Лаборатория моделирования биомолекулярных систем

Отдел структурной биологии

Руководитель: Ефремов Роман Гербертович, д. ф.-м. н., профессор
efremov@nmr.ru+7(495)336-20-00

model.nmr.ru

Молекулярное моделирование, метод молекулярного гидрофобного потенциала, мембранные и мембрано-активные белки и пептиды, структурная организация биологических мембран, молекулярный дизайн, докинг, молекулярная динамика, вычислительный эксперимент, структурная протеомика, технологии in silico, биоинформатика, трансмембранные альфа-спиральные димеры

Сотрудники лаборатории занимаются компьютерным моделированием основных «молекул жизни» и надмолекулярных систем: белков, нуклеиновых кислот и биомембран. Особый акцент делается именно на мембраны и на «населяющие» их белковые молекулы — рецепторы, ионные каналы и пр. Основной «прицел» исследований — установить, как организованы и как функционируют эти молекулы на уровне отдельных атомов, ведь такое знание позволяет не только объяснять, как устроена жизнь, но и осуществлять рациональное конструирование принципиально новых соединений, таких как биологически активные вещества или лекарства.

Компьютерный (или in silico – «в кремнии») эксперимент, в отличие от других методов анализа молекул, не требует создания реальных образцов белковых кристаллов или изотопно-меченых белков. Всю работу сотрудники ведут на многопроцессорных компьютерах, а также обращаются к вычислительным ресурсам Межведомственного суперкомпьютерного центра РАН и других центров коллективного пользования.

На компьютерах создают и изучают модели мембранных и мембрано-активных белков и пептидов, а также их взаимодействия между собой и с лигандами. Исследования этих моделей позволили определить особенности химического строения мембран архей (эти организмы могут использоваться людьми в экологической химии и фармакологии), а также создать на основе природных биологически активных пептидов прототипы новых лекарственных препаратов (например, аналоги латарцинов — антимикробных пептидов, не обладающих гемолитическими свойствами).

Моделирование пространственной структуры рецепторов – отдельное направление работы лаборатории. Особое внимание привлекают GPCR-рецепторы и рецепторные тирозинкиназы, поскольку они являются мишенью действия многочисленных лекарственных веществ, и их потенциал как фармакологических мишеней лишь начинает разрабатываться.

В своей работе исследователи применяют разные алгоритмы молекулярного моделирования: сопоставительное моделирование (на основе структуры белка-«родственника»), молекулярный докинг (для рассмотрения механизмов взаимодействия молекул между собой), молекулярную динамику и др. Чтобы оптимизировать компьютерные модели мембранных белков, сотрудники установили статистические закономерности упаковки мембранных белков.

В лаборатории создан банк динамических моделей липидных бислоев различного состава, в том числе, двухкомпонентных мембран, включающих отрицательно заряженные липиды. Такие структуры позволяют имитировать мембраны бактерий и изучать влияние разных веществ на них, чтобы узнать, какие вещества могут обладать антимикробной активностью и быть полезными в медицине, например, при создании антибиотиков.

Лаборатория активно сотрудничает как с другими подразделениями Института (например, отделами Молекулярных основ нейросигнализации и Молекулярной нейробиологии), так и с другими лабораториями в России и за рубежом.

Лаборатория была образована в 2007 году из группы молекулярного моделирования в составе лаборатории (ныне — отдела) структурной биологии.

Сейчас лаборатория моделирования биомолекулярных систем, равно как и метод компьютерного эксперимента, делает первые шаги в совершенствовании путей изучения важнейших мезоскопических систем и процессов, протекающих внутри клетки. Метод уже гармонично дополняет лабораторные эксперименты, а в будущем, возможно, сыграет решающую роль в лечении и даже предотвращении болезней.

Научно-популярная статья о работе Лаборатории: «Компьютерные игры в молекулярную биофизику биологических мембран».

Лаборатория занимается молекулярным моделированием пространственной структуры и динамики биомолекул. Основной областью специализации является изучение структуры и функций мембранных и мембрано-активных белков и пептидов, лиганд-рецепторных взаимодействий, а также рациональный компьютерный дизайн новых биологически активных соединений, в том числе действующих на мишени в биомембранах.

Большинство работ проводится в тесном сотрудничестве с экспериментальными группами, что обеспечивает максимальную эффективность теоретических исследований. Все молекулярные расчеты проводятся с использованием современного компьютерного оборудования, имеющегося в распоряжении Лаборатории (высокопроизводительные многопроцессорные кластеры под управлением Linux, рабочие станции и пр.) Лаборатория имеет доступ к вычислительным ресурсам Межведомственного суперкомпьютерного центра РАН.

1992—1997 гг. Количественная оценка и картирование пространственных гидрофобных свойств биомолекул. Для детальной характеризации гидрофобных/гидрофильных параметров белков и пептидов впервые применен метод молекулярного гидрофобного потенциала (МГП). МГП-подход также был успешно использован для изучения гидрофобной организации целого ряда водорастворимых и мембранных белков и пептидов, оценки межмолекулярных взаимодействий с их участием. Данные подходы реализованы в виде веб-приложения PLATINUM на сайте Лаборатории.

1998—2000 гг. Разработана модель неявно заданной мембраны. Для описания мембранного окружения в систему вводится дополнительный сольватационый потенциал, зависящий от одной из координат атомов. Модель позволяет изучать пространственную структуру мембранных белков и белок-мембранные взаимодействия с помощью конформационного поиска методом Монте-Карло. Модель неявно заданной мембраны реализована в программе FANMEM, созданной на базе пакета FANTOM (von Freyberg B., W. Braun 1991. J. Comp.Chem. 12:1065–1076).

2005—2008 гг. Созданы модели явно заданных липидных бислоев и мицелл детергентов различного молекулярного состава. Изучено взаимодействие мембрано-активных пептидов из разных классов (пептиды слияния, антимикробные, неспецифические переносчики) с данными моделями. Исследована структурная организация модельных мембран. Показана роль липидного состава и структурно-динамических свойств пептидов в процессе дестабилизации мембраны. Определена взаимосвязь структура-функция для ряда антимикробных пептидов, выделенных из яда паука Lachesana tarabaevi. Созданы пептиды с направленно измененной активностью.

2000—2004 гг. Проведено моделирование ряда мембрано-активных белков и пептидов (кардиотоксины, пептиды слияния, др.) с неявно заданной мембраной. Выявлены ключевые факторы (аминокислотный состав, гидрофобная организация, конформационная динамика), определяющие процесс связывания и геометрию молекул в мембране.

2004—2008 гг. Учет доменных движений бека-мишени и гидрофобных контактов при исследовании взаимодействий рецептор-лиганд методом молекулярного докинга. На основе оригинального метода оценки гидрофобного соответствия разработаны аденин-специфичные оценочные функции. Они эффективно выявляют наиболее правдоподобные решения задачи докинга даже в случае доменных движений рецептора, что было показано при моделирование комплексов АТФ с различными АТФазами Р-типа. Новые подходы реализованы в виде веб-приложения PLATINUM на сайте Лаборатории.

2006—2008 гг. Разработаны подходы для моделирования димеризации трансмембранных α-спиралей. Получены структуры димеров для трансмембранных фрагментов ряда белков (гликофорин, рецепторные тирозин-киназы) с помощью конформационного поиска в неявно заданной мембране методом Монте-Карло с помощью программы FANMEM. Проведено моделирование динамического поведения димера трансмембранных фрагментов про-апоптозного белка Bnip3 в явно заданном липидном бислое с использованием данных ЯМР-спектроскопии.

2006—2008 гг. Алгоритмы оценки качества упаковки α-спиральных сегментов в трехмерных моделях мембранных белков. Разработаны оценочные функции для моделей G-белок сопряженных рецепторов, построенных по гомологии. Метод позволяет выявить модель рецептора, наиболее близкую к его нативной (например, кристаллографической) структуре, среди большого числа некоректных моделей.

По результатам научной работы Лаборатории получено несколько патентов РФ.

Лаборатория моделирования биомолекулярных систем. В первом ряду (слева направо): студ. Фахрутдинова Г. Н., Балицкая Е. Д., Тарасова Н. К., асп. Пыркова Д. В., студ. Иванова И. Д. Во втором ряду: к. ф.-м. н., н. с. Чугунов А. О., зав. лаб., д. ф.-м. н., зам. дир. ИБХ Ефремов Р. Г., к. ф.-м. н., м. н. с. Пырков Т. В., к. ф.-м. н., н. с. Полянский А. А., к. ф.-м. н., с. н. с. Волынский П. Е. В дальнем ряду: асп. Новоселецкий В. Н., студ. Кузнецов А. С., Озеров И. В., м. н. с. Коншина А. Г., студ. Попов П. А.

 

Ф.И.О.ДолжностьКонтакты
Ефремов Роман Гербертович, д. ф.-м. н., профессоррук. подр.efremov@nmr.ru+7(495)336-20-00
Чугунов Антон Олегович, к. ф.-м. н.с.н.с.batch2k@yandex.ru+7(495)336-20-00
Крылов Николай Андреевичс.н.с.krna@rambler.ru
Волынский Павел Евгеньевич, к. ф.-м. н.с.н.с.pashuk@nmr.ru+7(495)336-20-00
Полянский Антон Александрович, к. ф.-м. н.с.н.с.newant@gmail.com+7(495)336-20-00
Нольде Дмитрий Евгеньевич, к. х. н.с.н.с.nolde@nmr.ru+7(916)179-1264
Дубовский Пётр Викторович, к. х. н.н.с.peter@nmr.ru+7(495)727-44-98
Табакмахер Валентин Михайлович, к. х. н.н.с.tabval@yandex.ru+7(495)3362000
Коншина Анастасия Геннадьевнам.н.с.nastya@nmr.ru
Замалетдинов Мифтах Фатиховичасп.miftakhz@gmail.com+7(495)3362000
Панина Ирина Сергеевнаасп.irinaspanina@gmail.com
Коробова Наталья Владимировнастуд.nvkorobova_1@edu.hse.ru+7(495)3362000
Покровский Виктор Игоревичстуд.vincheste@gmail.com+7(495)3362000
Смирнов Кирилл Валерьевичстуд.kvsmirnov@edu.hse.ru+7(495)3362000
Кузнецов Андрей Сергеевичинженерandrej.kuznecov@phystech.edu

Ранее здесь работали:

Пырков Тимофей Владимирович, к. ф.-м. н.м.н.с.tim.pyrkov@gmail.com
Пыркова Дарья Владимировнам.н.с.dpyrkova@gmail.com
Ширшиков Фёдор Владимировичасп.shrshkv@ya.ru

Избранные публикации

  1. Bocharov E.V., Bragin P.E., Pavlov K.V., Bocharova O.V., Mineev K.S., Polyansky A.A., Volynsky P.E., Efremov R.G., Arseniev A.S. (2017). The Conformation of the Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts to the Local Membrane Environment. Biochemistry 56 (12), 1697–1705 [+]

    The epidermal growth factor receptor (EGFR) family is an important class of receptor tyrosine kinases, mediating a variety of cellular responses in normal biological processes and in pathological states of multicellular organisms. Different modes of dimerization of the human EGFR transmembrane domain (TMD) in different membrane mimetics recently prompted us to propose a novel signal transduction mechanism based on protein-lipid interaction. However, the experimental evidence for it was originally obtained with slightly different TMD fragments used in the two different mimetics, compromising the validity of the comparison. To eliminate ambiguity, we determined the nuclear magnetic resonance (NMR) structure of the bicelle-incorporated dimer of the EGFR TMD fragment identical to the one previously used in micelles. The NMR results augmented by molecular dynamics simulations confirm the mutual influence of the TMD and lipid environment, as is required for the proposed lipid-mediated activation mechanism. They also reveal the possible functional relevance of a subtle interplay between the concurrent processes in the lipid and protein during signal transduction.

    ID:1780
  2. Kasheverov I.E., Chugunov A.O., Kudryavtsev D.S., Ivanov I.A., Zhmak M.N., Shelukhina I.V., Spirova E.N., Tabakmakher V.M., Zelepuga E.A., Efremov R.G., Tsetlin V.I. (2016). High-Affinity α-Conotoxin PnIA Analogs Designed on the Basis of the Protein Surface Topography Method. Sci Rep 6, 36848 [+]

    Despite some success for small molecules, elucidating structure-function relationships for biologically active peptides - the ligands for various targets in the organism - remains a great challenge and calls for the development of novel approaches. Some of us recently proposed the Protein Surface Topography (PST) approach, which benefits from a simplified representation of biomolecules' surface as projection maps, which enables the exposure of the structure-function dependencies. Here, we use PST to uncover the "activity pattern" in α-conotoxins - neuroactive peptides that effectively target nicotinic acetylcholine receptors (nAChRs). PST was applied in order to design several variants of the α-conotoxin PnIA, which were synthesized and thoroughly studied. Among the best was PnIA[R9, L10], which exhibits nanomolar affinity for the α7 nAChR, selectivity and a slow wash-out from this target. Importantly, these mutations could hardly be delineated by "standard" structure-based drug design. The proposed combination of PST with a set of experiments proved very efficient for the rational construction of new bioactive molecules.

    ID:1604
  3. Панина И.С., Нольде Д.Е., Чугунов А.О., Ефремов Р.Г. (2016). Структурно-динамическая модель комплекса лантибиотика низин с липидом-II в биомембране. Актуальные вопросы биологической физики и химии 1, 263–267 ID:1680
  4. Shulepko M.A., Lyukmanova E.N., Shenkarev Z.O., Dubovskii P.V., Astapova M.V., Feofanov A.V., Arseniev A.S., Utkin Y.N., Kirpichnikov M.P., Dolgikh D.A. (2016). Towards universal approach for bacterial production of three-finger Ly6/uPAR proteins: Case study of cytotoxin I from cobra N. oxiana. Protein Expr. Purif. 130, 13–20 [+]

    Cytotoxins or cardiotoxins is a group of polycationic toxins from cobra venom belonging to the 'three-finger' protein superfamily (Ly6/uPAR family) which includes small β-structural proteins (60-90 residues) with high disulfide bond content (4-5 disulfides). Due to a high cytotoxic activity for cancer cells, cytotoxins are considered as potential anticancer agents. Development of the high-throughput production methods is required for the prospective applications of cytotoxins. Here, efficient approach for bacterial production of recombinant analogue of cytotoxin I from N. oxiana containing additional N-terminal Met-residue (rCTX1) was developed. rCTX1 was produced in the form of E. coli inclusion bodies. Refolding in optimized conditions provided ∼6 mg of correctly folded protein from 1 L of bacterial culture. Cytotoxicity of rCTX1 for C6 rat glioma cells was found to be similar to the activity of wild type CTX1. The milligram quantities of (13)C,(15)N-labeled rCTX1 were obtained. NMR study confirmed the similarity of the spatial structures of recombinant and wild-type toxins. Additional Met residue does not perturb the overall structure of the three-finger core. The analysis of available data for different Ly6/uPAR proteins of snake and human origin revealed that efficiency of their folding in vitro is correlated with the number of proline residues in the third loop and the surface area of hydrophobic residues buried within the protein interior. The obtained data indicate that hydrophobic core is important for the folding of proteins with high disulfide bond content. Developed expression method opens new possibilities for structure-function studies of CTX1 and other related three-finger proteins.

    ID:1599
  5. Lyukmanova E.N., Shulepko M.A., Shenkarev Z.O., Kasheverov I.E., Chugunov A.O., Kulbatskii D.S., Myshkin M.Y., Utkin Y.N., Efremov R.G., Tsetlin V.I., Arseniev A.S., Kirpichnikov M.P., Dolgikh D.A. (2016). Central loop of non-conventional toxin WTX from Naja kaouthia is important for interaction with nicotinic acetylcholine receptors. Toxicon 119, 274–9 [+]

    'Three-finger' toxin WTX from Naja kaouthia interacts with nicotinic and muscarinic acetylcholine receptors (nAChRs and mAChRs). Mutagenesis and competition experiments with (125)I-α-bungarotoxin revealed that Arg31 and Arg32 residues from the WTX loop II are important for binding to Torpedo californica and human α7 nAChRs. Computer modeling suggested that loop II occupies the orthosteric binding site at α7 nAChR. The similar toxin interface was previously described as a major determinant of allosteric interactions with mAChRs.

    ID:1598
  6. Lyukmanova E.N., Shulepko M.A., Shenkarev Z.O., Bychkov M.L., Paramonov A.S., Chugunov A.O., Kulbatskii D.S., Arvaniti M., Dolejsi E., Schaer T., Arseniev A.S., Efremov R.G., Thomsen M.S., Dolezal V., Bertrand D., Dolgikh D.A., Kirpichnikov M.P. (2016). Secreted Isoform of Human Lynx1 (SLURP-2): Spatial Structure and Pharmacology of Interactions with Different Types of Acetylcholine Receptors. Sci Rep 6, 30698 [+]

    Human-secreted Ly-6/uPAR-related protein-2 (SLURP-2) regulates the growth and differentiation of epithelial cells. Previously, the auto/paracrine activity of SLURP-2 was considered to be mediated via its interaction with the α3β2 subtype of the nicotinic acetylcholine receptors (nAChRs). Here, we describe the structure and pharmacology of a recombinant analogue of SLURP-2. Nuclear magnetic resonance spectroscopy revealed a 'three-finger' fold of SLURP-2 with a conserved β-structural core and three protruding loops. Affinity purification using cortical extracts revealed that SLURP-2 could interact with the α3, α4, α5, α7, β2, and β4 nAChR subunits, revealing its broader pharmacological profile. SLURP-2 inhibits acetylcholine-evoked currents at α4β2 and α3β2-nAChRs (IC50 ~0.17 and >3 μM, respectively) expressed in Xenopus oocytes. In contrast, at α7-nAChRs, SLURP-2 significantly enhances acetylcholine-evoked currents at concentrations <1 μM but induces inhibition at higher concentrations. SLURP-2 allosterically interacts with human M1 and M3 muscarinic acetylcholine receptors (mAChRs) that are overexpressed in CHO cells. SLURP-2 was found to promote the proliferation of human oral keratinocytes via interactions with α3β2-nAChRs, while it inhibited cell growth via α7-nAChRs. SLURP-2/mAChRs interactions are also probably involved in the control of keratinocyte growth. Computer modeling revealed possible SLURP-2 binding to the 'classical' orthosteric agonist/antagonist binding sites at α7 and α3β2-nAChRs.

    ID:1597
  7. Bragin P.E., Mineev K.S., Bocharova O.V., Volynsky P.E., Bocharov E.V., Arseniev A.S. (2016). HER2 Transmembrane Domain Dimerization Coupled with Self-Association of Membrane-Embedded Cytoplasmic Juxtamembrane Regions. J. Mol. Biol. 428 (1), 52–61 [+]

    Receptor tyrosine kinases of the human epidermal growth factor receptor (HER or ErbB) family transduce biochemical signals across plasma membrane, playing a significant role in vital cellular processes and in various cancers. Inactive HER/ErbB receptors exist in equilibrium between the monomeric and unspecified pre-dimerized states. After ligand binding, the receptors are involved in strong lateral dimerization with proper assembly of their extracellular ligand-binding, single-span transmembrane, and cytoplasmic kinase domains. The dimeric conformation of the HER2 transmembrane domain that is believed to support the cytoplasmic kinase domain configuration corresponding to the receptor active state was previously described in lipid bicelles. Here we used high-resolution NMR spectroscopy in another membrane-mimicking micellar environment and identified an alternative HER2 transmembrane domain dimerization coupled with self-association of membrane-embedded cytoplasmic juxtamembrane region. Such a dimerization mode appears to be capable of effectively inhibiting the receptor kinase activity. This finding refines the molecular mechanism regarding the signal propagation steps from the extracellular to cytoplasmic domains of HER/ErbB receptors.

    ID:1369
  8. Kuzmenkov A.I., Krylov N.A., Chugunov A.O., Grishin E.V., Vassilevski A.A. (2016). Kalium: a database of potassium channel toxins from scorpion venom. Database (Oxford) 2016, [+]

    Kalium (http://kaliumdb.org/) is a manually curated database that accumulates data on potassium channel toxins purified from scorpion venom (KTx). This database is an open-access resource, and provides easy access to pages of other databases of interest, such as UniProt, PDB, NCBI Taxonomy Browser, and PubMed. General achievements of Kalium are a strict and easy regulation of KTx classification based on the unified nomenclature supported by researchers in the field, removal of peptides with partial sequence and entries supported by transcriptomic information only, classification of β-family toxins, and addition of a novel λ-family. Molecules presented in the database can be processed by the Clustal Omega server using a one-click option. Molecular masses of mature peptides are calculated and available activity data are compiled for all KTx. We believe that Kalium is not only of high interest to professional toxinologists, but also of general utility to the scientific community.Database URL:http://kaliumdb.org/.

    ID:1504
  9. Chugunov A.O., Volynsky P.E., Krylov N.A., Nolde D.E., Efremov R.G. (2016). Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains. Sci Rep 6, 33112 [+]

    Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of the organism. Despite the spatial structure of the channel in both open (O) and closed (C) states is known, microscopic nature of channel gating and mechanism of thermal sensitivity are still poorly understood. In this work, we used unrestrained atomistic molecular dynamics simulations of TRPV1 (without N- and C-terminal cytoplasmic domains) embedded into explicit lipid bilayer in its O- and C-states. We found that the pore domain with its neighboring loops undergoes large temperature-dependent conformational transitions in an asymmetric way, when fragments of only one monomer move with large amplitude, freeing the pore upon heating. Such an asymmetrical gating looks rather biologically relevant because it is faster and more reliable than traditionally proposed "iris-like" symmetric scheme of channel opening. Analysis of structural, dynamic, and hydrophobic organization of the pore domain revealed entropy growth upon TRPV1 gating, which is in line with current concepts of thermal sensitivity.

    ID:1558
  10. Dubovskii P.V., Vassilevski A.A., Kozlov S.A., Feofanov A.V., Grishin E.V., Efremov R.G. (2015). Latarcins: versatile spider venom peptides. Cell. Mol. Life Sci. 72 (23), 4501–22 [+]

    Arthropod venoms feature the presence of cytolytic peptides believed to act synergetically with neurotoxins to paralyze prey or deter aggressors. Many of them are linear, i.e., lack disulfide bonds. When isolated from the venom, or obtained by other means, these peptides exhibit common properties. They are cationic; being mostly disordered in aqueous solution, assume amphiphilic α-helical structure in contact with lipid membranes; and exhibit general cytotoxicity, including antifungal, antimicrobial, hemolytic, and anticancer activities. To suit the pharmacological needs, the activity spectrum of these peptides should be modified by rational engineering. As an example, we provide a detailed review on latarcins (Ltc), linear cytolytic peptides from Lachesana tarabaevi spider venom. Diverse experimental and computational techniques were used to investigate the spatial structure of Ltc in membrane-mimicking environments and their effects on model lipid bilayers. The antibacterial activity of Ltc was studied against a panel of Gram-negative and Gram-positive bacteria. In addition, the action of Ltc on erythrocytes and cancer cells was investigated in detail with confocal laser scanning microscopy. In the present review, we give a critical account of the progress in the research of Ltc. We explore the relationship between Ltc structure and their biological activity and derive molecular characteristics, which can be used for optimization of other linear peptides. Current applications of Ltc and prospective use of similar membrane-active peptides are outlined.

    ID:1395
  11. Lyukmanova E.N., Shenkarev Z.O., Shulepko M.A., Paramonov A.S., Chugunov A.O., Janickova H., Dolejsi E., Dolezal V., Utkin Y.N., Tsetlin V.I., Arseniev A.S., Efremov R.G., Dolgikh D.A., Kirpichnikov M.P. (2015). Structural Insight into Specificity of Interactions between Nonconventional Three-finger Weak Toxin from Naja kaouthia (WTX) and Muscarinic Acetylcholine Receptors. J. Biol. Chem. 290 (39), 23616–30 [+]

    Weak toxin from Naja kaouthia (WTX) belongs to the group of nonconventional "three-finger" snake neurotoxins. It irreversibly inhibits nicotinic acetylcholine receptors and allosterically interacts with muscarinic acetylcholine receptors (mAChRs). Using site-directed mutagenesis, NMR spectroscopy, and computer modeling, we investigated the recombinant mutant WTX analogue (rWTX) which, compared with the native toxin, has an additional N-terminal methionine residue. In comparison with the wild-type toxin, rWTX demonstrated an altered pharmacological profile, decreased binding of orthosteric antagonist N-methylscopolamine to human M1- and M2-mAChRs, and increased antagonist binding to M3-mAChR. Positively charged arginine residues located in the flexible loop II were found to be crucial for rWTX interactions with all types of mAChR. Computer modeling suggested that the rWTX loop II protrudes to the M1-mAChR allosteric ligand-binding site blocking the entrance to the orthosteric site. In contrast, toxin interacts with M3-mAChR by loop II without penetration into the allosteric site. Data obtained provide new structural insight into the target-specific allosteric regulation of mAChRs by "three-finger" snake neurotoxins.

    ID:1394
  12. Kuznetsov A.S., Polyansky A.A., Fleck M., Volynsky P.E., Efremov R.G. (2015). Adaptable Lipid Matrix Promotes Protein-Protein Association in Membranes. J. Chem. Theory Comput. 11 (9), 4415–26 [+]

    Трансмембранные домены играют важную роль в функционировании мембранных белков. Их взаимодействия определяют работу ряда важнейших рецепторов, в частности, рецепторных тирозинкиназ. В настоящей работе на примере гликофорина А и двух модельних пептидов показали, что липидный бислой играет важную роль в димеризации трансмембранных спиралей. Встраивание пептида в мембрану вызывает формирование характерных неоднородностей в последней. Таким образом, димеризация трансмембранных спиралей может носить энтропийный характер.

    ID:1342
  13. Kuznetsov A.S., Volynsky P.E., Efremov R.G. (2015). Role of the Lipid Environment in the Dimerization of Transmembrane Domains of Glycophorin A. Acta Naturae 7 (4), 122–7 [+]

    An efficient computational approach is developed to quantify the free energy of a spontaneous association of the α-helices of proteins in the membrane environment. The approach is based on the numerical decomposition of the free energy profiles of the transmembrane (TM) helices into components corresponding to protein-protein, protein-lipid, and protein-water interactions. The method was tested for the TM segments of human glycophorin A (GpA) and two mutant forms, Gly83Ala and Thr87Val. It was shown that lipids make a significant negative contribution to the free energy of dimerization, while amino acid residues forming the interface of the helix-helix contact may be unfavorable in terms of free energy. The detailed balance between different energy contributions is highly dependent on the amino acid sequence of the TM protein segment. The results show the dominant role of the environment in the interaction of membrane proteins that is changing our notion of the driving force behind the spontaneous association of TM α-helices. Adequate estimation of the contribution of the water-lipid environment thus becomes an extremely urgent task for a rational design of new molecules targeting bitopic membrane proteins, including receptor tyrosine kinases.

    ID:1396
  14. Kasheverov I.E., Kudryavtsev D.S., Ivanov I.A., Zhmak M.N., Chugunov A.O., Tabakmakher V.M., Zelepuga E.A., Efremov R.G., Tsetlin V.I. (2015). Rational design of new ligands for nicotinic receptors on the basis of α-conotoxin PnIA. Dokl. Biochem. Biophys. 461, 106–9 [+]

    A variety of different subtypes of nicotinic acetylcholine receptors (nAChRs) and their involvement in a number of diseases and pathologies (Parkinson’s and Alzheimer’s diseases, schizophrenia, myasthenia, nicotine addiction) dictates the needs in potent and selective ligands for each subtype. These ligands can be used as a tool for detection and characterization of the distinct nAChR subtypes, as well as be the basis for drug design. Novel cholinergic ligands can emerge in the result of search among natural sources or design (with the use of modern computer modeling) on the basis of known molecules. The significance of the first way was confirmed in our hands by the detection of affinities of a set of marine alkaloids from sponges and ascidians towards some receptor subtypes. The most active of them — makaluvamines — showed micromolar affinity for muscle and neuronal α7 nAChRs. Application of the recently presented Protein Surface Topography method to known natural antagonist of some neuronal nAChRs — α-conotoxin PnIA — resulted in design of new potent analogs with nanomolar affinities for α7 nAChR. Radioactive derivatives of these analogs were successfully applied in radioligand tests for characterization of novel compounds and could be perspective as well for detection of α7 nAChR in the various preparations. Combining these two ways (search and design) was demonstrated in the synthesis of small peptide compounds on the basis of discovered by us in venom of Burmese Viper linear peptide azemiopsin — powerful blocker of muscle-type nAChRs. Some designed peptides have retained a certain affinity to receptor and showed high practical potential: in the absence of toxicity they contributed to the reduction of facial wrinkles (patent application for cosmetic use RU2013102410; PCT/RU2014/000032).

    ID:1393
  15. Zhang L., Polyansky A., Buck M. (2015). Modeling transmembrane domain dimers/trimers of plexin receptors: implications for mechanisms of signal transmission across the membrane. PLoS ONE 10 (4), e0121513 [+]

    Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and -B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, -A3, -A4, -C1 and -D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 - trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures suggest experimental tests and will be useful for the interpretation of future studies.

    ID:1397
  16. Dubovskii V., Vorontsova V., Utkin N., Arseniev S., Efremov G., Feofanov V. (2014). Cobra cytotoxins: determinants of antibacterial activity. Mendeleev Communications 25 (1), 70–71 [+]

    The investigation of antibacterial activity of three-finger cobra cytotoxins towards Gram-negative and Gram-positive bacteria showed no activity against the former species, whereas M. luteus was found most susceptible to cytotoxins. A correlation was revealed between this activity and hydrophobicity of the toxins (HTL scores), total charge and its distribution over the toxin molecule: the absence of Glu-16 residue and the presence of positively charged residues (Lys30/His31) in the tip of the loop 2.

    ID:1398
  17. Ribeiro Ede.A. Jr, Pinotsis N., Ghisleni A., Salmazo A., Konarev P.V., Kostan J., Sjöblom B., Schreiner C., Polyansky A.A., Gkougkoulia E.A., Holt M.R., Aachmann F.L., Zagrovic B., Bordignon E., Pirker K.F., Svergun D.I., Gautel M., DjinovićCarugo K. (2014). The Structure and Regulation of Human Muscle α-Actinin. Cell 159 (6), 1447–60 [+]

    The spectrin superfamily of proteins plays key roles in assembling the actin cytoskeleton in various cell types, crosslinks actin filaments, and acts as scaffolds for the assembly of large protein complexes involved in structural integrity and mechanosensation, as well as cell signaling. α-actinins in particular are the major actin crosslinkers in muscle Z-disks, focal adhesions, and actin stress fibers. We report a complete high-resolution structure of the 200 kDa α-actinin-2 dimer from striated muscle and explore its functional implications on the biochemical and cellular level. The structure provides insight into the phosphoinositide-based mechanism controlling its interaction with sarcomeric proteins such as titin, lays a foundation for studying the impact of pathogenic mutations at molecular resolution, and is likely to be broadly relevant for the regulation of spectrin-like proteins.

    ID:1127
  18. Дубовский П.В., Уткин Ю.Н. (2014). Цитотоксины кобр: структурная организация и антибактериальная активность. Acta Naturae 6 (3), 12–19 ID:1125
  19. Alekseeva A.S., Korotaeva A.A., Samoilova E.V., Volynsky P.E., Vodovozova E.L., Boldyrev I.A. (2014). Secretory phospholipase A2 activity in blood serum: The challenge to sense. Biochem. Biophys. Res. Commun. 454 (1), 178–182 [+]

    Excess levels of secretory phospholipase A2 (sPLA2) is known to contribute to several inflammatory diseases including vascular inflammation correlating with coronary events in coronary artery disease. Thus a method to monitor sPLA2 activity in blood serum is urgently needed. Such method is still a challenge since existing fluorescent probes do not allow to monitor sPLA2 activity directly in blood serum. Here we analyze and overcome barriers in sPLA2 sensing methodology and report a fluorescent probe and a kinetic model of its hydrolysis by sPLA2. New probe is designed with a fluorophore and a quencher not interfering binding to the enzyme. At the same time phospholipid matrix bearing the probe promotes efficient initial quenching of the fluorophore. Kinetic model of probe hydrolysis takes into account signal change due to the side processes. The probe and the kinetic model applied together prove the concept that the activity of sPLA can be measured directly in blood serum.

    ID:1124
  20. Чугунов А.О., Ефремов Р.Г. (2014). Поверхность молекулы -- источник биологической информации. Природа  (10), 3–10 [+]

    Компьютерное моделирование биологических молекул зачастую основано не на квантовой механике, описывающей строение вещества максимально корректно, а на наборе приближений, уводящих нас от физических «истоков», но позволяющих решать практически важные задачи с использованием ЭВМ. Одним из таких упрощений является концепция молекулярных поверхностей, представляющая молекулу в виде твердого тела, на поверхности которого распределены какие-либо физические свойства. Несмотря на кажущийся примитивизм, этот подход является довольно плодотворным, внося свою лепту в решение актуальных проблем молекулярной биологии, — например, дизайна новых антибиотиков и изучения молекулярных механизмов заболеваний.

    ID:1092
  21. Кузнецов А.С., Дубовский П.В., Воронцова О.В., Феофанов А.В., Ефремов Р.Г. (2014). Взаимодействие линейных катионных пептидов с фосфолипидными мембранами и полимерами сиаловой кислоты. Биохимия 79 (5), 583–594583–594 ID:1123
  22. Koromyslova A.D., Chugunov A.O., Efremov R.G. (2014). Deciphering Fine Molecular Details of Proteins' Structure and Function with a Protein Surface Topography (PST) Method. Journal of chemical information and modeling 54 (4), 1189–99 [+]

    Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them-protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

    ID:1030
  23. Polyansky A.A., Chugunov A.O., Volynsky P.E., Krylov N.A., Nolde D.E., Efremov R.G. (2014). PREDDIMER: a web server for prediction of transmembrane helical dimers. Bioinformatics 30 (6), 889–90 [+]

    Here we present PREDDIMER, a web tool for prediction of dimer structure of transmembrane (TM) helices. PREDDIMER allows (i) reconstruction of a number of dimer structures for given sequence(s) of TM protein fragments, (ii) ranking and filtering of predicted structures according to respective values of a scoring function, (iii) visualization of predicted 3D dimer structures and (iv) visualization of surface hydrophobicity of TM helices and their contacting (interface) regions represented as 2D maps.

    ID:975
  24. Peter B., Polyansky A.A., Fanucchi S., Dirr H.W. (2014). A Lys-Trp cation-π interaction mediates the dimerization and function of the chloride intracellular channel protein 1 transmembrane domain. Biochemistry 53 (1), 57–67 [+]

    Chloride intracellular channel protein 1 (CLIC1) is a dual-state protein that can exist either as a soluble monomer or in an integral membrane form. The oligomerization of the transmembrane domain (TMD) remains speculative despite it being implicated in pore formation. The extent to which electrostatic and van der Waals interactions drive folding and association of the dimorphic TMD is unknown and is complicated by the requirement of interactions favorable in both aqueous and membrane environments. Here we report a putative Lys37-Trp35 cation-π interaction and show that it stabilizes the dimeric form of the CLIC1 TMD in membranes. A synthetic 30-mer peptide comprising a K37M TMD mutant was examined in 2,2,2-trifluoroethanol, sodium dodecyl sulfate micelles, and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine liposomes using far-ultraviolet (UV) circular dichroism, fluorescence, and UV absorbance spectroscopy. Our data suggest that Lys37 is not implicated in the folding, stability, or membrane insertion of the TMD peptide. However, removal of this residue impairs the formation of dimers and higher-order oligomers. This is accompanied by a 30-fold loss of chloride influx activity, suggesting that dimerization modulates the rate of chloride conductance. We propose that, within membranes, individual TMD helices associate via a Lys37-mediated cation-π interaction to form active dimers. The latter findings are also supported by results of modeling a putative TMD dimer conformation in which Lys37 and Trp35 form cation-π pairs at the dimer interface. Dimeric helix bundles may then associate to form fully active ion channels. Thus, within a membrane-like environment, aromatic interactions involving a polar lysine side chain provide a thermodynamic driving force for helix-helix association.

    ID:1126
  25. Chugunov A.O., Volynsky P.E., Krylov N.A., Boldyrev I.A., Efremov R.G. (2014). Liquid but Durable: Molecular Dynamics Simulations Explain the Unique Properties of Archaeal-Like Membranes. Sci Rep 4, 7462 [+]

    Археи, прежде известные как архебактерии, в основном являются экстремофилами: их среда обитания — это высокие температура, давление, соленость и кислотность. Возможно, «особый путь» архей был определен необычными свойствами их мембран, существенно отличающихся по составу от «обычных» фосфолипидов у бактерий и эукариот. В Лаборатории моделирования биомолекулярных систем ИБХ РАН провели компьютерное исследование архейных мембран, объяснив взаимосвязь между химической структурой липидов и физическими свойствами мембран. Статья опубликована в журнале Scientific Reports. По ее материалам написан пресс-релиз: «Прочные, но гибкие: молекулярная динамика объясняет уникальность биомембран архей».

    ID:1110
  26. Чугунов А.О., Василевский А.А. (2013). Эволюционная «гонка вооружений»: нейротоксины против ионных каналов. Наука и Жизнь 11, 42–48 [+]

    Биологическая эволюция — общая форма существования живой материи. При детальном рассмотрении оказывается, что виды почти никогда не эволюционируют поодиночке. Обычно в этом принимают участие их экологические партнёры. Таким образом, изменение происходит в парах: паразит — хозяин, хищник — жертва. Эволюционное изменение одного вида неизбежно приводит к изменению другого. Более того, взаимную эволюцию, когда один вид совершенствует систему нападения, а другой вслед за ним — систему защиты (и наоборот), часто можно проследить на молекулярном уровне. И здесь наиболее действенной и элегантной оказалась система нападения с помощью ядов, содержащих в своём составе нейротоксины — вещества, воздействующие на нервную систему и мышцы жертвы.

    ID:976
  27. Dubovskii P.V., Konshina A.G., Efremov R.G. (2013). Cobra Cardiotoxins: Membrane Interactions and Pharmacological Potential. Curr. Med. Chem. 21 (3), 270–287 [+]

    Natural polycationic membrane-active peptides typically lack disulfide bonds and exhibit fusion, cell-penetrating, antimicrobial activities. They are mostly unordered in solution, but adopt a helical structure, when bound to phospholipid membranes. Structurally different are cardiotoxins (or cytotoxins, СTs) from cobra venom. They are fully -structured molecules, characterized by the three-finger fold (TFF). Affinity of CTs to lipid bilayer was shown to depend on amino acid sequence in the tips of the three loops. In the present review, CT-membrane interactions are analyzed through the prism of data on binding of the toxins to phospholipid liposomes and detergent micelles, as well as their structural and computational studies in membrane mimicking environments. We assess different hydrophobicity scales to compare membrane partitioning of various CTs and their membrane effects. A comparison of hydrophobic/hydrophilic properties of CTs and linear polycationic peptides provides a key to their biological activity and creates a fundamental basis for rational design of new membrane-interacting compounds, including new promising drugs. For instance, since the viewpoint of the data obtained on model lipid membranes, cytotoxic activity of CTs against cancer cells is discussed.

    ID:974
  28. Krylov N.A., Pentkovsky V.M., Efremov R.G. (2013). Nontrivial behavior of water in the vicinity and inside lipid bilayers as probed by molecular dynamics simulations. ACS Nano 7 (10), 9428–42 [+]

    The atomic-scale diffusion of water in the presence of several lipid bilayers mimicking biomembranes is characterized via unconstrained molecular dynamics (MD) simulations. Although the overall water dynamics corresponds well to literature data, namely, the efficient braking near polar head groups of lipids, a number of interesting and biologically relevant details observed in this work have not been sufficiently discussed so far; for instance, the fact that waters "sense" the membrane unexpectedly early, before water density begins to decrease. In this "transitional zone" the velocity distributions of water and their H-bonding patterns deviate from those in the bulk solution. The boundaries of this zone are well preserved even despite the local (<1 nm size) perturbation of the lipid bilayer, thus indicating a decoupling of the surface and bulk dynamics of water. This is in excellent agreement with recent experimental data. Near the membrane surface, water movement becomes anisotropic, that is, solvent molecules preferentially move outward the bilayer. Deep in the membrane interior, the velocities can even exceed those in the bulk solvent and undergo large-scale fluctuations. The analysis of MD trajectories of individual waters in the middle part of the acyl chain region of lipids reveals a number of interesting rare phenomena, such as the fast (ca. 50 ps) breakthrough across the membrane or long-time (up to 750 ps) "roaming" between lipid leaflets. The analysis of these events was accomplished to delineate the mechanisms of spontaneous water permeation inside the hydrophobic membrane core. It was shown that such nontrivial dynamics of water in an "alien" environment is driven by the dynamic heterogeneities of the local bilayer structure and the formation of transient atomic-scale "defects" in it. The picture observed in lipid bilayers is drastically different from that in a primitive membrane mimic, a hydrated cyclohexane slab. The possible biological impact of such phenomena in equilibrated lipid bilayers is discussed.

    ID:973
  29. Chugunov A.O., Koromyslova A.D., Berkut A.A., Peigneur S., Tytgat J., Polyansky A.A., Pentkovsky V.M., Vassilevski A.A., Grishin E.V., Efremov R.G. (2013). Modular Organization of α-Toxins from Scorpion Venom Mirrors Domain Structure of Their Targets, Sodium Channels. J. Biol. Chem. 288 (26), 19014–27 [+]

    To gain success in the evolutionary "arms race," venomous animals such as scorpions produce diverse neurotoxins selected to hit targets in the nervous system of prey. Scorpion α-toxins affect insect and/or mammalian voltage-gated sodium channels (Navs) and thereby modify the excitability of muscle and nerve cells. Although more than 100 α-toxins are known and a number of them have been studied into detail, the molecular mechanism of their interaction with Navs is still poorly understood. Here, we employ extensive molecular dynamics simulations and spatial mapping of hydrophobic/hydrophilic properties distributed over the molecular surface of α-toxins. It is revealed that despite the small size and relatively rigid structure, these toxins possess modular organization from structural, functional, and evolutionary perspectives. The more conserved and rigid "core module" is supplemented with the "specificity module" (SM) that is comparatively flexible and variable and determines the taxon (mammal versus insect) specificity of α-toxin activity. We further show that SMs in mammal toxins are more flexible and hydrophilic than in insect toxins. Concomitant sequence-based analysis of the extracellular loops of Navs suggests that α-toxins recognize the channels using both modules. We propose that the core module binds to the voltage-sensing domain IV, whereas the more versatile SM interacts with the pore domain in repeat I of Navs. These findings corroborate and expand the hypothesis on different functional epitopes of toxins that has been reported previously. In effect, we propose that the modular structure in toxins evolved to match the domain architecture of Navs.

    ID:858
  30. Volynsky P.E., Polyansky A.A., Fakhrutdinova G.N., Bocharov E.V., Efremov R.G. (2013). Role of Dimerization Efficiency of Transmembrane Domains in Activation of Fibroblast Growth Factor Receptor 3. J. Am. Chem. Soc. , [+]

    Mutations in transmembrane (TM) domains of receptor tyrosine kinases are shown to cause a number of inherited diseases and cancer development. Here, we use a combined molecular modeling approach to understand molecular mechanism of effect of G380R and A391E mutations on dimerization of TM domains of human fibroblast growth factor receptor 3 (FGFR3). According to results of Monte Carlo conformational search in the implicit membrane and further molecular dynamics simulations, TM dimer of this receptor is able to form a number of various conformations, which differ significantly by the free energy of association in a full-atom model bilayer. The aforementioned mutations affect dimerization efficiency of TM segments and lead to repopulation of conformational ensemble for the dimer. Particularly, both mutations do not change the dimerization free energy of the predominant (putative "non-active") symmetric conformation of TM dimer, while affect dimerization efficiency of its asymmetric ("intermediate") and alternative symmetric (putative "active") models. Results of our simulations provide novel atomistic prospective of the role of G380 and A391E mutations in dimerization of TM domains of FGFR3 and their consecutive contributions to the activation pathway of the receptor.

    ID:972
  31. Chugunov A., Pyrkova D., Nolde D., Polyansky A., Pentkovsky V., Efremov R. (2013). Lipid-II forms potential "landing terrain" for lantibiotics in simulated bacterial membrane. Sci Rep 3, 1678 [+]

    Bacterial cell wall is targeted by many antibiotics. Among them are lantibiotics, which realize their function via interaction with plasma membrane lipid-II molecule - a chemically conserved part of the cell wall synthesis pathway. To investigate structural and dynamic properties of this molecule, we have performed a series of nearly microsecond-long molecular dynamics simulations of lipid-II and some of its analogs in zwitterionic single component and charged mixed simulated phospholipid bilayers (the reference and the mimic of the bacterial plasma membrane, respectively). Extensive analysis revealed that lipid-II forms a unique "amphiphilic pattern" exclusively on the surface of the simulated bacterial membrane (and not in the reference one). We hypothesize that many lantibiotics exploit the conserved features of lipid-II along with characteristic modulation of the bacterial membrane as the "landing site". This putative recognition mechanism opens new opportunities for studies on lantibiotics action and design of novel armament against resistant bacterial strains.

    ID:839
  32. Blanchevoye C., Floquet N., Scandolera A., Baud S., Maurice P., Bocquet O., Blaise S., Ghoneim C., Cantarelli B., Delacoux F., Dauchez M., Efremov R.G., Martiny L., Duca L., Debelle L. (2013). Interaction between the elastin peptide VGVAPG and human elastin binding protein. J. Biol. Chem. 288 (2), 1317–28 [+]

    The elastin binding protein (EBP), a spliced variant of lysosomal β-galactosidase, is the primary receptor of elastin peptides that have been linked to emphysema, aneurysm and cancer progression. The sequences recognized by EBP share the XGXXPG consensus pattern found in numerous matrix proteins, notably in elastin where the VGVAPG motif is repeated. To delineate the elastin binding site of human EBP, we built a homology model of this protein and docked VGVAPG on its surface. Analysis of this model suggested that Gln-97 and Asp-98 were required for interaction with VGVAPG because they contribute to the definition of a pocket thought to represent the elastin binding site of EBP. Additionally, we proposed that Leu-103, Arg-107, and Glu-137 were essential residues because they could interact with VGVAPG itself. Site-directed mutagenesis experiments at these key positions validated our model. This work therefore provides the first structural data concerning the interaction of the VGVAPG with its cognate receptor. The present structural data should now allow the development of EBP-specific antagonists.

    ID:814
  33. Aseev L.V., Chugunov A.O., Efremov R.G., Boni I.V. (2013). A single missense mutation in a coiled-coil domain of Escherichia coli ribosomal protein S2 confers a thermosensitive phenotype that can be suppressed by ribosomal protein S1. J. Bacteriol. 195 (1), 95–104 [+]

    Ribosomal protein S2 is an essential component of translation machinery, and its viable mutated variants conferring distinct phenotypes serve as a valuable tool in studying the role of S2 in translation regulation. One of a few available rpsB mutants, rpsB1, shows thermosensitivity and ensures enhanced expression of leaderless mRNAs. In this study, we identified the nature of the rpsB1 mutation. Sequencing of the rpsB1 allele revealed a G-to-A transition in the part of the rpsB gene which encodes a coiled-coil domain of S2. The resulting E132K substitution resides in a highly conserved site, TKKE, a so-called N-terminal capping box, at the beginning of the second alpha helix. The protruding coiled-coil domain of S2 is known to provide binding with 16S rRNA in the head of the 30S subunit and, in addition, to interact with a key mRNA binding protein, S1. Molecular dynamics simulations revealed a detrimental impact of the E132K mutation on the coiled-coil structure and thereby on the interactions between S2 and 16S rRNA, providing a clue for the thermosensitivity of the rpsB1 mutant. Using a strain producing a leaderless lacZ transcript from the chromosomal lac promoter, we demonstrated that not only the rpsB1 mutation generating S2/S1-deficient ribosomes but also the rpsA::IS10 mutation leading to partial deficiency in S1 alone increased translation efficiency of the leaderless mRNA by about 10-fold. Moderate overexpression of S1 relieved all these effects and, moreover, suppressed the thermosensitive phenotype of rpsB1, indicating the role of S1 as an extragenic suppressor of the E132K mutation.

    ID:812
  34. Чугунов А.О., Нольде Д.Е., Пыркова Д.В., Полянский А.А., Пентковский В.М., Ефремов Р.Г. (2013). На пути к новым антибиотикам. Суперкомпьютеры 12, 34–36 [+]

    Проблема резистентности бактерий к действию антибиотиков серьезна как никогда, и медицина всеми силами ищет пути к новым бактерицидным веществам, способным сохранять эффективность в течение долгих лет. Современная биофизика поможет ей в этом — наблюдение за молекулой антибиотика, которая «атакует» бактериальную клетку, подскажет ученым, как создать новые вещества, убивающие бактерий и безвредные для человеческого организма. Возможность для такого наблюдения дают суперкомпьютерные расчеты, а также современные физические модели и математические алгоритмы, предназначенные для изучения в вычислительном эксперименте структуры, динамики и функций сложнейших биологических супрамолекулярных систем. Исследователи из Института биоорганической химии РАН, используя ресурсы нового суперкомпьютера, установленного в лаборатории iScalare МФТИ, изучили на атомном уровне особенности организации мембраны бактерий, используя которые антибиотики преодолевают защитные системы клетки и оказывают антимикробное действие. Полученный результат указывает на возможность разработки нового поколения антибиотиков, избавленных от бремени резистентности.

    ID:816
  35. Чугунов А.О., Полянский А.А., Ефремов Р.Г. (2013). Физическая водобоязнь. Природа 1, 24–34 [+]

    Лист лотоса, по которому вода бегает, собравшись в шарики, водоотталкивающие поверхности и защитные составы для обуви, плавающие в бульоне кружки масла — всё это примеры свойства молекул, называемого гидрофобностью. Помимо этого, гидрофобный эффект играет важную биологическую роль: сворачивание и правильная работа белковых молекул, формирование биомембран, распознавание молекулами друг друга также «запрограммированы» с использованием гидрофобных свойств. Интересно, что гидрофобный эффект не сводится к «обычным» физическим взаимодействиям: за ним стоит Второй закон термодинамики и величина, именуемая энтропией.

    ID:817
  36. Pyrkova D.V., Tarasova N.K., Krylov N.A., Nolde D.E., Pentkovsky V.M., Efremov R.G. (2013). Dynamic clustering of lipids in hydrated two-component membranes: results of computer modeling and putative biological impact. J. Biomol. Struct. Dyn. 31 (1), 87–95 [+]

    Delineation and analysis of lateral clustering of lipids in model bilayers is an important step toward understanding of the physical processes underlying formation of lipid domains and rafts in cell membranes. Computer modeling methods represent a powerful tool to address the problem since they can detect clusters of only few lipid molecules - this issue still resists easy characterization with modern experimental techniques. In this work, we propose a computational method to detect and analyze parts of membrane with different packing densities and hydrogen bonding patterns. A series of one- and two-component fluid systems containing lipids with the same polar heads and different acyl chains, dioleoylphosphatidylcholine (18:1) and dipalmitoylphosphatidylcholine (16:0), or with same acyl chains and different polar heads, dioleoylphosphatidylserine (18:1) and dioleoylphosphatidylcholine (18:1), were studied via molecular dynamics simulations. Four criteria of clustering were considered. It was shown that the water-lipid interface of biomembranes represents a highly dynamic and "mosaic" picture, whose parameters depend on the bilayer composition. Some systems (e.g. with 20-30% of the anionic lipid) demonstrate unusual clustering properties and demand further investigation at molecular level. Lateral microheterogeneities in fluid lipid bilayers seem to be among the most important factors determining the nature of the membrane-water interface in a cell.

    ID:808
  37. Charlier L., Topin J., Ronin C., Kim S.K., Goddard W.A. 3rd, Efremov R., Golebiowski J. (2012). How broadly tuned olfactory receptors equally recognize their agonists. Human OR1G1 as a test case. Cell. Mol. Life Sci. 69 (24), 4205–13 [+]

    The molecular features that dominate the binding mode of agonists by a broadly tuned olfactory receptor are analyzed through a joint approach combining cell biology, calcium imaging, and molecular modeling. The odorant/receptor affinities, estimated through statistics accrued during molecular dynamics simulations, are in accordance with the experimental ranking. Although in many systems receptors recognize their target through a network of oriented interactions, such as H-bonding, the binding by broadly tuned olfactory receptors is dominated by non-polar terms. We show how such a feature allows chemicals belonging to different chemical families to similarly activate the receptors through compensations of interactions within the binding site.

    ID:811
  38. Polyansky A.A., Chugunov A.O., Vassilevski A.A., Grishin E.V., Efremov R.G. (2012). Recent Advances in Computational Modeling of α-Helical Membrane- Active Peptides. Curr. Protein Pept. Sci. 13 (7), 644–57 [+]

    Membrane-active peptides (MAPs) represent a broad variety of molecules, and biological functions of most are directly associated with their ability to interact with membranes. Taking into account the effect of MAPs on living cells they can be nominally divided into three major groups - fusion (FPs), antimicrobial/cytolytic (AMPs/CPs) and cellpenetrating (CPPs) peptides. Although spatial structure of different MAPs varies to a great extent, linear α-helical peptides represent the most studied class. These peptides possess relatively simple structural organization and share a set of similar molecular features, which make them very attractive to both experimental and computational studies. Here, we review different molecular modeling methods in prospective of their applications to study of α-helical MAPs. The most sophisticated of them, such as molecular dynamics simulations, give atomistic information about molecular interactions driving peptide binding to the water-lipid interface, cooperative mechanisms of membrane destabilization and thermodynamics of these processes. Significant progress has been achieved in this field during the last few years, resulting in a possibility to observe computationally MAPs action in realistic peptide-to-lipid ratios and over the microsecond timescale. Other relatively simple but powerful approaches allow assessment of important characteristics of MAPs such as α-helical propensity, amphiphilicity, total hydrophobicity, and spatial distribution of charge and hydrophobic/hydrophilic properties, etc. Altogether, computational methods provide efficient basis for rational design of MAPs with predefined properties and a spectrum of biological activities.

    ID:813
  39. Polyansky A.A., Volynsky P.E., Efremov R.G. (2012). Multistate organization of transmembrane helical protein dimers governed by the host membrane. J. Am. Chem. Soc. 134 (35), 14390–400 [+]

    Association of transmembrane (TM) helices taking place in the cell membrane has an important contribution to the biological function of bitopic proteins, among which receptor tyrosine kinases represent a typical example and a potent target for medical applications. Since this process depends on a complex interplay of different factors (primary structures of TM domains and juxtamembrane regions, composition and phase of the local membrane environment, etc.), it is still far from being fully understood. Here, we present a computational modeling framework, which we have applied to systematically analyze dimerization of 18 TM helical homo- and heterodimers of different bitopic proteins, including the family of epidermal growth factor receptors (ErbBs). For this purpose, we have developed a novel surface-based modeling approach, which not only is able to predict particular conformations of TM dimers in good agreement with experiment but also provides screening of their conformational heterogeneity. Using all-atom molecular dynamics simulations of several of the predicted dimers in different model membranes, we have elucidated a putative role of the environment in selection of particular conformations. Simulation results clearly show that each particular bilayer preferentially stabilizes one of possible dimer conformations, and that the energy gain depends on the interplay between structural properties of the protein and the membrane. Moreover, the character of protein-driven perturbations of the bilayer is reflected in the contribution of a particular membrane to the free energy gain. We have found that the approximated dimerization strength for ErbBs family can be related to their oncogenic ability.

    ID:810
  40. Konshina A.G., Dubovskii P.V., Efremov R.G. (2012). Structure and dynamics of cardiotoxins. Curr. Protein Pept. Sci. 13 (6), 570–84 [+]

    Cytotoxins (or cardiotoxins; CTs) are toxins from cobra venom characterized by the three-finger (TF) fold. CTs are on average 60-residue-long peptides, possessing as many as 4 disulfide bonds. The elements of antiparallel β-structure take origin from the hydrophobic core formed by the disulfides. The β-strands adopt the shape of the three loops, giving the name of the fold. While neurotoxins (NTs) - also TF proteins from snake venom - exert their effect through specific interactions with protein receptors, no specific protein target has been found for CTs. Unlike NTs, CTs are amphiphilic and cytotoxic against a variety of cells, including cancer ones. Thus, the hypothesis that the activity of CTs is caused by their interactions with lipid membranes is currently central. To understand molecular basis behind variations in toxicities of CTs highly homologous in their sequences, detailed knowledge of their structure and dynamics is required. The present review summarizes experimental and computational data on the spatial organization of CTs and their dynamics in various environments (aqueous solution, membranous milieus).

    ID:772
  41. Polyansky A.A., Zagrovic B. (2012). Protein Electrostatic Properties Predefining the Level of Surface Hydrophobicity Change upon Phosphorylation. J Phys Chem Lett 3, 973–976 [+]

    We use explicit-solvent, molecular dynamics simulations to study the change in polar properties of a solvent-accessible surface for proteins undergoing phosphorylation. We analyze eight different pairs of proteins representing different structural classes in native and phosphorylated states and estimate the polarity of their surface using the molecular hydrophobicity potential approach. Whereas the phosphorylation-induced hydrophobicity change in the vicinity of phosphosites does not vary strongly among the studied proteins, the equivalent change for complete proteins covers a surprisingly wide range of effects including even an increase in the overall hydrophobicity in some cases. Importantly, the observed changes are strongly related to electrostatic properties of proteins, such as the net charge per residue, the distribution of charged side-chain contacts, and the isoelectric point. These features predefine the level of surface hydrophobicity change upon phosphorylation and may thus contribute to the phosphorylation-induced alteration of the interactions between a protein and its environment.

    ID:815
  42. Чугунов А.О., Полянский А.А., Ефремов Р.Г. (2012). Липидный фундамент жизни. Природа  (3), 3–12 [+]

    Жизнь в том виде, в каком мы ее знаем, невозможно представить без биомембраны, разделяющей «внутренний мир» клетки и всё остальное пространство. Мембрана обеспечивает взаимодействие клетки с внешней средой, избирательно пропуская многие вещества, а также является средой протекания множества биохимических процессов. И хотя большую часть полезной работы выполняют белки, которыми мембрана буквально «нашпигована», роль липидного матрикса не стоит недооценивать. Липиды — это не просто «океан», в котором плавают белки. Это «умный» океан, чьи физико-химические свойства были тщательно подобраны в ходе эволюции так, чтобы создать эффективную платформу для функционирования и взаимодействия мембранных белков.

    ID:747
  43. Ostapchenko V.G., Gasparian M.E., Kosinsky Y.A., Efremov R.G., Dolgikh D.A., Kirpichnikov M.P. (2012). Dissecting structural basis of the unique substrate selectivity of human enteropeptidase catalytic subunit. J. Biomol. Struct. Dyn. 30 (1), 62–73 [+]

    Enteropeptidase is a key enzyme in the digestion system of higher animals. It initiates enzymatic cascade cleaving trypsinogen activation peptide after a unique sequence DDDDK. Recently, we have found specific activity of human enteropeptidase catalytic subunit (L-HEP) being significantly higher than that of its bovine ortholog (L-BEP). Moreover, we have discovered that L-HEP hydrolyzed several nonspecific peptidic substrates. In this work, we aimed to further characterize species-specific enteropeptidase activities and to reveal their structural basis. First, we compared hydrolysis of peptides and proteins lacking DDDDK sequence by L-HEP and L-BEP. In each case human enzyme was more efficient, with the highest hydrolysis rate observed for substrates with a large hydrophobic residue in P2-position. Computer modeling suggested enzyme exosite residues 96 (Arg in L-HEP, Lys in L-BEP) and 219 (Lys in L-HEP, Gln in L-BEP) to be responsible for these differences in enteropeptidase catalytic activity. Indeed, human-to-bovine mutations Arg96Lys, Lys219Gln shifted catalytic properties of L-HEP toward those of L-BEP. This effect was amplified in case of the double mutation Arg96Lys/Lys219Gln, but still did not cover the full difference in catalytic activities of human and bovine enzymes. To find a missing link, we studied monopeptide benzyl-arginine-β-naphthylamide hydrolysis. L-HEP catalyzed it with an order lower K (m) than L-BEP, suggesting the monopeptide-binding S1 site input into catalytic distinction between two enteropeptidase species. Together, our findings suggest structural basis of the unique catalytic properties of human enteropeptidase and instigate further studies of its tentative physiological and pathological roles.

    ID:809
  44. Semenova A.A., Chugunov A.O., Dubovskii P.V., Chupin V.V., Volynsky P.E., Boldyrev I.A. (2011). The role of chain rigidity in lipid self-association: Comparative study of dihexanoyl- and disorbyl-phosphatidylcholines. Chem. Phys. Lipids 165, 382–386 [+]

    In the course of structure-function investigations of lipids a phosphatidylcholine molecule with short and rigid tails, di-2,4-hexadienoylphosphatidylcholine (DiSorbPC), was synthesized and studied in comparison with its saturated analog, dihexanoylphosphatidylcholine (DHPC). Conjugated double bonds in the acyl chains in DiSorbPC reduce considerably the number of possible conformers of the lipid within an aggregate. This leads to impaired packing of unsaturated acyl chains and thus, to a surprisingly high (115Å(2)) area per molecule for DiSorbPC at the air-water interface and failure to form micelles of regular size and shape. Details on DiSorbPC aggregation and packing provided by a set of experimental techniques combined with molecular dynamics simulations are presented.

    ID:669
  45. Чугунов А.О., Ефремов Р.Г. (2010). Компьютерные игры в молекулярную биофизику. Природа  (12), 36–43 [+]

    Кконцу XX в. грань между «классическими» науками практически стерлась, исследования стали междисциплинарными. В текущем столетии тенденция усиливается — слияние «обычной» (хотя тоже междисциплинарной!) молекулярной биофизики и того, что называют theoretical computer science, породило необыкновенную область исследований — компьютерный, или in silico, эксперимент. Но прежде чем рассказать о методической подоплеке подхода in silico и о его конкретном использовании для имитационного изучения «жизни» биологических мембран и населяющих их белковых молекул, напомним предысторию.

    ID:746
  46. Chugunov A.O., Simms J., Poyner D.R., Dehouck Y., Rooman M., Gilis D., Langer I. (2010). Evidence that interaction between conserved residues in transmembrane helices 2, 3, and 7 are crucial for human VPAC1 receptor activation. Mol. Pharmacol. 78 (3), 394–401 [+]

    The VPAC(1) receptor belongs to family B of G protein-coupled receptors (GPCR-B) and is activated upon binding of the vasoactive intestinal peptide (VIP). Despite the recent determination of the structure of the N terminus of several members of this receptor family, little is known about the structure of the transmembrane (TM) region and about the molecular mechanisms leading to activation. In the present study, we designed a new structural model of the TM domain and combined it with experimental mutagenesis experiments to investigate the interaction network that governs ligand binding and receptor activation. Our results suggest that this network involves the cluster of residues Arg(188) in TM2, Gln(380) in TM7, and Asn(229) in TM3. This cluster is expected to be altered upon VIP binding, because Arg(188) has been shown previously to interact with Asp(3) of VIP. Several point mutations at positions 188, 229, and 380 were experimentally characterized and were shown to severely affect VIP binding and/or VIP-mediated cAMP production. Double mutants built from reciprocal residue exchanges exhibit strong cooperative or anticooperative effects, thereby indicating the spatial proximity of residues Arg(188), Gln(380), and Asn(229). Because these residues are highly conserved in the GPCR-B family, they can moreover be expected to have a general role in mediating function.

    ID:368
  47. Bocharov E.V., Mayzel M.L., Volynsky P.E., Mineev K.S., Tkach E.N., Ermolyuk Y.S., Schulga A.A., Efremov R.G., Arseniev A.S. (2010). Left-handed dimer of EphA2 transmembrane domain: Helix packing diversity among receptor tyrosine kinases. Biophys. J. 98 (5), 881–9 [+]

    The Eph receptor tyrosine kinases and their membrane-bound ephrin ligands control a diverse array of cell-cell interactions in the developing and adult organisms. During signal transduction across plasma membrane, Eph receptors, like other receptor tyrosine kinases, are involved in lateral dimerization and subsequent oligomerization presumably with proper assembly of their single-span transmembrane domains. Spatial structure of dimeric transmembrane domain of EphA2 receptor embedded into lipid bicelle was obtained by solution NMR, showing a left-handed parallel packing of the transmembrane helices (535-559)(2). The helices interact through the extended heptad repeat motif L(535)X(3)G(539)X(2)A(542)X(3)V(546)X(2)L(549) assisted by intermolecular stacking interactions of aromatic rings of (FF(557))(2), whereas the characteristic tandem GG4-like motif A(536)X(3)G(540)X(3)G(544) is not used, enabling another mode of helix-helix association. Importantly, a similar motif AX(3)GX(3)G as was found is responsible for right-handed dimerization of transmembrane domain of the EphA1 receptor. These findings serve as an instructive example of the diversity of transmembrane domain formation within the same family of protein kinases and seem to favor the assumption that the so-called rotation-coupled activation mechanism may take place during the Eph receptor signaling. A possible role of membrane lipid rafts in relation to Eph transmembrane domain oligomerization and Eph signal transduction was also discussed.

    ID:320
  48. Volynsky P.E., Mineeva E.A., Goncharuk M.V., Ermolyuk Y.S., Arseniev A.S., Efremov R.G. (2010). Computer simulations and modeling-assisted ToxR screening in deciphering 3D structures of transmembrane alpha-helical dimers: ephrin receptor A1. Phys Biol 7, 16014 [+]

    Membrane-spanning segments of numerous proteins (e.g. receptor tyrosine kinases) represent a novel class of pharmacologically important targets, whose activity can be modulated by specially designed artificial peptides, the so-called interceptors. Rational construction of such peptides requires understanding of the main factors driving peptide-peptide association in lipid membranes. Here we present a new method for rapid prediction of the spatial structure of transmembrane (TM) helix-helix complexes. It is based on computer simulations in membrane-like media and subsequent refinement/validation of the results using experimental studies of TM helix dimerization in a bacterial membrane by means of the ToxR system. The approach was applied to TM fragments of the ephrin receptor A1 (EphA1). A set of spatial structures of the dimer was proposed based on Monte Carlo simulations in an implicit membrane followed by molecular dynamics relaxation in an explicit lipid bilayer. The resulting models were employed for rational design of wild-type and mutant genetic constructions for ToxR assays. The computational and the experimental data are self-consistent and provide an unambiguous spatial model of the TM dimer of EphA1. The results of this work can be further used to develop new biologically active 'peptide interceptors' specifically targeting membrane domains of proteins.

    ID:312
  49. Чугунов А.О., Ефремов Р.Г. (2009). Предсказание пространственной структуры белков: акцент на мембранных мишенях. Биоорг. хим. 35 (6), 1–17 [+]

    Интегральные белки биологических мембран — объекты, пространственная структура которых с большим трудом поддаётся экспериментальному определению. Во многих случаях существует возможность теоретического предсказания строения белковых молекул, используя физические или эмпирические закономерности. В обзоре рассмотрены основные существующие приёмы предсказания пространственной структуры белков с использованием компьютерных алгоритмов; основной акцент сделан на наиболее «сложные» объекты — мембранных белки (МБ).

    Отдельно описаны идеология “de novo”-предсказаний, основывающаяся на эмпирических физических закономерностях, и подход сопоставительного моделирования (или моделирования на основании гомологии), в котором используется информация о трёхмерном строении родственных белков. В качестве примеров рассмотрены фармакологически важные классы G-белоксопряжённых рецепторов, рецепторных тирозинкиназ и другие МБ. Обсуждаются потенциальные сферы применения моделей белков и существующие подходы к оценке «качества» упаковки полипептидной цепи в моделях.

    ID:188
  50. Pyrkov T.V., Chugunov A.O., Krylov N.A., Nolde D.E., Efremov R.G. (2009). PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. Bioinformatics 25 (9), 1201–2 [+]

    The PLATINUM (Protein-Ligand ATtractions Investigation NUMerically) web service is designed for analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structures. Furthermore, PLATINUM provides a number of tools for quantitative characterization of the hydrophobic/hydrophilic match in biomolecular complexes e.g. in docking poses. These complement standard scoring functions. The calculations are based on the concept of empirical Molecular Hydrophobicity Potential (MHP). AVAILABILITY: The PLATINUM web tool as well as detailed documentation and tutorial are available free of charge for academic users at http://model.nmr.ru/platinum/. PLATINUM requires Java 5 or higher and Adobe Flash Player 9. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

    ID:184
  51. Polyansky A.A., Volynsky P.E., Arseniev A.S., Efremov R.G. (2009). Adaptation of a membrane-active peptide to heterogeneous environment. I. Structural plasticity of the peptide. The journal of physical chemistry. B 113 (4), 1107–19 [+]

    В статье приводится детальное описание различных факторов, определяющих процесс взаимодействия мембрано-активного пептида (неспецифический переносчик—пенетратин) с липидными бислоями разного состава. К ключевым факторам следует отнести: конформационную подвижность пептида, способность аминокислотных остатков образовывать специфические контакты с другими остатками пептида, а также полярными головками липидов.

    ID:125
  52. Polyansky A.A., Volynsky P.E., Arseniev A.S., Efremov R.G. (2009). Adaptation of a membrane-active peptide to heterogeneous environment. II. The role of mosaic nature of the membrane surface. The journal of physical chemistry. B 113 (4), 1120–6 [+]

    В статье постулируется мозаичная гидрофобно-гдрофильная организация поверхности липидной мембраны. Рассматривается влияние гетерогенности полярных свойств границы раздела вода-липиды на процесс связывания мембрано-активных агентов (на примере неспецифического пептидного переносчика — пенетратина).

    ID:126
  53. Farce A., Chugunov A.O., Logé C., Sabaouni A., Yous S., Dilly S., Renault N., Vergoten G., Efremov R.G., Lesieur D., Chavatte P. (2008). Homology modeling of MT1 and MT2 receptors. European journal of medicinal chemistry 43 (9), 1926–44 [+]

    Melatonin is a neurohormone synthesized and secreted mainly during the dark period of the circadian cycle by the pineal gland. It has already been proved to be involved in a number of chronobiological processes, most of them being mediated by its membranar receptors MT1 and MT2. Both are members of the GPCR class and, despite the interest they elicit, their 3D structure is still to be described. Models for both human MT1 and MT2 receptors have been constructed by homology modeling, using the X-ray structure of bovine rhodopsin as template. These models have been evaluated in terms of hydrophobic properties of the helices and refined to take into account the rearrangement of GPCRs necessary for their activation, thus leading to a putative activated model for each subtype.

    ID:179
  54. Dubovskii P.V., Volynsky P.E., Polyansky A.A., Karpunin D.V., Chupin V.V., Efremov R.G., Arseniev A.S. (2008). Three-dimensional structure/hydrophobicity of latarcins specifies their mode of membrane activity. Biochemistry 47 (11), 3525–33 [+]

    Latarcins, linear peptides from the Lachesana tarabaevi spider venom, exhibit a broad-spectrum antimicrobial activity, likely acting on the bacterial cytoplasmic membrane. We study their spatial structures and interaction with model membranes by a combination of experimental and theoretical methods to reveal the structure-activity relationship. In this work, a 26 amino acid peptide, Ltc1, was investigated. Its spatial structure in detergent micelles was determined by (1)H nuclear magnetic resonance (NMR) and refined by Monte Carlo simulations in an implicit water-octanol slab. The Ltc1 molecule was found to form a straight uninterrupted amphiphilic helix comprising 8-23 residues. A dye-leakage fluorescent assay and (31)P NMR spectroscopy established that the peptide does not induce the release of fluorescent marker nor deteriorate the bilayer structure of the membranes. The voltage-clamp technique showed that Ltc1 induces the current fluctuations through planar membranes when the sign of the applied potential coincides with the one across the bacterial inner membrane. This implies that Ltc1 acts on the membranes via a specific mechanism, which is different from the carpet mode demonstrated by another latarcin, Ltc2a, featuring a helix-hinge-helix structure with a hydrophobicity gradient along the peptide chain. In contrast, the hydrophobic surface of the Ltc1 helix is narrow-shaped and extends with no gradient along the axis. We have also disclosed a number of peptides, structurally homologous to Ltc1 and exhibiting similar membrane activity. This indicates that the hydrophobic pattern of the Ltc1 helix and related antimicrobial peptides specifies their activity mechanism. The latter assumes the formation of variable-sized lesions, which depend upon the potential across the membrane.

    ID:315
  55. Bocharov E.V., Mineev K.S., Volynsky P.E., Ermolyuk Y.S., Tkach E.N., Sobol A.G., Chupin V.V., Kirpichnikov M.P., Efremov R.G., Arseniev A.S. (2008). Spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 presumably corresponding to the receptor active state. J. Biol. Chem. 283 (11), 6950–6 [+]

    Proper lateral dimerization of the transmembrane domains of receptor tyrosine kinases is required for biochemical signal transduction across the plasma membrane. The spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 embedded into lipid bicelles was obtained by solution NMR, followed by molecular dynamics relaxation in an explicit lipid bilayer. ErbB2 transmembrane segments associate in a right-handed alpha-helical bundle through the N-terminal tandem GG4-like motif Thr652-X3-Ser656-X3-Gly660, providing an explanation for the pathogenic power of some oncogenic mutations.

    ID:314
  56. Vereshaga Y.A., Volynsky P.E., Pustovalova J.E., Nolde D.E., Arseniev A.S., Efremov R.G. (2007). Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study. Proteins 69 (2), 309–25 [+]

    Предложен вычислительный метод предсказания пространственной структуры димеров трансмембранных альфа-спиралей. Подход основан на применении модели неявно заданной мембраны и конформационного поиска методом Монте-Карло в пространстве двугранных углов пептидов. Эффективность метода продемонстрирована на примере трансмембранного домена проапоптотического митохондриального белка BNIP3.

    ID:124
  57. Efremov R.G., Volynsky P.E., Nolde D.E., Vergoten G., Arseniev A.S. (2007). The membrane-proximal fusion domain of HIV-1 GP41 reveals sequence-specific and fine-tuning mechanism of membrane binding. J. Biomol. Struct. Dyn. 25 (2), 195–205 [+]

    The membrane interface-partitioning region preceding the transmembrane anchor of the human immunodeficiency virus type 1 (HIV-1) gp41 envelope protein is one of the sites responsible for virus binding to its host cell membrane and subsequent fusion events. Here, we used molecular modeling techniques to assess membrane interactions, structure, and hydrophobic properties of the fusion-active peptide representing this region, several of its homologs from different HIV-1 strains, as well as a peptide - defective gp41 phenotype - unable to mediate cell-cell fusion and virus entry. It is shown that the wild-type peptides bind to the water-membrane interface in alpha-helical conformation, while the mutant adopts partly destabilized helix-break-helix structure on the membrane surface. The wild-type peptides reveal specific "tilted oblique-oriented" pattern of hydrophobicity on their surfaces - the property specific for fusion regions of other viruses. Fusion peptides penetrate into the membrane with their N-termini and reveal "fine-tuning" interactions with membrane and water environments: the shift of this balance (e.g., due to point mutations) may dramatically change the mode of membrane binding, and therefore, may cause loss of fusion activity. The modeling results agree well with experimental data and provide a strategy to delineate fusogenic regions in amino acid sequences of viral proteins.

    ID:313
  58. Chugunov A.O., Novoseletsky V.N., Nolde D.E., Arseniev A.S., Efremov R.G. (2007). Method to assess packing quality of transmembrane alpha-helices in proteins. 1. Parametrization using structural data. Journal of chemical information and modeling 47 (3), 1150–62 [+]

    Integral membrane proteins (MPs) are pharmaceutical targets of exceptional importance. Modern methods of three-dimensional protein structure determination often fail to supply the fast growing field of structure-based drug design with the requested MPs' structures. That is why computational modeling techniques gain a special importance for these objects. Among the principal difficulties limiting application of these methods is the low quality of the MPs' models built in silico. In this series of two papers we present a computational approach to the assessment of the packing "quality" of transmembrane (TM) alpha-helical domains in proteins. The method is based on the concept of protein environment classes, whereby each amino acid residue is described in terms of its environment polarity and accessibility to the membrane. In the first paper we analyze a nonredundant set of 26 TM alpha-helical domains and compute the residues' propensities to five predefined classes of membrane-protein environments. Here we evaluate the proposed approach only by various test sets, cross-validation protocols and ability of the method to delimit the crystal structure of visual rhodopsin, and a number of its erroneous theoretical models. More advanced validation of the method is given in the second article of this series. We assume that the developed "membrane score" method will be helpful in optimizing computer models of TM domains of MPs, especially G-protein coupled receptors.

    ID:1
  59. Chugunov A.O., Novoseletsky V.N., Nolde D.E., Arseniev A.S., Efremov R.G. (2007). Method to assess packing quality of transmembrane alpha-helices in proteins. 2. Validation by "correct vs misleading" test. Journal of chemical information and modeling 47 (3), 1163–70 [+]

    We describe a set of tests designed to check the ability of the new "membrane score" method (see the first paper of this series) to assess the packing quality of transmembrane (TM) alpha-helical domains in proteins. The following issues were addressed: (1) Whether there is a relation between the score (S(mem)) of a model and its closeness to the "nativelike" conformation? (2) Is it possible to recognize a correct model among misfolded and erroneous ones? (3) To what extent the score of a homology-built model is sensitive to errors in sequence alignment? To answer the first question, two test cases were considered: (i) Several models of bovine aquaporin-1 (target protein) were built on the structural templates provided by its homologs with known X-ray structure. (ii) Side chains in the spatial models of visual rhodopsin and cytochrome c oxidase were rebuilt based on the backbone scaffolds taken from their crystal structures, and the resulting models were iteratively fitted into the full-atom X-ray conformations. It was shown that the higher the S(mem) value of a model is, the lower its root-mean-square deviation is from the "correct" (crystal) structure of a target. Furthermore, the "membrane score" method successfully identifies the rhodopsin crystal structure in an ensemble of "rotamer-type" decoys, thus providing the way to optimize mutual orientations of alpha-helices in models of TM domains. Finally, being applied to a set of homology models of rhodopsin built on its crystal structure with systematically shifted alignment, the approach demonstrates a prominent ability to detect alignment errors. We therefore assume that the "membrane score" method will be helpful in optimization of in silico models of TM domains in proteins, especially those in GPCRs.

    ID:2
  60. Chugunov A.O., Novoseletsky V.N., Arseniev A.S., Efremov R.G. (2007). A novel method for packing quality assessment of transmembrane alpha-helical domains in proteins. Biochemistry Mosc. 72 (3), 293–300 [+]

    Here we present a novel method for assessment of packing quality for transmembrane (TM) domains of alpha-helical membrane proteins (MPs), based on analysis of available high-resolution experimental structures of MPs. The presented concept of protein-membrane environment classes permits quantitative description of packing characteristics in terms of membrane accessibility and polarity of the nearest protein groups. We demonstrate that the method allows identification of native-like conformations among the large set of theoretical MP models. The developed "membrane scoring function" will be of use for optimization of TM domain packing in theoretical models of MPs, first of all G-protein coupled receptors.

    ID:186
  61. Pyrkov T.V., Kosinsky Y.A., Arseniev A.S., Priestle J.P., Jacoby E., Efremov R.G. (2007). Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions. Proteins 66 (2), 388–98 [+]

    Анализ экспериментально установленных пространственных структур комплексов АТФ-белок был проведен с целью выявить основные закономерности, определяющие молекулярное узнавание аденин-белок. Было показано что основную роль играют гидрофобные котакты и стэкинг, и разработан эффективный метод учета этих взаимодействий в аденин-специфичной оценочной функции.

    ID:123
  62. Efremov R.G., Chugunov A.O., Pyrkov T.V., Priestle J.P., Arseniev A.S., Jacoby E. (2007). Molecular lipophilicity in protein modeling and drug design. Curr. Med. Chem. 14 (4), 393–415 [+]

    Hydrophobic interactions play a key role in the folding and maintenance of the 3-dimensional structure of proteins, as well as in the binding of ligands (e.g. drugs) to protein targets. Therefore, quantitative assessment of spatial hydrophobic (lipophilic) properties of these molecules is indispensable for the development of efficient computational methods in drug design. One possible solution to the problem lies in application of a concept of the 3-dimensional molecular hydrophobicity potential (MHP). The formalism of MHP utilizes a set of atomic physicochemical parameters evaluated from octanol-water partition coefficients (log P) of numerous chemical compounds. It permits detailed assessment of the hydrophobic and/or hydrophilic properties of various parts of molecules and may be useful in analysis of protein-protein and protein-ligand interactions. This review surveys recent applications of MHP-based techniques to a number of biologically relevant tasks. Among them are: (i) Detailed assessment of hydrophobic/hydrophilic organization of proteins; (ii) Application of this data to the modeling of structure, dynamics, and function of globular and membrane proteins, membrane-active peptides, etc. (iii) Employment of the MHP-based criteria in docking simulations for ligands binding to receptors. It is demonstrated that the application of the MHP-based techniques in combination with other molecular modeling tools (e.g. Monte Carlo and molecular dynamics simulations, docking, etc.) permits significant improvement to the standard computational approaches, provides additional important insights into the intimate molecular mechanisms driving protein assembling in water and in biological membranes, and helps in the computer-aided drug discovery process.

    ID:185
  63. Chugunov A.O., Farce A., Chavatte P., Efremov R.G. (2006). Differences in binding sites of two melatonin receptors help to explain their selectivity to some melatonin analogs: a molecular modeling study. J. Biomol. Struct. Dyn. 24 (2), 91–107 [+]

    Numerous diseases have been linked to the malfunction of G-protein coupled receptors (GPCRs). Their adequate treatment requires rational design of new high-affinity and high-selectivity drugs targeting these receptors. In this work, we report three-dimensional models of the human MT(1) and MT(2) melatonin receptors, members of the GPCR family. The models are based on the X-ray structure of bovine rhodopsin. The computational approach employs an original procedure for optimization of receptor-ligand structures. It includes rotation of one of the transmembrane alpha-helices around its axis with simultaneous assessment of quality of the resulting complexes according to a number of criteria we have developed for this purpose. The optimal geometry of the receptor-ligand binding is selected based on the analysis of complementarity of hydrophobic/hydrophilic properties between the ligand and its protein environment in the binding site. The elaborated "optimized" models are employed to explore the details of protein-ligand interactions for melatonin and a number of its analogs with known affinity to MT(1) and MT(2) receptors. The models permit rationalization of experimental data, including those that were not used in model building. The perspectives opened by the constructed models and by the optimization procedure in the design of new drugs are discussed.

    ID:187
  64. Volynsky P.E., Bocharov E.V., Nolde D.E., Vereshaga Y.A., Mayzel M.L., Mineev K.S., Mineeva E.V., Pustovalova Yu.E., Gagnidze I.A., Efremov R.G., Arseniev A.S. (2006). Solution of the Spatial Structure of Dimeric Transmembrane Domains of Proteins by Heteronuclear NMR Spectroscopy and Molecular Modeling. Biophysics 51 (S1), S23–S27 [+]

    Membrane proteins play an important role in various biological processes. An approach combining
    NMR spectroscopy with molecular modeling was used to study the spatial structure and intramolecular dynamics of protein transmembrane domains consisting of two interacting α-helices. The approach was tested with model transmembrane domains and yielded detailed atomic-level data on the protein–protein and protein–lipid interactions.

    ID:347
  65. Polyansky A.A., Volynsky P.E., Nolde D.E., Arseniev A.S., Efremov R.G. (2005). Role of lipid charge in organization of water/lipid bilayer interface: insights via computer simulations. The journal of physical chemistry. B 109 (31), 15052–9 [+]

    Anionic unsaturated lipid bilayers represent suitable model systems that mimic real cell membranes: they are fluid and possess a negative surface charge. Understanding of detailed molecular organization of water-lipid interfaces in such systems may provide an important insight into the mechanisms of proteins' binding to membranes. Molecular dynamics (MD) of full-atom hydrated lipid bilayers is one of the most powerful tools to address this problem in silico. Unfortunately, wide application of computational methods for such systems is limited by serious technical problems. They are mainly related to correct treatment of long-range electrostatic effects. In this study a physically reliable model of an anionic unsaturated bilayer of 1,2-dioleoyl-sn-glycero-3-phosphoserine (DOPS) was elaborated and subjected to long-term MD simulations. Electrostatic interactions were treated with two different algorithms: spherical cutoff function and particle-mesh Ewald summation (PME). To understand the role of lipid charge in the system behavior, similar calculations were also carried out for zwitterionic bilayer composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). It was shown that, for the charged DOPS bilayer, the PME protocol performs much better than the cutoff scheme. In the last case a number of artifacts in the structural organization of the bilayer were observed. All of them were attributed to inadequate treatment of electrostatic interactions of lipid headgroups with counterions. Electrostatic properties, along with structural and dynamic parameters, of both lipid bilayers were investigated. Comparative analysis of the MD data reveals that the water-lipid interface of the DOPC bilayer is looser than that for DOPS. This makes possible deeper penetration of water molecules inside the zwitterionic (DOPC) bilayer, where they strongly interact with carbonyls of lipids. This can lead to thickening of the membrane interface in zwitterionic as compared to negatively charged bilayers.

    ID:843
  66. Dioubankova N.N., Malakhov A.D., Stetsenko D.A., Gait M.J., Volynsky P.E., Efremov R.G., Korshun V.A. (2003). Pyrenemethyl ara-uridine-2'-carbamate: a strong interstrand excimer in the major groove of a DNA duplex. Chembiochem 4 (9), 841–7 [+]

    The synthesis of new nucleoside derivatives, ara-uridine-2'-carbamates, and their incorporation into synthetic DNA oligomers is described. The modification directs ligands into the major groove of duplex DNA and somewhat destabilizes the duplexes of modified oligonucleotides with complementary DNA or RNA. In the case of pyrenemethyl carbamate modification in DNA-DNA duplexes, the destabilization is considerably reduced. The pyrenemethyl derivative also shows remarkable spectral properties: a "reversed" absorbance change for pyrene at 350 nm in the course of denaturation of the DNA duplex, as compared to the change seen in the nucleotide absorbance at 260 nm. This derivatization also causes pronounced sequence-dependent excimer formation in the major groove.

    ID:768
  67. Efremov R.G., Nolde D.E., Vergoten G., Arseniev A.S. (1999). A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation. Biophys. J. 76 (5), 2448–59 [+]

    В работе дается описание неявно заданной модели мембраны. Показана эффективность модели в предсказании доли альфа-спиральной конформации для нескольких гомопептидов (поли-Leu, поли-Val, поли-Ile, поли-Gly) методом Монте-Карло.

    ID:122
  68. Efremov R.G., Vergoten G. (1995). The hydrophobic nature of membrane-spanning alpha-helices as revealed by Monte Carlo simulations and molecular hydrophobicity potential analysis. J. Phys. Chem. 99 (26), 10658–10666 [+]

    С помощью двух независимых подходов – метода молекулярного гидрофобного потенциала (МГП) и расчета поведения пептида в явно заданных растворителях с различной степенью полярности методом Монте-Карло – исследована гидрофобная организация альфа-спиральных трансмембранных сегментов нескольких белков. Показана высокая эффективность МГП-подхода в количественной характеризации и картировании гидрофобных/гидрофильных характеристик трансмембранных сегментов белков.

    ID:121

Ефремов Роман Гербертович

  • Москва, ул. Миклухо-Маклая, 16/10 — На карте
  • ИБХ РАН, корп. БОН, комн. 522
  • Тел.: +7(495)330-58-74
  • Эл. почта: efremov@nmr.ru

Температурная активация рецептора TRPV1: моделирование на компьютере (2016-11-19)

Ванилоидный рецептор типа 1 (TRPV1) — важнейший молекулярный сенсор нашего организма, реагирующий на повышение температуры, понижение pH (закисление), а также на капсаицин — вещество жгучего перца. Именно активации этого катионного канала мы обязаны ощущением «пожара» во рту от острой пищи, а также болевому ощущению при контакте с предметами горячее 43 °C. В этой работе 2016 года мы промоделировали температурную активацию рецептора TRPV1 с помощью молекулярной динамики (in silico эксперимент). Основываясь на определенных ранее структурах открытого и закрытого состояний TRPV1, мы создали компьютерную модель этого рецептора в липидной бислойной мембране, напоминающей нейрональную. В компьютерных экспериментах с повышением и понижением температуры мы идентифицировали серию событий «открывания» поры рецептора и чуть реже — «закрывания». Также мы предложили термодинамический механизм температурной активации белка, в котором важную роль играет экспонирование гидрофобных фрагментов в пору канала, в область контакта с растворителем. Еще одним интересным моментом стал механизм «асимметричного» открывания, который также следует из этих расчетов. Конечной целью работы можно считать создание в ближайшем будущем виртуального рецептора TRPV1, пригодного для предсказания структуры селективных лигандов. Ожидается, и не без основания, что такие лиганды найдут применение в медицине как анальгетические лекарства и будут лишены большинства побочных эффектов, свойственных современным препаратам группы нестероидных противовоспалительных средств. Подробнее о работе можно прочитать в пресс-релизе, опубликованном на сайте ИБХ.

Публикации

  1. Chugunov A.O., Volynsky P.E., Krylov N.A., Nolde D.E., Efremov R.G. (2016). Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains. Sci Rep 6, 33112 [+]

    Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of the organism. Despite the spatial structure of the channel in both open (O) and closed (C) states is known, microscopic nature of channel gating and mechanism of thermal sensitivity are still poorly understood. In this work, we used unrestrained atomistic molecular dynamics simulations of TRPV1 (without N- and C-terminal cytoplasmic domains) embedded into explicit lipid bilayer in its O- and C-states. We found that the pore domain with its neighboring loops undergoes large temperature-dependent conformational transitions in an asymmetric way, when fragments of only one monomer move with large amplitude, freeing the pore upon heating. Such an asymmetrical gating looks rather biologically relevant because it is faster and more reliable than traditionally proposed "iris-like" symmetric scheme of channel opening. Analysis of structural, dynamic, and hydrophobic organization of the pore domain revealed entropy growth upon TRPV1 gating, which is in line with current concepts of thermal sensitivity.

    ID:1558

Дизайн высокоаффинного аналога конотоксина PnIA на основе метода белковой топографии (2016-11-19)

Некоторое время назад мы предложили компьютерный алгоритм белковой топографии, применение которого позволило объяснить селективное действие α-нейротоксинов из яда скорпионов на потенциал-чувствительные натриевые каналы насекомых и млекопитающих. В этой работе (2016 года) мы применили описанный принцип — белковую топографию — для дизайна мутантной формы конотоксина PnIA, которая обладает самым высоким на сегодняшний день сродством к ацетилхолиновому рецептору никотинового типа (α7-нАХР). Основой для этого дизайна стал массив экспериментально полученных данных по активности различных конотоксинов по отношению к α7-нАХР, наработанный в Отделе молекулярных основ нейросигнализации (вместе с которым мы представляем это достижение). В этом же отделе проведено исчерпывающее функциональное тестирование предложенных аналогов PnIA, что вместе с применением компьютерного моделирования стало предпосылкой для успешного дизайна новых пептидов. В перспективе, подобный подход позволит создавать нейропептиды с требуемыми свойствами, которые найдут применение в исследованиях рецепторов и в медицине.

Публикации

  1. Kasheverov I.E., Chugunov A.O., Kudryavtsev D.S., Ivanov I.A., Zhmak M.N., Shelukhina I.V., Spirova E.N., Tabakmakher V.M., Zelepuga E.A., Efremov R.G., Tsetlin V.I. (2016). High-Affinity α-Conotoxin PnIA Analogs Designed on the Basis of the Protein Surface Topography Method. Sci Rep 6, 36848 [+]

    Despite some success for small molecules, elucidating structure-function relationships for biologically active peptides - the ligands for various targets in the organism - remains a great challenge and calls for the development of novel approaches. Some of us recently proposed the Protein Surface Topography (PST) approach, which benefits from a simplified representation of biomolecules' surface as projection maps, which enables the exposure of the structure-function dependencies. Here, we use PST to uncover the "activity pattern" in α-conotoxins - neuroactive peptides that effectively target nicotinic acetylcholine receptors (nAChRs). PST was applied in order to design several variants of the α-conotoxin PnIA, which were synthesized and thoroughly studied. Among the best was PnIA[R9, L10], which exhibits nanomolar affinity for the α7 nAChR, selectivity and a slow wash-out from this target. Importantly, these mutations could hardly be delineated by "standard" structure-based drug design. The proposed combination of PST with a set of experiments proved very efficient for the rational construction of new bioactive molecules.

    ID:1604

Определяющая роль мембраны в димеризации трансмембранных доменов белков: результаты молекулярного моделирования (2016-03-18)

Димеризация трансмембранных (ТМ) альфа-спиралей — важнейший процесс, определяющий функционирование широкого класса мембранных белков, в частности, рецепторных тирозинкиназ. Молекулярные аспекты механизма ассоциации спиральных доменов в липидном окружении до сих пор остаются неясными. Так, до последнего времени роль мембраны в процессе димеризации рассматривалась лишь поверхностно. В Лаборатории моделирования биомолекулярных систем провели компьютерное исследование структурно-динамических параметров липидного бислоя вблизи мономеров и димеров гликофорина А человека, который является характерной моделью для изучения димеризации ТМ доменов, двух его мутантных форм и двух модельных пептидов. С помощью метода молекулярной динамики были оценены неоднородности в распределении средней плотности липидов. Показано, что даже одиночные спирали вызывают формирование стабильных во времени неоднородностей распределения липидов в гидрофобной области бислоя. При димеризации белка картина усложняется, т. к. ацильные цепи липидов заполняют все неровности поверхности формирующегося димера. Расчёты вкладов различных типов взаимодействий в свободную энергию ассоциации показали, что именно взаимодействие ТМ доменов с липидным окружением вносит наибольший вклад. Таким образом, димеризация ТМ спиралей имеет энтропийную природу и во многом определяется способностью белка связывать липиды на своей поверхности. Впервые получены аргументы в пользу гипотезы об определяющей роли мембраны в процессах олигомеризации ТМ спиралей белков.

Публикации

  1. Kuznetsov A.S., Polyansky A.A., Fleck M., Volynsky P.E., Efremov R.G. (2015). Adaptable Lipid Matrix Promotes Protein-Protein Association in Membranes. J. Chem. Theory Comput. 11 (9), 4415–26 [+]

    Трансмембранные домены играют важную роль в функционировании мембранных белков. Их взаимодействия определяют работу ряда важнейших рецепторов, в частности, рецепторных тирозинкиназ. В настоящей работе на примере гликофорина А и двух модельних пептидов показали, что липидный бислой играет важную роль в димеризации трансмембранных спиралей. Встраивание пептида в мембрану вызывает формирование характерных неоднородностей в последней. Таким образом, димеризация трансмембранных спиралей может носить энтропийный характер.

    ID:1342
  2. Kuznetsov A.S., Volynsky P.E., Efremov R.G. (2015). Role of the Lipid Environment in the Dimerization of Transmembrane Domains of Glycophorin A. Acta Naturae 7 (4), 122–7 [+]

    An efficient computational approach is developed to quantify the free energy of a spontaneous association of the α-helices of proteins in the membrane environment. The approach is based on the numerical decomposition of the free energy profiles of the transmembrane (TM) helices into components corresponding to protein-protein, protein-lipid, and protein-water interactions. The method was tested for the TM segments of human glycophorin A (GpA) and two mutant forms, Gly83Ala and Thr87Val. It was shown that lipids make a significant negative contribution to the free energy of dimerization, while amino acid residues forming the interface of the helix-helix contact may be unfavorable in terms of free energy. The detailed balance between different energy contributions is highly dependent on the amino acid sequence of the TM protein segment. The results show the dominant role of the environment in the interaction of membrane proteins that is changing our notion of the driving force behind the spontaneous association of TM α-helices. Adequate estimation of the contribution of the water-lipid environment thus becomes an extremely urgent task for a rational design of new molecules targeting bitopic membrane proteins, including receptor tyrosine kinases.

    ID:1396
  3. Zhang L., Polyansky A., Buck M. (2015). Modeling transmembrane domain dimers/trimers of plexin receptors: implications for mechanisms of signal transmission across the membrane. PLoS ONE 10 (4), e0121513 [+]

    Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and -B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, -A3, -A4, -C1 and -D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 - trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures suggest experimental tests and will be useful for the interpretation of future studies.

    ID:1397

Прочные, но гибкие: молекулярная динамика объясняет уникальность биомембран архей (2015-01-03)

Археи в основном являются экстремофилами: их среда обитания — это высокие температура, давление, соленость и кислотность. Возможно, «особый путь» архей был определен необычными свойствами их мембран, существенно отличающихся по составу от «обычных» фосфолипидов у бактерий и эукариот. В Лаборатории моделирования биомолекулярных систем провели компьютерное исследование архейных мембран, объяснив взаимосвязь между химической структурой липидов и физическими свойствами мембран. В расчетах показано, что ключевой особенностью химического строения архейных липидов, определяющей исключительные физические свойства мембран на их основе, является изопреноидная природа гидрофобных фрагментов этих липидов (боковые метильные группы каждый четвертый углеродный атом «хвоста»). Подробнее об этом можно прочитать в пресс-релизе на сайте ИБХ.

Публикации

  1. Chugunov A.O., Volynsky P.E., Krylov N.A., Boldyrev I.A., Efremov R.G. (2014). Liquid but Durable: Molecular Dynamics Simulations Explain the Unique Properties of Archaeal-Like Membranes. Sci Rep 4, 7462 [+]

    Археи, прежде известные как архебактерии, в основном являются экстремофилами: их среда обитания — это высокие температура, давление, соленость и кислотность. Возможно, «особый путь» архей был определен необычными свойствами их мембран, существенно отличающихся по составу от «обычных» фосфолипидов у бактерий и эукариот. В Лаборатории моделирования биомолекулярных систем ИБХ РАН провели компьютерное исследование архейных мембран, объяснив взаимосвязь между химической структурой липидов и физическими свойствами мембран. Статья опубликована в журнале Scientific Reports. По ее материалам написан пресс-релиз: «Прочные, но гибкие: молекулярная динамика объясняет уникальность биомембран архей».

    ID:1110