Laboratory of Molecular Instruments for Neurobiology

Who are we?

The laboratory was formed in 2017 from a preexisting group that was officially organized in 2014 under the "Molecular and Cell Biology" Program of the Presidium of the Russian Academy of Sciences, concomitantly with the Department of Molecular Neurobiology (de facto the group was active since 2008). We are a young and ambitious team and we are always open for new members. Graduate and PhD students are most welcome!

What are we doing?

  1. Study of under-investigated natural venoms and poisons from jelly fish, centipedes, certain spiders, leaf beetles, sea urchins, and stingrays.
  2. Design and production of molecular instruments for neuroscience.
  3. Production of diagnostic tools and search for drug hits.

 

Our international partners:

Toxicology and Pharmacology, KU Leuven (Belgium). Head, Professor Jan Tytgat.

Experimental Anesthesiology and Pain Research, University Hospital of Cologne (Germany). Head, Professor Tim Hucho.

Maduke Lab, Stanford University (USA). Head, Professor Merritt Maduke.

Kullmann Lab, Institute of Neurology, University College London (UK). Head, Professor Dimitri Kullmann.

Sobolevsky Lab, the Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center (New York, USA). Head, Professor Alexander Sobolevsky.

NamePositionContacts
Alexander Vassilevski, Ph.D.Head of lab.avas@ibch.ru+7(495)336-65-40
Alexey Kuzmenkov, Ph.D.r. f.aleksey.kuzmenkov@gmail.com+7(495)336-65-40
Petr Oparin, Ph.D.r. f.spud-13@mail.ru+7(495)336-65-40
Anton KommerPhD stud.lipokuza@rambler.ru+7(903)6750157
Nikita Kuldyushevstud.nikita.kuldushev@phystech.edu+7(495)336-65-40
Mihail Chernyht. q. - lab. as.
Nikita Dobrohotovt. q. - lab. as.
Andrei Gigolaevres. eng.gig-andrey@yandex.ru
Zhanna Kanaevskayalab. as.zh-kanewskaya@yandex.ru+7(495)000-00-00

Former members:

Antonina Berkutj. r. f.Problemka2008@gmail.com
Maria Sachkova, Ph.D.j. r. f.sachkovamasha@mail.ru
Tat'yana Kotovat. q. - lab. as.
Daniil Lukyanovt. q. - lab. as.
Ivan Chudetskiyres. eng.ivan.chudetskiy@gmail.com

All publications (show selected)

Loading...

Alexander Vassilevski

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. 51, office. 365
  • Phone: +7(495)336-65-40
  • E-mail: avas@ibch.ru

Protein Surface Topography was used to improve a potassium channel blocker

In collaboration with Laboratory of biomolecular NMR-spectroscopy,  Laboratory of biomolecular modeling,  Group of in silico analysis of membrane proteins structure

Previously, for the design of peptides with a given function, we have proposed using a convenient structural framework, namely, the α-hairpinin fold, characteristic of toxins from scorpion venom and plant defense peptides. Now, the use of the Protein Surface Topography method that we developed, has significantly improved the properties of an artificial α-hairpinin, which blocks Kv1.3 potassium channels, an important pharmacological target. The joint application of two approaches, namely, scaffold engineering and protein surface topography, can be used to obtain optimized ion channel ligands.

Kalium 2.0, a database of all known polypeptide ligands of potassium channels

In collaboration with Laboratory of biomolecular modeling

Previously, we have created a comprehensive database of scorpion toxins acting on potassium channels, called Kalium. Now we have expanded it to include all known potassium channel ligands of peptide nature in general. Together with the Guide to PHARMACOLOGY resource, which contains information on low-molecular-mass ligands, Kalium 2.0 database provides researchers with full information on this most important group of compounds.

By tradition, our initiative has received widespread community approval, with leading international experts in the field of ion channel ligands acting as Kalium 2.0 experts. Kalium 2.0 database is available following this link.

Combinatorial selective incorporation of stable13C and 15N isotopes facilitates NMR spectra analysis and allows mapping of the binding interfaces between membrane receptors and their ligands

In collaboration with Group of in silico analysis of membrane proteins structure,  Laboratory of bioengineering of neuromodulators and neuroreceptors,  Laboratory of structural biology of ion channels

Combinatorial incorporation of stable 13C and 15N isotopes into protein molecules can significantly simplify the analysis of NMR spectra. For the first time, the problem was solved and the CombLabel algorithm was developed for calculating combinatorial 13C and 15N  labeling schemes with a minimum price. The application of the program allowed to assign 50% of the NMR signals of the backbone of the second voltage-sensing domain of human sodium channel Nav1.4 (VSD-II). Leak currents through mutant variants of Nav1.4 containing Arg675Gly mutation in VSD-II lead to the development of a hereditary disease – normokalemic periodic paralysis. Hm-3 toxin from the venom of spider Heriaeus melloteei is able to block leak currents in VSD-II. By the means of NMR spectroscopy the interaction interface between VSD-II and Hm-3 toxin was determined. According to the model of the VSD-II/Hm-3 complex, based on the NMR data, the toxin binds to the extracellular S1-S2 loop, destabilizing the state of the domain, at which leak currents are observed. Using the example of the complexes of Hm-3 toxin with VSD-I and VSD-II of the Nav1.4 channel, it has been shown that arachnid toxins can interact differently with different domains within the same sodium channel.

Spider toxin inhibits aberrant currents in mutant ion channels

In collaboration with Laboratory of structural biology of ion channels,  Laboratory of bioengineering of neuromodulators and neuroreceptors

Toxin from the venom of the crab spider Heriaeus melloteei may serve as a hit in drug discovery for hypokalemic periodic paralysis type 2; there is no reliable medication for all cases of this disease. It is caused by mutations in the gene encoding voltage-gated sodium channels NaV1.4, characteristic of skeletal muscles. As a result of the mutations, these channels conduct aberrant currents, the muscles are unable to respond to the signals of the nervous system, and weakness develops followed by paralysis. Hm-3 toxin was found to be able to selectively inhibit such currents through voltage-sensing domain I of mutant channels. Read more in the press release on the IBCh website.

Publications

  1. Männikkö R, Shenkarev ZO, Thor MG, Berkut AA, Myshkin MY, Paramonov AS, Kulbatskii DS, Kuzmin DA, Castañeda MS, King L, Wilson ER, Lyukmanova EN, Kirpichnikov MP, Schorge S, Bosmans F, Hanna MG, Kullmann DM, Vassilevski AA (2018). Spider toxin inhibits gating pore currents underlying periodic paralysis. Proc Natl Acad Sci U S A 115 (17), 4495–4500

Scorpion venom is rich in peptide blockers of voltage-gated potassium channels (KV), and we have reflected this diversity previously in Kalium, a database dedicated to such peptides. A high-affinity and selective blocker of KV1.2 channels, characteristic of the human central nervous system, was obtained from the venom of the scorpion Mesobuthus eupeus. Using molecular modeling and site-directed mutagenesis, the mechanism of selective interaction between the toxin and channels was investigated.

Molecular mechanism of action of acylpolyamines, glutamate receptor blockers

Spiders and wasps secrete in their venom acylpolyamines that act as high-affinity blockers of receptors for glutamate, the main excitatory neurotransmitter of the human brain. Under the leadership of Eugene Grishin in 1986, the first representative of acylpolyamines was described, namely, argiopin from the venom of the orb-weaver spider Argiope lobata. In 2018, the spatial structure of argiopin complex with a glutamate receptor was studied using cryo-electron microscopy. The obtained results will allow the creation of drugs for the treatment of neurodegenerative diseases. The study was featured on the cover of Neuron. Read more in the press release on the IBCh website.

Publications

  1. Twomey EC, Yelshanskaya MV, Vassilevski AA, Sobolevsky AI (2018). Mechanisms of Channel Block in Calcium-Permeable AMPA Receptors. Neuron 99 (5), 956–968.e4

MeKTx11-1, Kv1.2 channel –specific peptide blocker from the M.eupeus scorpion venom: structural basis of selectivity

In collaboration with Laboratory of biomolecular modeling,  Group of in silico analysis of membrane proteins structure,  Group of nanobioengineering,  Laboratory of optical microscopy and spectroscopy of biomolecules

A.V. Feofanov (Laboratory of optical microscopy and spectroscopy of biomolecules), О.V. Nekrasova, K.S.Kudryashova (Group of nanobioengineering, Bioengineering department), A.A. Vassilevski, A.I. Kuzmenkov, A.M. Gigolaev (Laboratory of molecular instruments for neurobiology), A.O. Chugunov, V.M. Tabakmakher, R.G. Efremov (Group of in silico analysis of membrane proteins structure, Laboratory of biomolecular modeling).

A unique high-affinity and highly selective peptide blocker of Kv1.2 channel, MeKTx11-1, from the scorpion venom Mesobuthus eupeus was studied. Peptide MeKTx11-1 and its mutant forms were produced in a recombinant form, and their receptor-binding activity was studied against a panel of Kv1-channels. Molecular modeling of interaction of these peptides with Kv1.2 channel was carried out, and key structural elements of the interactions were determined. Peptide MeKTx11-1 may be used as a novel efficient molecular tool in neurobiology to identify and study the activity of Kv1.2 channel in the presence of different isoforms of Kv1-channels.

In collaboration with S.Peigneur and J.Tytgat fromUniversity of Leuven, Belgium and A.F. Fradkov from Evrogen JSC.

MeKTx11-1, Kv1.2 channel –specific peptide blocker from the M.eupeus scorpion venom: structural basis of selectivity

In collaboration with Laboratory of optical microscopy and spectroscopy of biomolecules,  Group of in silico analysis of membrane proteins structure,  Group of nanobioengineering

Оksana V. Nekrasova, K.S.Kudryashova (Group of nanobioengineering, Bioengineering department), A.A. Vassilevski, A.I. Kuzmenkov, A.M. Gigolaev (Laboratory of molecular instruments for neurobiology), A.O. Chugunov, V.M. Tabakmakher, R.G. Efremov (Group of in silico analysis of membrane proteins structure, Laboratory of biomolecular modeling), A.V. Feofanov (Laboratory of optical microscopy and spectroscopy of biomolecules).

A unique high-affinity and highly selective peptide blocker of Kv1.2 channel, MeKTx11-1, from the scorpion venom Mesobuthus eupeus was studied. Peptide MeKTx11-1 and its mutant forms were produced in a recombinant form, and their receptor-binding activity was studied against a panel of Kv1-channels. Molecular modeling of interaction of these peptides with Kv1.2 channel was carried out, and key structural elements of the interactions were determined. Peptide MeKTx11-1 may be used as a novel efficient molecular tool in neurobiology to identify and study the activity of Kv1.2 channel in the presence of different isoforms of Kv1-channels.

In collaboration with S.Peigneur and J.Tytgat fromUniversity of Leuven, Belgium and A.F. Fradkov from Evrogen JSC.

KV1.2 Сhannel-Specific Blocker from Scorpion Venom: Structural Basis of Selectivity

In collaboration with Laboratory of optical microscopy and spectroscopy of biomolecules,  Group of nanobioengineering,  Group of in silico analysis of membrane proteins structure

Laboratory of Molecular Instruments for Neurobiology is known for systematic study of Arthropods’ venoms and derived peptides that specifically target various ion channels. Scorpions’ venom is abundant with potassium channels (Kv) blockers, and this diversity was described in previously released in Kalium database.

In cooperation with Laboratory of optical microscopy and spectroscopy of biomolecules and Group of nanobioengineering an unique screening system permitted identification in the Mesobuthus eupeus scorpion venom of Kv1.2 blocker: peptide MeKTx11-1 binging with high affinity (IC50 ≈0,2 nM) and specificity (effect on Kv1.1, 1.3 and 1.6 emerges at >100-fold higher concentrations). This peptide differs from the related MeKTx11-3 by just two residues, possessing substantially lower Kv1.2-specificity.

Finally, Group of in silico analysis of membrane proteins structure conducted a molecular modeling study of these two peptides interacting with Kv1.2 channel, immersed into an explicit lipid bilayer. This study uncovered mechanism of selective action of MeKTx11-1 peptide. The developed analysis technique will be of use for future design of selective ligands of Kv and other channels, which may be applied in fundamental studies of molecular basis of nervous system function and as drugs prototypes.

Interaction of gating modifier toxin Hm-3 with voltage-sensing domains of Nav1.4 sodium channel: structural view on the membrane-mediated binding

In collaboration with Laboratory of bioengineering of neuromodulators and neuroreceptors,  Laboratory of structural biology of ion channels

Voltage-gated Na+ channels (Nav) are essential for the functioning of cardiovascular, muscular, and nervous systems. Certain mutations trigger a leak current through voltage-sensing domains (VSDs) of Nav leading to various diseases. Hypokalemic periodic paralysis (HypoPP) type 2 is caused by mutations in the S4 segments of VSDs in the human skeletal muscle channel NaV1.4. The gating modifier toxin Hm-3 (crab spider Heriaeus melloteei) inhibits leak currents through such mutant channels. To investigate molecular basis of Hm-3 interaction with NaV1.4 channel, we studied isolated VSD-I by NMR spectroscopy in membrane mimicking environment. Hm-3/VSD-I complex was modeled using protein-protein docking guided by NMR restrains. The toxin initially anchors onto the membrane surface and then forms the complex with the S3b-S4 loop of the VSD-I. The Hm-3 binding blocks movement of the voltage-sensor helix S4 and induces some allosteric changes that prevent development of gating-pore currents. Our report is the first NMR study of structural interactions between gating modifier toxins and Nav channels.

Publications

  1. Männikkö R, Shenkarev ZO, Thor MG, Berkut AA, Myshkin MY, Paramonov AS, Kulbatskii DS, Kuzmin DA, Castañeda MS, King L, Wilson ER, Lyukmanova EN, Kirpichnikov MP, Schorge S, Bosmans F, Hanna MG, Kullmann DM, Vassilevski AA (2018). Spider toxin inhibits gating pore currents underlying periodic paralysis. Proc Natl Acad Sci U S A 115 (17), 4495–4500

Structure of two-domain spider toxins

In collaboration with Laboratory of biomolecular NMR-spectroscopy

Venoms of many spiders contain two-domain toxins that unite in their structure modules, which are similar to "simple" single-domain toxins. We conducted a detailed structural study of those toxins that consist of disulfide-rich (similar to ordinary neurotoxins) and linear (similar to conventional cytotoxins) modules. Linear modules can serve for the association of two-domain toxins with membranes due to the formation of amphiphilic helices, characteristic of membrane-active peptides. We propose a "membrane access" mode of action for two-domain toxins: linear modules interact with lipid bilayers, whereas disulfide-rich modules bind to protein receptors.