Laboratory of X-ray study

Department of Peptide and Protein Technologies

Head: Vladimir Pletnev, D.Sc
pletnev@ibch.ru+7(495)995-55-57#2073

X-ray study, protein crystallography, three dimensional structure, structure-fuctional relations

The Laboratory is involved in study of three dimensional (3D) structure of the protein-peptide nature compounds by high resolution X-ray methods supported by molecular mechanics/dynamics/graphics and bioinformatics methods. The Laboratory studies proteins of different functional nature with emphasis on the structure-functional aspects of specificity of the ligand/substrate recognition and binding.

The Laboratory collaborates with the Macromolecular Crystallography Laboratory of the National Cancer Institute of USA (Argonne, IL, USA). The laboratory of X-ray study was organized in 1990 from the X-ray group functioning since 1972.

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Laboratory employees.

In the present time, much attention in our lab is paid to structural study of the fluorescent proteins (FP) used as molecular bionanomarkers in cell biology, biotechnology and biomedicine for visualization and monitoring the internal processes within cells or whole organisms. A big series of FPs, emitting in green, yellow, red and far red spectral regions, has been studied in our Lab by high resolution X-ray methods. The following analysis of the structure-functional relation allowed to explain many experimentally observed properties and to design new mutant fluorescent variants with improved photophysical characteristics. The obtained results of the Laboratory are expanding considerably the structural base for rational design of the advanced fluorescent biomarkers for practical application.


The 3D structures of the cyclic depsipeptide ionophores differing by cycle size, nature and configuration of residues helped to understand the important details of the metal ion binding specificity and mechanism of the ion transport through biological membranes.

In collaboration with Hauptman-Woodward Medical Research Institute (Buffalo, USA) a number of research projects has been performed under the title “Rational proteomics of short chain dehydrogenases”. A general approach for identification of the 3D pattern of residues (fingerprints) responsible for the protein fold, cofactor and substrate binding was developed for this family.

A big series of FPs, emitting in green, yellow, red and far red spectral regions, has been studied in our lab by high resolution X-ray methods. The following analysis of the structure-functional relation allowed to explain many experimentally observed properties and to design new mutant fluorescent variants with improved photophysical characteristics.

Selected species of the marine button polyps — the source of fluorescent proteins (FP) (a); The principal structural fold of FPs is an 11-stranded β-barrel and a chromophore (matured from the three residue sequence) embedded in the middle of an internal α-helix going along the β-barrel axis (b).

Crystals of the fluorescent proteins for X-ray study

Unic examples of fluorescent proteins obtained in the laboratory

I. Study of the far red monomeric FP mKate has showed that the observed pH dependence of fluorescence is a consequence of cis-trans isomerization of the internal chromophore. Based on its 3D structure the new gene engineered variant mKate_S158A with almost 2 fold brighter fluorescence has been rationally designed. Currently, the photophysical characteristics of this variant succeed significantly over those of other known monomeric fluorescent biomarkers.

Structural study of the highly toxic red and orange FPs, KillerRed and KillerOrange, allowed to determine the chromophore adjacent key amino-acid residues participating in generation of the active oxygen forms, responsible for the phototoxic effect.

Amino acid environment of the internal chromophore in highly toxic red fluorescent protein KillerRed. Hydrogen bonds (≤3.3 Å) are shown as blue dashed lines, waters (W) as red spheres and van der Waals contacts (≤3.9 Å) as black “eyelashes”.

II. The intermediate form of chromophore biosynthesis has been observed in crystal structure of the colorless nonfluorescent FP, aceGFP-G222E. This new experimentally observed structure of the immature chromophore, characterized by the non-coplanar arrangement of the imidazolinone and phenolic rings, where cyclization of the protein backbone has occurred, but Tyr66 chromophore still stays in the native, non-oxidized form, with Cα and Cβ atoms in sp3 hybridization.

The trapped intermediate state (form III) for GFP chromophore biosynthesis found in the crystal structure of aceGFP-G222E

 III.

Red Fluorescent Protein laRFP from a lancelet. Chromophore Gly58-Tyr59-Gly60 (GYG; shown in yellow) in 2Fo-Fc electron density (density cutoff ρ= 2.0σ). laRFP showing the presence of the covalent bond between chromophore (Tyr59)Cβ and proximal (Tyr62)O. Potential proton acceptor Asp142 forms H-bond (shown in dashed red line), mediated by water molecule (W), with the Tyr62 hydroxyl. Arg89 forms H-bond with the Tyr62 hydroxyl that assumingly may facilitate proton transfer to Asp142 prior to reaction.

IV.

Канал простирающейся вдоль β-бочонка  заполнен цепочкой из связанных водородными связями молекул воды, выполняющей роль транспортной системы для фотогенерируемых токсичных супероксид анионов.

V. For the first time, the three-dimensional structure of the native green and UV irradiated photoconverted red forms of DendFP (Dendronephthya sp.) has been determined,  the latter showing cleavage of the main chain before chromophore

Chromophore structure (His62-Trp63-Gly64) in the green form of DendGFP (a) and the red form of DendRFP (b).

VI. In international collaboration three new bright far-red and near infrared genetically engineered biomarkers (from plant photoreceptors - phytochromes), providing high permeability of emission through biological tissues - miRFP670 (em ~ 670nm ), miRFP703 (703 nm) and miRFP709 (709 nm), have been studied by X-ray method with resolution 1.33, 1.35 and 1.34Å, respectively. Three-dimensional structure and structure-functional relations of these biomarkers have been established

Superimposed structures of miRFP703 (in green) and miRFP709 (in red) showing chromophores in the binding pocket

NamePositionContacts
Vladimir Pletnev, D.Scdepart. dir.pletnev@ibch.ru+7(495)995-55-57#2073
Ekaterina Goryacheva, Ph.D.r. f.goryacheva@ibch.ru+7(499)793-51-22
Igor' Artem'evr. f.artem1@ibch.ru+7(495)335-16-77
Svetlana Arhipovar. f.arhipova@ibch.ru+7(495)335-75-10
Alexey Rossohinsen. eng.

Former members:

Igor' Tsygannik, Ph.D.s. r. f.

Selected publications (show all)

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Vladimir Pletnev

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. 52, office. 155
  • Phone: +7(495)995-55-57#2073
  • E-mail: pletnev@ibch.ru








































 

Tree dimensional structure and structure-functional relation of the green fluorescent protein WasCFP. (2018-11-22)

The three-dimensional structure of the pH dependent green fluorescent protein of WasCFP with the Trp based chromophore has been determined by X-ray method (resolution 1.3Å) at extremely low value of pH 2.0 (earlier, we determined the crystal structures of WasCFP at pH 10.0, 8.0 и 5.5). It was shown, that stepwise shift of pH from 10.0 to 2.0 is accompanied by the synchronous change of side chain conformations of residues from the chromophore nearest environment. Role of interactions of the chromophore with the key amino-acid residues from nearest environment has been studied by quantum chemistry calculations.

Crystal structure of the protein protease inhibitor Alocasin from the rhizomes Alocasia (2018-11-22)

Three dimensional structure of the β-structural protein Alocasin from the rhizomes Alocasia has been determined by X-ray method at 2.5 Å resolution. Alocasin demonstrates the profound inhibitory activity towards trypsin and chymotrypsin and to midgut proteases of the mosquitos (Aedes aegypti) and presents a promising tool for the anti Ae. aegypti activity.

Publications

  1. Vajravijayan S, Pletnev S, Pletnev VZ, Nandhagopal N, Gunasekaran K (2018). Crystal structure of a novel Kunitz type inhibitor, alocasin with anti-Aedes aegypti activity targeting midgut proteases. Pest Manag Sci 74 (12), 2761–2772

Three-dimensional structure and structure-functional relations of fluorescent proteins (2017-11-21)

Fig. legend: (A) Superimposed structures of miRFP703 (in green) and miRFP709 (in red) showing chromophores in the binding pocket. (B) Emission spectra of miRFP703 (in green), miRFP709 (in red), and miRFP709/Y210F (in magenta)

Three new bright far-red and near infrared genetically engineered biomarkers (from plant photoreceptors - phytochromes), providing high permeability of emission through biological tissues - miRFP670 (lem ~ 670nm ), miRFP703 (703 nm) and miRFP709 (709 nm), have been studied by X-ray method with resolution 1.33, 1.35 and 1.34Å, respectively. Three-dimensional structure and structure-functional relations of these biomarkers have been established

Publications

  1. Baloban M, Shcherbakova DM, Pletnev S, Pletnev VZ, Lagarias JC, Verkhusha VV (2017). Designing brighter near-infrared fluorescent proteins: Insights from structural and biochemical studies. Chem Sci 8 (6), 4546–4557

A new phototoxic fluorescent biomarker with Trp-based chromophore (2016-03-03)

Three dimensional structure of two new phototoxic orange fluorescent proteins, dimeric KillerOrange and monomeric m KillerOrange, have been determined by X-ray method at resolution 1.81Å and 1.57 Å, respectively. They are first orange-emitting protein photosensitizers with a tryptophan-based chromophore (Gln65-Trp66-Gly67). The β-barrel structure of both orange photosensitizers has an internal channel extending along the β-barrel axis. It is filled with a chain of hydrogen-bonded water molecules providing an outlet for the photo-generated reactive oxygen spices. Trp66 of the chromophore in KillerOrange/mKillerOrange adopts an unusual high energy trans-cis conformation stabilized by H-bond with the nearby Gln159. The observed trans-cis isomer of Trp66 presents first example among those found in known Trp-based chromophores. This conformation was suggested a key structural feature for generation of bright orange emission and phototoxicity.