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A S Arsen'ev

Publications and source records attributed to A S Arsen'ev.

At least 19 recordsLinked to original sources
PubMed2000

[Modeling of peptides and proteins in membrane environment. I. A solvation model mimicking a lipid bilayer].

A theoretical solvation model of peptides and proteins that mimics the heterogeneous membrane-water system was proposed. Our approach is based on the combined use of atomic parameters of solvation for water and hydrocarbons, which approximates the hydrated polar groups and acyl chains of lipids, respectively. This model was tested in simulations of several peptides: a nonpolar 20-mer polyleucine, a hydrophobic peptide with terminal polar groups, and a strongly amphiphilic peptide. The conformational space of the peptides in the presence of the membrane was studied by the Monte Carlo method. Unlike a polar solvent and vacuum, the membrane-like environment was shown to stabilize the alpha-helical conformation: low-energy structures have a helicity index of 100% in all cases. At the same time, the energetically most favorable orientations of the peptides relative to the membrane depend on their hydrophobic properties: nonpolar polyleucine is entirely immersed in the bilayer and the hydrophobic peptide with polar groups at the termini adopts a transbilayer orientation, whereas the amphiphilic peptide lies at the interface parallel to the membrane plane. The results of the simulations agree well with the available experimental data for these systems. In the following communications of this series, we plan to describe applications of the solvation model to membrane-bound proteins and peptides with biologically important functional activities.

Cell Membrane↗
PubMed2000

[Modeling of peptides and proteins in a membrane environment.II. Structural and energetic aspects of Glycophorin A in a lipid bilayer].

The conformational space of a hydrophobic peptide fragment of glycophorin A in a lipid membrane was studied with the Monte Carlo method using the solvation model described in the first communication of this series. The simulation was performed for various starting orientations of the peptide relative to the membrane bilayer: outside, inside, partially immersed, and transbilayer. We showed that the membrane substantially stabilizes the alpha-helical conformation of the central hydrophobic part of the glycophorin A molecule, which for the most part is immersed in the apolar core of the bilayer. For various conformational states, energy values were calculated and the orientations of the peptide relative to the membrane were characterized. Depending on the thickness of the bilayer, either an entirely alpha-helical conformation in transbilayer orientation or a conformation with a kink in the central part of the helix with the N- and C-termini exposed on one side of the membrane corresponds to the minimal-energy structure. The transmembrane orientation of glycophorin A is energetically advantageous when the membrane thickness is close to the length of its hydrophobic helical portion, which is consistent with the effect of "hydrophobic match" observed experimentally. The prospects for further refinement of the model are discussed.

Animals↗
PubMed2000

[Study of solid-phase catalytic isotopic exchange of hydrogen in alpha-conotoxin G1 under the effect of spillover-tritium].

Tritium-labeled alpha-conotoxin G1 with a molar radioactivity of 35 Ci/mmol and full biological activity (according to the binding to nicotinic acetylcholine receptor) was obtained by the high-temperature solid-state catalytic isotope exchange (HSCIE). The tritium distribution in the molecule of alpha-conotoxin G1 was revealed by 3H NMR spectroscopy. Tritium was found in all amino acid residues except for the Asn4-Pro5-Ala6 fragment. The data on the comparative reactivity of C-H bonds, the ab initio quantum-chemical calculation of the hydrogen exchange reaction, and the information on the spatial structures of alpha-conotoxin G1 in solution and in crystal state allowed us to establish that the reactivity of H atoms may be increased by their interaction with the electron donor O and N atoms at the transition state of the HSCIE reaction. A decrease in the rate of the HSCIE reaction could be caused by both a poor spatial accessibility of C-H bonds and a limited mobility of the peptide fragment containing these bonds.

Amino Acid Sequence↗
PubMed1997

[The rational evolution of scorpion toxins].

A theoretical method for the rational design of a "universal" scorpion toxin with a wider spectrum of specificity for K+ channels and a more stable alpha/beta-folding than in its natural homologues is described. On the basis of the analysis of molecular hydrophobic potentials (MHP) of the protein spatial structures, structural features for a family of five short scorpion toxins were revealed. The analysis of the maps of two-dimensional intramolecular MHP contacts allowed the identification of amino acid residues responsible for the folding of the protein and/or for the manifestation of its specific function. The theoretically predicted structure-function roles of the residues were compared with experimental data on the mutagenesis of charybdotoxin. Based on the results of MHP calculations and with the theory of protein molecular evolution used as an additional criterion for the selection of mutations, the amino acid sequence and the spatial structure of a "universal" scorpion toxin were determined.

Amino Acid Sequence↗
PubMed1997

[Spatial structure of bacterioopsin 87-136 fragment].

The [Nle18]-(87-136)-bacterioopsin, a fragment of bacterioopsin from Halobacterium salinarium synthesized by solid phase technique, was solubilized in a 1:1 chloroform-methanol mixture containing 0.1 M LiClO4 and studied by two-dimensional 1H NMR spectroscopy. The complete assignment of proton resonances was performed in the DQF-COSY, TOCSY, and NOESY spectra of this peptide, and its spatial structure was computed. As a result, two helical regions (92-100 and 108-130) were identified, which correspond to the C-terminal part of segment C and to segment D of bacteriorhodopsin, respectively. The 92-100 region forms a right-handed alpha-helix, and the 108-130 region can adopt right-handed alpha-helical, 3(10)-helical, and combined (from the two) conformations. A comparison of the structure computed with the bacteriorhodopsin model deduced from the electron cryomicroscopy data showed good agreement in the 91-100 region (the root-mean-square deviation of the backbone atoms was less than 0.51 A) and considerable differences in the 108-130 region (1.82 A). A dynamic model of the conformation of the D transmembrane segment was suggested, and the accordance of the model to the functional dynamics of bacteriorhodopsin was discussed.

Amino Acid Sequence↗
PubMed1997

[Secondary structure of binase in solution by 1H NMR].

Nearly all resonances were assigned in the two-dimensional 1H NMR spectra of binase, guanylospecific ribonuclease from Bacillus intermedius containing 109 amino acid residues. The exchange rates of amide protons with the solvent deuterium were measured in 2H2O at pH 6.7 and 30 degrees C. Coupling constants 3J of H-NC alpha-H, NOE contacts, solvent exchange rates of amide protons, and indices of C alpha H chemical shifts were measured, and the binase secondary structure was deduced from these data. It involves three alpha-helices in the N-terminal part (the 6-16, 26-31, and 41-45 segments) and a beta-sheet formed by five antiparallel beta-strands (51-55, 71-75, 86-90, 95-99, and 104-108 segments). The binase secondary structure was compared with that of its closest homologue, barnase from B. amyloliquefaciens.

Amino Acid Sequence↗
PubMed1997

[1H-15N NMR signal assignment and secondary structure of bacteriorhodopsin (1-231) in solution].

15N-Labeled de-(232-248)-bacteriorhodopsin [BR(1-231)] was solubilized in 1:1 chloroform-methanol solvent mixture that contained 1.0 M 2HCO2N2H4 and mimic membrane medium. Resonances in the 1H-15N heteronuclear multiple-quantum coherence (HMQC) spectrum of BR (1-231) were assigned using the data of two- and three-dimensional NMR experiments. Of 117 cross-peaks present in the 1H-15N HMQC spectrum, 98 were assigned to residues in 1-75 and 193-231 segments of the protein. Almost all cross-peaks that correspond to the 76-192 segment were absent in the HMQC spectrum (except for six cross-peaks from the side chains and 14 cross-peaks from the backbone). Deuterium exchange rates of amide protons and cross-peaks of nuclear Overhauser effect helped to localize helices A (residues 8-30), B (residues 40-65), and G (residues 198-226). The periodicity in the rates of deuterium exchange of NH protons of helices A, B, and G was explained by the compact arrangement of these helices in the protein globule. The broadening of signals from six residues in helix G, which, according to the electron cryomicroscopy model of bacteriorhodopsin, is in contact with the NMR-unobservable bundle of helices CDEF, indicates specific interactions of the helices in BR(1-231). These data suggest that BR(1-231) solubilized in an organic medium has a spatial structure similar to that in the electron cryomicroscopy model of BR.

Amino Acids↗
PubMed1996

[Secondary structure and conformational heterogeneity of Naja naja oxiana cytotoxin II].

The proton resonances of cytotoxin II from Naja naja oxiana were sequentially assigned in 2D 1H NMR spectra for all of its 60 amino acid residues of both major and minor components of the spectra. The presence of the minor component was shown to be due to a conformational heterogeneity of the cytotoxin. The proton-deuterium exchange rates of amide groups were measured in 2H2O at a pH of 5.0 and at 10 degrees C. Experimental data obtained (d-connectivities, H-NC alpha-H coupling constants and long-range NOEs) allowed for the determination of the secondary structure of the two cytotoxin conformers. Both conformer structures contain two antiparallel beta-sheets. The first beta-sheet involves two antiparallel beta-strands comprising the residues 2-5 and 10-13. The second sheet involves three antiparallel strands consisting of the residues 20-26, 35-39, and 49-55; its peripheral beta-strands are connected by cross-over. The most striking structural difference between these conformers is the nature of the beta-turn 6-9, which has trans- and cis-forms of the Val7-Pro8 peptide bond in the major and minor conformer, respectively. The structures of other beta-turns, some of which are ascribed to standard types, and the C-termini are almost the same for the both conformers.

Amino Acid Sequence↗
PubMed1995

[NMR spectroscopy in the study of the spatial structure of membrane peptides and proteins].

The review covers the field of the spatial structure determination of membrane-associated peptides and proteins by the High-Resolution NMR Spectroscopy. The membrane-bound conformations of several hormones, neuropeptides, lipopeptides, peptide antibiotics, bacteriophage coat proteins, transmembrane domains of receptors and others are considered. To mimic the biomembrane environment the appropriate artificial media (organic solvents, micelles of detergents of lipid vesicles) must be adjusted. In that case NMR spectroscopy is a powerful tool for the spatial structure and dynamics investigations of membrane associated peptides and proteins constituting the bases for unraveling of their structure-function relationships.

Magnetic Resonance Spectroscopy↗
PubMed1995

[Refinement of the spatial structure of neurotoxin II from Naja naja oxiana venom].

A set of 19 conformations of the neurotoxin II from Naja naja oxiana was determined by conformational energy minimization using constraints derived from experimental 1H NMR data. The pairwise average root-mean-square deviations were 0.86 A for the backbone heavy atoms and 1.48 A for all heavy atoms of these conformations. A model of the neurotoxin II dimer is proposed to account for the relatively slow deuterium exchange rates of the Val45 and Leu51 amide protons, which are exposed to the solvent in the calculated conformations of monomeric neurotoxin II. Both the monomeric and dimeric models of neurotoxin II may be useful for detailed studies of the functional, hydrophobic, and electrostatic properties of this molecule.

Amino Acid Sequence↗
PubMed1995

[Spatial structure of bacterioopsin transmembrane segments C, E, and G from two-dimensional 1H-NMR data].

The spatial structure of synthetic peptides with transmembrane segment sequences C (residues 67-106), E (128-162), and G (190-233) of bacterioopsin from Halobacterium halobium solubilized in methanol-chloroform 1:1 containing 0.1 M LiClO4 was computed based on 2D 1H NMR data. Segment C forms a right alpha-helix between Pro77 and Val101. The residue Pro91 within the alpha-helix induces a 25 degrees "kink". Segment E forms a right alpha-helix between Val136 and Ser158. Segment G includes alpha-helical region, which begins from CO of Ile198 and ends at N alpha-H of Arg227. The torsion angles, chi 1, of the side chains were unambiguously determined for most of the residues within the alpha-helical regions. Conformations of some side chains of the transmembrane segment residues in the solution were found to differ from their previously reported conformations determined by electron microscopy. Conformations of the sites terminating the C and E segment alpha-helices were refined.

Amino Acid Sequence↗
PubMed1993

[Conformation of fragment 66-72 of interleukin-2 complexed with a monoclonal antibody to interleukin-2].

1H-NMR spectra of the interleukin-2 synthetic fragment Ac-Leu66-Glu-Glu-Val-Leu-Asn-Leu72-OCH3 in the presence or absence of the monoclonal antibody were analysed. The data obtained are consistent with an extended unordered conformation of the free peptide. Measurements of NOESY cross-peak intensities allowed us to determine the spatial structure of the peptide bound to the antibody. The peptide has an amphiphilic surface with hydrophobic and hydrophilic amino acid side chains clustered on the opposite sides of its alpha-helical-like structure. The hydrophobic and hydrophilic clusters are located on the opposite sides of the bound peptide's surface. The hydrophobic side chains contact the antibody surface, while the hydrophilic ones are oriented into the solvent (T. A. Balashova et al. (1991) Bioorgan. Khim. (USSR), v. 17, p. 1470-1486). Hydrolysis of the methyl ester slowly ocurs in the presence of the antibody. This process does not alter the conformation of the peptide bounded with the antibody, though decreases the peptide's affinity to the antibody.

Amino Acid Sequence↗
PubMed1993

[2D-1H-NMR-study of the conformation of transmembrane segments of C, E, and G bacteriorhodopsin].

Conformations of synthetic peptides, analogues of the membrane spanning segments C (residues 67-106), E (128-162) and G (190-233) of bacteriorhodopsin Halobacterium halobium were studied by two-dimensional 1H-NMR spectroscopy. Peptides were solubilized in the mixture chloroform-methanol (1:1), 0.1 M LiC1O4. The spectrum resonances were assigned by means of phase-sensitive DQF-COSY, TOCSY and NOESY techniques. Interproton nuclear Overhauser effects were derived from NOESY spectra. Amide protons with slow deuterium exchange rates were determined. Analysis of the obtained data showed that segments C, E and G form right-handed alpha-helices including residues 77-101, 131-159 and 198-227, respectively.

Amino Acid Sequence↗
PubMed1992

[Refinement of the spatial structure of the gramicidin A ion channel].

The spatial structure of the gramicidin A (GA) transmembrane ion-channel was refined on the base of cross-peak volumes measured in NOESY spectra (mixing time tau m = 100 and 200 ms). The refinement methods included the comparison of experimental cross-peak volumes with those calculated for low-energy GA conformations, dynamic averaging of the low-energy conformation set and restrained energy minimization. Accuracy of the spatial structure determination was estimated by the penalty function Fr defined as a root mean square deviation of interproton distances corresponding to the calculated and experimental cross-peak volumes. As the initial conformation we used the right-handed pi 6,3 LD pi 6,3 LD helix established on the base of NMR data regardless of the cross-peak volumes. The conformation is in a good agreement with NOE cross-peak volumes (Fr 0.2 to 0.5 A depending on NOESY spectrum). For a number of NOEs formed by the side chain protons, distances errors were found as much as 0.5-2.0 A. Restrained energy minimization procedure had little further success. However some of these errors were eliminated by the change in torsional angle chi 2 of D-Leu12 and dynamic averaging of the Val7 side chain conformations. Apparently, majority of deviations of the calculated and experimental cross-peak volumes are due to the intramolecular mobility of GA and cannot be eliminated within the framework of rigid globule model. In summary the spatial structure of GA ion-channel can be thought as a set of low-energy conformations, differing by the side chain torsion angles chi 1 Val7 and chi 2 D-Leu4 and D-Leu10 and the orientation of the C-terminal ethanolamine group. Root mean square differences between the atomic coordinates of conformations are in the range of 0.3-0.8 A.

Cell Membrane↗
PubMed1991

[Conformational analysis of a segment in bacterioopsin by two-dimensional (1)H-NMR spectroscopy].

The spatial structure of a synthetic peptide, an analogue of the membrane spanning segment B (residues 34-65) of bacterioopsin from Halobacterium halobium, has been refined. Backbone torsion angles were derived from intensities of short-range interproton NOEs. These, together with a complete set of the NOEs integral intensities formed the basis for the three-dimensional structure refinement by the energy minimization with consideration of NOE penalty functions. Analysis indicates the right-handed alpha-helical conformation of segment B extending from Asp-38 to Tyr-64 with a kink of the helical axis (27 degrees) at Pro-50. The most stable region with an average root-mean-square deviation of 0.43 A between the backbone atoms includes residues 42-60 in six energy refined structures. The N-terminal part of segment B (residues 34-37) has no ordered conformation. The inferred structure is in close agreement with the electron cryomicroscopy structure of bacteriorhodopsin, differing from it in conformations of most of the side chains.

Amino Acid Sequence↗
PubMed1991

[Determination of the spatial structure of insectotoxin 15A from Buthus erpeus by (1)H-NMR spectroscopy data].

The solution structure of insectotoxin 15A (35 residues) from scorpion Buthus eupeus was determined on the basis of 386 interproton distance restraints 12 hydrogen-bonding restraints and 113 dihedral angle restraints derived from 1H NMR experiments. A group of 20 structures was calculated with the distance geometry program DIANA followed by the restrained energy minimization with the program CHARMM. The atomic RMS distribution about the mean coordinate position is 0.64 +/- 0.11 A for the backbone atoms and 1.35 +/- 0.20 A for all atoms. The structure contains an alpha-helix (residues 10-20) and a three-stranded antiparallel beta-sheet (residues 2-5, 24-28 and 29-33). A pairing of the eight cysteine residues of insectotoxin 15A was established basing on NMR data. Three disulfide bridges (residues 2-19, 16-31 and 20-33) connect the alpha-helix with the beta-sheet, and the fourth one (5-26) joins beta-strands together. The spatial fold of secondary structure elements (the alpha-helix and the beta-sheet) of the insectotoxin 15A is very similar to those of the other short and long scorpion toxins in spite of a low (about 20%) sequence homology.

Amino Acid Sequence↗
PubMed1990

[Determination of the local structure of the protein insectotoxin I5A from the scorpion Buthus eupeus from 1H-NMR spectroscopy data].

The local structure (torsion angles phi, psi and chi 1 of amino acid residues) of insectotoxin I5A (35 residues) of scorpion Buthus eupeus has been determined from cross-peak integral intensities in two-dimensional nuclear Overhauser enhancement (NOESY) spectra and spin coupling constants of vicinal H--NC alpha--H and H--C alpha C beta--H protons. The local structure determination was carried out by fitting complete relaxation matrix of peptide unit protons (protons of a given residue and NH proton of the next residue in the amino acid sequence) with experimental NOESY cross-peak intensities. The obtained intervals of backbone torsional angles phi and psi consistent with NMR data were determined for all but Gly residues. The predominant C alpha--C beta rotamer of the side chain has been unambiguously determined for 42% of the insectotoxin amino acid residues whereas for another 46% residues experimental data are fitted equally well with two rotamers. Stereospecific assignments were obtained for 38% of beta-methylene groups. The determined torsional angles phi, psi and chi 1 correspond to the sterically allowed conformations of the amino acid residues and agree with the insectotoxin secondary structure established earlier by 1H NMR spectroscopy.

Amino Acids↗