Human EGF-derived direct and reverse short linear motifs: conformational dynamics insight into the receptor-binding residues.

Short linear motifs (SLiMs) have been recognized to perform diverse functions in a variety of regulatory proteins through the involvement in protein-protein interactions, signal transduction, cell cycle regulation, protein secretion, etc. However, detailed molecular mechanisms underlying their functions including roles of definite amino acid residues remain obscure. In our previous studies, we demonstrated that conformational dynamics of amino acid residues in oligopeptides derived from regulatory proteins such as alpha-fetoprotein (AFP), carcino-embryonic antigen (CEA), and pregnancy specific β1-glycoproteins (PSGs) contributes greatly to their biological activities.

Modeling of three dimensional structure of human alpha-fetoprotein complexed with diethylstilbestrol: docking and molecular dynamics simulation study.

It has been long experimentally demonstrated that human alpha-fetoprotein (HAFP) has an ability to bind immobilized estrogens with the most efficiency for synthetic estrogen analog - diethylstilbestrol (DES). However, the question remains why the human AFP (HAFP), unlike rodent AFP, cannot bind free estrogens. Moreover, despite the fact that AFP was first discovered more than 50 years ago and is presently recognized as a "golden standard" among onco-biomarkers, its three-dimensional (3D) structure has not been experimentally solved yet.

[The structural and dynamic model of the serotonin 5-HT3 receptor. Comparative analysis of the structure of the channel domain of pentameric ligand-gated ion channels].

The three-dimensional structure of the 5-HT3 receptor is currently unknown. An available structure of the nicotinic acetylcholine receptor closely related by homology to the 5-HT3 receptor was used as a template for the computer-based homology modeling of the 5-HT3 receptor. The study of the ion migration through the channel by the stirred molecular dynamics method has shown that the steric factor in the region of residue THR 279 and the region of GLU 272, ASP 293 influences the ion transmission.

[A molecular dynamics study of the interaction between domain I-BAR of the IRSp53 protein and negatively charged membranes].

The methods of computer simulation in full-atomic and large-grain approximations have been used to study specific interactions of the isolated domain I-BAR of the actin-binding protein IRSp53 and model membranes containing neutral phospholipids, as well as membranes containing high amounts of negatively charged PI(4,5)P2 phospholipids. It has been shown that the I-BAR domain does not interact with neutral lipids but induces the bending of the synthetic membrane rich in negatively charged phospholipids. A clusterization of charged lipids on the surface of the membrane at the sites of its interaction with the protein has been observed.

Interaction of zervamicin IIB with lipid bilayers. Molecular dynamics study.

In this work we have studied the interaction of zervamicin IIB (ZrvIIB) with the model membranes of eukaryotes and prokaryotes using all-atom molecular dynamics. In all our simulations zervamicin molecule interacted only with lipid headgroups but did not penetrate the hydrophobic core of the bilayers. During the interaction with the prokaryotic membrane zervamicin placed by its N-termini towards the lipids and rotated at an angle of 40° relatively to the bilayer surface.

[Comparative studies of structural properties of melittin in water and trifluroethanol/water mixture by the molecular dynamics method].

The structural properties and dynamic behavior of the antimicrobial peptide melittin in hydrophobic and polar environments have been investigated. The main characteristics of the secondary structure of melittin in different media have been analyzed, and compared with the data on the ideal alpha-helix. It has been shown that melittin is an alpha-helix bent in the region of residue Pro14; in this case, the N-terminus of the peptide tends to unfold, while the C-terminal segment (residues 14-23) retains the helical structure for 20 ns of the simulation.

[Molecular dynamics of zervamicin II and its analogues in water and methanol].

A comparative study of the molecular dynamics of zervamicin II (an antimicrobial peptide from the peptaibol group, which has the channel-forming activity) in water and methanol has been performed. The influence of amino acid substitutions on the dynamics and stability of the peptide structure has been investigated. The amino acid sequence responsible for the absence of swivel motions in short peptaibols has been determined.

[Molecular dynamics of oligopeptides. A comparative study of the interactions of amino acid residues in dipeptide structures].

A comparative study of the molecular dynamics of dipeptides consisting of natural amino acid residues has been carried out. Molecular dynamics protocols were used that do not violate the principle of equidistribution of energy by degrees of freedom. Autocorrelation functions of complex exponential curves from dihedrals were used for the comparative analysis.

Steered molecular dynamics simulations of cobra cytotoxin interaction with zwitterionic lipid bilayer: no penetration of loop tips into membranes.

Cobra cytotoxins, small proteins of three-fingered toxin family, unspecifically damage membranes in different cells and artificial vesicles. However, the molecular mechanism of this damage is not yet completely understood. We used steered molecular dynamics simulations to study the interaction of cardiotoxin A3 from Naja atra cobra venom with hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) bilayer.

Computer modeling of binding of diverse weak toxins to nicotinic acetylcholine receptors.

Weak toxins are the "three-fingered" snake venoms toxins grouped together by having an additional disulfide in the N-terminal loop I. In general, weak toxins have low toxicity, and biological targets have been identified for some of them only, recently by detecting the effects on the nicotinic acetylcholine receptors (nAChR). Here the methods of docking and molecular dynamics simulations are used for comparative modeling of the complexes between four weak toxins of known spatial structure (WTX, candoxin, bucandin, gamma-bungarotoxin) and nAChRs.

A model for short alpha-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica.

Short- and long-chain alpha-neurotoxins from snake venoms are potent blockers of nicotinic acetylcholine receptors (nAChRs). Short alpha-neurotoxins consist of 60-62 amino acid residues and include 4 disulfide bridges, whereas long alpha-neurotoxins have 66-75 residues and 5 disulfides. The spatial structure of these toxins is built by three loops, I-III "fingers," confined by four disulfide bridges; the fifth disulfide of long-chain alpha-neurotoxins is situated close to the tip of central loop II.

[Molecular dynamics of oligopeptides 6. A comparative study of poincare cross-section of monopeptide frames in media with different hydrophobicity].

A comparative study of the molecular dynamics of natural amino acid residues and their closest homologues and isomers was carried out. Molecular dynamics protocols not interfering with the principle of equidistribution of energy with respect to degrees of freedom were used. Poincare cross-sections, auto- and cross-correlation of complex exponential curves as a function of dihedrons were considered.

A model for short alpha-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica: comparison with long-chain alpha-neurotoxins and alpha-conotoxins.

Short-chain alpha-neurotoxins from snakes are highly selective antagonists of the muscle-type nicotinic acetylcholine receptors (nAChR). Although their spatial structures are known and abundant information on topology of binding to nAChR is obtained by labeling and mutagenesis studies, the accurate structure of the complex is not yet known. Here, we present a model for a short alpha-neurotoxin, neurotoxin II from Naja oxiana (NTII), bound to Torpedo californica nAChR.