Team: Structural biophysics of cell

Laboratory of Biophysics and Engineering of Cell

Team: Structural biophysics of cell
Head of the team — V.G. Veresov, D.Sc, leading research scientist.

Main research trends:

  • Development of methods, algorithms, computer programs for simulating spatial structure of intracellular proteins. Detection of interrelations: “structure-activity” and “structure-property”.
  • Development of methods, algorithms, computer programs for simulating interactions of intracellular proteins with membranes of intracellular organelles.
  • Development of methods, algorithms, computer programs for simulating interactions between intracellular proteins.
  • Structural biology of apoptosis. Simulation of apoptotic processes.
  • Computer-based drug design and virtual screening of chemical compound
    The main achievements:

The creation of algorithms and program packages for:

  • simulations of protein structure and dynamics
  • simulations of transport of ions and molecules in channels by Brownian and molecular dynamics techniques
  • simulations of protein-membrane interaction
  • simulations of intracellular calcium dynamics

The main achievements:

  • The computer modeling of the structure and dynamics of a number of voltage-gated and ligand- gated channels;
  • The creation of algorithms and the program package WERCAL1 for simulations of the structure and dynamics of inositol-1,4,5-triphosphate-sensitive and ryanodine-sensitive calcium channels by a number of methods;
  • The modeling of the structure and domain dynamics of inositol 1,4,5-binding region of inositol 1,4,5-sensitive calcium channel (receptor) after their binding with coagonists: inositol 1,4,5-triphosphaete (IP3) and Ca2 +;
  • The modeling of the structure and domain organization of ryanodine receptor (ryanodine-sensitive calcium channel) of brain neuron (RyR3 human);
  • The modeling of kinetics of Ca2+ binding to calcium-binding sites EF3bIP3R and EF3bIP3R of the inositol 1,4,5-triphosphate receptor and to the calcium-binding sites EF1RyR, EF2RyR, EF3aRyR, EF3bRyR as well as of the dynamics of transmembrane helices of the ryanodine receptor by Monte-Carlo method;
  • The modeling of the generation and coding of intracellular calcium signal in brain neurons and in plant cells;
  • The modeling of the 3D-structure of protein tBid bound to mitochondrial outer membrane and of the dynamics of the direct activation of Bax by tBid and cardiolipins of mitochondrial outer membrane. A novel model of Bax activation by tBid was predicted by the simulations. In this model, tBid binds to Bax at an interaction site formed by Bax helices  α1, α2, α3 and α5 leading, due to interaction of the positively charged N-terminal fragment of tBid with anionic lipid headgroups, to Bax reorientation such that a hydrogen bonded pair of residues Asp98 and Ser184 is brought into close proximity with negatively charged lipid headgroups. The interaction with these headgroups destabilizes the hydrogen bond that results in the release of helix 9 from the Bax binding groove, its insertion into the membrane followed by insertion into the membrane of the α5-α6 helical hairpin;
  • The establishment of mechanisms of the antiapoptotic action of antiapoptotic proteins;
  • The modeling of the dynamics of IP3-receptor after the IP3 binding;
  • Modeling of mechanisms of proapoptotic action of antitumor drugs;
  • Computer-based-structure-based of new highly-effective inhibitors of the proteins Bcl-2, Bcl-xL, Bcl-w, as potent anticancer drugs;
  • Modeling apoptosis in hCNS neurons;
  • Modeling of apoptosis processes regulated by mitochondrial receptors MTCH2, VDAC2 and the TOM complex.

    Ongoing studies are directed at the refinement of the structure-based atomic-level  insights  into  understanding the regulation of apoptotic processes by MOM proteins as well as the in silico development of antitumor drugs.

    “Structural Biology Group” is open for collaboration on national or international levels in areas of all types of Structural Biology, Protein modeling, Modeling of Cellular processes, Modeling of Ca-release receptors, apoptosis, membrane channels, computer-based drug design, virtual screening of drugs, software development for above purposes. Collaboration is possible as joint projects, short-term visit exchange (up to 3 months), etc
    Responsible person: Dr. Valery Veresov (phone: (37517)-2842252, e-mail: