[Oligoglycine surface structures: molecular dynamics simulation].

The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.

Conformation-dependent sequence design: evolutionary approach.

A new modification of evolutionary approach to sequence design of copolymers has been proposed. A model of step-by-step evolution of a two-letter ( HP) copolymer sequence has been studied by means of a coarse-grained Monte Carlo algorithm. The conditions for accepting a change in the primary sequence depend on the spatial conformation of HP-copolymer chain. This leads to a coupling between sequence and conformation and to formation of protein-like conformations and primary sequences (for some values of parameters of the model) independently of initial sequence and/or conformation. Simple theory describing these computer simulation observations is developed.

Coil-globule transition for regular, random, and specially designed copolymers: Monte Carlo simulation and self-consistent field theory.

The coil-globule transition has been studied for A-B copolymer chains both by means of lattice Monte Carlo (MC) simulations using bond fluctuation algorithm and by a numerical self-consistent-field (SCF) method. Copolymer chains of fixed length with A and B monomeric units with regular, random, and specially designed (proteinlike) primary sequences have been investigated. The dependence of the transition temperature on the AB sequence has been analyzed. A proteinlike copolymer is more stable than a copolymer with statistically random sequence. The transition is more sharp for random copolymers. It is found that there exists a temperature below which the chain appears to be in the lowest energy state (ground state). Both for random and proteinlike sequences and for regular copolymers with a relatively long repeating block, a molten globule regime is found between the ground state temperature and the transition temperature. For regular block copolymers the transition temperature increases with block size. Qualitatively, the results from both methods are in agreement. Differences between the methods result from approximations in the SCF theory and equilibration problems in MC simulations. The two methods are thus complementary.

Primary sequences of proteinlike copolymers: Levy-flight-type long-range correlations.

We consider the statistical properties of primary sequences of two-letter HP copolymers (H for hydrophobic and P for polar) designed to have water soluble globular conformations with H monomers shielded from water inside the shell of P monomers. We show, both by computer simulations and by exact analytical calculation, that for large globules and flexible polymers such sequences exhibit long-range correlations which can be described by Levy-flight statistics.

[Electron computer modeling of membrane structure and distribution of admixture particles in the lipid bilayer]. / Modelirovanie na EVM struktury membran i raspredeleniia primesnykh chastits v lipidnom bisloe.

A simple molecular model of double lipid layer of the membrane is proposed. Equilibrium distribution of small hydrophilic particles between bilayer and contacting solution was studied by computer modeling. Connection between the concentration profile of the particles and its structural organization was considered. Special role of the bilayer central region was found. The results obtained qualitatively agree with the known experimental data.

[Study of the permeability of bilayer lipid membranes by the Monte-Carlo method]. / Izuchenie pronitsaemosti bisloinykh lipidnykh membran metodom Monte-Karlo.

Results are presented of computer modelling of small molecules transfer through the double lipid layer of the membrane. The problem is considered on the basis of "kink" theory. Dependence of the permeability coefficient P on temperature T and area A per one lipid chain on the interface surface was studied. It has been shown that with T and (or) A decrease the value P decreases. The P values calculated, as well as probabilities of "kinks" and gauche-isomers for the chains in liquid--crystal bilayer well agree with the experimental data. It has been shown that the admixture molecules introduced between the bilayer lipid chains decrease its permeability.

[Coil--globule transition in a linear macromolecule]. / O perekhode klubok--globula v lineinoi makromolekule.

Effect of chain length and rigidity on characteristics of coil-globule in a linear macromolecule was considered taking into account the data of computer experiment. It was shown that with a temperature decrease a sufficiently long chain passes from a developed conformation into the globule close to theta-point. Relative withdrawal of theta-temperature from that of coil-globule transition is changed in proportion to the persistent length of the chain. The role of intramolecular orientation ordering during the formation of the protein globule is discussed.