R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, G. Verkhivker, H. Li, A. Ulitsky.
MOIL: A molecular dynamics program with emphasis on conformational search and reaction path calculations.
In NATO ASI Ser., Ser. B, 325 ( Statistical Mechanics, Protein Structure and Protein Substrate Interactions). Plenum Press, p.165-191 1994.
ABSTRACT: The field of computational biology has expanded considerably in the last few years. Insight to the dynamics of biomolecules, the design of new drugs and the interactions that lead to stability of macromolecules has been obtained. Crucial in bringing these changes was the introduction of “user friendly” computer programs so that the number of potential users expanded considerably. It is now possible to visualize complex molecules and to study their structure and thermodynamics properties. The strength of this approach and what makes it so attractive is the possibility of studying the behavior of a variety of molecules using essentially the same set of tools. Constructing a large number of molecules was made possible by the use of a data base of molecular pieces: Different molecules are described using common fragments. For example, all proteins are constructed from the same monomers — amino acids. Another example of repeating fragments is found in the base-pairs of DNA. The fragment solution is chemically intuitive, however, it is approximate. In general the intramolecular interactions in an amino acid are influenced by its neighborhood. For example the charge distribution is determined not only by the identity of the amino acid (as is usually assumed) but also by the solvent, the nearby amino acids and the specific conformation of the fragment. Nevertheless, this approximate approach has a number of successes that are documented in the literature1 and therefore not covered in this manuscript.
Computer charts of diffusing molecules.
Science News, The weekly news magazine of Science, 142, p.132-133, August 29, 1992 (featured editorial about my research).
G. Verkhivker, R. Elber, Q.H. Gibson.
Microscopic modeling of ligand diffusion through the protein leghemoglobin: Computer simulations and experiments.
J . Am. Chem. Soc. 114 (20):7866-7878, 1992.
ABSTRACT: The diffusion of carbon monoxide through lupine leghhemoglobin was investigated. The potential of mean force, the transition-state theory rate constant, the friction kernel, the transmission coefficient, and the diffusion constant were calculated. The computations are based on our previous explorationof the diffusion dynamics using the mean field method and on our calculation of the reaction coordinate. The back of the heme pocket is a shallow free energy minimum for the dissociated ligand. The minimum is directly accessible (without a barrier) from the binding site. The barrier for escaping from the free energy minimum to the CE loop is low. Once the ligand leaves the pocket, the diffusion is barrierless. The ligand escapes in two steps. In the first step the ligand is hopping from the heme pocket to the protein interior, and in the second step it diffuses throught the protein matrix to the surface of the macromolecule. The transition-state theory is used for the first part of the process. For the second part a diffusion model is constructed. The calculated friction kernel and its power spectrum strongly depend on the reaction coordinate. The power spectrum is consistent with previous interpretations of the diffusion dynamics. In the second step significant coupling to low-frequency modes is observed, and the diffusion coordinate is dominated by motions of the C and the G helices of the protein. Experimental results of ligand rebinding kinetics in lupine leghemoglobin are reported. It is shown that different diatomic ligands have an unusually fast diffusion rate in accord with theory.
G. Verkhivker, R. Elber, W. Novak.
Locally Enhanced Sampling in free energy calculations. Application of a mean field approximation to accurate calculation of free energy differences.
J. Chem. Phys. 97(10) 7838-7841, 1992.
ABSTRACT: Mean field approximation is employed for accurate calculation of free energy differences. Significantly enhanced sampling is obtained for local changes. In an example for the mutation of a residue in a protein, the increase in the sampling yielded converged results at a significantly lower computational cost than the usual approach.
V.E. Kuzmin, I.S. Rublev, S.V. Korovin, G.M. Verkhivker.
Analysis of complexation ability of 12-crown-4 by the method of the molecular electrostatic potential.
Soviet Progress in Chemistry 56 (2): 76-79, 1990. (Translated from Ukrainski Khimicheski Zhurnal (Russ. Ed.) 56 (2): 180-183, 1990.)
V.E. Kuzmin, I.S. Rublev, G.M. Verkhivker, S.V. Korovin.
Analysis of complexation ability of 18-crown-6 by the molecular electrostatic potential method.
Soviet Progress in Chemistry 56(3): 114-116, 1990.
I.S. Rublev, G.M. Verkhivker.
A program for conformational analysis and computing thermodynamic parameters of hydration of macromolecules.
In “Molecular interactions and conformational analysis “ (In Russian), Novosibirsk, Russia, p.103-105, 1990.
G.M. Verkhivker, I.S. Rublev, V.E. Kuzmin.
Conformational factors of complexation for the cryptand [2.2.2] and its acyclic analogs Analysis of hydration effects.
In “Molecular interactions and conformational analysis” (In Russian), Novosibirsk, Russia, p.106-108, 1990.
V.V. Kuznezov, A.P. Klusky, Y.E. Shapiro, G.M. Verkhivker, A.I. Gren, S.A. Bochkor, V.I. Larionov, E.A. Cantor.
Conformational pathways of interconversion for six-membered heterocycles.
In “Molecular interactions and conformational analysis” (In Russian), Novosibirsk, Russia, p.109-112, 1990.
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