A New Approach for the Calculation of the Energy of van der Waals Interactions in Macromolecules of Globular Proteins

Abstract Van der Waals interaction energy in globular proteins is presented by the interaction energies between regions of protein spatial structure with homogenous medium density distribution. We introduce a notion of the local medium permittivity as a function of absorptance of molecular groups with particular conformation. Proposed theory avoids shortcomings which are typical for the calculations on the basis of the pairwise additive approximation. The approach takes into account local peculiarities of protein spatial structure and physical-chemical characteristics of amino acid residues and molecular groups.

[1]  M. Sippl.  Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.

[2]  H. Scheraga,et al.  Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids , 1983 .

[3]  J. Israelachvili.  Van der Waals forces in biological systems , 1973, Quarterly Reviews of Biophysics.

[4]  Evgenii Mikhailovich Lifshitz,et al.  General theory of van der Waals' forces , 1961 .

[5]  A. Wada,et al.  A theoretical study of the dielectric constant of protein. , 1988, Protein engineering.

[6]  Determination of Nonbonded Potential Parameters for Peptides , 1995 .

[7]  A. Kuznetsov,et al.  Electrostatics of proteins: Description in terms of two dielectric constants simultaneously , 1997, Proteins.

[8]  Thomas A. Halgren,et al.  The representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters , 1992 .

[9]  Gordon M. Crippen.  Failures of inverse folding and threading with gapped alignment , 1996 .

[10]  M Vendruscolo,et al.  Efficient dynamics in the space of contact maps. , 1998, Folding & design.

[11]  C. Roth,et al.  Van der Waals interactions involving proteins. , 1996, Biophysical journal.

[12]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[13]  A. Ben-Naim.  STATISTICAL POTENTIALS EXTRACTED FROM PROTEIN STRUCTURES : ARE THESE MEANINGFUL POTENTIALS? , 1997 .

[14]  K. Dill,et al.  Statistical potentials extracted from protein structures: how accurate are they? , 1996, Journal of molecular biology.

[15]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[16]  V A Namiot,et al.  Hierarchy of the interaction energy distribution in the spatial structure of globular proteins and the problem of domain definition. , 1999, Journal of biomolecular structure & dynamics.

[17]  G. Casari,et al.  Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. , 1990, Journal of molecular biology.

[18]  R. Beyer,et al.  Soviet Physics—JETP , 1960 .

[19]  V. Tumanyan,et al.  Representation of amino acid sequences in terms of interaction energy in protein globules , 1997, FEBS letters.

[20]  R. A. Silverman,et al.  Methods of Quantum Field Theory in Statistical Physics , 1964 .