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Internal force field in proteins

Authors:
Damian Marchewka
Irena Roterman

Keywords: Internal force field; External force field; Interactions in protein; 3-D Gauss function; Information theory

Abstract:
The proteins representing the structures of ordered form in respect to their tertiary structure are discussed. The hydrophobic core of 3-D Gauss function (“fuzzy oil drop” model) appeared to be present in some proteins. The proteins of the structure with ordered form of vdW and/or electrostatic internal interaction in protein body are discussed in the paper. The vdW interaction distribution in proteins appeared to be accordant with assumed 3-D Gauss function while the electrostatic represents the distribution of random form. This characteristics allows interpretation of the tertiary structure as the effect of external/internal force field influence expressed by 3-D Gauss function in respect to hydrophobic and/or vdW interaction. It is postulated that the additional introduction of 3-D Gauss function representing the influence of external environment (in contrast to internal force field of protein body) in the simulation of protein folding process in silico may simplify the optimization procedure leading to the appropriate order on the level of tertiary structure of protein molecule and directing the hydrophobic residues toward the center of the protein body with the exposure of hydrophilic residues on the surface. The procedure minimize the differences between internal interactions and the idealized one expressed by external force field.

Pages: 110 to 115

Copyright: Copyright (c) IARIA, 2011

Publication date: May 22, 2011

Published in: conference

ISSN: 2308-4383

ISBN: 978-1-61208-137-3

Location: Venice/Mestre, Italy

Dates: from May 22, 2011 to May 27, 2011