The Journal of Biological Physics and Chemistry

2004

Volume 4, Number 1, p. 3338

G. Managadze, B. Vishnepolsky and M. Pirtskhalava


Institute of Molecular Biology and Biological Physics, Georgian Academy of Sciences, 12 Gotua Street, 0160 Tbilisi, Georgia

Side chain orientations as a characteristic of native protein structure

Revealing a new feature of native protein structure is interesting in the light of the construction of simple potentials for threading. According to the conventional model of folding, the hydrophobic effect is a dominant force in the process of stabilization of the native structure. Our earlier investigations showed that a protein can be stabilized by more than one group of hydrophobic residues (cores). These results led us to examine the possibility of using the orientations of side chains in relation to the geometrical centres of the hydrophobic core as a hallmark of the native structure of globular proteins. Statistical features observed in 73 native structures of monomeric non-membrane globular proteins, and also threading tests of these structures, show that the side chains orientations are an effective characteristic of the native states. The simplicity of this characteristic makes it useful in attempts to derive simple threading potentials.

Keywords: side chain orientation, statistical analysis, threading

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