ISSN:
0887-3585
Keywords:
accessible and molecular surfaces
;
fractal and topological dimensions
;
yardstick
;
Chemistry
;
Biochemistry and Biotechnology
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Medicine
Notes:
In an earlier publication [Serdyuk, I.N. et al., Biofizika, in press, 1997] we demonstrated that the asymmetry extent of globular proteins does not change with increasing their sizes, and the observed nontrivial dependence of the protein accessible surface area on the molecular mass [Miller, S., J. Mol. Biol. 196:641-656, 1987] (As - M dependence) is a reflection of the protein surface relief peculiarities. To clarify these peculiarities, an analysis of the molecular surface on the basis of high-resolution x-ray data has been done for 25 globular proteins not containing prosthetic groups. The procedure was based on studying the dependence of the minimal number (N) of probe bodies (here cubes) covering the entire protein surface, both on their size (N - R dependence) and on the value of dry protein volume (N - V dependence). Two levels of protein surface organization have been detected by molecular surface analysis. On the micro scale (2-7 Å), the surface is characterized by a D = 2.1 fractal dimension which is intrinsic to surfaces with weak deformations and reflects the local atomic group packing. On the macro scale, large-scale surface defects are revealed that are interpreted as the result of secondary structure elements packing. A simple model of protein surface representation reflecting large-scale irregularities has been proposed. Proteins 28:194-201, 1997. © 1997 Wiley-Liss Inc.
Additional Material:
5 Ill.
Type of Medium:
Electronic Resource
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