ROUGHNESS OF THE GLOBULAR PROTEIN SURFACE - ANALYSIS OF HIGH-RESOLUTION X-RAY DATA

In an earlier publication [Serdyuk, I.N. et al., Biofizika, in press, 1997] we demonstrated that the asymmetry extent of globular proteins d oes not change with increasing their sizes, and the observed nontrivia l dependence of the protein accessible surface area on the molecular m ass [Miller, S., J. Mol, Biol. 196:641-656, 1987] (A(s) - M dependence ) is a reflection of the protein surface relief peculiarities. To clar ify these peculiarities, an analysis of the molecular surface on the b asis of high-resolution x-ray data has been done for 25 globular prote ins not containing prosthetic groups. The procedure was based on study ing the dependence of the minimal number (N) of probe bodies (here cub es) covering the entire protein surface, both on their size (N - R dep endence) and on the value of dry protein volume (N - V dependence). Tw o levels of protein surface organization have been detected by molecul ar surface analysis. On the micro scale (2-7 Angstrom), the surface is characterized by a D = 2.1 fractal dimension which is intrinsic to su rfaces with weak deformations and reflects the local atomic group pack ing. 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-sc ale irregularities has been proposed. (C) 1997 Wiley-Liss, Inc.