Characterizing oriented protein structural sites using biochemical properties

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abstract: A protein site is a region of a three-dimensional protein structure, with adistinguishing functional or structural role. Certain sites recur indifferent protein structures (for example catalytic sites, calcium bindingsites, and some types of turns), but maintain critical shared features. Tofacilitate the analysis of such protein sites, we have developed a system foranalyzing the spatial distributions of biochemical properties around a site. Simply put, the system takes a set of similar sites and a set of controlnonsites, and finds differences between them. Specifically, it compares distributions of the properties surrounding the sites with those surroundingthe nonsites, and reports significant differences. In this paper, we applyour method to analysis of the features of the active site of the serineprotease enzymes. We compare the use of radial distributions (shells) with3-D grids (blocks) in the analysis of the active site. We demonstrate threedifferent strategies for focusing attention on significant findings, based onproperties of interest, spatial volumes of interest, and on the level ofstatistical significance. Finally, we show that the program automaticallyidentifies conserved sequential, secondary structural and biophysical featuresof the serine protease active site, using noncatalytic histidine residues as acontrol environment.

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