IDENTIFICATION OF A PATTERN IN PROTEIN-STRUCTURE BASED ON ENERGETIC AND STATISTICAL CONSIDERATIONS

We carry out a statistical analysis of the nonbonded interactions in 1 0 high-resolution nonhomologous protein structures, using original alg orithms, We observe a tendency of nonbonded interactions which contrib ute significantly (i.e., with an energy lower than the average value, referred to as ''strong'') to protein stability, to be concentrated in clusters of residues that are strongly sequence correlated, We charac terize this sequence correlation and subsequently define a ''system'' as the pattern that describes these clusters. In order to study the di stribution of the systems in the proteins we build a matrix for each p rotein and for each term of the empirical potential function used to c ompute the nonbonded interactions; each ij element is the number of co mmon residues between the systems i and j. The analysis of the matrice s shows the presence of compact blocks that define units in the protei n structure which concentrate strong and weak interactions inside the unit itself and display relative independence with respect to the rest of the protein, Comparing the blocks defined by the three nonbonded e nergy components (electrostatic, hydrogen bonds, and van der Waals int eractions) we observe a one-to-one correspondence between the blocks o f different energy components with an average overlap of 90% of the re sidues forming each block. (C) 1996 Wiley-Liss, Inc.