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Main-chain complementarity in protein-protein recognition
Vakser, Ilya A.
Vakser, Ilya A.
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Abstract
We present a statistical analysis of protein structures based on interatomic Ca distances. The overall distance distributions reflect in detail the contents of sequence-specific substructures maintained by local interactions (such as α-helixes) and longer range interactions (such as disulfide bridges and β-sheets). We also show that a volume scaling of the distances makes distance distributions for protein chains of different length superimposable. Distance distributions were also calculated specifically for amino acids separated by a given number of residues. Specific features in these distributions are visible for sequence separations of up to 20 amino acid residues. A simple representation, which preserves most of the information in the distance distributions, was obtained using six parameters only. The parameters give rise to canonical distance intervals and when predicting coarse-grained distance constraints by methods such as data-driven artificial neural networks, these should preferably be selected from these intervals. We discuss the use of the six parameters for determining or reconstructing 3-D protein structures.
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This is the publisher's version, also available electronically from "http://peds.oxfordjournals.org".
Date
1996-09-01
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Oxford University Press
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Vakser, I. (1996). Main-chain complementarity in protein-protein recognition. "Protein Engineering, Design and Selection", 9(9), 741-744. http://www.dx.doi.org/10.1093/protein/9.9.741