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J Mol Biol. 1987 Sep 20;197(2):331-48.

Analysis of sequence-similar pentapeptides in unrelated protein tertiary structures. Strategies for protein folding and a guide for site-directed mutagenesis.

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European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany.


From the most recent Brookhaven Protein Co-ordinate Databank, 229 sequence-identical pentapeptide pairs, each found in two unrelated protein structures, were collected; 9115 such pairs differing in only one residue were also gathered. For both samples the main-chain fold was conserved about 20% of the time, despite the different atomic environments presented by the unrelated protein architectures. An analysis of the substituted residues as well as the composition of the sequence-similar pentapeptides allowed several suggestions regarding protein folding mechanisms. An examination of the most frequently observed residue substitutions and their correlation with structural changes in the oligopeptide pairs yields a possible guide for site-directed mutagenesis experiments, especially when no tertiary structural information is at hand.

[Indexed for MEDLINE]

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