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On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations.

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On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Kabsch, W. Sander, C.
Abstract	The search for amino acid sequence homologies can be a powerful tool for predicting protein structure. Discovered sequence homologies are currently used in predicting the function of oncogene proteins. To sharpen this tool, we investigated the structural significance of short sequence homologies by searching proteins of known three-dimensional structure for subsequence identities. In 62 proteins with 10,000 residues, we found that the longest isolated homologies between unrelated proteins are five residues long. In 6 (out of 25) cases we saw surprising structural adaptability: the same five residues are part of an alpha-helix in one protein and part of a beta-strand in another protein. These examples show quantitatively that pentapeptide structure within a protein is strongly dependent on sequence context, a fact essentially ignored in most protein structure prediction methods: just considering the local sequence of five residues is not sufficient to predict correctly the local conformation (secondary structure). Cooperativity of length six or longer must be taken into account. Also, we are warned that in the growing practice of comparing a new protein sequence with a data base of known sequences, finding an identical pentapeptide sequence between two proteins is not a significant indication of structural similarity or of evolutionary kinship.
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	4
Volume Number	81
Language	English
Publisher	National Academy of Sciences
Publisher Date	1984-04-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Amino Acid Sequence Oligopeptides Protein Conformation Proteins Animals Carbonic Anhydrases Models, Molecular Prealbumin Probability Structure-Activity Relationship Comparative Study Multidisciplinary
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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