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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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http://pubman.mpdl.mpg.de/cone/persons/resource/persons93650

Kabsch,  Wolfgang
Emeritus Group Biophysics, Max Planck Institute for Medical Research, Max Planck Society;
Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Max Planck Society;

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Zitation

Kabsch, W., & Sander, C. (1984). On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proceedings of the National Academy of Sciences of the United States of America, 81(4), 1075-1078. Retrieved from http://www.pnas.org/content/81/4/1075.


Zitierlink: http://hdl.handle.net/11858/00-001M-0000-0019-AF88-6
Zusammenfassung
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.