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The interwinding nature of protein-protein interfaces and its implication for protein complex formation.

ABSTRACT: MOTIVATION: Structural features at protein-protein interfaces can be studied to understand protein-protein interactions. It was noticed that in a dataset of 45 multimeric proteins the interface could either be described as flat against flat or protruding/interwound. In the latter, residues within one chain were surrounded by those in other chains, whereas in the former they were not. RESULTS: A simple method was developed that could distinguish between these two types with results that matched those made by a human annotator. Applying this automatic method to a large dataset of 888 structures, chains at interfaces were categorized as non-surrounded or surrounded. It was found that the surrounded set had a significantly lower folding tendency using a sequence based measure, than the non-surrounded set. This suggests that before complexation, surrounded chains are relatively unstable and may be involved in 'fly-casting'. This is supported by the finding that terminal regions are overrepresented in the surrounded set. AVAILABILITY: http://cib.cf.ocha.ac.jp/DACSIS/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUBMITTER: Yura K

PROVIDER: S-EPMC2778332 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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The interwinding nature of protein-protein interfaces and its implication for protein complex formation.

Yura Kei K Hayward Steven S

Bioinformatics (Oxford, England) 20090929 23

<h4>Motivation</h4>Structural features at protein-protein interfaces can be studied to understand protein-protein interactions. It was noticed that in a dataset of 45 multimeric proteins the interface could either be described as flat against flat or protruding/interwound. In the latter, residues within one chain were surrounded by those in other chains, whereas in the former they were not.<h4>Results</h4>A simple method was developed that could distinguish between these two types with results t ...[more]

PMID: 19789269

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The interwinding nature of protein-protein interfaces and its implication for protein complex formation.

Publications

The interwinding nature of protein-protein interfaces and its implication for protein complex formation.

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