Journal Article

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

Kei Yura and Steven Hayward

in Bioinformatics

Volume 25, issue 23, pages 3108-3113
Published in print December 2009 | ISSN: 1367-4803
Published online September 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp563

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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/

Contact: yura.kei@ocha.ac.jp; sjh@cmp.uea.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  4706 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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