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

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 on...

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Bibliographic Details
Published in:Bioinformatics 2009-12, Vol.25 (23), p.3108-3113
Main Authors: Yura, Kei, Hayward, Steven
Format: Article
Language:English
Subjects:
Binding Sites
Bioinformatics
Biological and medical sciences
Chains
Complexation
Computational Biology - methods
Contact
Databases, Protein
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Multiprotein Complexes - chemistry
On-line systems
Original Papers
Protein Conformation
Protein Interaction Mapping - methods
Proteins
Proteins - chemistry
Proteins - metabolism
Residues
Terminals
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Summary: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.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btp563