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


BACKGROUND
http://cib.cf.ocha.ac.jp/DACSIS/.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Computational Biology, Graduate School of Humanities and Sciences, Center for Informational Biology, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan. yura.kei@ocha.ac.jp
Kei
K
Yura
Steven
S
Hayward
D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D046912:Multiprotein Complexes / Q000737:chemistry*; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000378:metabolism
D046912:Multiprotein Complexes; D011506:Proteins