Campus Units
Genetics, Development and Cell Biology, Bioinformatics and Computational Biology, Biochemistry, Biophysics and Molecular Biology, Computer Science
Document Type
Article
Publication Version
Accepted Manuscript
Publication Date
2008
Journal or Book Title
The Protein Journal
Volume
27
Issue
1
First Page
59
Last Page
70
DOI
10.1007/s10930-007-9108-x
Abstract
We analyze the characteristics of protein–protein interfaces using the largest datasets available from the Protein Data Bank (PDB). We start with a comparison of interfaces with protein cores and noninterface surfaces. The results show that interfaces differ from protein cores and non-interface surfaces in residue composition, sequence entropy, and secondary structure. Since interfaces, protein cores, and non-interface surfaces have different solvent accessibilities, it is important to investigate whether the observed differences are due to the differences in solvent accessibility or differences in functionality. We separate out the effect of solvent accessibility by comparing interfaces with a set of residues having the same solvent accessibility as the interfaces. This strategy reveals residue distribution propensities that are not observable by comparing interfaces with protein cores and noninterface surfaces. Our conclusions are that there are larger numbers of hydrophobic residues, particularly aromatic residues, in interfaces, and the interactions apparently favored in interfaces include the opposite charge pairs and hydrophobic pairs. Surprisingly, Pro-Trp pairs are over represented in interfaces, presumably because of favorable geometries. The analysis is repeated using three datasets having different constraints on sequence similarity and structure quality. Consistent results are obtained across these datasets. We have also investigated separately the characteristics of heteromeric interfaces and homomeric interfaces.
Copyright Owner
Springer Science+Business Media, LLC
Copyright Date
2007
Language
en
File Format
application/pdf
Recommended Citation
Yan, Changhui; Wu, Feihong; Jernigan, Robert L.; Dobbs, Drena; and Honavar, Vasant, "Characterization of Protein–Protein Interfaces" (2008). Genetics, Development and Cell Biology Publications. 110.
https://lib.dr.iastate.edu/gdcb_las_pubs/110
Included in
Biochemistry, Biophysics, and Structural Biology Commons, Bioinformatics Commons, Cell and Developmental Biology Commons, Computational Biology Commons
Comments
This is a manuscript of an article from The Protein Journal 27 (2008): 59. The final publication is available at Springer via http://dx.doi.org/10.1007/s10930-007-9108-x.