title: A study of interface roughness of heteromeric obligate and non-obligate protein-protein complexes.
abstract: A number of studies aimed to distinguish the structural patterns at the interfaces of obligate and non-obligate protein-protein complexes. These studies revealed better geometric complementarity of protomers in obligate complexes over non-obligates. We showed that protein surface roughness can be used to explain this observation. Using smoothened atomic fractal dimension (SAFD) as a descriptor, this work investigates the role of interface roughness in the molecular recognition of these two types of protein-protein complexes. We studied 52 obligate and 62 nonobligate heteromeric high quality crystal structures from benchmark data sets. We found that distribution of interface roughness values obligate and non-obligates are quite similar. However, we observed a distinct preference for obligate protomers to complex with chains having similar roughness. The roughness pairing is correlated in obligates only. The later indicates, an increase/decrease of roughness in one chain causes a proportional change in roughness in its binding partner. Based on these observations we proposed that similar and correlated roughness pairing leads to more interdigitation and contacts at the interface leading to better geometric fit in obligates. We propose that roughness information can find useful application in improving machine learning based complex type classifiers and filtering protein-protein docking solutions.
authors.affiliation: Structural Biology & Bioinformatics Division, Indian Institute of Chemical Biolgy, Jadavpur, Kolkata 700032, India.
authors.forename: Indrani
authors.initials: I
authors.lastname: Bera
authors.forename: Somak
authors.initials: S
authors.lastname: Ray
references.citation: J Mol Biol. 2003 Jan 10;325(2):377-87
references.pmid: 12488102
references.citation: J Mol Graph. 1992 Jun;10(2):120-3, 111
references.pmid: 1637749
references.citation: Proteins. 2007 Jul 1;68(1):170-86
references.pmid: 17393392
references.citation: Proteins. 2003 Nov 15;53(3):629-39
references.pmid: 14579354
references.citation: BMC Bioinformatics. 2006 Jan 19;7:27
references.pmid: 16423290
references.citation: Nucleic Acids Res. 2005 Jan 12;33(1):244-59
references.pmid: 15647507
references.citation: Science. 1985 Dec 6;230(4730):1163-5
references.pmid: 4071040
references.citation: J Mol Biol. 1999 Jan 29;285(4):1377-82
references.pmid: 9917382
references.citation: Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):13-20
references.pmid: 8552589
references.citation: Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10930-5
references.pmid: 16043700
references.citation: J Mol Biol. 2003 Jan 31;325(5):991-1018
references.pmid: 12527304
references.citation: BMC Struct Biol. 2005 Aug 16;5:15
references.pmid: 16105176
references.citation: J Mol Biol. 2007 Jun 8;369(3):863-79
references.pmid: 17451744