Interface - 整理

Protein–Protein Interfaces: Analysis of Amino Acid Conservation in Homodimers

WilliamS. J. Valdar^1* and Janet M. Thornton^1,2

PROTEINS: Structure, Function, and Genetics 42:108–124 (2001)

The classes are assigned on the basis of solvent accessibility, which is calculated using NACCESS an implementation of the Lee and Richards algorithm, with a

probe sphere of radius 1.4Å. A residue is deemed accessible if its relative accessible surface area (RSA) is < 5%, a cut-off devised and optimized by Miller et al.⁴⁷ If a residue is accessible in the protomer it is in the Surface set, otherwise it is Core. If a residue in the Surface set loses RSA upon complexation it is in the Interface set, otherwise it is Exposed. If a residue in the Interface set is inaccessible (i.e.< 5% RSA) in the multimer complex, it is in the Buried set, else it is Partially Buried.

47. Miller S, Lesk AM, Janin J, Chothia C. The accessible surfacearea

and stability of oligomeric proteins. Nature 1987;328:834–836.

An evolution based classifier for prediction of protein interfaces without using protein structures

I. Reš, I. Mihalek and O. Lichtarge

Vol. 21 no. 10 2005, pages 2496–2501 doi:10.1093/bioinformatics/bti340

Interface residues were defined as surface residues that lost relative surface

accessible areas (RSAs) upon complex formation. Surface residues were

defined as those for which RSA ≥5% (Valdar and Thornton, 2001). The

solvent accessibility was calculated using the program NACCESS (Hubbard

and Thornton, 1993), which implements the Lee and Richards algorithm,

with a probe sphere of radius 1.4 Å (Lee and Richards, 1971). Valdar,V. and Thornton,J.M. (2001) Protein–protein interfaces: analysis of amino acid

conservation in homodimers. Proteins, 42, 108–124.

X-ray crystallographic analysis of the sulfur carrier protein SoxY from Chlorobium limicolaf. thiosulfatophilum reveals a tetrameric structure

JAN STOUT, GONZALEZ VAN DRIESSCHE, SAVVAS N. SAVVIDES, AND JOZEF VAN BEEUMEN

Protein Science (2007), 16:589–601. Published by Cold Spring Harbor Laboratory Press. Copyright _ 2007 The Protein Society

Accessible surface areas (ASA) were calculated with the programs ACCESS and ACCFMT (Lee and Richards 1971). Atoms losing 0.1 Ų in a protein–protein

interaction were identified as interface atoms, and atoms having 0 Ų in a protein–protein interface were classified as buried interface atoms. Surface residues having >5% of their relative accessible surface area (RSA), calculated for each amino acid by Miller et al. (1987), were defined as exposed to the solvent. Fully buried interface residues have a maximum of 5% of their RSA exposed upon oligomerization. Residues having >5% RSA exposed in the interface are partially buried interface residues.