Fast accurate evaluation of protein solvent exposure

Proteins
Naigong ZhangNed S Wingreen

Abstract

Protein solvation energies are often taken to be proportional to solvent-accessible surface areas. Computation of these areas is numerically demanding and may become a bottleneck for folding and design applications. Fast graph-based methods, such as dead-end elimination (DEE), become possible if all energies, including solvation energies, are expressed as single-residue and pair-residue terms. To this end, Street and Mayo originated a pair-residue approximation for solvent-accessible surface areas (Street AG, Mayo SL. Pairwise calculation of protein solvent accessible surface areas. Fold Des 1998;3:253-258). The dominant source of error in this method is the overlapping burial of side-chain surfaces in the protein core. Here we report a new pair-residue approximation, which greatly reduces this overlap error by the use of optimized generic side-chains. We have tested the generic-side-chain method for the ten proteins studied by Street and Mayo and for 377 single-domain proteins from the CATH database (Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-A hierarchic classification of protein domain structures. Structure 1997;5:1093-1108). With little additional cost in computation, the new method consistentl...Continue Reading

References

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Citations

Feb 24, 2009·Journal of Molecular Modeling·Elizabeth DurhamJens Meiler
Nov 30, 2012·Journal of Molecular Modeling·Xiaoqiang HuangYushan Zhu
Mar 10, 2012·The Journal of Chemical Physics·Ariel Fernández
Dec 13, 2007·Journal of Computational Chemistry·Christina L VizcarraStephen L Mayo
Feb 8, 2007·Journal of Computational Chemistry·Andrew Leaver-FayBrian Kuhlman
May 2, 2007·Journal of Computational Chemistry·Edda KloppmannTorsten Becker
Mar 21, 2008·Journal of Computational Chemistry·Naigong Zhang, Chen Zeng
Jun 17, 2008·Protein Science : a Publication of the Protein Society·Mingyang LuJianpeng Ma
May 8, 2013·Protein Science : a Publication of the Protein Society·Xiaoqiang HuangYushan Zhu
Jun 10, 2011·Journal of Computational Chemistry·Konstantin V KleninWolfgang Wenzel
Jun 30, 2011·Protein Science : a Publication of the Protein Society·Yulin LeiYushan Zhu
Jan 5, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yao-Ming Huang, Christopher Bystroff
Jul 18, 2006·Current Opinion in Structural Biology·Alan M Poole, Rama Ranganathan
Nov 1, 2005·Current Opinion in Chemical Biology·Christina L Vizcarra, Stephen L Mayo
Aug 16, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Robert G Endres, Ned S Wingreen
Jun 12, 2012·Physical Review Letters·Ariel Fernández

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