Computational protein design is a challenge for implicit solvation models

Biophysical Journal
Alfonso Jaramillo, S J Wodak

Abstract

Increasingly complex schemes for representing solvent effects in an implicit fashion are being used in computational analyses of biological macromolecules. These schemes speed up the calculations by orders of magnitude and are assumed to compromise little on essential features of the solvation phenomenon. In this work we examine this assumption. Five implicit solvation models, a surface area-based empirical model, two models that approximate the generalized Born treatment and a finite difference Poisson-Boltzmann method are challenged in situations differing from those where these models were calibrated. These situations are encountered in automatic protein design procedures, whose job is to select sequences, which stabilize a given protein 3D structure, from a large number of alternatives. To this end we evaluate the energetic cost of burying amino acids in thousands of environments with different solvent exposures belonging, respectively, to decoys built with random sequences and to native protein crystal structures. In addition we perform actual sequence design calculations. Except for the crudest surface area-based procedure, all the tested models tend to favor the burial of polar amino acids in the protein interior over no...Continue Reading

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Citations

Nov 30, 2012·Journal of Molecular Modeling·Xiaoqiang HuangYushan Zhu
Jul 3, 2009·Systems and Synthetic Biology·María SuárezAlfonso Jaramillo
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