Protein stability prediction: a Poisson-Boltzmann approach

The Journal of Physical Chemistry. B
Yu-Hong Tan, Ray Luo

Abstract

Most proteins are only marginally stable at physiological temperatures. Thus a common defect due to mutation is the loss of protein stability, resulting in loss of their well-defined structures and functions at their functioning temperatures. Quantification of protein stability change upon mutation has attracted a large number of experimental and theoretical studies. In this work, we have extended the Poisson-Boltzmann theory that is originally used for predicting stability changes of charged mutations to predicting stability changes of all mutations. To achieve this, we have proposed a free energy model covering both electrostatic and hydrophobic interactions. A Gõ-like model for the denatured state that incorporates both nativeness and randomness of the denatured state has been used to calculate the hydrophobic contribution to protein stability. The new model is computationally simple and fast, and performs well for charged and hydrophobic mutations for all four tested proteins. Future directions for extending the method into pH-dependent effect and more accurate prediction for polar mutations are discussed.

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Citations

Jun 30, 2009·PMC Biophysics·Yuhong Tan, Ray Luo
Apr 20, 2010·Current Opinion in Structural Biology·Daniel M JordanShamil R Sunyaev
May 11, 2010·Biochemical and Biophysical Research Communications·Yunqi Li, Jianwen Fang
May 30, 2017·Journal of Chemical Theory and Computation·Ruxi QiRay Luo
Jun 1, 2017·Journal of Chemical Theory and Computation·Li XiaoRay Luo
Jan 26, 2018·Frontiers in Molecular Biosciences·Changhao WangRay Luo
Jul 7, 2016·Protein Engineering, Design & Selection : PEDS·Jyotica BatraHuan-Xiang Zhou
Mar 21, 2017·Journal of Computational Chemistry·Changhao WangRay Luo
Aug 12, 2016·Journal of Computational Chemistry·Changhao WangRay Luo
Oct 14, 2008·Journal of Chemical Theory and Computation·Harianto Tjong, Huan-Xiang Zhou
Dec 10, 2016·The Journal of Physical Chemistry. B·D'Artagnan GreeneRay Luo
Dec 15, 2018·Journal of Chemical Information and Modeling·Ruxi Qi, Ray Luo

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