Protein Stability Prediction: A Poisson−Boltzmann Approach

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.