Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC

Abstract

The accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to predict the change in melting temperature {Delta}Tm upon point mutations, given the protein structure and, when available, the melting temperature Tm of the wild-type protein. The key ingredients of our model structure are standard and temperature-dependent statistical potentials, which are combined with the help of an artificial neural network. The model structure was chosen on the basis of a detailed thermodynamic analysis of the system. The parameters of the model were identified on a set of more than 1,600 mutations with experimentally measured {Delta}Tm. The performance of our method was tested using a strict 5-fold cross-validation procedure, and was found to be significantly superior to that of competing methods. We obtained a root mean square deviation between predicted and experimental {Delta}Tm values of 4.2{degrees}C that reduces to 2.9{degrees}C when ten percent outliers are removed. A webserver-based tool is freely available for non-commercial use at soft.dezyme.com.