Negative and Positive Design in Protein Folding and Thermodynamic Stability: Insights from Computational Mutagenesis and Simulations

Abstract

Negative and positive components of protein design are crucial for stability and uniqueness of native proteins. The main goal of this work is to investigate mutual work of positive and negative components of design via the effects of non-specific single and multiple mutations on protein thermodynamic stability and folding dynamics. Proteins representing all four major fold types are under consideration. All mutations are done according to single-nucleotide polymorphism, and coarse-grained protein models with Cα representation are constructed based on native-centric approach and are used in Molecular Dynamic (MD) simulations with Langevin dynamics. Inclusion of non-native interactions to the protein dynamics increases the folding/unfolding transition temperatures compared to the model without non-native interactions regardless of protein type. Depending on mutation types and where they are located, changes in thermodynamic stability consistent with experiments are observed. Mutations can also affect the population of transition-state conformations and folding/unfolding dynamics. Positive and negative components are indispensible parts of protein design, and they should be considered in all experimental and computational studies of protein structure and folding. In particular, specific roles of non-native repulsive interactions illuminated in this work calls for in-depth exploration of the role of unfolded conformations in thermodynamic stability and kinetics of protein folding.