Description
Comparing the folding mechanisms of proteins with similar secondary structures yet with different sequences can provide fundamental insights in understanding important properties of proteins. Molecular Dynamics (MD) is a computational tool used to analyze protein dynamics and, in our study, the thermal stability of proteins on an atomistic level. Here, we describe the use of the AMBER 14 MD package to carry out computer simulations on two sets of protein mutants in order to understand the effect that point mutations (in the core of a protein) have on surrounding secondary structure elements and on overall protein thermal stability. The two sets of proteins are mutants that are derived from the β1 domain of streptococcal protein-G and the human protein ubiquitin. MD simulations were conducted on a series of different mutants at simulated temperatures that ranged from 200K to 500K in 25K increments. The purpose was to study and analyze the energies and conformational changes that occur within the series of mutant test proteins at increasing temperatures. The results of these calculations enhanced our understanding of the effect that core point mutations have on β-hairpin secondary structure elements common to both test proteins. The resulting MD trajectories were analyzed for retention of main-chain hydrogen bonds for β-hairpin secondary structure elements as a function of increasing temperature. In an interesting case, the retention of main chain hydrogen bonds for the wild type variant was actually greater in comparison to the most thermostable variant. This emphasizes the unique packing and high structural specificity inherent to the wild type protein. Computational results on the analysis of thermal stability for these mutants were found by analyzing their conformational changes during the course of these simulations. We were able to adapt this form of dynamic simulations to provide computational results that are complementary to experimental data. The goal is to apply rigorous analysis that can be used as a pipeline for guiding protein design projects by providing a robust bridge between theory and experiment.
