Using Molecular Dynamics Simulation to Analyze Protein Stability and Dynamic Properties in Solution

Abstract

In solution, the native structure of a protein is actually an ensemble of structures in their lowest energy conformation. Compared to experimental studies, theoretical studies using molecular dynamics have the potential to characterize such ensemble properties in atomic detail. In this study, we are trying to find common dynamic properties across different folds. The dynamic properties of 20 amino acids are categorized based on different secondary structure as well as hydrogen bonds between polar groups and water molecules. In our simulation, we find that packing is not optimized for folded proteins. All 20 amino acids exhibit similar packing variations regardless of their secondary structure. Alpha helices show the least conformation flexibility, while turns and random coils exhibits the most flexibility. Also, different residues display different packing preference in different secondary structures. More hydrogen bonds were made between polar groups and water, less between buried and exposed polar groups, and the least between 2 buried polar groups. The proportion of hydrogen bonds made between different groups remains constant across protein folds. More interestingly, all hydrogen bonds between the water and protein show larger surface areas than those between polar groups, which suggests higher packing in the solution interface. All folded protein share similarity in hydration with high packing