Engineering Protein Dynamics through Mutational Energy Landscape Traps

Abstract

Protein dynamics is essential for various biological processes, influencing functions such as enzyme activity, molecular recognition, and signal transduction. However, traditional protein engineering methods often focus on static structures, lacking tools to precisely manipulate dynamic behaviors. Here, we developed Mutational Energy Landscape Trap (MELT), a novel method designed to control protein dynamics by combining Normal Mode Analysis (NMA) and in silico mutagenesis. MELT works by displacing protein structures along low-frequency normal modes and introducing mutations to either lock proteins in these conformations or increase dynamics along the chosen normal modes. We tested MELT using hen-egg lysozyme as a model system. The method was validated by monitoring relevant collective coordinates during molecular dynamics simulations and evaluation of the collective movements of each construct. Our experiments showed that MELT was able to consistently create new protein sequences with the desired dynamical behavior in simulations. It demonstrates its potential for applications in the field of protein engineering, being an unprecedented way of manipulating protein features.