AbstractIn this study, we provide a time-dependent (td-) mechanical model, taking advantage of molecular dynamics (MD) simulations, quasiharmonic analysis of MD trajectories and td-linear response theories (td-LRT) to describe vibrational energy redistribution within the protein matrix. The theoretical description explains the observed biphasic responses of specific residues in myoglobin to CO-photolysis and photoexcitation on heme. The fast responses are found triggered by impulsive forces and propagated mainly by principal modes <40 cm-1. The predicted fast responses for individual atoms are then used to study signal propagation within protein matrix and signals are found to propagate ∼ 8 times faster across helices (4076 m/s) than within the helices, suggesting the importance of tertiary packing in proteins’ sensitivity to external perturbations. We further develop a method to integrate multiple intramolecular signal pathways and discover frequent “communicators”. These communicators are found evolutionarily conserved including those distant from the heme.
Molecular dynamics simulations and linear response theories jointly describe biphasic responses of myoglobin relaxation and reveal evolutionarily conserved frequent communicators
