著者
Bang-Chieh Huang Lee-Wei Yang
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.16, pp.473-484, 2019 (Released:2019-11-29)
参考文献数
59
被引用文献数
1 3

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