Paper Citing NAMD - Abstract
Mino, German; Barriga, Raul; Gutierrez, Gonzalo
Hydrogen Bonds and Heat Diffusion in alpha-Helices: A Computational Study
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10025-10034, AUG 28 2014
Recent evidence has shown a correlation between the heat diffusion pathways and the known allosteric communication pathways in proteins. Allosteric communication in proteins is a central, yet unsolved, problem in biochemistry, and the study and characterization of the structural determinants that mediate energy transfer among different parts of proteins is of major importance. In this work, we characterized the role of hydrogen bonds in diffusivity of thermal energy for two sets of a-helices with different abilities to form hydrogen bonds. These hydrogen bonds can be a constitutive part of the a-helices or can arise from the lateral chains. In our in vacuo simulations, it was observed that alpha-helices with a higher possibility of forming hydrogen bonds also had higher rates of thermalization. Our simulations also revealed that heat readily flowed through atoms involved in hydrogen bonds. As a general conclusion, according to our simulations, hydrogen bonds fulfilled an important role in heat diffusion in structural patters of proteins.
