Hydrogen bonds and heat diffusion in α-helices: a computational study.

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 α-helices with different abilities to form hydrogen bonds.

Effect of mutation at the interface of Trp-repressor dimeric protein: a steered molecular dynamics simulation.

The strength of key interfacial contacts that stabilize protein-protein interactions have been studied by computer simulation. Experimentally, changes in the interface are evaluated by generating specific mutations at one or more points of the protein structure. Here, such an evaluation is performed by means of steered molecular dynamics and use of a dimeric model of tryptophan repressor and in-silico mutants as a test case.

On the role of short and strong hydrogen bonds on the mechanism of action of a model chymotrypsine active site.

The electronic properties of a chemical model that mimics the His-57...