Thermodynamic calculations in biological systems.
The ability to compute intra- and inter-molecular interactions provides the opportunity to gain a deeper understanding of previously intractable problems in biochemistry and biophysics. This review presents three examples in which molecular dynamics calculations were used to gain insight into the atomic detail underlying important experimental observations. The three examples are the following: (1) Entropic contribution to rate acceleration that results from conformational constraints imposed on the reactants; (2) Mechanism of force unfolding of a small protein molecule by the application of a force that separates its N- and C-terminals; and (3) Loss of translational entropy experienced by small molecules when they bind to proteins.
Amzel
L Mario
LM
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, United States. mario@neruda.med.jhmi.edu
Siebert
Xavier
X
Armstrong
Anthony
A
Pabon
German
G
D008954:Models, Biological; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012996:Solutions; D013816:Thermodynamics
D011506:Proteins; D012996:Solutions