Conformational equilibria of valine studied by dynamics simulation.
The conformational probability distribution of a valine residue in the valine dipeptide and of the valine side chain in an alpha-helix, as well as the change in helix stability for replacing alanine with valine, has been calculated by molecular dynamics simulations of explicitly hydrated systems: dipeptide, tetrapeptide and 10-, 14- and 18-residue oligoalanine helices. All computed free-energy differences are means from at least eight separate slow-growth simulations, four in each direction and are reported with their root-mean-square deviations. Different values for the change in free energy of folding (delta delta G degrees) have been calculated with the use of forcefields having an all-atom and a central-atom representation of methyl groups, etc. The value obtained with the all-atom forcefield agrees well with new experimental values (3 kJ/mol = 0.7 kcal/mol). Furthermore, the most stable valine side-chain rotamer in the helix is different for these two representations. The most stable rotamer for the all atom conformation is the same one that predominates for valines in alpha-helices in proteins of known conformation. The lower conformational freedom of the valine side chain in the helix contributes 1 kJ/mol to the difference in stability computed with the all-atom potential; unfavorable interactions of the side chain with helix, even in the most stable conformation, further increase delta delta G degrees.
Yun
R H
RH
Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill 27599-7260.
Hermans
J
J
D000409:Alanine / Q000737:chemistry*; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry; D008956:Models, Chemical; D009842:Oligopeptides / Q000737:chemistry*; D011336:Probability; D011487:Protein Conformation; D014633:Valine / Q000737:chemistry*
D004151:Dipeptides; D009842:Oligopeptides; C034792:valylvaline; D014633:Valine; D000409:Alanine