Association lifetimes of hydrophobic amino acid pairs measured directly from molecular dynamics simulations.
Unrestrained molecular dynamics simulations have been used to estimate the lifetimes and equilibrium constants for association of six different pairs of hydrophobic amino acids in aqueous solution. The results indicate that current computational resources are sufficient that the thermodynamics of association of small molecules in water can be routinely measured, thus demonstrating that the development of molecular force fields to reproduce aqueous phase binding data is now an achievable goal.
Yang
Hongbo
H
Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA.
Elcock
Adrian H
AH
D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D007930:Leucine / Q000737:chemistry*; D008715:Methionine / Q000737:chemistry*; D013816:Thermodynamics; D014633:Valine / Q000737:chemistry*
D004151:Dipeptides; D008715:Methionine; D007930:Leucine; D014633:Valine