Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations.
The temperature dependence of thermodynamic quantities, such as heat capacity, entropy and free enthalpy, may be obtained by using well-known equations that relate these quantities to the enthalpy of the molecular system of interest at a range of temperatures. In turn, the enthalpy of a molecular system can be estimated from molecular dynamics simulations of an appropriate model. To demonstrate this, we have investigated the temperature dependence of the enthalpy, heat capacity, entropy and free enthalpy of a system that consists of a beta-heptapeptide in methanol and have used the statistical mechanics relationships to describe the thermodynamics of the folding/unfolding equilibrium of the peptide. The results illustrate the power of current molecular simulation force fields and techniques in establishing the link between thermodynamic quantities and conformational distributions.
Boned
Ricard
R
Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
van Gunsteren
Wilfred F
WF
Daura
Xavier
X
D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D013696:Temperature; D013816:Thermodynamics
D010455:Peptides