Effect of chain connectivity on the structure of Lennard-Jones liquid and its implicationon statistical potentials for protein folding.
Statistical contact potentials and bead-spring models have been widely used for computational studies of protein folding. However, there has been speculation that systematic error may arise in the contact energy calculations when the statistical potentials are deduced under the assumption that the chain connectivity in proteins can be ignored. To address this issue, we have performed molecular-dynamics simulations to study the structure and dynamics of a simple liquid system in which the beads are either connected or unconnected with springs. Results from the present study provide useful information for assessing the accuracy of the statistical potentials for protein structure simulations.
Lu
W C
WC
Ames Laboratory and Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, USA.
Wang
C Z
CZ
Ho
K M
KM
D001483:Base Sequence; D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012996:Solutions / Q000737:chemistry*
D011506:Proteins; D012996:Solutions