Effect of chain connectivity on the structure of Lennard-Jones liquid and its implication on statistical potentials for protein folding

Abstract

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.

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“…To reduce such artifacts, the protein structures from PDBs need to be modified by adding the missing Ca residues using molecular dynamics simulations in which the coordinates of the additional residues are optimized to fill the broken gaps whereas the coordinates of the residues from the PDB are kept intact. The interactions among the Cas in the molecular dynamics simulations are the same as those we previously used in simulations in a single‐bead protein model 22. These interactions describe reasonably well the backbone configurations of a protein.…”