Paper Citing NAMD - Abstract
Lin, Ying-Wu; Nie, Chang-Ming; Liao, Li-Fu
Folding behaviors of apocytochrome b(5) and its mutants: Insights from high temperature molecular dynamics simulations
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 910:154-162, SEP 30 2009
Apocytochrome b(5) (apocyt b(5)) with heme removal from the heme-binding core 1, and its mutants with amino acid replaced in the hydrophobic core 2, namely apocyt b(5) Y7P, P81A and H15R/S20E, have been subjected to molecular dynamics (MD) simulation at high temperature (500 K) for elucidating their folding behaviors. The early events upon thermal induced unfolding were found to be in good agreement with available experimental results, and the lowest stability of Y7P was predicted among the four apoproteins. The influences of these key residues on protein folding behavior were compared directly at an atomic level. At the same time, the influences of non-native interactions of hydrogen bonds and salt-bridges on protein stabilities were analyzed in detail. The insights from current MD simulations are valuable for understanding the apoprotein folding and the holoprotein formation in terms of heme proteins. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.
