A coarse-grained dynamic Monte Carlo (MC) simulation method is used to inve
stigate the conformational dynamics of chymotrypsin inhibitor 2 (CI2). Each
residue is represented therein by two interaction sites, one at the alpha-
carbon and the other on the amino acid side-chain. The energy and geometry
parameters extracted from databank structures are used. The calculated rms
fluctuations of alpha-carbon atoms are in good agreement with crystallograp
hic temperature factors. The two regions of the protein that pack against e
ach other to form the main hydrophobic core exhibit negatively correlated f
luctuations. The conformational dynamics could efficiently be probed by the
time-delayed orientational and conformational correlation functions of the
virtual bonds: the active site loop, excluding the active site bond, the t
urn region, and the N-terminal of the alpha-helix are relatively more mobil
e regions of the structure. A correlation is observed between the hydrogen/
deuterium (H/D) exchange behavior and the long-time orientational and confo
rmational autocorrelation function values for CI2. A cooperativity in the r
otations of the bonds near in sequence is observed at all time windows, whe
reas the cooperative rotations of the bonds far along the sequence appear a
t long time windows; these correlations contribute to the stability of the
secondary structures and the tertiary structure, respectively. Proteins 199
9;37:454-464. (C) 1999 Wiley-Liss, Inc.