Paper Citing NAMD - Abstract
Hua, Lan; Zhou, Ruhong; Thirumalai, D.; Berne, B. J.
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:16928-16933, NOV 4 2008
The mechanism of denaturation of proteins by urea is explored by using all-atom microseconds molecular dynamics simulations of hen lysozyme generated on BlueGene/L. Accumulation of urea around lysozyme shows that water molecules are expelled from the first hydration shell of the protein. We observe a 2-stage penetration of the protein, with urea penetrating the hydrophobic core before water, forming a "dry globule." The direct dispersion interaction between urea and the protein backbone and side chains is stronger than for water, which gives rise to the intrusion of urea into the protein interior and to urea's preferential binding to all regions of the protein. This is augmented by preferential hydrogen bond formation between the urea carbonyl and the backbone amides that contributes to the breaking of intrabackbone hydrogen bonds. Our study supports the "direct interaction mechanism" whereby urea has a stronger dispersion interaction with protein than water.
