Paper Citing NAMD - Abstract
Gao, Meng; She, Zhen-Su; Zhou, Ruhong
Key Residues that Play a Critical Role in Urea-Induced Lysozyme Unfolding
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15687-15693, DEC 2 2010
In this paper, we have developed a simple sensitivity score, based on the relative population of solvent molecules near each residue, to analyze the detailed motions of both urea and water around the hen egg-while lysozyme protein (W62G mutant) during its early stage of urea-induced unfolding for a better understanding of the atomic picture of the chemical denaturation process. Our simulation and analysis show that some hydrophobic core residues can keep dry from water for tens of nanoseconds in 8 M urea, while their contacts with urea increase significantly at the same time, forming a molten dry-globule-like state. Also, different from previously proposed actions that urea molecules preferentially absorb onto charged residues, our analysis shows that the noncharged residues, rather than the charged ones, attract more urea molecules in their surroundings (acting as attractants for urea), which is consistent with our earlier findings that urea molecules preferentially bind to protein through their stronger dispersion interactions than water. Once the initial adsorption surrounding the protein surface is accomplished, the further intrusion is found to be facilitated by a group of key residues, including Leu8, Met12, Val29, and Ala95, which play a critical role in the formation of the dry-globule structure. These hydrophobic dry residues form a local contact map which excludes the intrusion of water but accommodates a e presence of urea due to their stronger binding to protein during this swelling process, thus maintaining an interesting transient dry-globule state.
