Collapse of unfolded proteins in a mixture of denaturants.
Both urea and guanidinium chloride (GdmCl) are frequently used as protein denaturants. Given that proteins generally adopt extended or unfolded conformations in either aqueous urea or GdmCl, one might expect that the unfolded protein chains will remain or become further extended due to the addition of another denaturant. However, a collapse of denatured proteins is revealed using atomistic molecular dynamics simulations when a mixture of denaturants is used. Both hen egg-white lysozyme and protein L are found to undergo collapse in the denaturant mixture. The collapse of the protein conformational ensembles is accompanied by a decreased solubility and increased non-native self-interactions of hydrophobic residues in the urea/GdmCl mixture. The increase of non-native interactions rather than the native contacts indicates that the proteins experience a simple collapse transition from the fully denatured states. During the protein collapse, the relatively stronger denaturant GdmCl displays a higher tendency to be absorbed onto the protein surface due to their stronger electrostatic interactions with proteins. At the same time, urea molecules also accumulate near the protein surface, resulting in an enhanced "local crowding" for the protein near its first solvation shell. This rearrangement of denaturants near the protein surface and crowded local environment induce the protein collapse, mainly by burying their hydrophobic residues. These findings from molecular simulations are then further explained by a simple analytical model based on statistical mechanics.
Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.
Zhen
Z
Xia
Payel
P
Das
Eugene I
EI
Shakhnovich
Ruhong
R
Zhou
D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry*; D002645:Chickens; D004268:DNA-Binding Proteins / Q000737:chemistry*; D019791:Guanidine / Q000737:chemistry*; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry*; D010460:Peptococcus / Q000737:chemistry*; D011487:Protein Conformation; D058767:Protein Unfolding; D014508:Urea / Q000737:chemistry*
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C116593:L-protein, Peptococcus magnus; D014508:Urea; C421864:hen egg lysozyme; D009113:Muramidase; D019791:Guanidine