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Collapse of Unfolded Proteins in a Mixture of Denaturants

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† Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
‡ Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
§ Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
⊥ Department of Chemistry, Columbia University, New York, New York 10027, United States
[email protected]; [email protected]
Cite this: J. Am. Chem. Soc. 2012, 134, 44, 18266–18274
Publication Date (Web):October 11, 2012
https://doi.org/10.1021/ja3031505
Copyright © 2012 American Chemical Society
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    Abstract

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    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.

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    Appendix providing a more complete analytical theory to explain the protein collapse phenomenon with a model polymer in a mixture of water, urea, and GdmCl, time dependence of radius of gyration in “6 M urea + 2 M GdmCl” and “4 M urea + 4 M GdmCl” mixture for another two independent simulations of lysozyme, protein solvent-accessible surface area of different types of residues in “4 M urea + 4 M GdmCl” mixture for protein L, time dependence of the backbone–backbone hydrogen bonds formed by the residue pairs of hydrophobic–hydrophobic, hydrophilic–hydrophilic, and hydrophobic–hydrophilic in “4 M urea + 4 M GdmCl” mixture for lysozyme, protein solvent-accessible surface area of different types of residues in “0 M urea + 6 M GdmCl” single denaturant system for lysozyme, protein solvent-accessible surface area of different types of residues in “0 M urea + 6 M GdmCl single denaturant system for protein L, secondary structure content (as a percentage of residues in α-helices and β-sheets) for lysozyme and protein L, time-dependent density of urea and guanidinium molecules at the first solvation shell of lysozyme for another independent trajectory, time-dependent density of urea and guanidinium molecules at the first solvation shell of protein L, time-dependent radial distribution functions of urea and GdmCl to charged side chains in “4 M urea + 4 M GdmCl” mixture, time-dependent pair radial distribution function between the hydrogen atom (HR) at the side chain of arginine and the oxygen atom of urea (OU) or the nitrogen atom (NG) of Gdm+, and protein lysozyme collapse in pre-equilibrated “4 M urea + 4 M GdmCl” mixture. This material is available free of charge via the Internet at http://pubs.acs.org.

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