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Quantitative Assessments of the Distinct Contributions of Polypeptide Backbone Amides versus Side Chain Groups to Chain Expansion via Chemical Denaturation

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† Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, Missouri 63130, United States
‡ TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad, 500075, India
§ Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-5807, Zurich, Switzerland
[email protected]
Cite this: J. Am. Chem. Soc. 2015, 137, 8, 2984–2995
Publication Date (Web):February 9, 2015
https://doi.org/10.1021/ja512062h
Copyright © 2015 American Chemical Society
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    Abstract

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    In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones, and therefore, backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations of denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of side chains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that side chains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of side chain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation.

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    Includes versions of Figures 1 and 4 with error bars, analysis of the relative occupancies for peptides in 8 m GdmCl, and a discussion of the analysis of the amino acid compositional biases in generic foldable proteins. This material is available free of charge via the Internet at http://pubs.acs.org.

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