title: Probing Selection Mechanism of the Most Favorable Conformation of a Dipeptide in Chaotropic and Kosmotropic Solution.
abstract: Chaotropes like urea and guanidinium chloride (GdmCl) tend to destabilize, and kosmotropes like proline tend to stabilize folded structures of peptides and proteins. Here, we combine fluorescence anisotropy decay measurements and molecular dynamics simulations to gain a microscopic understanding of the molecular mechanism for shifting conformational preferences in aqueous, GdmCl, urea, and proline solutions of a simple model dipeptide, N-acetyl-tryptophan-amide (NATA). Measured anisotropy decay of NATA as a function of temperature, pH, and cosolvent concentrations showed reorientations moderately slower in GdmCl and urea and substantially slower in proline compared to those of aqueous environment. A small change in pH significantly slows orientation time in water and GdmCl and less markedly in urea. Computationally, we use molecular dynamics with dihedral restraints to separately analyze the motions and interactions of the representative NATA conformers in the four different solvent environments. This novel analysis provides a dissection of the observed overall diffusion rates into contributions from individual dipeptide conformations. The variation of rotational diffusion rates with conformation are quite large. Population-weighted averaging or using properties of the major cluster reproduces the dynamical features of the full unrestrained dynamics. Additionally, we correlate the observable diffusion rates with microscopic features of conformer size, shape, and solvation. This analysis uncovered underlying differences in detailed atomistic behavior of the three cosolvents-urea, GdmCl, and proline. For both urea and the pure water system we find good agreement with hydrodynamic theory, with diffusion rates primarily correlated with conformer size and shape. In contrast, for GdmCl and proline solutions, the variation in conformer diffusion rates was mostly determined by specific interactions with the cosolvents. We also find preferences for different molecular shapes by the three cosolvents, with increased preferential solvation of smaller and more spherical conformers by urea and larger and more elongated conformers by GdmCl and proline. Additionally, our results provide a basis for a simple approximate model of the effects of pH lowering on dipeptide conformational equilibria. The translational diffusion rates of NATA are less sensitive to conformations, but variation with solvation strength is similar to rotational diffusion. Our results, combining experiment and simulation, show that we can identify the individual peptide conformers with definite microscopic properties of shape, size, and solvation, that are responsible for producing physical observables, such as translational and orientational diffusion in the complex solvent environments of denaturants and osmolytes.
authors.affiliation: Department of Pharmaceutical Chemistry, The University of Kansas , Lawrence, Kansas 66047, United States.
authors.forename: Gouri S
authors.initials: GS
authors.lastname: Jas
authors.affiliation: Department of Pharmaceutical Chemistry, The University of Kansas , Lawrence, Kansas 66047, United States.
authors.forename: C Russell
authors.initials: CR
authors.lastname: Middaugh
authors.affiliation: Department of Chemistry, The University of Kansas , Lawrence, Kansas 66045, United States.|Department of Molecular Biosciences, The University of Kansas , Lawrence, Kansas 66045, United States.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Kuczera
mesh_terms: D004151:Dipeptides / Q000737:chemistry* / Q000378:metabolism; D005454:Fluorescence Polarization; D019791:Guanidine / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D056004:Molecular Dynamics Simulation; D013696:Temperature; D013816:Thermodynamics; D014508:Urea / Q000737:chemistry
chemical_list: D004151:Dipeptides; D014508:Urea; D019791:Guanidine