Interactions of Urea with Native and Unfolded Proteins: A Volumetric Study

All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.

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“…117 High pressure induced conformational changes (like unfolding) are distinct from those induced by urea. 118–119…”

Section: Thermodynamic Principle Of Protein Moleculesmentioning

confidence: 99%

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

et al. 2016

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“…Therefore, understanding the pathways of protein unfolding using HEWL may help develop treatments for such degenerative diseases. Urea is one of the small molecules known to unfold proteins, but the exact mechanism of unfolding is not understood despite a variety of theoretical and experimental studies56789101112131415161718192021. Urea-denaturation curves can be explained equally well by two different thermodynamic models: the solvent-exchange model and the site-binding model22232425.…”

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confidence: 99%

Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation

Raskar

Khavnekar

Hosur

2016

Sci Rep

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Temporal binding of urea to lysozyme was examined using X-ray diffraction of single crystals of urea/lysozyme complexes prepared by soaking native lysozyme crystals in solutions containing 9 M urea. Four different soak times of 2, 4, 7 and 10 hours were used. The five crystal structures (including the native lysozyme), refined to 1.6 Å resolution, reveal that as the soaking time increased, more and more first-shell water molecules are replaced by urea. The number of hydrogen bonds between urea and the protein is similar to that between protein and water molecules replaced by urea. However, the number of van der Waals contacts to protein from urea is almost double that between the protein and the replaced water. The hydrogen bonding and van der Waals interactions are initially greater with the backbone and later with side chains of charged residues. Urea altered the water-water hydrogen bond network both by replacing water solvating hydrophobic residues and by shortening the first-shell intra-water hydrogen bonds by 0.2 Å. These interaction data suggest that urea uses both ‘direct’ and ‘indirect’ mechanisms to unfold lysozyme. Specific structural changes constitute the first steps in lysozyme unfolding by urea.

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“…Pressure, by itself or in conjunction with temperature and denaturant, , is a useful but perhaps underutilized probe in protein biophysics. In principle, pressure can facilitate either protein unfolding or folding, depending on which conformational state has a smaller partial molar volume. − ,− High pressure has also been applied to study folding intermediates , and to dissociate multimeric proteins and protein aggregates to study protein–protein interactions.…”

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confidence: 99%

Volumetric Physics of Polypeptide Coil–Helix Transitions

2016

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Volumetric properties of proteins bear directly on their biological functions in hyperbaric environments and are useful in general as a biophysical probe. To gain insight into conformation-dependent protein volume, we developed an implicit-solvent atomic chain model that transparently embodies two physical origins of volume: (1) a fundamental geometric term capturing the van der Waals volume of the protein and the particulate, finite-size nature of the water molecules, modeled together by the volume encased by the protein's molecular surface, and (2) a physicochemical term for other solvation effects, accounted for by empirical proportionality relationships between experimental partial molar volumes and solvent-accessible surface areas of model compounds. We tested this construct by Langevin dynamics simulations of a 16-residue polyalanine. The simulated trajectories indicate an average volume decrease of 1.73 ± 0.1 Å/residue for coil-helix transition, ∼80% of which is caused by a decrease in geometric void/cavity volume, and a robust positive activation volume for helical hydrogen bond formation originating from the transient void created by an approaching donor-acceptor pair and nearby atoms. These findings are consistent with prior experiments with alanine-rich peptides and offer an atomistic analysis of the observed overall volume changes. The results suggest, in general, that hydrostatic pressure likely stabilizes helical conformations of short peptides but slows the process of helix formation. In contrast, hydrostatic pressure is more likely to destabilize natural globular proteins because of the void volume entrapped in their folded structures. The conceptual framework of our model thus affords a coherent physical rationalization for experiments.

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Interactions of Urea with Native and Unfolded Proteins: A Volumetric Study

Cited by 17 publications

References 71 publications

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation

Volumetric Physics of Polypeptide Coil–Helix Transitions

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