Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding

Hua, Lan; Zhou, Ruhong; Thirumalai, D.; Berne, B. J.

doi:10.1073/pnas.0808427105

Cited by 496 publications

(698 citation statements)

References 40 publications

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“…Some previous simulations show urea hydrogen bonding with the peptide carbonyl group, 22,44,45 whereas others see more significant hydrogen bonding with the peptide amides as opposed to the peptide carbonyl group. 46 To provide a further description of the nature of osmolyte and backbone correlations, we have calculated the solvent density profile around the peptide. The densities in Figure 6 correspond to regions of high probability for the particular solvent species to reside.…”

Section: Resultsmentioning

confidence: 99%

“…There has been confusion over the dominant free energy component of the direct mechanism of interaction between osmolytes and proteins: some have suggested interactions are driven by electrostatics, 40,44,45 whereas others have shown a dominant role of vdW interactions. 46 From our simulated solvation free energies, and the subsequent highly precise transfer free energy calculations, we are able to decompose the contributions of the dispersion and electrostatic interactions to the free energy of transfer of both protecting and denaturing osmolytes. We have shown that upon the transfer of the peptide backbone models from water to urea, the electrostatic component is actually highly unfavorable.…”

Section: Resultsmentioning

confidence: 99%

“…46 Those authors found a shift towards more favorable vdW potential energy of urea within the first solvation shell as compared to the bulk solvent, with no corresponding shift in the electrostatic component. 46 The analysis demonstrates that interaction of urea with peptide groups should be described by more than just the electrostatic terms. Though the electrostatic interactions are obviously important for hydrogen bonding to occur within this type of model it is clear that the vdW aspects of these interactions plays an integral role.…”

Section: Discussionmentioning

confidence: 96%

“…In addition to this increased contact with the peptide backbone by urea, these collisions occur for longer periods of time, indicating stronger correlations. Several previous simulations have demonstrated the direct interaction of urea with peptide or protein 22,45,46,[50][51][52] as well as the lack of interaction between TMAO and a cyclic 53 and long peptide backbone model. 38 Similarly, solution hydrogen bonds with the peptide backbone models demonstrate very little hydrogen bonding of TMAO with the peptide backbone, whereas urea forms about 1/2 hydrogen bond per glycine residue.…”

Section: Discussionmentioning

confidence: 98%

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Backbone additivity in the transfer model of protein solvation

et al. 2010

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The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (DG tr ) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and DG tr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of 254 cal/mol/M compares quite favorably with 243 cal/mol/M determined experimentally.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 96%

Section: Discussionmentioning

confidence: 98%

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Backbone additivity in the transfer model of protein solvation

et al. 2010

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“…Computer simulations have suggested that a denaturant can unfold a protein either by binding directly to the protein via hydrogen bonding, electrostatic, or van der Waals interactions, or by altering the solvent environment (35)(36)(37)(38). A very recent NMR study of HX at the peptide groups of dialanine has shown that GdnHCl, unlike urea, does not hydrogen bond to the peptide group (13).…”

Section: Unfolding Begins Similarly In Zero and High Denaturant Concementioning

confidence: 99%

Native state dynamics drive the unfolding of the SH3 domain of PI3 kinase at high denaturant concentration

Wani

Udgaonkar²

2009

Proc. Natl. Acad. Sci. U.S.A.

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Little is known about the role of protein dynamics in directing protein unfolding along a specific pathway and about the role played by chemical denaturants in modulating the dynamics and the initiation of unfolding. In this study, deuterium-hydrogen exchange (HX) detected by electrospray ionization mass spectrometry (ESI-MS) was used to study the unfolding of the SH3 domain of the PI3 kinase. Unfolding on the principal unfolding pathway occurs in 2 steps, both in the absence and in the presence of 1.8 M guanidine hydrochloride (GdnHCl). In both cases, the first step leads to the formation of an intermediate, I N, with 5 fewer protected amide hydrogen sites than in N. In the second step, IN loses the structure protecting the remaining 14 amide hydrogen sites from HX as it unfolds completely. ESI-MS analysis of fragments of the protein created by proteolytic digestion, after completion of the HX reaction, shows that I N has lost protection against HX in the same segments of native structure during unfolding in the absence and presence of 1.8 M GdnHCl. Hence, GdnHCl does not appear to play a direct active role in the initiation of unfolding. However, at higher GdnHCl concentrations, a second unfolding pathway is shown to compete effectively with the N 7 IN 7 U pathway. In this way, the denaturant modulates the energy landscape of unfolding.hydrogen exchange ͉ mass spectrometry ͉ protein unfolding ͉ partially unfolded conformation ͉ native-state exchange F olded proteins possess dynamic structures, and the lowest energy conformation of a folded protein exists at equilibrium with many high energy conformational substates, which are Boltzmann-distributed in the folded protein ensemble (1-4). Fluctuations in protein structure appear not to be random. They may be directed toward enhancing function (3-7), but their role in preferentially directing protein folding and unfolding reactions on to specific pathways is poorly understood (8). Even less is known about how the thermal fluctuations that lead to protein unfolding are perturbed by denaturants such as guanidine hydrochloride (GdnHCl) and urea. Protein denaturants may act indirectly by disrupting the structure of water, thereby making hydrophobic groups more readily solvated (9, 10), or directly by interacting more strongly than water with the protein backbone and side chains (11-13). To understand how denaturants act, it is necessary to determine whether the mechanism of unfolding of a protein, as well as the thermal fluctuations that enable unfolding, are the same in the absence of a chemical denaturant and in the presence of a high concentration of the denaturant.Structural characterization of protein unfolding in the presence, as well as absence, of denaturant becomes possible when the hydrogen exchange (HX) experiment is carried out in conjunction with NMR spectroscopy or MS. HX-NMR experiments have been carried out on many different proteins under conditions where HX is rate-limited by the intrinsic exchange rate constant (k int ) of the fully solvent-exposed a...

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