Proteins in Mixed Solvents:  A Molecular-Level Perspective

Baynes, Brian M.; Trout, Bernhardt L.

doi:10.1021/jp0363996

Cited by 151 publications

(285 citation statements)

References 39 publications

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“…For longer repeats of the backbone model the preferential interaction parameter is usually negative indicating a significant decrease in the overall amount of TMAO as compared to bulk solution, but this depends on conformation and is quite noisy. The high relative error seen is common behavior for the preferential interaction parameter as evidenced by the calculations of others, [36][37][38] because the nature of the calculation depends upon the local number fluctuations at increasing distances. The inherent nosiness of the parameter, and the subsequent lack in statistical confidence of the interpretation, caused us to look at shorter ranged events that are less susceptible to artifacts caused by large local number fluctuations.…”

Section: Resultsmentioning

confidence: 85%

“…For our calculation of the preferential interaction parameter, we have chosen a local cutoff distance to be 8.0Å beyond which the correlations are no longer strong. 36 At this distance, we have included around three hydration layers of the peptide backbone, thus providing a satisfactory view of the overall hydration of the backbone. From Eq.…”

Section: Resultsmentioning

confidence: 99%

“…This analysis gives a connection between structure, thermodynamics, and dynamics, which is a result of direct interaction, and focuses on shorter distances than that used to determine the preferential interaction parameter. 36 Contact events are defined to be when any atom on the osmolyte molecule is within 3.0Å from any atom on the peptide backbone models. Figure 5(a) presents the average number of contact events for the backbone models in both osmolyte solutions per simulation snapshot.…”

Section: Resultsmentioning

confidence: 99%

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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: 85%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Backbone additivity in the transfer model of protein solvation

et al. 2010

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“…An alternative approach is to study cosolvent binding at low denaturant concentrations so as to avoid populating the denatured state. [28] In addition, the individual values of N 21 and N 23 can be extracted from the above expressions using the KB results for the partial molar volume (V ) of the solute at infinite dilution in terms of properties of the reference solution,…”

Section: Background and Theorymentioning

confidence: 99%

Preferential interaction parameters in biological systems by Kirkwood–Buff theory and computer simulation

Kang

Smith

2007

Fluid Phase Equilibria

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Recent results concerning the formulation and evaluation of preferential interactions in biological systems in terms of Kirkwood-Buff (KB) integrals are presented.In particular, experimental and simulated preferential interactions of a cosolvent with a biomolecule in the presence of water are described. It is argued that the preferential interaction parameter defined in a system open to both cosolvent and solvent corresponds to the situation most relevant to the analysis of computer simulation results of cosolvent interactions with proteins and small peptides. Hence, KB theory provides a path from quantities determined from simulation data to the corresponding thermodynamic data.

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“…[19][20][21] For protein systems, the effects of various salts and other small molecules, e.g., the "salting in" and "salting out" effects associated with the Hofmeister series, 9,22-26 have been documented in great detail, although a unifying theory that can quantitatively predict the effect of salt concentration on the stability of protein is not yet available. [27][28][29][30][31][32] The importance of salt on protein stability was also illustrated in several molecular dynamics simulations. 33,34 Although including counter ions for proteins with a low overall charge was shown not as important, 35 proteins with a higher overall charge are more sensitive to the ionic environment.…”

Section: Introductionmentioning

confidence: 97%

Effects of Temperature and Salt Concentration on the Structural Stability of Human Lymphotactin: Insights from Molecular Simulations

Formaneck

Cui

2006

J. Am. Chem. Soc.

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Extensive molecular dynamics (MD) simulations (∼ 70 ns total) with explicit solvent molecules and salt ions are carried out to probe the effects of temperature and salt concentration on the structural stability of the human Lymphotactin (hLtn). The distribution of ions near the protein surface and the stability of various structural motifs are observed to exhibit interesting dependence on the local sequence and structure. Whereas chloride association to the protein is overall enhanced as the temperature increases, the sodium distribution in the C-terminal helical region and, to a smaller degree, the chloride distribution in the same region are found higher at the lower temperature. The similar trend is also observed in non-linear Poisson-Boltzmann calculations with a temperaturedependent water dielectric constant, once conformational averaging over a series of MD snapshots is done. The unexpected temperature dependence in the ion distribution is explained based on the cancellation of association entropy for ion-sidechain pairs of opposite-charge and like-charge characters, which have positive and negative contributions, respectively. The C-terminal helix is observed to partially melt while a short • strand forms at the higher temperature with little salt dependence. The N-termal region, by contrast, develops partial helical structure at a higher salt concentration. These observed behaviors are consistent with solvent and salt screening playing an important role in stabilizing the canonical chemokine fold of hLtn.

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Proteins in Mixed Solvents: A Molecular-Level Perspective

Cited by 151 publications

References 39 publications

Backbone additivity in the transfer model of protein solvation

Backbone additivity in the transfer model of protein solvation

Preferential interaction parameters in biological systems by Kirkwood–Buff theory and computer simulation

Effects of Temperature and Salt Concentration on the Structural Stability of Human Lymphotactin: Insights from Molecular Simulations

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