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

Kang, Myungshim; Smith, Paul E.

doi:10.1016/j.fluid.2006.11.003

Cited by 54 publications

(63 citation statements)

References 36 publications

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“…An excess of cosolvent molecules correlates with a higher preferential interaction parameter with a positive sign, whereas a deficit of cosolvent yields a negative value. The preferential interaction parameter between osmolyte and peptide backbone is defined as: 66 C os;bb ¼ n local osmolyte À n local water n bulk osmolyte À n local osmolyte n bulk water À n local water 8 > > > : 9 > > > ; * + :…”

Section: Discussionmentioning

confidence: 99%

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: Discussionmentioning

confidence: 99%

Backbone additivity in the transfer model of protein solvation

et al. 2010

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“…The OPLS and KBFF models are probably the most popular urea models, 7,8,[15][16][17][18]20,23,[33][34][35][36][37] and there are some previous studies on the comparison of these two models. 15,[34][35][36][37] The CHARMM urea model is also widely used to study the process and mechanism of urea-induced denaturation of proteins. 9, 14,19,22,38 The AMBER* urea model has been used to study the urea-mediated dewetting between hydrophobic plates.…”

Section: Model and Methodsmentioning

confidence: 99%

Urea-Induced Drying of Hydrophobic Nanotubes: Comparison of Different Urea Models

et al. 2011

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In a previous study, we performed the molecular dynamics (MD) simulations of various carbon nanotubes solvated in 8 M urea and observed a striking phenomenon of urea-induced drying of hydrophobic nanotubes, which resulted from the stronger dispersion interaction of urea than water with nanotube (Das, P.; Zhou, R. H. J. Phys. Chem. B2010, 114, 5427-5430). In this paper, we have compared five different urea models to investigate if the above phenomenon is sensitive to the urea models used. We demonstrate through MD simulations that the drying phenomenon and its physical mechanism are qualitatively independent of the urea models. Consistent with our previous study, our current analyses with both interaction potential energy and association free energy indicate that there is a "dry state" inside the carbon nanotubes, which is caused by the urea's preferential binding to nanotubes through stronger dispersion interactions. These results also have implications for understanding the urea-induced protein denaturation by providing further evidence of the potential existence of a "dry globule"-like transient state during protein unfolding and the "direct interaction mechanism" (whereby urea attacks protein directly, rather than disrupts water structure as a "water breaker"). In addition, our study highlights the crucial role of dispersion interaction in the selective absorption of molecules in hydrophobic nanopores and may have significance for nanoscience and nanotechnology.

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“…As an example of a preferential binding parameter analysis we will discuss a recently performed simulation study of 8 M urea around native lysozyme [167]. The experimental data indicates that C N3 ¼ 16 for this system at pH 7 and the protein remains folded even in 8 M urea [86].…”

Section: Computer Simulation Of Cosolvent Effectsmentioning

confidence: 99%

Recent Applications of Kirkwood–Buff Theory to Biological Systems

Pierce

Kang

Aburi

et al. 2007

Cell Biochem Biophys

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The effect of cosolvents on biomolecular equilibria has traditionally been rationalized using simple binding models. More recently, a renewed interest in the use of Kirkwood-Buff (KB) theory to analyze solution mixtures has provided new information on the effects of osmolytes and denaturants and their interactions with biomolecules. Here we review the status of KB theory as applied to biological systems. In particular, the existing models of denaturation are analyzed in terms of KB theory, and the use of KB theory to interpret computer simulation data for these systems is discussed.

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

Cited by 54 publications

References 36 publications

Backbone additivity in the transfer model of protein solvation

Backbone additivity in the transfer model of protein solvation

Urea-Induced Drying of Hydrophobic Nanotubes: Comparison of Different Urea Models

Recent Applications of Kirkwood–Buff Theory to Biological Systems

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