Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy

Helms, Volkhard; Wade, Rebecca C.

doi:10.1002/(sici)1096-987x(199703)18:4<449::aid-jcc1>3.0.co;2-t

Cited by 37 publications

(26 citation statements)

References 55 publications

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“…59 This conditioning radius is also close to the conditioning radius of = 3.35 Å obtained for the methyl groups of neopentane in water at 298 K and 1 bar using the SPC/E potential model for water. This radius was found to give normally distributed p͑ i ͉ n =0͒ and ex = 2.25 kcal/ mol for propane in water at 298 K and 1 bar, which falls between the value of 2.02 kcal/mol derived from the measured solubility of propane in water 58 and the value of 2.4 kcal/mol estimated from molecular simulations of OPLS propane in TIP3P water at the same temperature and pressure.…”

Section: Methodssupporting

confidence: 80%

Cooperative hydrophobic/hydrophilic interactions in the hydration of dimethyl ether

Utiramerur

Paulaitis

2010

The Journal of Chemical Physics

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Cooperative interactions in the hydration of dimethyl ether (DME) relative to its purely hydrophobic analog, propane, are analyzed by expressing the free energy of hydration in terms of an "inner-shell" contribution from water molecular packing and chemical association, and an "outer-shell" contribution described by the mean binding energy of the solute to the solution and fluctuations in this binding energy. We find that nonadditive, cooperative interactions associated with strong correlations in the binding energy fluctuations of the methyl groups and ether oxygen play a dominant role in the hydration of DME relative to propane. The electrostatic nature of these interactions is revealed in a multi-Gaussian analysis of hydration substates, which shows that the formation of favorable ether oxygen-water hydrogen bonds is correlated with less favorable methyl group-water interactions, and vice versa. We conclude that the group additive distinction between the hydrophobic hydration of the DME methyl groups and hydrophilic hydration of the ether oxygen is lost in the context of these cooperative interactions. Our results also suggest that the binding energy fluctuations of constituent hydrophobic/hydrophilic groups are more sensitive than local water density fluctuations for characterizing the hydration of heterogeneous interfaces.

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Section: Methodssupporting

confidence: 80%

Cooperative hydrophobic/hydrophilic interactions in the hydration of dimethyl ether

Utiramerur

Paulaitis

2010

The Journal of Chemical Physics

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“…For camphor the parameters were obtained from the XPLO-2D program (Kleywegt and Jones 1997) and the partial charges of camphor were taken from Helms and Wade (1997). The simulations were performed using the CHARMM program (Brooks et al 1983).…”

Section: The Force Field Parametersmentioning

confidence: 99%

CO migration pathways in cytochrome P450_cam studied by molecular dynamics simulations

Mouawad¹,

Tétreau²,

Abdel‐Azeim³

et al. 2007

Protein Science

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Previous laser flash photolysis investigations between 100 and 300 K have shown that the kinetics of CO rebinding with cytochrome P450 cam (camphor) consist of up to four different processes revealing a complex internal dynamics after ligand dissociation. In the present work, molecular dynamics simulations were undertaken on the ternary complex P450 cam (cam)(CO) to explore the CO migration pathways, monitor the internal cavities of the protein, and localize the CO docking sites. One trajectory of 1 nsec with the protein in a water box and 36 trajectories of 1 nsec in the vacuum were calculated. In each trajectory, the protein contained only one CO ligand on which no constraints were applied. The simulations were performed at 200, 300, and 320 K. The results indicate the presence of seven CO docking sites, mainly hydrophobic, located in the same moiety of the protein. Two of them coincide with xenon binding sites identified by crystallography. The protein matrix exhibits eight persistent internal cavities, four of which corresponding to the ligand docking sites. In addition, it was observed that water molecules entering the protein were mainly attracted into the polar pockets, far away from the CO docking sites. Finally, the identified CO migration pathways provide a consistent interpretation of the experimental rebinding kinetics. (Srajer et al. 2001;Bourgeois et al. 2003;Schotte et al. 2003;Hummer et al. 2004), cryocrystallography (Brunori et al. 2000Chu et al. 2000;Ostermann et al. 2000;Schlichting 2000), spectroscopy (Engler et al. 2000;Lamb et al. 2002;Nienhaus et al. 2002;Kriegl et al. 2003), kinetic competition experiments with xenon (Scott and Gibson 1997;Scott et al. 2001; Nienhaus et al. 2003a,b;Tetreau et al. 2004, and molecular dynamics (MD) simulations (Elber and Karplus 1990;Carlson et al. 1996;Meller and Elber 1998;Amara et al. 2001;Mouawad et al. 2005). Article published online ahead of print. Article and publication date are at

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“…Alternatively, force field parameters may be fit to experimental data such as crystal structure, energy and lattice dynamics, infrared, X-ray data on small molecules, liquid properties like density and enthalpy of vaporization, free energy of solvation, NMR data, etc. [8] OPLS, [10] CHARMM, [11] GROMOS, [12] AMBER [13] and CVFF [14] are examples of the most popular force fields and have been critically evaluated [15][16][17][18][19].…”

Section: Current Force Fields For Biomolecular Systemsmentioning

confidence: 99%

On the application of simple explicit water models to the simulations of biomolecules

Guimarães¹,

Barreiro²,

Oliveira³

et al. 2004

Braz. J. Phys.

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Computer simulations of biomolecular systems have achieved a significant importance in science as they provide information regarding structure, dynamics, and energetics of biomolecules that are inaccessible to experimental measuring techniques. In this work, some important aspects of the simulation of biomolecular systems are described. An overview of the most popular protein force fields, simple explicit water models for the simulation of liquid water, and different approaches to treat the boundaries of the system is presented. Also, studies conducted in our group illustrating successful simulations of three biomolecules (thrombin, L-type calcium channel and human Cytomegalovirus protease) through the application of simple explicit water models combined with protein force fields are discussed.

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Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy

Cited by 37 publications

References 55 publications

Cooperative hydrophobic/hydrophilic interactions in the hydration of dimethyl ether

Cooperative hydrophobic/hydrophilic interactions in the hydration of dimethyl ether

CO migration pathways in cytochrome P450_cam studied by molecular dynamics simulations

On the application of simple explicit water models to the simulations of biomolecules

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Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy

Cited by 37 publications

References 55 publications

Cooperative hydrophobic/hydrophilic interactions in the hydration of dimethyl ether

Cooperative hydrophobic/hydrophilic interactions in the hydration of dimethyl ether

CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations

On the application of simple explicit water models to the simulations of biomolecules

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Product

Resources

About

CO migration pathways in cytochrome P450_cam studied by molecular dynamics simulations