Reduction of the hydrophobic attraction between charged solutes in water

Dzubiella, J.; Hansen, Jean‐Pierre

doi:10.1063/1.1632902

Cited by 34 publications

(51 citation statements)

References 11 publications

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“…29,30 Their solute model slightly differs from the one used in the previous section: the solute-solvent interaction potential is purely repulsive and is given by U i ͑r͒ = k B T͑r − R 0 ͒ −12 , while the solute-solute interaction is hard-spherelike with a hard sphere radius R 0 . The solutes are neutral or carry opposite charges Q homogeneously distributed over the sphere volume.…”

Section: Comparison Of Mean Forces To Previous MD Simulationsmentioning

confidence: 99%

“…Importantly, this demonstrates that the present formalism captures the sensitivity of dewetting phenomena to specific solvent-solute interactions as reported in previous studies. 20,21,26,27,29,31,32 Note that the optimal shape function at ͉z͉Ӎ2 Å is closer to the solutes in VI compared to V due to the proximity of the charge to the interface. Clearly, the observed effects, particularly the transition from III to VI, cannot be described by existing solvation models which use the surface area ͑GB/SA or PB/SA͒ ͑Ref.…”

Section: Behavior Of the Shape Functionmentioning

confidence: 99%

“…The same trend has been observed recently in explicit water simulations of a similar system of charged hydrophobic nanosolutes. 29,30 Now we turn our attention to varying the intersolute distance. The pmfs and solute-solute mean forces F = ‫ץ‬W͑s 0 ͒ / ‫ץ‬s 0 versus a range of s 0 are shown for systems I-VI in Fig.…”

Section: Potential Of Mean Forcementioning

confidence: 99%

“…20,21,26,27,29,31,32 The dewetting in our model is driven by the interfacial term which favors minimizing the solute-solvent interface. A comment must be made here regarding the sensitivity of dewetting to the particular solvent-solute interactions.…”

Section: -9mentioning

confidence: 99%

“…[19][20][21] A similar sensitivity was found in systems where the solutes carry charges or are exposed to an external electric field, e.g., electrostatic interactions have been shown to strongly affect the dewetting behavior of hydrophobic channels [26][27][28] and hydrophobic spherical nanosolutes. 29,30 Furthermore, two recent simulations of proteins supported the importance of solvent dewetting and its sensitivity in realistic biomolecular systems. First, a simulation of the two-domain BphC enzyme showed that the region between the two domains was completely dewetted when vdW and electrostatic interactions were turned off, but accommodated 30% of the bulk density with the addition of vdW attraction ͑water was found mainly at the edges of the considered volume, while the central region was still empty͒, and 85%-90% with the addition of electrostatic interactions.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Coupling nonpolar and polar solvation free energies in implicit solvent models

Dzubiella

Swanson

McCammon

2006

The Journal of Chemical Physics

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129

194

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Recent studies on the solvation of atomistic and nanoscale solutes indicate that a strong coupling exists between the hydrophobic, dispersion, and electrostatic contributions to the solvation free energy, a facet not considered in current implicit solvent models. We suggest a theoretical formalism which accounts for coupling by minimizing the Gibbs free energy of the solvent with respect to a solvent volume exclusion function. The resulting differential equation is similar to the Laplace-Young equation for the geometrical description of capillary interfaces but is extended to microscopic scales by explicitly considering curvature corrections as well as dispersion and electrostatic contributions. Unlike existing implicit solvent approaches, the solvent accessible surface is an output of our model. The presented formalism is illustrated on spherically or cylindrically symmetrical systems of neutral or charged solutes on different length scales. The results are in agreement with computer simulations and, most importantly, demonstrate that our method captures the strong sensitivity of solvent expulsion and dewetting to the particular form of the solvent-solute interactions.

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Section: Comparison Of Mean Forces To Previous MD Simulationsmentioning

confidence: 99%

Section: Behavior Of the Shape Functionmentioning

confidence: 99%

Section: Potential Of Mean Forcementioning

confidence: 99%

Section: -9mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Coupling nonpolar and polar solvation free energies in implicit solvent models

Dzubiella

Swanson

McCammon

2006

The Journal of Chemical Physics

Self Cite

129

194

View full text Add to dashboard Cite

show abstract

Transhepatic pulmonary artery stenting via a short intravascular sheath following neonatal repair of truncus arteriosus

Abrams

Rigby

2005

Cathet. Cardiovasc. Intervent.

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Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: Calculation of structural and dynamic properties

Hassan

Mehler

2005

Proteins

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Long dynamics simulations were carried out on the B1 immunoglobulin-binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens-of-nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen-bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all-atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP-based implicit solvent model (SCP-ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40-ns trajectories were stable, yielding C α root mean square deviations (RMSD) of about 1.0 and 0.8 Å respectively along the entire simulation time, compared to 0.8 Å for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30-ns simulation, with a C α RMSD of ≈ 1.4 Å, while the PAR22/LD trajectory became unstable early in the simulation, reaching a C α RMSD of about 2.7 Å and remaining at this value until the end of the simulation; the C α RMSD of the EW/MD simulation was about 1.5 Å. The source of the instabilities of the BPTI trajectories in the PAR22/LD simulations was explored by an analysis of the backbone torsion angles. To further validate the findings from this analysis of BPTI, a 35-ns SCP-ISM simulation of Ubiquitin (Ubq) was carried out. For this protein, the CMAP/LD simulation was stable for the entire simulation time (C α RMSD of ≈1.0 Å), while the PAR22/LD trajectory showed a trend similar to that in BPTI, reaching a C α RMSD of ≈1.5 Å at 7 ns. All the calculated properties were found to be in agreement with the corresponding experimental values, although local deviations were also observed. HB patterns were also well reproduced by all the continuum solvent simulations with the exception of solvent-exposed side chain-side chain (sc-sc) HB in ProtG, where several of the HB interactions observed in the crystal structure and in the EW/MD simulation wer...

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Reduction of the hydrophobic attraction between charged solutes in water

Cited by 34 publications

References 11 publications

Coupling nonpolar and polar solvation free energies in implicit solvent models

Coupling nonpolar and polar solvation free energies in implicit solvent models

Transhepatic pulmonary artery stenting via a short intravascular sheath following neonatal repair of truncus arteriosus

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: Calculation of structural and dynamic properties

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