A Kirkwood–Buff force field for the aromatic amino acids

Ploetz, Elizabeth A.; Smith, Paul E.

doi:10.1039/c1cp21883b

Cited by 44 publications

(51 citation statements)

References 98 publications

(252 reference statements)

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“…81,91,94,[96][97][98][99][100][101] The results showed that without introducing polarization good agreement with experimental KB data can be obtained. The present study demonstrated that the polarizable Drude force field, which was not developed by targeting experimental KB data, can also achieve almost the same degree of accuracy compared to KBFF, except for activity derivative and excess Gibbs free energy, which will be the focus in our future force field optimization efforts.…”

Section: Discussionsupporting

confidence: 71%

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Lin

Lopes

Roux

et al. 2013

The Journal of Chemical Physics

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Kirkwood-Buff analysis was performed on aqueous solutions of N-methylacetamide and acetamide using the Chemistry at HARvard Molecular Mechanics additive and Drude polarizable all-atom force fields. Comparison of a range of properties with experimental results, including Kirkwood-Buff integrals, excess coordination numbers, solution densities, partial molar values, molar enthalpy of mixing, showed both models to be well behaved at higher solute concentrations with the Drude model showing systematic improvement at lower solution concentrations. However, both models showed difficulties reproducing experimental activity derivatives and the excess Gibbs energy, with the Drude model performing slightly better. At the molecular level, the improved agreement of the Drude model at low solute concentrations is due to increased structure in the solute-solute and solute-solvent interactions. The present results indicate that the explicit inclusion of electronic polarization leads to improved modeling of dilute solutions even when those properties are not included as target data during force field optimization.

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Section: Discussionsupporting

confidence: 71%

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Lin

Lopes

Roux

et al. 2013

The Journal of Chemical Physics

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“…ffiffiffiffiffiffiffiffi r i r j ph NVT;ij ð0Þ ¼ ffiffiffiffiffiffiffiffi r i r j p ð drh ij ðrÞ ¼ Àd ij (18) Then, combining eqn (16)- (18), and using the mole fractions defined as x i = hN i i/N, we get e ij ¼ 1 Nr 1 x i x j @r i @bm j ! TVm k which gives the results in Section 2.1 eqn (2) and (3).…”

Section: Mixturesmentioning

confidence: 99%

Simple and complex disorder in binary mixtures with benzene as a common solvent

Požar

Seguier

Guerche

et al. 2015

Phys. Chem. Chem. Phys.

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Substituting benzene for water in computer simulations of binary mixtures allows one to study the various forms of disorder, without the complications often encountered in aqueous mixtures. In particular, we study the relationship between the local order generated by different types of molecular interactions and the nature of the global disorder, by analyzing the relationship between the concentration fluctuations and the correlation functions and the associated structure factors. Alkane-benzene mixtures are very close to ideal mixtures, despite appreciable short range shape mismatch interactions, acetone-benzene mixtures appear as a good example of regular mixtures, and ethanol-benzene mixtures show large micro-segregation. In the latter case, we can unambiguously demonstrate, unlike in the case of water, the appearance of domain-domain correlations, both in the correlation functions and the structure factor calculated in computer simulations. This finding helps to confirm the existence of a pre-peak in the structure factor associated with the micro-heterogeneity, which was speculated from several of our previous simulations of aqueous-alcohol mixtures. The fact that benzene as a solvent allows us to solve some of the problems that could not be solved with water points towards some of the particularities of water as a solvent, which we discuss herein. The concept of molecular emulsion put forward in our earlier work is useful in formulating these differences between water and benzene through the analogy with direct and inverse micellar aggregates.

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“…29 A series of model compounds resembling chemical moieties commonly found in amino acids have been studied to retrieve non-bonded interactions parameters from the use of KBIs, therefore prompting the arising of a new Kirkwood-Buff derived forcefield (KBFF). 27,[30][31][32][33][34][35] The novelty of KBFF resides in its approach to model force field parameters by reproducing the chemical potential of the parametrized compound. Practically, this translates into retrieving parameters by taking into account solution effects that tend to modulate molecular polarities.…”

Section: Introductionmentioning

confidence: 99%

Kirkwood–Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields

et al. 2015

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Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.

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A Kirkwood–Buff force field for the aromatic amino acids

Cited by 44 publications

References 98 publications

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Simple and complex disorder in binary mixtures with benzene as a common solvent

Kirkwood–Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields

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