Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy

Oliveira, Denílson Mendes de; Zukowski, Samual R.; Palivec, Vladimír; Hénin, Jérôme; Martinez‐Seara, Hector; Ben‐Amotz, Dor; Jungwirth, Pavel; Duboué-Dijon, Elise

doi:10.1039/d0cp02987d

Cited by 41 publications

(56 citation statements)

References 109 publications

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“…Another simple case is when a restraining potential is applied on the distance between the ligand and receptor. ∆G V • →rest decoupled can then be numerically estimated by integration of the restraint potential U rest : 49,50…”

Section: ∆G •mentioning

confidence: 99%

“…Eq. 12 can be simply numerically estimated on the fully coupled simulation window if the binding site is well sampled in presence of the restraints (as was for instance done by us and others, 49,50 where a simplified version of Eq. 12 was reported, which in those cases is numerically equivalent to Eq.…”

Section: ∆G •mentioning

confidence: 99%

“…We will discuss in detail such a situation, showing how it relates and differs from the previous one, on the typical case of ion binding to a symmetric carboxylate group-acetate for the sake of simplicity-that we recently encountered, and for which we needed binding predictions to help interpret experiments. 50 Different modes of cation binding to carboxylate groups have been described. 61,62 A cation can interact directly with either with both carboxylate oxygen atoms in the bidentate binding mode, or with only one of the two oxygens in the monodentate mode.…”

Section: Analytical Treatment Under Simplifying Assumptionsmentioning

confidence: 99%

“…3. The distance d between the carbon atom of the carboxylate group and the cation is the natural coordinate, previously used in the literature, 49,50,63,64 to define the monodentate binding mode and separate it from bidentate and solvent-shared binding modes. For instance, in the case of Mg 2+ binding to acetate, monodentate bound geometries correspond to 2.8 < d < 3.8 Å, bidentate complexes typically have d < 2.8 Å, and solvent-shared ion pairs correspond to d > 4 Å.…”

Section: Analytical Treatment Under Simplifying Assumptionsmentioning

confidence: 99%

“…The simulations were performed in the constant temperature/constant pressure (NpT) ensemble, using the same setup as previously reported. 50 Water molecules were described by the SPC/E force field, 74 and two different force fields 65,66 for Mg 2+ , giving rise to two different behaviors with respect to sampling of one or both symmetric sites, were used. Note that these force fields are known to strongly overestimate ion-acetate binding, as we discussed in a previous work, 50 and their use here is only meant to illustrate typical issues encountered in free energy calculations.…”

Section: Computational Detailsmentioning

confidence: 99%

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Building intuition for binding free energy calculations: bound state definition, restraints, and symmetry

Duboué-Dijon,

Hénin

2021

Preprint

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The theory behind computation of absolute binding free energies using explicit-solvent molecular simulations is wellestablished, yet somewhat complex, with counter-intuitive aspects. This leads to frequent frustration, common misconceptions, and sometimes, erroneous numerical treatment. To improve this, we present the main practically relevant segments of the theory with constant reference to physical intuition. We pinpoint the role of the implicit or explicit definition of the bound state (or the binding site), to make a robust link between an experimental measurement and a computational result. We clarify the role of symmetry, and discuss cases where symmetry number corrections have been misinterpreted. In particular, we argue that symmetry corrections as classically presented are a source of confusion, and could be advantageously replaced by restraint free energy contributions. We establish that contrary to a common intuition, partial or missing sampling of some modes of symmetric bound states does not affect the calculated decoupling free energies. Finally, we review these questions and pitfalls in the context of a few common practical situations: binding to a symmetric receptor (equivalent binding sites), binding of a symmetric ligand (equivalent poses), and formation of a symmetric complex, in the case of homodimerization.

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Section: ∆G •mentioning

confidence: 99%

Section: ∆G •mentioning

confidence: 99%

Section: Analytical Treatment Under Simplifying Assumptionsmentioning

confidence: 99%

Section: Analytical Treatment Under Simplifying Assumptionsmentioning

confidence: 99%

Section: Computational Detailsmentioning

confidence: 99%

See 3 more Smart Citations

Building intuition for binding free energy calculations: bound state definition, restraints, and symmetry

Duboué-Dijon,

Hénin

2021

Preprint

Self Cite

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Investigating oil solubilization into nonionic micelles by Raman multivariate curve resolution

et al. 2023

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Hydrophobic hydration, whereby water spontaneously structures around hydrophobic and amphiphilic molecules, plays a key role in the process of surfactant micelle formation and micellar oil solubilization. Using vibrational Raman multivariate curve resolution spectroscopy, we characterized changes in the hydrophobic hydration occurring within nonionic alkylphenol ethoxylate surfactant Tergitol NP‐12 micelles as a function of oil solubilization. We report trends in the changes of hydrophobic hydration depending on the chain length of the oil as well as the presence of a halogen atom in the oil chemical structure. Changes in hydrophobic hydration directly correlate to changes in the physical properties of the micellar solution, including cloud point and micelle hydrodynamic diameter. We compare hydrophobic hydration of Tergitol NP‐12 to nonionic linear alkyl ethoxylate surfactant Makon TD‐12 and ionic sodium dodecyl sulfate and observe similar trends; the molecular structure of the oil has the largest impact on the hydrophobic hydration. We believe these studies contribute to a fundamental understanding of the importance of hydrophobic hydration in surfactant and oil aggregates, especially as it relates to micellar oil solubilization, and provide insight into how the molecular solubilizate can impact micellar structure, size, and stability.

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Hofmeister Effects of Group II Cations as Seen in the Unfolding of Ribonuclease A

et al. 2022

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This work studies the effects of alkaline-earth cation addition on the unfolding free energy of a model protein, pancreatic Ribonuclease A (RNase A) by differential scanning calorimetry analysis. RNase A was chosen because: a) it does not specifically bind Mg 2 + , Ca 2 + and Sr 2 + cations and b) maintains its structural integrity throughout a large pH range. We have measured and compared the effects of NaCl, MgCl 2 , CaCl 2 and SrCl 2 addition on the melting point of RNase A. Our results show that even though the addition of group II cations to aqueous solvent reduces the solubility of nonpolar residues (and enhances the hydrophobic effect), their interactions with the amide moieties are strong enough to "salt-them-in" the solvent, thereby causing an overall protein stability reduction. We demonstrate that the amide-cation interactions are a major contributor to the observed "Hofmeister Effects" of group II cations in protein folding. Our analysis suggests that protein folding "Hofmeister Effects" of group II cations, are mostly the aggregate sum of how cation addition simultaneously salts-out hydrophobic moieties by increasing the cavitation free energy, while promoting the salting-in of amide moieties through contact pair formation.

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Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy

Abstract: In spite of the biological importance of the binding of Zn2+, Ca2+, and Mg2+ to the carboxylate group, cation-acetate binding affinities and binding modes remain actively debated. Here, we report...

Cited by 41 publications

References 109 publications

Building intuition for binding free energy calculations: bound state definition, restraints, and symmetry

Building intuition for binding free energy calculations: bound state definition, restraints, and symmetry

Investigating oil solubilization into nonionic micelles by Raman multivariate curve resolution

Hofmeister Effects of Group II Cations as Seen in the Unfolding of Ribonuclease A

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