Force field parametrization of hydrogenoxalate and oxalate anions with scaled charges

Kroutil, Ondřej; Předota, Milan; Kabeláč, Martin

doi:10.1007/s00894-017-3490-x

Cited by 19 publications

(30 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The O-C-C-O dihedral angle of the oxalate ion in the occluded binding site became ~90˚ after the Gln34 flip (Extended Data Fig. 9A), which is the value observed in solution 41 . This contrasts with the other two trajectories without the Gln34 flip, where the oxalate dihedral angle remained around 40-50˚ (and its inverted position at 130-140˚; Extended Data Fig.…”

Section: Substrate-binding Hydrophobic Gates and Conformational Dynamics Of Oxltmentioning

confidence: 52%

Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

Jaunet-Lahary

Shimamura

Hayashi

et al. 2021

Preprint

View full text Add to dashboard Cite

Oxalobacter formigenes is an oxalate-degrading bacterium in the gut microbiota that absorbs food-derived oxalate to use this as a carbon and energy source and thereby helps reduce the risk of kidney stone formation of the host animals 1–4. The bacterial oxalate transporter OxlT uptakes oxalate from the gut to bacterial cells and excrete formate as a degradation product, with a strict discrimination from other carboxylates that serve as nutrients 5–7. Nevertheless, the underlying mechanism remains unclear. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two different conformations, occluded and outward-facing states. The oxalate binding site contains two basic residues that form salt bridges with a dicarboxylate substrate while preventing the conformational switch to the occluded state without an acidic substrate, a ‘disallowed’ state for an antiporter 8, 9. The occluded ligand-binding pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the binding pocket are completely blocked by extensive interdomain hydrophobic and ionic interactions. Nevertheless, a molecular dynamics simulation showed that a flip of a single side chain neighbouring the substrate is sufficient to trigger the gate opening. The OxlT structure indicates the underlying metabolic interactions enabling favourable symbiosis at a molecular level.

show abstract

Section: Substrate-binding Hydrophobic Gates and Conformational Dynamics Of Oxltmentioning

confidence: 52%

Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

Jaunet-Lahary

Shimamura

Hayashi

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…In this regards, a proper refinement of the force fields related to charged (both positive and negative) amino acids, which properly introduces polarization and screening effects with the ECC method, appears to be of paramount importance. A simple approach already pursued by researchers in this area involves the rescaling of the partial charges on the functional group of charged residues by a factor 0.75 . Together with the models here presented, an effective parametrization of charged amino acids will provide a consistent force field based on the ECC modeling process.…”

Section: Discussionmentioning

confidence: 99%

“…A simple approach already pursued by researchers in this area involves the rescaling of the partial charges on the functional group of charged residues by a factor 0.75. [28,29] Together with the models here presented, an effective parametrization of charged amino acids will provide a consistent force field based on the ECC modeling process.…”

Section: Discussionmentioning

confidence: 99%

“…Within such formalism, the presence of the medium is considered through a simple scaling of ionic integer charges by a factor equal to the inverse square root of the electronic part of the dielectric constant of the surrounding solvent. This approach has been fruitfully applied to the description of salts in water solution, to charged organic molecules and to the investigation of biological processes involving metal ions . In a work recently published by the present authors, the same theoretical procedure has been applied to model the zinc ion in water and within the active site of two zinc proteins.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction

Nikitin

Frate

2019

J Comput Chem

View full text Add to dashboard Cite

The parametrization of classical nonbonded models of metal ions has been widely addressed in the recent years. Despite the continuous development of novel and more physically inspired functional forms, the 12‐6 Lennard‐Jones plus Coulomb potential is still the most adopted force field in molecular dynamics (MD) codes, owing to its simple form and easy implementation. However, due to the integer formal charge, unpolarizable force fields of ions may suffer from overestimated interatomic electrostatic interactions, leading to nonphysical clustering or repulsion between such full charges. The electronic continuum correction (ECC) can fix this problem through a simple inclusion of solvent polarization effects via ionic charge rescaling. In this work, the development of novel nonbonded models for mono, divalent, and highly charged metal ions is presented. For each metal species, the ionic charge has been scaled, according to the ECC. Lennard‐Jones parameters have been optimized using experimental structural and thermodynamic properties as target quantities. Performances of the proposed models are discussed and compared with the literature data, while transferability attitudes among different and well‐known water models are evaluated. © 2019 Wiley Periodicals, Inc.

show abstract

“…As mentioned previously, the oxalate anion can be regarded as a complex of a proton (H + ) and an oxalate dianion (C 2 O 4 2− ) and has been previously studied experimentally and theoretically due to its unique structure [7][8][9][10][11][12][13][14][15]. The oxalate anion has two stable minima on the potential energy surface.…”

Section: Introductionmentioning

confidence: 99%

On-the-Fly Ring-Polymer Molecular Dynamics Calculations of the Dissociative Photodetachment Process of the Oxalate Anion

et al. 2021

View full text Add to dashboard Cite

The dissociative photodetachment dynamics of the oxalate anion, C2O4H− + hν → CO2 + HOCO + e−, were theoretically studied using the on-the-fly path-integral and ring-polymer molecular dynamics methods, which can account for nuclear quantum effects at the density-functional theory level in order to compare with the recent experimental study using photoelectron–photofragment coincidence spectroscopy. To reduce computational time, the force acting on each bead of ring-polymer was approximately calculated from the first and second derivatives of the potential energy at the centroid position of the nuclei beads. We find that the calculated photoelectron spectrum qualitatively reproduces the experimental spectrum and that nuclear quantum effects are playing a role in determining spectral widths. The calculated coincidence spectrum is found to reasonably reproduce the experimental spectrum, indicating that a relatively large energy is partitioned into the relative kinetic energy between the CO2 and HOCO fragments. This is because photodetachment of the parent anion leads to Franck–Condon transition to the repulsive region of the neutral potential energy surface. We also find that the dissociation dynamics are slightly different between the two isomers of the C2O4H− anion with closed- and open-form structures.

show abstract

Force field parametrization of hydrogenoxalate and oxalate anions with scaled charges

Cited by 19 publications

References 45 publications

Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction

On-the-Fly Ring-Polymer Molecular Dynamics Calculations of the Dissociative Photodetachment Process of the Oxalate Anion

Contact Info

Product

Resources

About