Introduction to the Empirical Valence Bond Approach

Duarte, Fernanda; Pabis, Anna; Kamerlin, Shina Caroline Lynn

doi:10.1002/9781119245544.ch2

Cited by 4 publications

(26 citation statements)

References 129 publications

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“…Since pkDAAO and hDAAO have a buried active site and product egress is their rate-limiting step, we concentrated on the initial analysis on their active sites, secondary binding sites and surroundings [ 3 , 4 ]. Solvent access investigations presented substantial details and identified critical residues, which were congruent with available literature data on (i) the structure and functional characterization of DAAOs [ 1 – 24 , 28 – 37 ], (ii) the analysis of the dynamics of the D-amino acid oxidase–benzoate complex of pkDAAO [ 44 ] and (iii) the aromatic cage regulating active site access and modulating the features of monoamine oxidase (MAO) [ 45 ].…”

Section: Introductionsupporting

confidence: 74%

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access

et al. 2018

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D-amino acid oxidase (DAAO) degrades D-amino acids to produce α-ketoacids, hydrogen peroxide and ammonia. DAAO has often been investigated and engineered for industrial and clinical applications. We combined information from literature with a detailed analysis of the structure to engineer mammalian DAAOs. The structural analysis was complemented with molecular dynamics simulations to characterize solvent accessibility and product release mechanisms. We identified non-obvious residues located on the loops on the border between the active site and the secondary binding pocket essential for pig and human DAAO substrate specificity and activity. We engineered DAAOs by mutating such critical residues and characterised the biochemical activity of the resulting variants. The results highlight the importance of the selected residues in modulating substrate specificity, product egress and enzyme activity, suggesting further steps of DAAO re-engineering towards desired clinical and industrial applications.

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Section: Introductionsupporting

confidence: 74%

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access

et al. 2018

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“…The Empirical Valence Bond (EVB) method [20][21][22][23][24][25] offers, instead, a simple general framework 1 Indeed, designing RFFs requires a high level of expertise to tackle a multi-dimensional problem, 11 where the modelled interactions are often expressed by complicated functional forms with many strongly coupled parameters that are optimized via the use of sophisticated tools. [12][13][14][15][16][17][18] 2 to model reactive processes through the coupling of multiple non-reactive FFs, where each FF corresponds to a different chemical state for the system.…”

Section: Introductionmentioning

confidence: 99%

“…We refer the interested reader to ref. 24 and references therein for a detailed list of applications investigated with EVB.…”

Section: Introductionmentioning

confidence: 99%

Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble

2020

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Please cite only the published version using the reference above. This is the citation assigned by the publisher at the time of issuing the AAM. Please check the publisher's website for any updates. This is the author's final, peer-reviewed manuscript as accepted for publication (AAM). The version presented here may differ from the published version, or version of record, available through the publisher's website. This version does not track changes, errata, or withdrawals on the publisher's site.

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“…The Empirical Valence Bond (EVB) method [20][21][22][23][24][25] offers, instead, a simple general framework to model reactive processes through the coupling of multiple non-reactive FFs, where each FF corresponds to a different chemical state for the system. In this method, a suitable EVB matrix is built using the computed energies of the involved chemical states as well as appropriate coupling terms.…”

Section: Introductionmentioning

confidence: 99%

“…30 This convenient feature of the EVB method has widely increased its recognition as a powerful tool within the computational chemistry community. 24 For condensed phase systems, reported MD simulations with the EVB method (herein, MD-EVB simulations) are conducted either in the microcanonical (NVE) or the canonical (NVT) ensemble. However, MD-EVB simulations at constant pressure and temperature, i.e.…”

Section: Introductionmentioning

confidence: 99%

Reactive molecular dynamics at constant pressure via non-reactive force fields: extending the Empirical Valence Bond method to the isothermal-isobaric ensemble

Scivetti,

Sen,

Elena

et al. 2020

Preprint

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The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of non-reactive force fields. However, most of the implemented functional forms for the coupling terms depend on complex spatial coordinates, which precludes the computation of the stress tensor for condensed phase systems and prevents the possibility to carry out EVB molecular dynamics in the isothermal-isobaric (NPT) ensemble. In this work, we make use of coupling terms that depend on the energy gaps, defined as the energy differences between the participating non-reactive force fields, and derive an expression for the EVB stress tensor suitable for computations. Implementation of this new methodology is tested for a model of a single reactive malonaldehyde solvated in non-reactive water. Computed densities and classical probability distributions in the NPT ensemble reveals a negligible role of the reactive potential in the limit of low concentrated solutions, thus corroborating the validity of standard approximations customarily adopted for EVB simulations.

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Introduction to the Empirical Valence Bond Approach

Cited by 4 publications

References 129 publications

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access

Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble

Reactive molecular dynamics at constant pressure via non-reactive force fields: extending the Empirical Valence Bond method to the isothermal-isobaric ensemble

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