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Loss of Hyperconjugative Effects Drives Hydride Transfer during Dihydrofolate Reductase Catalysis
In this paper, we studied hydride transfer, a widespread process in nature with significant importance in applied research, focusing on …
A. Angelastro , J. Javier Ruiz-Pernía , Iñaki Tuñón , V. Moliner , L.Y.P. Luk , R.K. Allemann
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Loss of Hyperconjugative Effects Drives Hydride Transfer during Dihydrofolate Reductase Catalysis
Why are some enzymes dimers? Flexibility and catalysis in thermotoga maritima dihydrofolate reductase
In this work, we studied the dihydrofolate reductase from Thermotoga maritima (TmDHFR), a dimeric thermophilic enzyme that catalyzes …
J. Javier Ruiz-Pernía , Iñaki Tuñón , V. Moliner , R.K. Allemann
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Why are some enzymes dimers? Flexibility and catalysis in thermotoga maritima dihydrofolate reductase
Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions
In this present work, we explored the potential of enzymatic catalysis for the chemical industry, addressing the limitations of enzymes …
J. Navarro-Sanchez , N. Almora-Barrios , B. Lerma-Berlanga , J. Javier Ruiz-Pernía , V.A. Lorenz-Fonfria , Iñaki Tuñón , C. Marti-Gastaldo
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Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions
A molecular dynamics study on the role of the protonation state in the biosynthesis of R-PAC by AHAS
In this work, we studied the effect of the protonation state of the hydroxyl-ethylthiamin diphosphate intermediate (HEThDP) on …
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A molecular dynamics study on the role of the protonation state in the biosynthesis of R-PAC by AHAS
Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase
Here we explored the origin of the catalytic power of enzymes, focusing on the controversial role of protein dynamics in enzymatic …
Maite Roca , J. Javier Ruiz-Pernía , R. Castillo , M. Oliva , V. Moliner
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Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase
Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State
In this work, we studied the origin of substrate preference in promiscuous enzymes by studying the alcohol dehydrogenase from …
E. M. Behiry , J. Javier Ruiz-Pernía , L.Y.P Luk , Iñaki Tuñón , V. Moliner , R.K. Allemann
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Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State
Modeling caspase-1 inhibition: Implications for catalytic mechanism and drug design
The metabolic product of caspase-1, IL-1β, is an important mediator in inflammation and pyroptosis cell death process. …
DOI
Adaptive Finite Temperature String Method in Collective Variables
Here we present a modified version of the on-the-fly string method for the localization of the minimum free energy path in a space of …
DOI
Adaptive Finite Temperature String Method in Collective Variables
QM/MM study of l-lactate oxidation by flavocytochrome: B2
In the present work, we studied the mechanism of L-lactate oxidation by flavocytochrome b2 (Fcb2) using molecular dynamics simulations …
N. Guillet , J. Javier Ruiz-Pernía , A. De La Lande , B. Levy , F. Lederer , I. Demachy , V. Moliner
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QM/MM study of l-lactate oxidation by flavocytochrome: B2
Minimization of dynamic effects in the evolution of dihydrofolate reductase
Here we investigated the role of protein isotope labeling as a powerful technique to probe functionally important motions in enzyme …
J. Javier Ruiz-Pernía , E. Behiry , L.Y.P. Luk , E.J. Loveridge , Iñaki Tuñón , V. Moliner , R.K Allemann
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Minimization of dynamic effects in the evolution of dihydrofolate reductase