Free Energy Landscape and Proton Transfer Pathways of the Transimination Reaction at the Active site of the Serine Hydroxymethyltransferase Enzyme in Aqueous Medium

Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II

(2020) Srabani Taraphder et al.   CHEMPHYSCHEM

A QM / MM simulation study of transamination reaction at the active site of aspartate aminotransferase: Free energy landscape and proton transfer pathways

(2020) Sindrila Dutta Banik et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Transimination Reaction at the Active Site of Aspartate Aminotransferase: A Proton Hopping Mechanism through Pyridoxal 5'-Phosphate

(2019) Kumari Soniya et al.   ACS Catalysis

Free energy landscapes of prototropic tautomerism in pyridoxal 5′-phosphate schiff bases at the active site of an enzyme in aqueous medium

(2018) Kumari Soniya et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The catalytic mechanism of the Serine Hydroxymethyltransferase – a computational ONIOM QM/MM study

(2018) Henrique Silva Fernandes et al.   ACS Catalysis

The GTPase hGBP1 converts GTP to GMP in two steps via proton shuttle mechanisms

(2017) Ravi Tripathi et al.   Chemical Science

Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme

(2017) Steven Dajnowicz et al.   Nature Communications

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

Differential 3-bromopyruvate inhibition of cytosolic and mitochondrial human serine hydroxymethyltransferase isoforms, key enzymes in cancer metabolic reprogramming

(2016) Alessandro Paiardini et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Free-Energy Landscape and Proton Transfer Pathways in Oxidative Deamination by Methylamine Dehydrogenase

(2016) Theodros Zelleke et al.   CHEMPHYSCHEM

Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics

(2016) Shalini Awasthi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

(2016) Garima Jindal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

cMyc-mediated activation of serine biosynthesis pathway is critical for cancer progression under nutrient deprivation conditions

(2015) Linchong Sun et al.   CELL RESEARCH

Screening and In Vitro Testing of Antifolate Inhibitors of Human Cytosolic Serine Hydroxymethyltransferase

(2015) Alessandro Paiardini et al.   ChemMedChem

Mechanism of Meropenem Hydrolysis by New Delhi Metallo β-Lactamase

(2015) Ravi Tripathi et al.   ACS Catalysis

A QM/MM Study of the l-Threonine Formation Reaction of Threonine Synthase: Implications into the Mechanism of the Reaction Specificity

(2014) Mitsuo Shoji et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

PLP undergoes conformational changes during the course of an enzymatic reaction

(2014) Ho-Phuong-Thuy Ngo et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

NMR Studies of Protonation and Hydrogen Bond States of Internal Aldimines of Pyridoxal 5′-Phosphate Acid–Base in Alanine Racemase, Aspartate Aminotransferase, and Poly-l-lysine

(2013) Monique Chan-Huot et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanism of Acyl–Enzyme Complex Formation from the Henry–Michaelis Complex of Class C β-Lactamases with β-Lactam Antibiotics

(2013) Ravi Tripathi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations

(2013) Matthew J. McGrath et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure-Based Mechanism for Early PLP-Mediated Steps of Rabbit Cytosolic Serine Hydroxymethyltransferase Reaction

(2013) Martino L. Di Salvo et al.   Biomed Research International

Critical hydrogen bonds and protonation states of pyridoxal 5′-phosphate revealed by NMR

(2011) Hans-Heinrich Limbach et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

In silico and in vitro validation of serine hydroxymethyltransferase as a chemotherapeutic target of the antifolate drug pemetrexed

(2011) Frederick Daidone et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Computational Mechanistic Studies Addressed to the Transimination Reaction Present in All Pyridoxal 5′-Phosphate-Requiring Enzymes

(2011) N. M. F. S. A. Cerqueira et al.   Journal of Chemical Theory and Computation

DFT Studies on Schiff Base Formation of Vitamin B6 Analogues. Reaction between a Pyridoxamine-Analogue and Carbonyl Compounds

(2010) J. Ortega-Castro et al.   JOURNAL OF PHYSICAL CHEMISTRY A

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Quantum Mechanical/Molecular Mechanical Study on the Catalysis of the Pyridoxal 5′-Phosphate-Dependent Enzymel-Serine Dehydratase

(2008) Zheng Zhao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS