Computational Enzymology

Mashhadi, N.; Taylor, K.T.*; Biswas, N.; Meister, P.J.; Gauld, J.W. (2019) Oligomerization of 3-substituted quinolines by catalytic activity of soybeanperoxidase as a wastewater treatment. Product formation and computationalstudies Chem. Engineer. J. 364, 340-348

Sekhar, S.C.; Venkatesh, J.; Cheriyan, V.T.; Muthu, M.; Levi, E.; Assad, H.; Meister, P.J.; Undyala, v.v.; Gauld, J.W.; Rishi, A.K.* (2019) A H2AX-CARP-1 Interaction Regulates Apoptosis Signaling Following DNA Damage Cancers, 11, 221

Nikoo, S.; Meister, P. J.; Hayward, J. J.; Gauld J. W.* (2018) An Assessment of Computational Methods for Calculating Accurate Structures and Energies of Bio-Relevant Polysulfur/Selenium-Containing Compounds Molecules, 23, 3323

Aboelnga, M.; Hayward, J. J.; Gauld J. W.* (2017) Unraveling the Critical Role Played by Ado762 OH in the Post-Transfer Editing by Archaeal Threonyl-tRNA Synthetase J. Phys. Chem. 122, 1092-1101

Aboelnga, M.; Hayward, J. J.; Gauld J. W.* (2017) A Water-Mediated and Substrate-Assisted Aminoacylation Mechanism in The Discriminating Aminoacyl-tRNA Synthetase GlnRS and Non-Discriminating GluRS Phys. Chem. Chem. Phys. 19, 25598-25609

Aboelnga, M.; Hayward, J. J.; Gauld J. W.* (2017) Enzymatic Post-Transfer Editing Mechanism of E. coli Threonyl-tRNA Synthetase (ThrRS): A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Investigation ACS. Catal., 7, 5180-5193

Gauld J. W. (2017) Book Review: "Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis", I. Tuñón and V. Moliner (Eds.), The Royal Society of Chemistry Publishing, UK, 2017. Computational and Theoretical Chemistry, 1112, 67-68

Dokainish, H.; Simard, D.; Gauld J. W.* (2017) A Pseudo-Hypervalent Sulfur Intermediate As An Oxidative Protective Mechanism In The Archaea Peroxiredoxin Enzyme ApTPx J. Phys. Chem. B. 121, 6570-6579

Aboelnga, M.; Gauld J. W.* (2017) The Roles of the Active Site Zn(II) and Residues in Substrate Discrimination by Threonyl-tRNA Synthetase: An MD and QM/MM Investigation J. Phys. Chem. B., 121, 6163-6174

Wei, W.; Gauld J. W.*; Monard, G.* (2017) Computational Insights Into Substrate Binding and Catalytic Mechanism of the Glutaminase Domain of Glucosamine-6-Phosphate Synthase (GlmS) RSC Advances, 7, 29626-29638

Wei, W.; Gauld J. W.*; Monard, G.* (2017) Pretransfer Editing in Threonyl-tRNA Synthetase: Roles of Differential Solvent Accessibility and Intermediate Stabilization ACS Catal. 7, 3102-3112

Ion, B. F.; Aboelnga, M. M. and Gauld, J. W. * (2016) Insights From Molecular Dynamics on Substrate Binding and Effects of Active Site Mutations in Δ1-Pyrroline-5-Carboxylate Dehydrogenase. Can J. Chem. 94,1151. (Invited/Journal Cover/2017 CJC Best Paper Award)

Jarosz, A. P., Wei, W., Gauld, J. W., Auld, J., Özcan, F.,Aslan, M., Mutus, B.* (2015) Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is inactivated by S-sulfuration in vitro. Free Radic. Biol. Med, 89, 512

Fortowsky, G.; Simard, D.; Aboelnga, M. and Gauld, J.W. * (2015) Substrate-Assisted and Enzymatic Pretransfer Editing of Nonstandard Amino Acids by Methionyl-tRNA Synthetase Biochemistry, 54, 5757

Dokainish, H.; Gauld, J.W.* (2015) Formation of a Stable Iminol Intermediate in the Redox Regulation Mechanism of Protein Tyrosine Phosphatase 1B (PTP1B) ACS Catalysis, 5, 2195-2202.Invited.

Bogdan F. Ion.; Erum Kazim; Gauld, J.W.* (2014) A Multi-Scale Computational Study on the Mechanism of Streptococcus pneumoniae Nicotinamidase (SpNic) Molecules, 19, 15735-15753. Invited / Journal Cover.

Aboelnga, M.; Awad M.; Gauld, J.W.; Moustafa M.(2014) An assessment to evaluate the validity of different methods for the description of some corrosion inhibitors J Mol. Model., 20, 2422.

Macdonald, C. A.; Bushnell, E.; Gauld, J.W.; Boyd, R.* (2014) The catalytic Mechanism of leukotriene C4: a critical step in inflammatory processes. Phys. Chem. Chem. Phys.16,16284

Dokainish, H.; Ion, B.F; Gauld, J.W.* (2014) Computational investigations on the catalytic mechanism of maleate isomerase: the role of the active site cysteine residues Phys. Chem. Chem. Phys., 16, 12462-12474.

Gherib, R.; Dokainish, H. M.; Gauld, J.W.* (2014) Multi-Scale Computational Enzymology: Enhancing Our Understanding of Enzymatic Catalysis.Int. J. Mol. Sci.15, 40-422.

De Luna P.; Bushnell, E.; Gauld J.W.* (2013) A Molecular Dynamics Examination on Mutation-Induced Catalase Activity in Coral Allene Oxide Synthase.J. Phys. Chem. B, 117, 14635.

Bushnell, E.A.C.; Gherib, R.; Gauld, J.W.* (2013) Insights into the Catalytic Mechanism of Coral Allene Oxide Synthase: A Dispersion Corrected Density Functional Theory Study. J. Phys. Chem. B, 117, 6701-6710.

De Luna, P.; Bushnell, E.; Gauld, J.W.* (2013) A Density Functional Theory Investigation into the Binding of the Antioxidants Ergothioneine and Ovothiol to Copper. J. Phys. Chem. A, 117, 4057-4065.

Dokainish, H.; Gauld, J.W.* (2013) An MD and QM/MM study on the Catalytic Reductase Mechanism of Methionine Sulfoxide Reductase A (MsrA): Formation and Reduction of a Sulfenic Acid. Biochemistry 52 (10) 1814-1827.

Bushnell, E.A.C.; Jamil, R.; Gauld, J.W.* (2013) Gaining Insight into the Chemistry of Lipoxygenases (LOXs): A Computational Investigation Into The Catalytic Mechanism of 8R-LOX. J. Biol. Inorg. Chem. 18 (3) 343-355.

Bushnell, E.A.C.; Fortowsky, G.B.; Gauld, J.W.* (2012) Iron-Oxo Species and the Oxidation of Imidazole: Insights into the Mechanism of OvoA and EgtB. Inorg. Chem.51(24) 13351 - 13356.

Huang, W.J.; Gauld, J.W.* (2012) Tautomerization in the UDP-Galactopyranose Mutase Mechanism: A DFT-Cluster and QM/MM Investigation. J. Phys. Chem. B 116(48) 14040 - 14050.

Ion, B.F.; Bushnell, E.A.C.; De Luna, P.; Gauld, J.W.* (2012) An MD and QM/MM Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums. Int. J. Mol. Sci., 13, 12994-13011. Invited.

Bushnell, E.A.C.; Gauld, J. W.* (2012) An Assessment of Standard, Hybrid, Meta and Hybrid-Meta GGA Density Functional Theory Methods for Open-Shell Systems: the Case of the Non-Heme Iron Enzyme 8R-LOX. J. Comput. Chem 34 (2) 141-148

Huang, W.J.; Gherib, R.; Gauld, J.W.* (2012) An Active Site Water Broadens Substrate Specificity in S-Ribosylhomocysteinase (LuxS): A Docking, MD, and QM/MM Study. J. Phys. Chem. B, 116, 8916-8929.

Bushnell, E.A.C.; Huang, W.J.; Llano, J.; Gauld, J.W.* (2012) Molecular Dynamics Investigation into Substrate Binding and Identity of the Catalytic Base in the Mechanism of Threonyl-tRNA Synthetase. J. Phys. Chem. B, 116, 4205-5212.

Almasi, J.; Bushnell, E.A.C.; Gauld, J.W.* (2011). A QM/MM-based Computational Investigation on the Catalytic Mechanism of Saccharopine Reductase. Molecules, 16, 8569-8589. Invited.

Huang, W.J.; Bushnell, E.A.C.; Francklyn, C.S.; Gauld, J.W.* (2011). The α-Amino Group of the Threonine Substrate as The General Base During tRNA Aminoacylation: A New Version of Substrate-Assisted Catalysis Predicted by Hybrid DFT, J. Phys. Chem. B, 115, 13050-13060 Invited.

Robinet, J.J.; Dokainish, H.; Paterson, D.J.; Gauld, J.W.* (2011) . A Sulfonium Cation Intermediate in the Mechanism of Methionine Sulfoxide Reductase B: A DFT Study, J. Phys. Chem. B, 115, 9202-9212.

Erdtman, E.; Bushnell, E.A.C.; Gauld, J.W.; Eriksson, L.A.* (2011) Computational Studies on Schiff Base Formation: Implications for the Catalytic Mechanism of Porphobilinogen Synthase, Comp. Theor. Chem., 963, 479-489. *highlighted by editors as part of the celebration of the 1000th volume.

Amiralaei, S.; Gauld, J.; Green, J.R.* (2011). Dehydrotropylium-Co2(CO)6 Ion. Generation, Reactivity and Evaluation of Cation Stability. Chem. Eur. J., 17, 4157-4165.

Bushnell, E.A.C.; Erdtman, E.; Llano, J.; Eriksson, L.A.; Gauld, J.W.* (2011). The First Branching Point in Porphyrin Biosynthesis: A Systematic Docking, MD and QM/MM Study of Substrate Binding and Mechanism of Uroporphyrinogen-III Decarboxylase. J. Comput. Chem., 32, 822-834.

Huang, W.J.; Llano, J.; Gauld, J.W.* (2010). A DFT Study on the Catalytic Mechanism of UDP, Can. J. Chem., 88, 804-814. Invited: Special issue in honour of Prof. R. Boyd .

Erdtman, E.; Bushnell, E.A.C.; Gauld, J.W.; Eriksson, L.A.* (2010). Computational Insights into the Mechanism of Porphobilinogen Synthase, J. Phys. Chem. B, 114, 16860-16870.

Huang, W.J.; Llano, J.; Gauld, J.W.* (2010) . Redox Mechanisms of Glycosidic-Bond Hydrolysis Catalyzed by 6-Phospho-a-Glucosidase (GlvA): A DFT Study, J. Phys. Chem. B, 114, 11196-11206.

Liu, H.; Llano, J.; Gauld, J.W.* (2009). A DFT Study of Nucleobase Dealkylation by the DNA Repair Enzyme AlkB, J. Phys. Chem. B, 113, 4887-4898.

Liu, H.; Gauld, J.W.* (2009). Protonation of Guanine Quartets and Quartet Stacks: Insights from DFT Studies, Phys. Chem. Chem. Phys., 11, 278-287.

Robinet, J.J.; Cho, K.-B.; Gauld, J.W.* (2008) A Density Functional Theory Investigation on the Mechanism of the Second Half-Reaction of Nitric Oxide Synthase, J. Am. Chem. Soc., 130, 3328-3334.

Robinet, J.J.; Gauld, J.W.* (2008). DFT Investigation on the Mechanism of the Deacetylation Reaction Catalyzed bt LpxC, J. Phys. Chem. B, 112, 3462-3469.

Liu, H.; Gauld, J.W.* (2008). Substrate-Assisted Catalysis in the Aminoacyl Transfer mechanism of Histidyl-tRNA Synthetase: A Density Functional Theory Study, J. Phys. Chem. B, 112, 3462-3469.

Robinet, J.J.; Baciu, C.; Cho, K.-B.; Gauld, J.W.* (2007). A Computational Study on the Interaction of the Nitric Oxide Ions NO+ and NO- with Aromatic Amino Acids, J. Phys. Chem. A, 111, 1981-1989.

Liu. H.; Robinet, J.J.; Ananvoranich, S.; Gauld, J.W.* (2007). Density Functional Theory Investigation on the Mechanism of the Hepatitis Delta Virus Ribozyme, J. Phys. Chem. B, 111, 439-445.

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Other refereed publications (Reviews / Chapters / Letters)

Ban, F.; Gauld, J.W.; Wetmore, S.D.; Boyd, R.J.* The Calculation of the Hyperfine Coupling Tensors of Biological Radicals. In EPR of Free Radicals in Solids: Trends in Methods and Applications, Lund, A. and Shiotani, M. (Eds.); Springer 2012 (37 pages; In Press).

Bushnell, E.A.C.; Huang, W.J.; Gauld, J.W.* (2012). Applications of Potential Energy Surfaces In The Study of Enzymatic Reactions, Adv. Phys. Chem. 2012 (15 pages; doi:10.1155/2012/867409) Invited: Special issue Accurate Potential Energy Surfaces and Beyond: Chemical Reactivity, Binding, Long-Range Interactions, and Spectroscopy.

Robinet, J.J.; Dokainish, H.; Paterson, D.J.; Gauld, J.W.* (2011). Reply to the "Comment on 'A Sulfonium Cation Intermediate in the Mechanism of Methionine Sulfoxide Reductase B: A DFT Study'", J. Phys. Chem. B, 115, 10776-10777.

Bushnell, E.A.C.; Llano, J.; Eriksson, L.A.; Gauld, J.W.* (2011). Mechanisms of Mutagenic DNA Nucleobase Damages and Their Chemical and Enzymatic Repairs Investigated by Quantum Chemical Methods In Selected Topics in DNA Repair, Clark C. Chen (Ed.), InTech (ISBN: 978-953-307-606-5).Invited.

Llano, J.; Gauld, J.W.* (2010) Mechanistics of Enzyme Catalysis: From Small to Large Active-Site Models In Quantum Biochemistry: Electronic Structure and Biological Activity, Matta, C. (Ed.), Wiley-VCH Verlag GmbH & Co. KGaA, p. 643-666. Invited due to our extensive work in computational enzymology.

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