Publications

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Identification of the Initial Steps in Signal Transduction in the α4β2 Nicotinic Receptor: Insights from Equilibrium and Nonequilibrium Simulations
Oliveira, A. S.O., Shoemark, D. K., Rego Campello, H., Wonnacott, S., Gallagher, T., Sessions, R. B. and Mulholland A.J.
Structure, 2019 just accepted
DOI: 10.1016/j.str.2019.04.008

Visualizing protein–ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site
Raza, S., Ranaghan, K.E., van der Kamp, M.W., Woods, C.J., Mulholland, A.J., and Azam, S.S.
J. Comput. Aided. Mol. Des. 2019
DOI: 10.1007/s10822-019-00200-4

Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate.
Nutho, B., Mulholland, A. J., and Rungrotmongkol, T.
J. Phys. Chem. B. 2019 Just Accepted Manuscript
DOI:10.1021/acs.jpcb.9b02157

Simulations of Shikimate Dehydrogenase from Mycobacterium tuberculosis in Complex with 3-dehydroshikimate and NADPH Suggest Strategies for MtbSDH inhibition.
Punkvang, A., Kamsri, P., Mulholland, A. J., Spencer, J., Hannongbua, S., and Pungpo, P.
J. Chem. Inf. Model. 2019 Just Accepted Manuscript
DOI: 10.1021/acs.jcim.8b00834

Projector-based embedding eliminates density functional dependence for QM/MM calculations of reactions in enzymes and solution
Ranaghan, K. E.,  Shchepanovska, D., Bennie, S. J.,  Lawan, N., Macrae, S. J., Zurek, J., Manby, F. R. and Mulholland, A. J.
J. Chem. Inf. Model., Just Accepted Manuscript
DOI: 10.1021/acs.jcim.8b00940

A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Unfolding of G-Quadruplex DNA
O’Hagan, M. P., Haldar, S., Duchi, M., Oliver, T. A. A., Mulholland, A. J., Morales, J. C., and Galan, M.C.
Angewandte Chemie Int. Ed., 2019 (in press)
DOI:10.1002/anie.201900740

2018

Loop Motion in Triosephosphate Isomerase is not a Simple Open and Shut Case
Liao, Q.,  Kulkarni, Y., Sengupta, U., Petrović, D., Mulholland, A. J., van der Kamp, M. W., Strodel, B., and Kamerlin, S. C.  L.
J. Am. Chem. Soc., Just Accepted Manuscript
DOI: 10.1021/jacs.8b09378

QM/MM Simulations Show Saccharide Distortion is Required for Reaction in Hen Egg-White Lysozyme.
Limb,  M..A. L., Suardiaz, R., Grant, I. M., Mulholland, A. J.
Chem. Eur. J., 2018
DOI: 10.1002/chem.201805250.

Maintaining and breaking symmetry in homomeric coiled-coil assemblies
Rhys, G. G., Wood, C. W., Lang, E. J. M., Mulholland, A. J., Brady, R. L., Thomson, A. R. and Woolfson, D. N.
Nature Communications, 2018, 9, 4132
https://www.nature.com/articles/s41467-018-06391-y

Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
Huggins, D. J., Biggin, P. C., Dämgen, M. A., Essex, J. W., Harris, S. A., Henchman, R. H., Khalid, S., Kuzmanic, A., Laughton, C. A.,  Michel, J., Mulholland, A. J., Rosta, E., Sansom, M. S. P., van der Kamp, M. W.
WIREs Computational Molecular Science, 2018
DOI:  10.1002/wcms.1393

A Multiscale Simulation Approach to Modelling Drug-Protein Binding Kinetics
Haldar, S., Comitani, F., Saladino, G., Woods, C. J., van der Kamp, M. W., Mulholland, A. J. and Gervasio, F. L.
J. Chem. Theory Comput., 2018, Just Accepted Manuscript
DOI: 10.1021/acs.jctc.8b00687

Combined Quantum Mechanics and Molecular Mechanics Studies of Enzymatic Reaction Mechanisms
Ainsley, J., Lodola, A., Mulholland, A. J., Christov, C. Z., and Karabencheva-Christova, T. G.
Advances in Protein Chemistry and Structural Biology, 2018, Vol. 113, Pages 1-32
DOI: 10.1016/bs.apcsb.2018.07.001

Sampling molecular conformations and dynamics in a multiuser virtual reality framework
O’Connor M., Deeks, H. M., Dawn, E., Metatla, O., Roudaut, A., Sutton, M., May Thomas, L., Glowacki, B. R., Sage, R., Tew, P., Wonnacott, M., Bates, P., Mulholland, A. J., and David R. Glowacki, D. R.
Science Advances, 2018, Vol. 4, no. 6, eaat2731
DOI: 10.1126/sciadv.aat2731

De novo designed α-helical barrels as receptors for small molecules
Thomas, F., Dawson, W. M., Lang, E. J. M., Burton, A. J., Bartlett, G. J., Rhys, G., Mulholland, A. J., and Woolfson, D. N.
ACS Synth. Biol. 2018 [Epub ahead of print]
DOI: 10.1021/acssynbio.8b00225

Unlocking Nicotinic Selectivity via Direct C‒H Functionalization of (−)-Cytisine
Rego Campello, H., Del Villar, S. G., Honraedt, A., Minguez, T., Oliveira, A. S. F., Ranaghan, K. E., Shoemark, D. K., Bermudez, I., Gotti, C., Sessions, R. B., Mulholland, A. J., Wonnacott, S., and Gallagher T.
Chem, 2018, In press
DOI: 10.1016/j.chempr.2018.05.007

Multiscale simulations of clavulanate inhibition identify the reactive complex in class A β-lactamases and predict efficiency of inhibition
Fritz, R.,  Alzate-Morales, J. H., Spencer, J.,  Mulholland, A. J. and van der Kamp, M. W.
Biochemistry, Just Accepted Manuscript
https://pubs.acs.org/doi/10.1021/acs.biochem.8b00480

Understanding complex mechanisms of enzyme reactivity: the case of Limonene-1,2-epoxide hydrolases.
Rinaldi, S., van der Kamp, M. W., Ranaghan, K. E., Mulholland, A. J. and Colombo, G.
ACS Catal., Just Accepted Manuscript
DOI: 10.1021/acscatal.8b00863

QM/MM simulations identify the determinants of catalytic activity differences between type ii dehydroquinase enzymes
Quintana, E. L., van der Kamp, M. W., González-Bello, C. and Mulholland, A. J.
Organic & Biomolecular Chemistry, 2018, Advance Article
DOI: 10.1039/C8OB00066B

Structural Insights from Molecular Dynamics Simulations of Tryptophan 7-Halogenase and Tryptophan 5-Halogenase
Ainsley, J., Mulholland, A. J., Black, G. W., Sparagano, O., Christov, C. Z., and Karabencheva-Christova T. G.
ACS Omega, 2018, 3 (5), pp 4847–4859
DOI: 10.1021/acsomega.8b00385

Multiscale methods in drug design bridge chemical and biological complexity in the search for cures
Amaro, R. E., and Mulholland, A. J.
Nature Reviews Chemistry, 2018, 2, 0148
https://www.nature.com/articles/s41570-018-0148

Experiment and simulation reveal how mutations in functional plasticity regions guide plant monoterpene product outcome
Leferink, N. G. H.,  Ranaghan, K. E., Karrupiah, V., Currin, A.,  van der Kamp, M. W., Mulholland, A.J. and Scrutton, N. S.
ACS Catalysis, 2018, 8 (5), 3780-3791
https://pubs.acs.org/doi/10.1021/acscatal.8b00692

Dynamical origins of heat capacity changes in enzyme-catalysed reactions
van der Kamp, M. W., Prentice, E. J., Kraakman, K. L., Connolly, M., Mulholland, A. J., and Arcus, V. L.
Nature Communications, 2018, 9, 1177
https://www.nature.com/articles/s41467-018-03597-y

Biocatalytic Routes to Lactone Monomers for Polymer Production
Messiha, H. L., Ahmed, S. T., Karuppiah, V.,  Suardiaz, R.,  Ascue Avalos, G. A., Fey, N.,  Yeates, S.,  Toogood, H. S.,  Mulholland, A. J. and Scrutton, N. S.
Biochemistry, 2018
https://pubs.acs.org/doi/abs/10.1021/acs.biochem.8b00169

P450-Catalyzed Regio- and Diastereoselective Steroid Hydroxylation: Efficient Directed Evolution Enabled by Mutability Landscaping
Acevedo-Rocha, C. G., Gamble, C. G., Lonsdale, R., Li, A., Nett, N., Hoebenreich, S., Lingnau, J. B., Wirtz, C., Fares, C., Hinrichs, H., Deege, A., Mulholland, A. J., Nov, Y., Leys, D., McLean, K. J., Munro, A. W., and Reetz, M.T.
ACS Catalysis, Articles ASAP (As Soon As Publishable), pp 3395–3410
https://pubs.acs.org/doi/abs/10.1021/acscatal.8b00389

L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib
Callegari, D., Ranaghan, K. E., Woods, C.,  Minari, R., Tiseo, M., Mor, M.,  Mulholland A. J. and Lodola, A.
Chemical Science, 2018
http://pubs.rsc.org/en/content/articlepdf/2018/SC/C7SC04761D

Multiscale analysis of enantioselectivity in enzyme-catalysed ‘lethal synthesis’ using projector-based embedding
Zhang, X., Bennie, S. J., van der Kamp, M. W., Glowacki, D. R., Manby, F. R., and Mulholland A. J.
Royal Society Open Science, 5:171390
http://dx.doi.org/10.1098/rsos.171390

2017

Mechanistic Insights into the Reaction of Chlorination of Tryptophan Catalyzed by Tryptophan 7-Halogenase
Karabencheva-Christova, T. G., Torras, J., Mulholland, A. J., Lodola, A., and Christov, C. Z.
Scientific Reports, 2017, 7:17395
http://dx.doi.org/10.1038/s41598-017-17789-x

Quantum Mechanics/Molecular Mechanics Simulations Identify the Ring-Opening Mechanism of Creatininase
Jitonnom, J., Mujika, J. I., van der Kamp, M. W., and Mulholland, A. J.
Biochemistry, 2017, 56 (48), 6377-6388
http://pubs.acs.org/doi/10.1021/acs.biochem.7b01032

Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations.
Ge, Y., van der Kamp, M. W., Malaisree, M., Liu, D., Liu, Y., Mulholland, A. J.
J Comput Aided Mol Des.,2017, 31(11):995-1007.
http://dx.doi.org/10.1007/s10822-017-0073-y 

Ab Initio QM/MM Modelling of the Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic Amine Dehydrogenase
Ranaghan K. E., Morris, W. G., Masgrau, L.,  Senthilkumar, K., Johannissen, L. O., Scrutton, N. S.,  Harvey, J. N., Manby, F. R. and Mulholland, A. J.
J. Phys. Chem. B, 2017, Just Accepted Manuscript
DOI:10.1021/acs.jpcb.7b06892

Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme
Watkins, D., Jenkins, J.,  Grayson, K., Wood, N., Steventon, J., Le Vay, K., Goodwin, M., A. Mullen, A., Bailey, H., Crump, M., MacMillan, F.,  Mulholland, A., Cameron, G., Sessions, R., Mann, S. & Anderson J.
Nature Communications, 2017, in press
doi:10.1038/s41467-017-00541-4

Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase
Karuppiah, V., Ranaghan, K.E., Leferink, N.G.H., Johannissen, L.O., Shanmugam, M., Ní Cheallaigh, A., Bennett, N.J, Kearsey, L.J., Takano, E., Gardiner, J.M., van der Kamp, M.W., Hay, S., Mulholland, A. J., Leys, D., and Scrutton, N.S.
ACS Catalysis, 2017, in press
http://pubs.acs.org/doi/10.1021/acscatal.7b01924

Molecular Dynamics, Quantum Mechanics and Combined Quantum Mechanics / Molecular Mechanics Methods for Drug Discovery and Development
Lang, E.J. and Mulholland A.J.
Comprehensive Medicinal Chemistry III
https://www.elsevier.com/books/comprehensive-medicinal-chemistry-iii/chackalamannil/978-0-12-803200-8

Rapid Estimation of Catalytic Efficiency by Cumulative Atomic Multipole Moments: Application to Ketosteroid Isomerase Mutants
Beker, W., van der Kamp, M.W., Mulholland, A.J. and Sokalski, W.A.
Chem. Theor. Comput., 2017, 13, 2, 945-955.
http://dx.doi.org/10.1021/acs.jctc.6b01131

Insights into the Mechanistic Basis of Plasmid-Mediated Colistin Resistance from Crystal Structures of the Catalytic Domain of MCR-1
Hinchcliffe, P., Yang, Q.E., Portal, E., Young, T., Li, H., Tooke, C.L., Carvalho, M.J., Paterson, N.G., Brem, J., Niumsup, P.R., Tansawai, U., Lei, L., Li, M., Shen, Z.Q., Wang, Y., Schofield, C.J., Mulholland, A.J., Shen, J.Z., Fey, N., Walsh, T.R., and Spencer, J.
Scientific Reports, 2017, 7, 39392
http://doi.dx.org/10.1038/srep39392

2016

Elucidation of Nonadditive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study
Calabro, G., Woods, C.J., Powlesland, F., Mey, A.S.J.S., Mulholland, A.J. and Michel, J.
Phys. Chem. B, 2016, 120, 24, 5340-5350.
http://dx.doi.org/10.1021/acs.jpcb.6b03296

QM/MM Methods for Simulating Enzyme Reactions
Ranaghan K.E. and Mulholland, A.J.
Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis
http://dx.doi.org/10.1039/9781782626831-00375

A projector embedding approach for multi scale coupled-cluster calculations applied to citrate synthase.
Bennie, S., van der Kamp, M. W., Pennifold, R., Stella, M., Manby, F. R., and Mulholland, A.J.
Chem. Theor. Comput., 2016, in press.
http://dx.doi.org/10.1021/acs.jctc.6b00285

Quantum mechanics/molecular mechanics modelling of drug metabolism: Mexiletine N-hydroxylation by cytochrome P450 1A2.
Lonsdale, R., Fort, R., Rydberg, P., Harvey, J. N. and Mulholland, A. J.
Chemical Research in Toxicology, 2016, in press.
http://dx.doi.org/10.1021/acs.chemrestox.5b00514

The catalytic mechanism of a natural Diels-Alderase revealed in molecular detail.
Byrne, M., Lees, N., Han, L.-C.,van der Kamp, M. W., Mulholland, A. J., Stach, J. E., Willis, C. and Race, P.
J. Am. Chem. Soc. 2016, in press.
http://dx.doi.org/10.1021/jacs.6b00232

On the temperature dependence of enzyme-catalysed rates.
Arcus, V. L., Prentice, E. J.,Hobbs, J. K., Mulholland, A. J., van der Kamp, M. W., Pudney, C. R., Parker, E. J., Schipper, L. A.
Biochemistry, 2016, 55, 1681-1688.
http://pubs.acs.org/doi/abs/10.1021/acs.biochem.5b01094

Dispelling the effects of a sorceress in enzyme catalysis.
Mulholland, A. J.
Proc. Natl. Acad. Sci. USA, 2016, 113, 9, 2328-2330.
http://www.pnas.org/content/113/9/2328

2015

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.
Gray, A., Harlen, O. G., Harris, S. A., Khalid, S., Leung, Y. M., Lonsdale, R., Mulholland A. J., Pearson, A. R., Read, D. J. and Richardson, R. A.
Acta Cryst. 2015, D71, 162-172.
http://scripts.iucr.org/cgi-bin/paper?S1399004714026777

High-Level QM/MM Calculations Support the Concerted Mechanism for Michael Addition and Covalent Complex Formation in Thymidylate Synthase.
Kaiyawet, N., Lonsdale, R., Rungrotmongkol, T., Mulholland, A. J., & Hannongbua, S.
Chem. Theory and Comput. 2015, 11, 713-722.
http://pubs.acs.org/doi/abs/10.1021/ct5005033″

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.
Wells, S. A., van der Kamp, M. W., McGeagh, J. D., & Mulholland, A. J.
Plos One 2015, 10(8).
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0133372

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations for Protein-Ligand Complexes: Free Energies of Binding of Water Molecules in Influenza Neuraminidase.
Woods, C. J., Shaw, K. E., & Mulholland, A. J.
Phys. Chem. B 2015, 119(3), 997-1001.
http://dx.doi.org/10.1021/jp506413j

2014

Large-Scale Density Functional Theory Transition State Searching in Enzymes
Lever G, Cole DJ, Lonsdale R, Ranaghan KE, Wales DJ, Mulholland AJ, Skylaris CK, Payne MC.
Phys. Chem. Lett. 2014, 5 (21), 3614-3619
http://pubs.acs.org/doi/abs/10.1021/jz5018703

Comparison of DFT and ab intio QM/MM methods for modelling reaction in chorismate synthase
Lawan N, Ranaghan KE, Manby FR, Mulholland AJ
Chem. Phys. Lett., 2014, (4), pp 380-385
http://www.sciencedirect.com/science/article/pii/S0009261414005041

Trends in predicted chemoselectivity of cytochrome P450 oxidation: B3LYP barrier heights for epoxidation and hydroxylation reactions.
Rydberg, P., Lonsdale, R., Harvey, J. N., and Mulholland, A. J.
Journal of Molecular Graphics and Modelling, 2014, 52, 30-35.
http://www.sciencedirect.com/science/article/pii/S1093326314000989

A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes
By: Lonsdale, Richard; Rouse, Sarah L.; Sansom, Mark S. P.; et al.
PLoS Comput. Biol., 2014, 10 (7)
http://www.ncbi.nlm.nih.gov/pubmed/25033460

QM/MM Free-Energy Simulations of Reaction in Serratia marcescens Chitinase B Reveal the Protonation State of Asp142 and the Critical Role of Tyr214.
Jitonnom J, Limb MA, Mulholland AJ.
J Phys Chem B, 118(18):4771-83.
http://pubs.acs.org/doi/abs/10.1021/jp500652x

Reaction Mechanism of N-Acetylneuraminic Acid Lyase Revealed by a Combination of Crystallography, QM/MM Simulation, and Mutagenesis.
Daniels AD, Campeotto I, van der Kamp MW, Bolt AH, Trinh CH, Phillips SE, Pearson AR, Nelson A, Mulholland AJ, Berry A.
ACS Chem Biol. 2014,9(4):1025-32.
http://www.ncbi.nlm.nih.gov/pubmed/24521460

QM/MM simulations indicate that Asp185 is the likely catalytic base in the enzymatic reaction of HIV-1 reverse transcriptase
Rungrotmongkol T, Mulholland AJ, Hannongbua S.
Med. Chem. Commun., 2014, 5, 593-596
http://pubs.rsc.org/en/content/articlelanding/md/2014/c3md00319a#!divAbstract

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme
Vojtěch Mlýnský, Pavel Banáš, Jiří Šponer, Marc W. van der Kamp, Adrian J. Mulholland, and Michal Otyepka
Chem. Theory Comput., 2014,(4), pp 1608–1622
http://pubs.acs.org/doi/abs/10.1021/ct401015e?prevSearch=%255BContrib%253A%2Bmulholland%255D&searchHistoryKey=

A catalytic role for methionine revealed by a combination of computation and experiments on phosphite dehydrogenase
Kara E. Ranaghan, John E. Hung, Gail J. Bartlett, Tiddo J. Mooibroek, Jeremy N. Harvey, Derek N. Woolfson, Wilfred A. van der Donk and Adrian J. Mulholland
Chem. Sci., 2014, Advance Article
http://pubs.rsc.org/en/Content/ArticleLanding/2014/SC/C3SC53009D#!divAbstract

Role of Active Site Residues in Promoting Cobalt-Carbon Bond Homolysis in Adenosylcobalamin-Dependent Mutases Revealed through Experiment and Computation.
Román-Meléndez GD, von Glehn P, Harvey JN, Mulholland AJ, Marsh EN.
Biochemistry (2014), vol 53, pp 169-177
http://pubs.acs.org/doi/abs/10.1021/bi4012644

QM/MM simulations as an assay for carbapenemase activity in class A beta-lactamases.
Chudyk, E. I., Limb, M. A. L., Jones, C., Spencer, J., van der Kamp, M. W., and Mulholland A. J.
Chem. Comm., 2014, 50, 14736-14739.
http://pubs.rsc.org/en/Content/ArticleLanding/2014/CC/C4CC06495J#!divAbstract

Rapid decomposition and visualisation of protein-ligand binding free energies by residue and by water.
Woods, C. J., Malaisree, M., Michel, J., Long, B., McIntosh-Smith, S., and Mulholland, A. J.
Farad. Discuss., 2014, 169, 477-499.
http://pubs.rsc.org/en/Content/ArticleLanding/2014/FD/C3FD00125C#!divAbstract

QM/MM Modelling of Drug-Metabolizing Enzymes
Lonsdale R., Mulholland AJ.
Curr. Top. Med. Chem., 2014, 14 (11), pp 1339-1347
http://www.ncbi.nlm.nih.gov/pubmed/24805066

2013

Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity.
Woods CJ, Malaisree M, Long B, McIntosh-Smith S, Mulholland AJ.
Sci Rep. (2013), 3, 3561
http://www.nature.com/srep/2013/131220/srep03561/full/srep03561.html

Analysis and assay of oseltamivir-resistant mutants of influenza neuraminidase via direct observation of drug unbinding and rebinding in simulation
Woods CJ, Malaisree M, Long B, McIntosh-Smith S, Mulholland AJ.
Biochemistry, (2013), vol 52, 88105-8164
http://www.ncbi.nlm.nih.gov/pubmed/24128064

Conformational change and ligand binding in the aristolochene synthase catalytic cycle
van der Kamp MW, Sirirak J, Żurek J, Allemann RK, Mulholland AJ.
Biochemistry, (2013), vol 52, pp 8094-8105
http://pubs.acs.org/doi/abs/10.1021/bi400898k

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis.
Luk LY, Javier Ruiz-Pernía J, Dawson WM, Roca M, Loveridge EJ, Glowacki DR, Harvey JN, Mulholland AJ, Tuñón I, Moliner V, Allemann RK.
Proc. Natl. Acad. Sci. USA. 2013 Sep 24.
http://dx.doi.org/10.1073/pnas.1312437110

QM/MM Modeling of Regioselectivity of Drug Metabolism in Cytochrome P450 2C9
Lonsdale R, Houghton KT, Zurek J, Bathelt CM, Foloppe N, de Groot MJ, Harvey JN, Mulholland AJ.
J. Am. Chem. Soc., (2013), vol. 135, pp 8001–8015
http://dx.doi.org/10.1021/ja402016p

Non-Empirical Energetic Analysis of Reactivity and Covalent Inhibition of Fatty Acid Amide Hydrolase
Chudyk EI, Dyguda-Kazimierowicz E, Langner KM, Sokalski WA, Lodola A, Mor M, Sirirak J, Mulholland AJ
J. Phys. Chem. B, (2013), vol. 117, pp 6656-6666
http://dx.doi.org/10.1021/jp401834v

Quantum mechanics/molecular mechanics modeling of fatty acid amide hydrolase reactivation distinguishes substrate from irreversible covalent inhibitors.
Lodola A, Capoferri L, Rivara S, Tarzia G, Piomelli D, Mulholland AJ, Mor M.
J. Med. Chem., (2013) vol. 56, pp. 2500-12
http://dx.doi.org/10.1021/jm301867x

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology.
van der Kamp MW, Mulholland AJ
Biochemistry, (2013), vol. 52, pp. 2708-2728
http://dx.doi.org/10.1021/bi400215w

Conformational Effects on the pro-S Hydrogen Abstraction Reaction in Cyclooxygenase-1: An Integrated QM/MM and MD Study.
Christov CZ, Lodola A, Karabencheva-Christova TG, Wan S, Coveney PV, Mulholland AJ.
Biophys J. (2013) vol. 104, pp.L5-7.
http://dx.doi.org/10.1016/j.bpj.2013.01.040

QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis.
van der Kamp MW, Chaudret R, Mulholland AJ.
FEBS J., (2013), vol. 280, pp. 3120-3131
http://dx.doi.org/10.1111/febs.12158

Computational enzymology
Lodola A, Mulholland AJ
Methods Mol. Biol., (2013), vol. 924, pp. 67-89
http://www.ncbi.nlm.nih.gov/pubmed/23034746

2012

Protein dynamics and enzyme catalysis: the ghost in the machine?
Glowacki DR, Harvey JN, Mulholland AJ
Biochem. Soc. Trans., (2012), vol. 40, pp. 515-521

The Basis for Carbapenem Hydrolysis by Class A Beta-Lactamases: A Combined Investigation using Crystallography and Simulations
Fonseca F, Chudyk EI, van der Kamp MW, Correia A, Mulholland AJ, Spencer J
J. Am. Chem. Soc., (2012), vol. 134, pp. 18275-18285
http://dx.doi.org/10.1021/ja304460j

Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions
Lonsdale R, Harvey JN, Mulholland AJ
J. Chem. Theory Comput., (2012), vol. 8, pp. 4637-4645
http://dx.doi.org/10.1021/ct300329h

Long Time Scale GPU Dynamics Reveal the Mechanism of Drug Resistance of the Dual Mutant I223R/H275Y Neuraminidase from h2N1-2009 Influenza Virus
Woods CJ, Malaisree M, Pattarapongdilok N, Sompornpisut P, Hannongbua S, Mulholland AJ
Biochemistry, (2012), vol. 51, pp 4364-4375
ttp://dx.doi.org/10.1021/bi300561n

Insights into conformational changes of procarboxypeptidase A and B from simulations: a plausible explanation for different intrinsic activity
Jitonnom J, Mulholland AJ
Theor. Chem. Account. (2012), vol. 131, pp. 1224-1229
http://dx.doi.org/10.1007/s00214-012-1224-9

Taking Ockham’s razor to enzyme dynamics and catalysis
Glowacki DR, Harvey JN, Mulholland AJ
Nature Chemistry (2012), vol. 4, pp. 169-176
http://dx.doi.org/10.1038/nchem.1244

Determinants of Reactivity and Selectivity in Soluble Epoxide Hydrolase from QM/MM Modeling
Lonsdale R, Hoyle S, Grey DT, Ridder L, Mulholland AJ
Biochemistry (2012), vol. 51, pp. 1774-1786
http://dx.doi.org/10.1021/bi201722j

A practical guide to modelling enzyme-catalysed reactions
Lonsdale R, Harvey JN, Mulholland AJ
Chem. Soc. Rev. (2012), vol. 41, pp. 3025-3038
http://dx.doi.org/10.1039/C2CS15297E

Mechanism of C-terminal intein cleavage in protein splicing from QM/MM molecular dynamics simulations
Mujika JI, Lopez X, Mulholland AJ
Org. Biomol. Chem. (2012), vol. 10, pp. 1207-1218
http://dx.doi.org/10.1039/C1OB06444D

2011

QM/MM Studies of Cytochrome P450 Systems: Application to Drug Metabolism
Lonsdale R, Harvey JN, Mulholland AJ
Iron-Containing Enzymes: Versatile Catalysts of Hydroxylation Reactions in Nature, (2011) pp. 366-399
http://dx.doi.org/10.1039/9781849732987-00366

Does Compound I Vary Significantly between Isoforms of Cytochrome P450?
Lonsdale R, Olah J, Mulholland AJ, Harvey JN
J. Am. Chem. Soc. (2011), vol. 133, pp. 15464-15474
http://pubs.acs.org/doi/abs/10.1021/ja203157u

“Lethal Synthesis” of Fluorocitrate by Citrate Synthase Explained through QM/MM Modeling.
van der Kamp MW, McGeagh JD, Mulholland AJ.
Angew. Chem. Int. Ed. Engl. (2011), vol. 50, pp. 10349-10351
http://dx.doi.org/10.1002/anie.201103260

Quantum Mechanics/Molecular Mechanics Modeling of Substrate-Assisted Catalysis in Family 18 Chitinases: Conformational Changes and the Role of Asp142 in Catalysis in ChiB.
Jitonnom J, Lee VS, Nimmanpipug P, Rowlands HA, Mulholland AJ.
Biochemistry (2011), vol. 50, pp. 4697
http://dx.doi.org/10.1021/bi101362g

Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450.
Olah J, Mulholland AJ, Harvey JN.
Proc. Natl. Acad. Sci. USA (2011), vol. 108, pp. 6050
http://dx.doi.org/10.1073/pnas.1010194108

Application of a SCC-DFTB QM/MM approach to the investigation of the catalytic mechanism of fatty acid amide hydrolase.
Capoferri L, Mor M, Sirirak J, Chudyk E, Mulholland AJ, Lodola A.
J Mol Model. (2011), vol. 17, pp. 2375
http://dx.doi.org/10.1007/s00894-011-0981-z

Protein dynamics and enzyme catalysis: insights from simulations
McGeagh JD, Ranaghan KE, Mulholland AJ
Biochim. Biophys. Acta (2011), vol. 1814, pp. 1077
http://www.sciencedirect.com/science/article/pii/S1570963910003134

Hybrid QM/MM study on the deglycosylation step of chitin hydrolysis catalysed by chitinase B from Serratia marcescens
Jitonnom J, Mulholland AJ, Nimmanpipug P, Lee VS
Maejo Int. J. Sci. Technol. (2011), vol. 5, pp. 47
http://www.mijst.mju.ac.th/vol5/

Understanding the role of carbamate reactivity in fatty acid amide hydrolase inhibition by QM/MM mechanistic modelling
Lodola A, Capoferri L, Rivara S, Chudyk E, Sirirak J, Dyguda-Kazimierowicz E, Sokalski WA, Mileni M, Tarzia G, Piomelli D, Mor M, Mulholland AJ
Chem. Commun. (2011) vol. 47, pp. 2517
http://dx.doi.org/10.1039/C0CC04937A

Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions
Claeyssens F, Ranaghan KE, Lawan N, Macrae SJ, Manby FR, Harvey JN, Mulholland AJ
Org. Biomol. Chem. (2011) vol. 9, pp. 1578
http://dx.doi.org/10.1039/C0OB00691B

A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies
Woods CJ, Malaisree M, Hannongbua S, Mulholland AJ
J. Chem. Phys. (2011) vol. 134, pp. 054114
http://dx.doi.org/10.1063/1.3519057

Comment on “A stationary-wave model of enzyme catalysis” by Carlo Canepa.
Lonsdale R, Harvey JN, Manby FR, Mulholland AJ
J. Comput. Chem. (2011) vol. 32, pp. 368-369
http://dx.doi.org/10.1002/jcc.21618

2010

Enzyme Dynamics and Catalysis: Insights from Simulations
McGeagh JD, Mulholland AJ
Kinetics and Dynamics
Challenges and Advances in Computational Chemistry and Physics (2010) vol.12, pp. 375-395
http://www.springerlink.com/content/x24g0470541540m1/

QM and QM/MM Approaches to Evaluating Binding Affinities.
Shaw KE, Woods CJ, Mulholland AJ
Burger’s Medicinal Chemistry, Drug Discovery and Development. 2010
http://dx.doi.org/10.1002/0471266949.bmc143

Inclusion of Dispersion Effects Significantly Improves Accuracy of Calculated Reaction Barriers for Cytochrome P450 Catalyzed Reactions.
Lonsdale R, Harvey JN, Mulholland AJ
J. Phys. Chem. Lett. (2010) vol. 1 pp. 3232-3237
http://dx.doi.org/10.1021/jz101279n

Testing High-Level QM/MM Methods for Modeling Enzyme Reactions: Acetyl-CoA Deprotonation in Citrate Synthase.
van der Kamp MW, Zurek J, Manby FR, Harvey JN, Mulholland AJ
J. Phys. Chem. B (2010) vol. 114 pp. 11303-11314
http://dx.doi.org/10.1021/jp104069t 

Structural Fluctuations in Enzyme-Catalyzed Reactions: Determinants of Reactivity in Fatty Acid Amide Hydrolase from Multivariate Statistical Analysis of Quantum Mechanics/Molecular Mechanics Paths.
Lodola A, Sirirak J, Fey N, Rivara S, Mor M, Mulholland AJ
J. Chem. Theor. Comput. (2010) vol. 6 pp. 2948-2960
http://pubs.acs.org/doi/abs/10.1021/ct100264j

Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics/Molecular Mechanics Liquid Water Simulations.
Shaw KE, Woods CJ, Mulholland AJ.
J. Phys. Chem. Lett. (2010) vol. 1 (1) pp. 219-223
http://dx.doi.org/10.1021/jz900096p

Optimal control design of laser pulses for mode specific vibrational excitation in an enzyme-substrate complex
Ren Q, Ranaghan KE, Mulholland AJ, Harvey JN, Manby FR, Balint-Kurti GG.
Chem. Phys. Lett. (2010) vol. 491 (4-6) pp. 230-236
http://dx.doi.org/10.1016/j.cplett.2010.03.089

Computer simulations of quantum tunnelling in enzyme-catalysed hydrogen transfer reactions.
Ranaghan KE, Mulholland AJ.
Interdiscip. Sci. Comput. Life Sci. (2010) vol. 2 (1) pp. 78-97
http://dx.doi.org/10.1007/s12539-010-0093-y

Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods.
Ranaghan KE, Mulholland AJ.
Int. Rev. Phys. Chem. (2010) vol. 29 (1) pp. 65-133
http://www.informaworld.com/smpp/content~db=all~content=a918979200

Computational enzymology.
Lonsdale R, Ranaghan KE, Mulholland AJ.
Chem. Commun. (2010) vol. 46 (14) pp. 2354
http://www.rsc.org/Publishing/Journals/CC/article.asp?doi=b925647d

Compound I Reactivity Defines Alkene Oxidation Selectivity in Cytochrome P450cam.
Lonsdale R, Harvey JN, Mulholland AJ.
J. Phys. Chem. B (2010) vol. 114 (2) pp. 1156-62
http://pubs.acs.org/doi/abs/10.1021/jp910127j

2009

Computational Methods: Modeling of Reactivity in Zn-Containing Enzymes
Mujika JI, Mulholland AJ, Harvey JN
Encylopedia of Inorganic Chemistry
http://dx.doi.org/10.1002/0470862106.ia627

Computational Methods: Modeling of Reactivity in Zn-Containing Enzymes
Mujika JI, Mulholland AJ, Harvey JN
in Computational Inorganic and Bioinorganic Chemistry, edited by E. I. Solomon, R. A. Scott and R. B. King, Chichester, UK: John Wiley and Sons, Ltd., 2009, pp. 343-352.
http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470699973.html

QM/MM study on the mechanism of peptide hydrolysis by carboxypeptidase A.
Szeto MWY, Mujika JI, Zurek J, Mulholland AJ, Harvey JN.
Theochem (2009) vol. 898 (1-3) pp. 106-114
http://dx.doi.org/10.1016/j.theochem.2008.06.033

Lennard-Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid Bases.
Pentikainen U, Shaw KE, Senthilkumar K, Woods CJ, Mulholland AJ.
J. Chem. Theory. Comput. (2009) vol. 5 (2) pp. 396-410
http://dx.doi.org/10.1021/ct800135k

High Level QM/MM Modeling of the Formation of the Tetrahedral Intermediate in the Acylation of Wild Type and K73A Mutant TEM-1 Class A beta-Lactamase.
Hermann JC, Pradon J, Harvey JN, Mulholland AJ.
J. Phys. Chem. A (2009) vol. 113 (43) pp. 11984-11994
http://dx.doi.org/10.1021/jp9037254

Modeling Protein Splicing: Reaction Pathway for C-Terminal Splice and Intein Scission.
Mujika JI, Lopez X, Mulholland AJ.
J. Phys. Chem. B (2009) vol. 113 (16) pp. 5607-5616
http://dx.doi.org/10.1021/jp808911p

Insights into the mechanism and inhibition of fatty acid amide hydrolase from quantum mechanics/molecular mechanics (QM/MM) modelling.
Lodola A, Mor M, Sirirak J, Mulholland AJ.
Biochem. Soc. Trans. (2009) vol. 37 pp. 363-367
http://dx.doi.org/10.1042/BST0370363

2008

Multiscale modelling of biological systems
Woods CJ, Mulholland AJ
Royal Society of Chemistry Special Periodicals Review: Chemical Modelling: Application and Theory, Ed. Hinchliffe A., 5, 13-50, 2008
http://dx.doi.org/10.1039/b608778g

Applications and Advances of QM/MM Methods in Computational Enzymology.
Lodola A, Woods CJ, Mulholland AJ.
In: Ralph A. Wheeler and David C. Spellmeyer, editors, Annual Reports in Computational Chemistry, Volume 4.
Amsterdam: Elsevier, 2008, p. 155
ISBN: 978-0-444-53250-3

QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate.
Bowman AL, Grant IM, Mulholland AJ.
Chem. Commun. (2008) (37) pp. 4425-4427
http://dx.doi.org/10.1039/b810099c

High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase.
van der Kamp MW, Perruccio F, Mulholland AJ.
Chem. Commun. (2008) (16) pp. 1874-1876
http://dx.doi.org/10.1039/b800496j

Identification of productive inhibitor binding orientation in fatty acid amide hydrolase (FAAH) by QM/MM mechanistic modelling.
Lodola A, Mor M, Rivara S, Christov C, Tarzia G, Piomelli D, Mulholland AJ.
Chem. Commun. (2008) (2) pp. 214-216
http://dx.doi.org/10.1039/b714136j

Computational and experimental studies on the catalytic mechanism of biliverdin-IX beta reductase.
Smith LJ, Browne S, Mulholland AJ, Mantle TJ.
Biochem. J. (2008) vol. 411 pp. 475-484
http://dx.doi.org/10.1042/BJ20071495

Introduction. Biomolecular simulation.
Mulholland AJ
J. R. Soc. Interface (2008) vol. 5 pp. S169-S172
http://dx.doi.org/10.1098/rsif.2008.0385.focus

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies.
Woods CJ, Manby FR, Mulholland AJ.
J. Chem. Phys. (2008) vol. 128 (1) pp. 014109
http://dx.doi.org/10.1063/1.2805379

Computational enzymology: modelling the mechanisms of biological catalysts.
Mulholland AJ.
Biochem. Soc. Trans. (2008) vol. 36 pp. 22-26
http://dx.doi.org/10.1042/BST0360022

QM/MM Modeling of Benzene Hydroxylation in Human Cytochrome P450 2C9.
Bathelt CM, Mulholland AJ, Harvey JN.
J. Phys. Chem. A (2008) vol. 112 (50) pp. 13149-13156
http://dx.doi.org/10.1021/jp8016908

Biomolecular simulation and modelling: status, progress and prospects.
van der Kamp MW, Shaw KE, Woods CJ, Mulholland AJ.
J. R. Soc. Interface (2008) vol. 5 pp. S173-S190
http://dx.doi.org/10.1098/rsif.2008.0105.focus

Computational enzymology: insight into biological catalysts from modelling.
van der Kamp MW, Mulholland AJ.
Nat. Prod. Rep. (2008) vol. 25 (6) pp. 1001-1014
http://dx.doi.org/10.1039/b600517a

Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds.
Senthilkumar K, Mujika JI, Ranaghan KE, Manby FR, Mulholland AJ, Harvey JN.
J. R. Soc. Interface (2008) vol. 5 pp. S207-S216
http://dx.doi.org/10.1098/rsif.2008.0243.focus

Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations.
Pentikaeinen U, Pentikaeinen OT, Mulholland AJ.
Proteins (2008) vol. 70 (2) pp. 498-508
http://dx.doi.org/10.1002/prot.21540

2007

Computational Enzymology: Insights into Enzyme Mechanism and Catalysis from Modelling
Mulholland AJ, Grant IM
Chapter 5 in Molecular Materials with Specific Interactions – Modeling and Design
Challenges and Advances in Computational Chemistry and Physics, (2007), vol. 4, pp. 275-304
<http://www.springerlink.com/content/k776wn0n455788x1/>

Analysis of classical and quantum paths for deprotonation of methylamine by methylamine dehydrogenase.
Ranaghan KE, Masgrau L, Scrutton NS, Sutcliffe MJ, Mulholland AJ.
Chemphyschem (2007) vol. 8 (12) pp. 1816-1835
http://dx.doi.org/10.1002/cphc.200700143

Conformational effects in enzyme catalysis: Reaction via a high energy conformation in fatty acid amide hydrolase.
Lodola A, Mor M, Zurek J, Tarzia G, Piomelli D, Harvey JN, Mulholland AJ.
Biophys. J. (2007) vol. 92 (2) pp. L20-L22
http://dx.doi.org/10.1529/biophysj.106.098434

Tunneling and classical paths for proton transfer in an enzyme reaction dominated by tunneling: Oxidation of tryptamine by aromatic amine dehydrogenase.
Masgrau L, Ranaghan KE, Scrutton NS, Mulholland AJ, Sutcliffe MJ.
J. Phys. Chem. B (2007) vol. 111 (11) pp. 3032-3047
http://dx.doi.org/10.1021/jp067898k

Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions.
Mulholland AJ.
Chem. Cent. J. (2007) vol. 1 pp. 19
http://dx.doi.org/10.1186/1752-153X-1-19

Quantum chemical analysis of reaction paths in chorismate mutase: Conformational effects and electrostatic stabilization.
Szefczyk B, Claeyssens F, Mulholland AJ, Sokalski WA.
Int. J. Quantum Chem. (2007) vol. 107 (12) pp. 2274-2285
http://dx.doi.org/10.1002/qua.21354

Molecular determinants of xenobiotic metabolism: QM/MM simulation of the conversion of 1-chloro-2,4-dinitrobenzene catalyzed by M1-1 glutathione S-transferase.
Bowman AL, Ridder L, Rietjens IMCM, Vervoort J, Mulholland AJ.
Biochemistry (2007) vol. 46 (21) pp. 6353-6363
http://dx.doi.org/10.1021/bi0622827

Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase.
van der Kamp MW, Perruccio F, Mulholland AJ.
J. Mol. Graphics Modell. (2007) vol. 26 (3) pp. 676-690
http://dx.doi.org/10.1016/j.jmgm.2007.04.002

Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex.
Rungrotmongkol T, Mulholland AJ, Hannongbua S.
J. Mol. Graphics Modell. (2007) vol. 26 (1) pp. 1-13
http://dx.doi.org/10.1016/j.jmgm.2006.09.004

Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl-CoA enolization in citrate synthase.
van der Kamp MW, Perruccio F, Mulholland AJ.
Proteins (2007) vol. 69 (3) pp. 521-535
http://dx.doi.org/10.1002/prot.21482

Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate.
Rodriguez A, Oliva C, Gonzalez M, van der Kamp MW, Mulholland AJ.
J. Phys. Chem. B (2007) vol. 111 (44) pp. 12909-12915
http://dx.doi.org/10.1021/jp0743469

2006

Simulating Enzyme-Catalyzed Reactions
Bowman AL, Mulholland AJ.
Chapter 7, pp. 305-359 in Handbook of Theoretical and Computational Nanotechnology,
Vol. 6, M. Rieth and W. Schommers, Eds.
American Scientific Publishers, 2006.
http://www.aspbs.com/tcn.html

Modelling Biological Systems
Mulholland AJ.
Chem. Modell. (2006) vol. 4, pp. 23-68
Chemical Modelling: Applications and Theory, Volume 4
RSC Specialist Periodicals Reports, 2006
A. Hinchliffe, Ed. RSC 2006.
http://www.rsc.org/publishing/ebooks/2006/9780854042432.asp

High-accuracy computation of reaction barriers in enzymes.
Claeyssens F, Harvey JN, Manby FR, Mata RA, Mulholland AJ, Ranaghan KE, Schutz M, Thiel S, Thiel W, Werner HJ.
Angew. Chem. Int. Ed. (2006) vol. 45 (41) pp. 6856-9
http://dx.doi.org/10.1002/anie.200602711

QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase.
Harvey JN, Bathelt CM, Mulholland AJ.
J. Comput. Chem. (2006) vol. 27 (12) pp. 1352-1362
http://dx.doi.org/10.1002/jcc.20446

QM and QM/MM studies of selectivity in organic and bioorganic chemistry.
Harvey JN, Aggarwal VK, Bathelt CM, Carreon-Macedo JL, Gallagher T, Holzmann N, Mulholland AJ, Robiette R.
J. Phys. Org. Chem. (2006) vol. 19 (8-9) pp. 608-615
http://dx.doi.org/10.1002/poc.1030

The Fe-CO bond energy in myoglobin: a QM/MM study of the effect of tertiary structure.
Strickland N, Mulholland AJ, Harvey JN.
Biophys. J. (2006) vol. 90 (4) pp. L27-9
http://dx.doi.org/10.1529/biophysj.105.078097

Mechanisms of reaction in cytochrome P450: hydroxylation of camphor in P450cam.
Zurek J, Foloppe N, Harvey JN, Mulholland AJ.
Org. Biomol. Chem. (2006) vol. 4 (21) pp. 3931-3937
http://dx.doi.org/10.1039/b611653a

Atomic description of an enzyme reaction dominated by proton tunneling.
Masgrau L, Roujeinikova A, Johannissen LO, Hothi P, Basran J, Ranaghan KE, Mulholland AJ, Sutcliffe MJ, Scrutton NS, Leys D.
Science (2006) vol. 312 (5771) pp. 237-241
http://dx.doi.org/10.1126/science.1126002

Molecular mechanisms of antibiotic resistance: QM/MM modelling of deacylation in a class A beta-lactamase.
Hermann JC, Ridder L, Hotje HD, Mulholland AJ.
Org. Biomol. Chem. (2006) vol. 4 (2) pp. 206-210
http://dx.doi.org/10.1039/b512969a

Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: flavoprotein and quinoprotein systems.
Sutcliffe MJ, Masgrau L, Roujeinikova A, Johannissen LO, Hothi P, Basran J, Ranaghan KE, Mulholland AJ, Leys D, Scrutton NS.
Philos. Trans. R. Soc B. (2006) vol. 361 (1472) pp. 1375-1386
http://dx.doi.org/10.1098/rstb.2006.1878

2005

QM/MM studies of the electronic structure of the compound I intermediate in cytochrome c peroxidase and ascorbate peroxidase.
Bathelt CM, Mulholland AJ, Harvey JN.
Dalton Trans. (2005) (21) pp. 3470-6
http://pubs.rsc.org/en/content/articlelanding/2005/dt/b505407a

QM/MM modelling of oleamide hydrolysis in fatty acid amide hydrolase (FAAH) reveals a new mechanism of nucleophile activation.
Lodola A, Mor M, Hermann JC, Tarzia G, Piomelli D, Mulholland AJ.
Chem. Commun. (2005) (35) pp. 4399-4401
http://dx.doi.org/10.1039/b503887a

Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization.
Claeyssens F, Ranaghan KE, Manby FR, Harvey JN, Mulholland AJ.
Chem. Commun. (2005) (40) pp. 5068-5070
http://dx.doi.org/10.1039/b508181e

Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling.
Bathelt CM, Zurek J, Mulholland AJ, Harvey JN.
J. Am. Chem. Soc. (2005) vol. 127 (37) pp. 12900-12908
http://dx.doi.org/10.1021/ja0520924

Mechanisms of antibiotic resistance: QM/MM modeling of the acylation reaction of a class A beta-lactamase with benzylpenicillin.
Hermann JC, Hensen C, Ridder L, Mulholland AJ, Holtje HD.
J. Am. Chem. Soc. (2005) vol. 127 (12) pp. 4454-4465
http://dx.doi.org/10.1021/ja044210d

Modelling enzyme reaction mechanisms, specificity and catalysis.
Mulholland AJ.
Drug discovery today (2005) vol. 10 (20) pp. 1393-1402
http://dx.doi.org/10.1016/S1359-6446(05)03611-1

2004

Mechanism and structure-reactivity relationships for aromatic hydroxylation by cytochrome P450.
Bathelt CM, Ridder L, Mulholland AJ, Harvey JN.
Org. Biomol. Chem. (2004) vol. 2 (20) pp. 2998-3005
http://www.rsc.org/publishing/journals/OB/article.asp?doi=b410729b

Conformational effects in enzyme catalysis: QM/MM free energy calculation of the ‘NAC’ contribution in chorismate mutase.
Ranaghan KE, Mulholland AJ.
Chem. Commun. (2004) (10) pp. 1238-1239
http://dx.doi.org/10.1039/b402388a

Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.
Ranaghan KE, Ridder L, Szefczyk B, Sokalski WA, Hermann JC, Mulholland AJ.
Org. Biomol. Chem. (2004) vol. 2 (7) pp. 968-980
http://dx.doi.org/10.1039/b313759g

Differential transition-state stabilization in enzyme catalysis: Quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field.
Szefczyk B, Mulholland AJ, Ranaghan KE, Sokalski WA.
J. Am. Chem. Soc. (2004) vol. 126 (49) pp. 16148-16159
http://dx.doi.org/10.1021/ja049376t

MM and QM/MM modeling of threonyl-tRNA synthetase: Model testing and simulations.
Zurek J, Bowman AL, Sokalski WA, Mulholland AJ.
Struct. Chem. (2004) vol. 15 (5) pp. 405-414
http://dx.doi.org/10.1023/B:STUC.0000037896.80027.2c

2003

Quantum-mechanical/Molecular-mechanical Methods in Medicinal Chemistry
Perruccio F, Ridder L, Mulholland AJ
Chapter 6, pp. 177-198 in ‘Quantum Medicinal Chemistry’, P. Carloni & F. Alber, Eds., Wiley-VCH, Weinheim (2003).

Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: From structure to activity.
Ridder L, Mulholland AJ.
Curr. Top. Med. Chem. (2003) vol. 3 (11) pp. 1241-1256
http://www.ingentaconnect.com/content/ben/ctmc/2003/00000003/00000011/art00005

Aromatic hydroxylation by cytochrome P450: Model calculations of mechanism and substituent effects.
Bathelt CM, Ridder L, Mulholland AJ, Harvey JN.
J. Am. Chem. Soc. (2003) vol. 125 (49) pp. 15004-15005
http://dx.doi.org/10.1021/ja035590q

Ab initio QM/MM modeling of the hydroxylation step in p-hydroxybenzoate hydroxylase.
Ridder L, Harvey JN, Rietjens IMCM, Vervoort J, Mulholland AJ.
J. Phys. Chem. B (2003) vol. 107 (9) pp. 2118-2126
http://dx.doi.org/10.1021/jp026213n

Insights into enzyme catalysis from QM/MM modelling: transition state stabilization in chorismate mutase.
Ranaghan KE, Ridder L, Szefczyk B, Sokalski WA, Hermann JC, Mulholland AJ.
Mol. Phys. (2003) vol. 101 (17) pp. 2695-2714
http://dx.doi.org/10.1080/00268970310001593286

Identification of Glu166 as the general base in the acylation reaction of class A beta-lactamases through QM/MM modeling.
Hermann JC, Ridder L, Mulholland AJ, Holtje HD.
J. Am. Chem. Soc. (2003) vol. 125 (32) pp. 9590-9591
http://dx.doi.org/10.1021/ja034434g

2002 and earlier

Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide.
Ridder L, Rietjens IMCM, Vervoort J, Mulholland AJ.
J. Am. Chem. Soc. (2002) vol. 124 (33) pp. 9926-9936
http://dx.doi.org/10.1021/ja0256360

The QM/MM Approach to Enzymatic Reactions
Mulholland AJ.
Chapter 14, pp. 597-653 in ‘Theoretical Biochemistry’, L.A. Erikkson, Ed., Elsevier, Amsterdam (2001).

A quantum mechanical/molecular mechanical study of the hydroxylation of phenol and halogenated derivatives by phenol hydroxylase.
Ridder L, Mulholland AJ, Rietjens IMCM, Vervoort J.
J. Am. Chem. Soc. (2000) vol. 122 (36) pp. 8728-8738
http://dx.doi.org/10.1021/ja0007814

Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved.
Mulholland AJ, Lyne PD, Karplus M.
J. Am. Chem. Soc. (2000) vol. 122 (3) pp. 534-535
http://dx.doi.org/10.1021/ja992874v

Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase.
Ridder L, Mulholland AJ, Rietjens IMCM, Vervoort J.
J. Mol. Graphics Model. (1999) vol. 17 (3-4) pp. 163
http://dx.doi.org/10.1016/S1093-3263(99)00027-3

Active-site dynamics of ASADH – A bacterial biosynthetic enzyme.
Hadfield AT, Mulholland AJ.
Int. J. Quantum Chem. (1999) vol. 73 (2) pp. 137-146
http://www3.interscience.wiley.com/journal/55003512/abstract

Modeling the Citrate Synthase Reaction: QM/MM and Small Model Calculations
Mulholland AJ, Richards WG.
Transition State Modeling for Catalysis, Chapter 35, 1999, pp 448-461
ACS Symposium Series, Volume 721
DOI: 10.1021/bk-1999-0721.ch035

Calculations on the substrates of citrate synthase – I. Oxaloacetate.
Mulholland AJ, Richards WG.
Theochem (1998) vol. 429 pp. 13-21
http://dx.doi.org/10.1016/S0166-1280(97)00294-7

A model of the condensation step in the citrate synthase reaction.
Mulholland AJ, Richards WG.
Theochem (1998) vol. 427 pp. 175-184
http://dx.doi.org/10.1016/S0166-1280(97)00200-5

Correlation of calculated activation energies with experimental rate constants for an enzyme catalyzed aromatic hydroxylation.
Ridder L, Mulholland AJ, Vervoort J, Rietjens IMCM.
J. Am. Chem. Soc. (1998) vol. 120 (30) pp. 7641-7642
http://dx.doi.org/10.1021/ja980639r

Modeling enzyme reaction intermediates and transition states: Citrate synthase.
Mulholland AJ, Richards WG.
J. Phys. Chem. B (1998) vol. 102 (34) pp. 6635-6646
http://dx.doi.org/10.1021/jp981121c

Acetyl-CoA enolization in citrate synthase: A quantum mechanical molecular mechanical (QM/MM) study.
Mulholland AJ, Richards WG.
Proteins (1997) vol. 27 (1) pp. 9-25
http://dx.doi.org/10.1002/(SICI)1097-0134(199701)27:13.0.CO;2-D

Combined quantum and molecular mechanical study of DNA cross-linking by nitrous-acid.
Elcock AH, Lyne PD, Mulholland AJ, Nandra A, Richards WG.
J. Am. Chem. Soc. (1995) vol. 117 (16) pp. 4706-4707
http://dx.doi.org/10.1021/ja00121a029

Insights into chorismate mutase catalysis from a combined QM/MM simulation of the enzyme reaction.
Lyne PD, Mulholland AJ, Richards WG.
J. Am. Chem. Soc. (1995) vol. 117 (45) pp. 11345-11350
http://dx.doi.org/10.1021/ja00150a037

A comparison of semiempirical and ab initio transition states for HF elimination in unimolecular decompositions.
Mulholland AJ, Richards WG.
Int. J. Quantum Chem. (1994) vol. 51 (3) pp. 161-172
http://dx.doi.org/10.1002/qua.560510306

Computer modelling of enzyme catalysed reaction mechanisms.
Mulholland AJ, Grant GH, Richards WG.
Protein Eng. (1993) vol. 6 (2) pp. 133-147
http://dx.doi.org/10.1093/protein/6.2.133

The calculation of product quantum state distributions and partial cross-sections in time-dependent molecular collision and photodissociation theory.
Balint-Kurti GG, Dixon RN, Marston CC, Mulholland AJ
Computer Physics Communications (1991) vol. 63 pp. 126-134
http://dx.doi.org/10.1016/0010-4655(91)90244-F