Publications
2013
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 Jan 29 [Epub ahead of print]
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
http://dx.doi.org/10.1042/BST20120047
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 H1N1-2009 Influenza Virus
Woods CJ, Malaisree M, Pattarapongdilok N, Sompornpisut P, Hannongbua S, Mulholland AJ
Biochemistry, (2012), vol. 51, pp 4364-4375
http://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.
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)27:1<9::AID-PROT3>3.0.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
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