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Items: 1 to 50 of 140

1.

Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case.

Liao Q, Kulkarni Y, Sengupta U, Petrović D, Mulholland AJ, van der Kamp MW, Strodel B, Kamerlin SCL.

J Am Chem Soc. 2018 Nov 21;140(46):15889-15903. doi: 10.1021/jacs.8b09378. Epub 2018 Nov 8.

PMID:
30362343
2.

QM/MM Simulations Show Saccharide Distortion is Required for Reaction in Hen Egg-White Lysozyme.

Limb MAL, Suardiaz R, Grant IM, Mulholland AJ.

Chemistry. 2018 Oct 22. doi: 10.1002/chem.201805250. [Epub ahead of print]

PMID:
30347479
3.

Maintaining and breaking symmetry in homomeric coiled-coil assemblies.

Rhys GG, Wood CW, Lang EJM, Mulholland AJ, Brady RL, Thomson AR, Woolfson DN.

Nat Commun. 2018 Oct 8;9(1):4132. doi: 10.1038/s41467-018-06391-y.

4.

Broadband 1-3 Piezoelectric Composite Transducer Design using Sierpinski Gasket Fractal Geometry.

Fang H, Qiu Z, Mulholland AJ, OrLeary RL, Gachagan A.

IEEE Trans Ultrason Ferroelectr Freq Control. 2018 Oct 8. doi: 10.1109/TUFFC.2018.2874384. [Epub ahead of print]

PMID:
30296221
5.

A Multiscale Simulation Approach to Modeling Drug-Protein Binding Kinetics.

Haldar S, Comitani F, Saladino G, Woods C, van der Kamp MW, Mulholland AJ, Gervasio FL.

J Chem Theory Comput. 2018 Nov 13;14(11):6093-6101. doi: 10.1021/acs.jctc.8b00687. Epub 2018 Oct 2.

PMID:
30208708
6.

Combined Quantum Mechanics and Molecular Mechanics Studies of Enzymatic Reaction Mechanisms.

Ainsley J, Lodola A, Mulholland AJ, Christov CZ, Karabencheva-Christova TG.

Adv Protein Chem Struct Biol. 2018;113:1-32. doi: 10.1016/bs.apcsb.2018.07.001. Epub 2018 Aug 13.

PMID:
30149903
7.

"Pipe Organ" Inspired Air-Coupled Ultrasonic Transducers With Broader Bandwidth.

Zhu B, Tiller BP, Walker AJ, Mulholland AJ, Windmill JFC.

IEEE Trans Ultrason Ferroelectr Freq Control. 2018 Oct;65(10):1873-1881. doi: 10.1109/TUFFC.2018.2861575. Epub 2018 Jul 31.

PMID:
30072320
8.

Sampling molecular conformations and dynamics in a multiuser virtual reality framework.

O'Connor M, Deeks HM, Dawn E, Metatla O, Roudaut A, Sutton M, Thomas LM, Glowacki BR, Sage R, Tew P, Wonnacott M, Bates P, Mulholland AJ, Glowacki DR.

Sci Adv. 2018 Jun 29;4(6):eaat2731. doi: 10.1126/sciadv.aat2731. eCollection 2018 Jun.

9.

De Novo-Designed α-Helical Barrels as Receptors for Small Molecules.

Thomas F, Dawson WM, Lang EJM, Burton AJ, Bartlett GJ, Rhys GG, Mulholland AJ, Woolfson DN.

ACS Synth Biol. 2018 Jul 20;7(7):1808-1816. doi: 10.1021/acssynbio.8b00225. Epub 2018 Jul 10.

PMID:
29944338
10.

Multiscale Simulations of Clavulanate Inhibition Identify the Reactive Complex in Class A β-Lactamases and Predict the Efficiency of Inhibition.

Fritz RA, Alzate-Morales JH, Spencer J, Mulholland AJ, van der Kamp MW.

Biochemistry. 2018 Jul 3;57(26):3560-3563. doi: 10.1021/acs.biochem.8b00480. Epub 2018 Jun 7.

PMID:
29812917
11.

QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes.

Lence E, van der Kamp MW, González-Bello C, Mulholland AJ.

Org Biomol Chem. 2018 Jun 20;16(24):4443-4455. doi: 10.1039/c8ob00066b.

12.

L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib.

Callegari D, Ranaghan KE, Woods CJ, Minari R, Tiseo M, Mor M, Mulholland AJ, Lodola A.

Chem Sci. 2018 Feb 12;9(10):2740-2749. doi: 10.1039/c7sc04761d. eCollection 2018 Mar 14.

13.

Dynamical origins of heat capacity changes in enzyme-catalysed reactions.

van der Kamp MW, Prentice EJ, Kraakman KL, Connolly M, Mulholland AJ, Arcus VL.

Nat Commun. 2018 Mar 21;9(1):1177. doi: 10.1038/s41467-018-03597-y.

14.

Biocatalytic Routes to Lactone Monomers for Polymer Production.

Messiha HL, Ahmed ST, Karuppiah V, Suardíaz R, Ascue Avalos GA, Fey N, Yeates S, Toogood HS, Mulholland AJ, Scrutton NS.

Biochemistry. 2018 Apr 3;57(13):1997-2008. doi: 10.1021/acs.biochem.8b00169. Epub 2018 Mar 22.

PMID:
29533655
15.

Multiscale analysis of enantioselectivity in enzyme-catalysed 'lethal synthesis' using projector-based embedding.

Zhang X, Bennie SJ, van der Kamp MW, Glowacki DR, Manby FR, Mulholland AJ.

R Soc Open Sci. 2018 Feb 14;5(2):171390. doi: 10.1098/rsos.171390. eCollection 2018 Feb.

16.

Mechanistic Insights into the Reaction of Chlorination of Tryptophan Catalyzed by Tryptophan 7-Halogenase.

Karabencheva-Christova TG, Torras J, Mulholland AJ, Lodola A, Christov CZ.

Sci Rep. 2017 Dec 12;7(1):17395. doi: 10.1038/s41598-017-17789-x.

17.

Quantum Mechanics/Molecular Mechanics Simulations Identify the Ring-Opening Mechanism of Creatininase.

Jitonnom J, Mujika JI, van der Kamp MW, Mulholland AJ.

Biochemistry. 2017 Dec 5;56(48):6377-6388. doi: 10.1021/acs.biochem.7b01032. Epub 2017 Nov 21.

PMID:
29140090
18.

Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations.

Ge Y, van der Kamp M, Malaisree M, Liu D, Liu Y, Mulholland AJ.

J Comput Aided Mol Des. 2017 Nov;31(11):995-1007. doi: 10.1007/s10822-017-0073-y. Epub 2017 Oct 9.

PMID:
28994029
19.

Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase.

Karuppiah V, Ranaghan KE, Leferink NGH, Johannissen LO, Shanmugam M, Ní Cheallaigh A, Bennett NJ, Kearsey LJ, Takano E, Gardiner JM, van der Kamp MW, Hay S, Mulholland AJ, Leys D, Scrutton NS.

ACS Catal. 2017 Sep 1;7(9):6268-6282. doi: 10.1021/acscatal.7b01924. Epub 2017 Aug 9.

20.

Ab Initio QM/MM Modeling of the Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic Amine Dehydrogenase.

Ranaghan KE, Morris WG, Masgrau L, Senthilkumar K, Johannissen LO, Scrutton NS, Harvey JN, Manby FR, Mulholland AJ.

J Phys Chem B. 2017 Oct 26;121(42):9785-9798. doi: 10.1021/acs.jpcb.7b06892. Epub 2017 Oct 17.

PMID:
28930453
21.

Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme.

Watkins DW, Jenkins JMX, Grayson KJ, Wood N, Steventon JW, Le Vay KK, Goodwin MI, Mullen AS, Bailey HJ, Crump MP, MacMillan F, Mulholland AJ, Cameron G, Sessions RB, Mann S, Anderson JLR.

Nat Commun. 2017 Aug 25;8(1):358. doi: 10.1038/s41467-017-00541-4.

22.

Rapid Estimation of Catalytic Efficiency by Cumulative Atomic Multipole Moments: Application to Ketosteroid Isomerase Mutants.

Beker W, van der Kamp MW, Mulholland AJ, Sokalski WA.

J Chem Theory Comput. 2017 Feb 14;13(2):945-955. doi: 10.1021/acs.jctc.6b01131. Epub 2017 Feb 2.

PMID:
28103023
23.

Insights into the Mechanistic Basis of Plasmid-Mediated Colistin Resistance from Crystal Structures of the Catalytic Domain of MCR-1.

Hinchliffe P, Yang QE, Portal E, Young T, Li H, Tooke CL, Carvalho MJ, Paterson NG, Brem J, Niumsup PR, Tansawai U, Lei L, Li M, Shen Z, Wang Y, Schofield CJ, Mulholland AJ, Shen J, Fey N, Walsh TR, Spencer J.

Sci Rep. 2017 Jan 6;7:39392. doi: 10.1038/srep39392.

24.

Non-adiabatic reactions: general discussion.

Althorpe SC, Ananth N, Angulo G, Astumian RD, Beniwal V, Blumberger J, Bolhuis PG, Ensing B, Glowacki DR, Habershon S, Hammes-Schiffer S, Hele TJ, Makri N, Manolopoulos DE, McKemmish LK, Miller TF III, Miller WH, Mulholland AJ, Nekipelova T, Pollak E, Richardson JO, Richter M, Roy Chowdhury P, Shalashilin D, Szabla R.

Faraday Discuss. 2016 Dec 22;195:311-344. doi: 10.1039/c6fd90078j. No abstract available.

PMID:
27929583
25.

The detection of flaws in austenitic welds using the decomposition of the time-reversal operator.

Cunningham LJ, Mulholland AJ, Tant KM, Gachagan A, Harvey G, Bird C.

Proc Math Phys Eng Sci. 2016 Apr;472(2188):20150500.

26.

Elucidation of Nonadditive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study.

Calabrò G, Woods CJ, Powlesland F, Mey AS, Mulholland AJ, Michel J.

J Phys Chem B. 2016 Jun 23;120(24):5340-50. doi: 10.1021/acs.jpcb.6b03296. Epub 2016 Jun 14.

PMID:
27248478
27.

A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase.

Bennie SJ, van der Kamp MW, Pennifold RC, Stella M, Manby FR, Mulholland AJ.

J Chem Theory Comput. 2016 Jun 14;12(6):2689-97. doi: 10.1021/acs.jctc.6b00285. Epub 2016 May 19.

28.

The Catalytic Mechanism of a Natural Diels-Alderase Revealed in Molecular Detail.

Byrne MJ, Lees NR, Han LC, van der Kamp MW, Mulholland AJ, Stach JE, Willis CL, Race PR.

J Am Chem Soc. 2016 May 18;138(19):6095-8. doi: 10.1021/jacs.6b00232. Epub 2016 May 6.

PMID:
27140661
29.

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2.

Lonsdale R, Fort RM, Rydberg P, Harvey JN, Mulholland AJ.

Chem Res Toxicol. 2016 Jun 20;29(6):963-71. doi: 10.1021/acs.chemrestox.5b00514. Epub 2016 May 10.

PMID:
27064685
30.

Dispelling the effects of a sorceress in enzyme catalysis.

Mulholland AJ.

Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):2328-30. doi: 10.1073/pnas.1601276113. Epub 2016 Feb 16. No abstract available.

31.

On the Temperature Dependence of Enzyme-Catalyzed Rates.

Arcus VL, Prentice EJ, Hobbs JK, Mulholland AJ, Van der Kamp MW, Pudney CR, Parker EJ, Schipper LA.

Biochemistry. 2016 Mar 29;55(12):1681-8. doi: 10.1021/acs.biochem.5b01094. Epub 2016 Mar 8.

PMID:
26881922
32.

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 AJ, Hannongbua S.

J Chem Theory Comput. 2015 Feb 10;11(2):713-22. doi: 10.1021/ct5005033. Epub 2015 Jan 20.

PMID:
26579604
33.

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.

J Phys Chem Lett. 2014 Nov 6;5(21):3614-9. doi: 10.1021/jz5018703. Epub 2014 Oct 9.

PMID:
26278727
34.

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.

Wells SA, van der Kamp MW, McGeagh JD, Mulholland AJ.

PLoS One. 2015 Aug 4;10(8):e0133372. doi: 10.1371/journal.pone.0133372. eCollection 2015.

35.

A model-based approach to crack sizing with ultrasonic arrays.

Tant KM, Mulholland AJ, Gachagan A.

IEEE Trans Ultrason Ferroelectr Freq Control. 2015 May;62(5):915-26. doi: 10.1109/TUFFC.2014.006809.

PMID:
25965684
36.

A fractional Fourier transform analysis of the scattering of ultrasonic waves.

Tant KM, Mulholland AJ, Langer M, Gachagan A.

Proc Math Phys Eng Sci. 2015 Mar 8;471(2175):20140958.

37.

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

Gray A, Harlen OG, Harris SA, Khalid S, Leung YM, Lonsdale R, Mulholland AJ, Pearson AR, Read DJ, Richardson RA.

Acta Crystallogr D Biol Crystallogr. 2015 Jan 1;71(Pt 1):162-72. doi: 10.1107/S1399004714026777. Epub 2015 Jan 1.

38.

Rapid decomposition and visualisation of protein-ligand binding free energies by residue and by water.

Woods CJ, Malaisree M, Michel J, Long B, McIntosh-Smith S, Mulholland AJ.

Faraday Discuss. 2014;169:477-99. doi: 10.1039/c3fd00125c. Epub 2014 May 27.

PMID:
25340314
39.

Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

Woods CJ, Shaw KE, Mulholland AJ.

J Phys Chem B. 2015 Jan 22;119(3):997-1001. doi: 10.1021/jp506413j. Epub 2014 Nov 7.

PMID:
25340313
40.

QM/MM simulations as an assay for carbapenemase activity in class A β-lactamases.

Chudyk EI, Limb MA, Jones C, Spencer J, van der Kamp MW, Mulholland AJ.

Chem Commun (Camb). 2014 Dec 7;50(94):14736-9. doi: 10.1039/c4cc06495j.

PMID:
25321894
41.

A multiscale approach to modelling drug metabolism by membrane-bound cytochrome P450 enzymes.

Lonsdale R, Rouse SL, Sansom MS, Mulholland AJ.

PLoS Comput Biol. 2014 Jul 17;10(7):e1003714. doi: 10.1371/journal.pcbi.1003714. eCollection 2014 Jul.

42.

Trends in predicted chemoselectivity of cytochrome P450 oxidation: B3LYP barrier heights for epoxidation and hydroxylation reactions.

Rydberg P, Lonsdale R, Harvey JN, Mulholland AJ, Olsen L.

J Mol Graph Model. 2014 Jul;52:30-5. doi: 10.1016/j.jmgm.2014.06.002. Epub 2014 Jun 23.

PMID:
25000094
43.

QM/MM modelling of drug-metabolizing enzymes.

Lonsdale R, Mulholland AJ.

Curr Top Med Chem. 2014;14(11):1339-47. Review.

PMID:
24805066
44.

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. 2014 May 8;118(18):4771-83. doi: 10.1021/jp500652x. Epub 2014 Apr 29.

PMID:
24730355
45.

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme.

Mlýnský V, Banáš P, Šponer J, van der Kamp MW, Mulholland AJ, Otyepka M.

J Chem Theory Comput. 2014 Apr 8;10(4):1608-22. doi: 10.1021/ct401015e.

PMID:
26580373
46.

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 Apr 18;9(4):1025-32. doi: 10.1021/cb500067z. Epub 2014 Feb 21.

47.

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 Dec 20;3:3561. doi: 10.1038/srep03561.

48.

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 Jan 14;53(1):169-77. doi: 10.1021/bi4012644. Epub 2013 Dec 20.

49.

Explicit error bounds for the α-quasi-periodic Helmholtz problem.

Lord NH, Mulholland AJ.

J Opt Soc Am A Opt Image Sci Vis. 2013 Oct 1;30(10):2111-23. doi: 10.1364/JOSAA.30.002111.

PMID:
24322866
50.

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 Nov 12;52(45):8150-64. doi: 10.1021/bi400754t. Epub 2013 Oct 30.

PMID:
24128064

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