M. W. van der Kamp

发表

Dynameomics: a comprehensive database of protein dynamics.

R Dustin Schaeffer, David A C Beck, Valerie Daggett, 2010, Structure.

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

Simon J. Bennie, M. W. van der Kamp, A. Mulholland, 2016, Journal of chemical theory and computation.

Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

Richard H. Henchman, P. Biggin, J. Essex, 2018, WIREs Computational Molecular Science.

On the Temperature Dependence of Enzyme-Catalyzed Rates.

Adrian J Mulholland, Vickery L Arcus, Emily J Parker, 2016, Biochemistry.

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

M. W. van der Kamp, A. Mulholland, Ushnish Sengupta, 2018, Journal of the American Chemical Society.

Reaction Mechanism of N-Acetylneuraminic Acid Lyase Revealed by a Combination of Crystallography, QM/MM Simulation, and Mutagenesis

Adrian J. Mulholland, Adam Nelson, Alan Berry, 2014, ACS chemical biology.

Simulations of membrane‐bound diglycosylated human prion protein reveal potential protective mechanisms against misfolding

V. Daggett, M. W. van der Kamp, B. Schiøtt, 2017, Journal of neurochemistry.

Pathogenic mutations in the hydrophobic core of the human prion protein can promote structural instability and misfolding.

V. Daggett, M. W. van der Kamp, 2010, Journal of molecular biology.

Dynameomics: protein dynamics and unfolding across fold space

Amanda L. Jonsson, V. Daggett, R. D. Schaeffer, 2010, Biomolecular concepts.

Crystal structure of the putative cyclase IdmH from the indanomycin nonribosomal peptide synthase/polyketide synthase

M. W. van der Kamp, J. Obajdin, G. R. Hemsworth, 2019, IUCrJ.

QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes† †Electronic supplementary information (ESI) available: Fig. S1–S5, Tables S1–S3 and extra details on umbrella sampling simulations. See DOI: 10.1039/c8ob00066b

C. González‐Bello, M. W. van der Kamp, A. Mulholland, 2018, Organic & biomolecular chemistry.

Specificity of bispecific T cell receptors and antibodies targeting peptide-HLA.

T. Blicher, B. Jakobsen, M. W. van der Kamp, 2020, The Journal of clinical investigation.

Exposing the Interplay Between Enzyme Turnover, Protein Dynamics, and the Membrane Environment in Monoamine Oxidase B.

S. Wells, M. W. van der Kamp, Hannah B. L. Jones, 2019, Biochemistry.

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

M. W. van der Kamp, A. Mulholland, Jitrayut Jitonnom, 2017, Biochemistry.

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

Christopher J. Woods, F. Gervasio, G. Saladino, 2018, Journal of chemical theory and computation.

Visualizing the protons in a metalloenzyme electron proton transfer pathway

M. W. van der Kamp, A. Mulholland, P. Moody, 2020, Proceedings of the National Academy of Sciences.

Multiscale Simulations Identify Origins of Differential Carbapenem Hydrolysis by the OXA-48 β-Lactamase

M. W. van der Kamp, A. Mulholland, J. Spencer, 2021, ACS catalysis.

The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis

G. Moreno-Hagelsieb, M. W. van der Kamp, Geoff P. Horsman, 2019, Nature Communications.

Cryptic β-Lactamase Evolution Is Driven by Low β-Lactam Concentrations

M. W. van der Kamp, H. Leiros, P. Johnsen, 2020, mSphere.

Small Changes in Hydration Determine Cephalosporinase Activity of OXA-48 β-Lactamases

M. W. van der Kamp, A. Mulholland, J. Spencer, 2020, ACS Catalysis.

Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases

M. W. van der Kamp, A. Hengge, S. C. Kamerlin, 2020, Journal of the American Chemical Society.

QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-Lactamases

Ewa I. Chudyk, Michael A. L. Limb, M. W. van der Kamp, 2022, ACS infectious diseases.

Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen

J. Haidar, J. Dukes, M. W. van der Kamp, 2022, Nature Communications.

Peptide cargo tunes a network of correlated motions in human leucocyte antigens

V. Arcus, A. Sewell, M. W. van der Kamp, 2020, The FEBS journal.

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

S. Wells, M. W. van der Kamp, A. Mulholland, 2015, PloS one.

Catalytic mechanism of the colistin resistance protein MCR-1†

M. W. van der Kamp, A. Mulholland, J. Spencer, 2020, Organic & biomolecular chemistry.

Conformation control of the histidine kinase BceS of Bacillus subtilis by its cognate ABC‐transporter facilitates need‐based activation of antibiotic resistance

M. W. van der Kamp, C. Pudney, S. Gebhard, 2020, Molecular microbiology.

Experiment and Simulation Reveal How Mutations in Functional Plasticity Regions Guide Plant Monoterpene Synthase Product Outcome.

N. Scrutton, A. Currin, M. W. van der Kamp, 2018, ACS catalysis.

Evolution of dynamical networks enhances catalysis in a designer enzyme

D. Hilvert, V. Arcus, M. W. van der Kamp, 2020, bioRxiv.

Structurally Informed Mutagenesis of a Stereochemically Promiscuous Aldolase Produces Mutants That Catalyze the Diastereoselective Syntheses of All Four Stereoisomers of 3-Deoxy-hexulosonic Acid

S. Crennell, M. W. van der Kamp, M. Danson, 2022, ACS catalysis.

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

E. Takano, N. Scrutton, L. Johannissen, 2017, ACS catalysis.

Computational enzymology: insight into biological catalysts from modelling.

M. W. van der Kamp, A. Mulholland, 2008, Natural product reports.

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

M. Byrne, M. W. van der Kamp, A. Mulholland, 2016, Journal of the American Chemical Society.

Enzyme evolution and the temperature dependence of enzyme catalysis.

V. Arcus, M. W. van der Kamp, A. Mulholland, 2020, Current opinion in structural biology.

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

Adrian J Mulholland, Michal Otyepka, Pavel Banáš, 2014, Journal of chemical theory and computation.

Affinity of Avr2 for tomato cysteine protease Rcr3 correlates with the Avr2-triggered Cf-2-mediated hypersensitive response.

B. Thomma, M. W. van der Kamp, J. Beekwilder, 2011, Molecular plant pathology.

A Rieske oxygenase/epoxide hydrolase-catalysed reaction cascade creates oxygen heterocycles in mupirocin biosynthesis

M. W. van der Kamp, T. J. Simpson, C. Willis, 2018, Nature Catalysis.

Antimicrobial Resistance Conferred by OXA-48 β-Lactamases: Towards a Detailed Mechanistic Understanding

M. W. van der Kamp, J. Spencer, Viivi H. A. Hirvonen, 2021, Antimicrobial Agents and Chemotherapy.

Dynamical origins of heat capacity changes in enzyme-catalysed reactions

E. Prentice, V. Arcus, M. W. van der Kamp, 2018, Nature Communications.

Multiscale analysis of enantioselectivity in enzyme-catalysed ‘lethal synthesis’ using projector-based embedding

Adrian J Mulholland, Xinglong Zhang, Frederick R Manby, 2018, Royal Society Open Science.

"Lethal synthesis" of fluorocitrate by citrate synthase explained through QM/MM modeling.

Adrian J Mulholland, Marc W van der Kamp, M. W. van der Kamp, 2011, Angewandte Chemie.

Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology.

M. W. van der Kamp, A. Mulholland, Marc W. van der Kamp, 2013, Biochemistry.

Enzymatic synthesis of natural (+)-aristolochene from a non-natural substrate.

M. W. van der Kamp, S. Leoni, R. Allemann, 2016, Chemical communications.

Variability in mitochondrial import, mitochondrial health and mtDNA copy number using Type II and Type V CRISPR effectors

M. W. van der Kamp, M. Szczelkun, J. Lane, 2020, bioRxiv.

Mitochondrial import, health and mtDNA copy number variability seen when using type II and type V CRISPR effectors

M. W. van der Kamp, M. Szczelkun, J. Lane, 2020, Journal of Cell Science.

Influence of pH on the human prion protein: insights into the early steps of misfolding.

V. Daggett, M. W. van der Kamp, 2010, Biophysical journal.

Intercellular exchange of lysosomal enzymes: enzyme assays in single human fibroblasts after co-cultivation.

H. Galjaard, M. W. van der Kamp, D. Halley, 1976, Biochemical and biophysical research communications.

The consequences of pathogenic mutations to the human prion protein.

V. Daggett, M. W. van der Kamp, 2009, Protein engineering, design & selection : PEDS.

Molecular Rules Underpinning Enhanced Affinity Binding of Human T Cell Receptors Engineered for Immunotherapy

A. Sewell, M. W. van der Kamp, C. Pudney, 2020, Molecular therapy oncolytics.

Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations

V. Daggett, M. W. van der Kamp, Marc W. van der Kamp, 2013 .

Structural and dynamic properties of the human prion protein.

V. Daggett, Wei Chen, M. W. van der Kamp, 2014, Biophysical journal.

An Esterase-like Lyase Catalyzes Acetate Elimination in Spirotetronate/Spirotetramate Biosynthesis.

M. Byrne, M. W. van der Kamp, J. Stach, 2019, Angewandte Chemie.

The basis for carbapenem hydrolysis by class A β-lactamases: a combined investigation using crystallography and simulations.

Ewa I. Chudyk, M. W. van der Kamp, A. Mulholland, 2012, Journal of the American Chemical Society.

Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase.

M. W. van der Kamp, A. Mulholland, F. Perruccio, 2007, Journal of molecular graphics & modelling.

Biomolecular simulation and modelling: status, progress and prospects

Christopher J. Woods, Adrian J Mulholland, Marc W van der Kamp, 2008, Journal of The Royal Society Interface.

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model.

Aaron Sisto, Edward G Hohenstein, Simon McIntosh-Smith, 2017, Physical chemistry chemical physics : PCCP.

Dynamical origins of heat capacity changes in enzyme-catalysed reactions

E. Prentice, V. Arcus, M. W. van der Kamp, 2017, Nature Communications.

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

Ewa I. Chudyk, Michael A. L. Limb, M. W. van der Kamp, 2014, Chemical communications.

Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA

M. W. van der Kamp, C. Pudney, D. Cole, 2021, bioRxiv.

Conformational change and ligand binding in the aristolochene synthase catalytic cycle.

Adrian J Mulholland, Marc W van der Kamp, M. W. van der Kamp, 2013, Biochemistry.

Diverse effects on the native β-sheet of the human prion protein due to disease-associated mutations.

V. Daggett, Wei Chen, M. W. van der Kamp, 2010, Biochemistry.

Path to Actinorhodin: Regio- and Stereoselective Ketone Reduction by a Type II Polyketide Ketoreductase Revealed in Atomistic Detail

Stefano A. Serapian, M. W. van der Kamp, J. Crosby, 2021, JACS Au.

How Static Disorder Mimics Decoherence in Anisotropy Pump-Probe Experiments on Purple-Bacteria Light Harvesting Complexes.

N. Linden, M. W. van der Kamp, F. Manby, 2016, The journal of physical chemistry. B.

Sensing Enzyme Activation Heat Capacity at the Single-Molecule Level Using Gold-Nanorod-Based Optical Whispering Gallery Modes

V. Arcus, M. W. van der Kamp, C. Pudney, 2021, ACS applied nano materials.

Redesigning the Molecular Choreography to Prevent Hydroxylation in Germacradien-11-ol Synthase Catalysis

David J. Miller, M. W. van der Kamp, Prabhakar L. Srivastava, 2021, ACS catalysis.

Conformation control of the histidine kinase BceS of Bacillus subtilis by its cognate ABC-transporter facilitates need-based activation of antibiotic resistance

M. W. van der Kamp, C. Pudney, S. Gebhard, 2020, bioRxiv.

4‐Thiaproline accelerates the slow folding phase of proteins containing cis prolines in the native state by two orders of magnitude

M. W. van der Kamp, M. Rubini, Kirill Zinovjev, 2023, bioRxiv.

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

Jans H. Alzate-Morales, M. W. van der Kamp, A. Mulholland, 2018, Biochemistry.

Promiscuous recognition of MR1 drives self-reactive mucosal-associated invariant T cell responses

G. Besra, M. W. van der Kamp, R. Calogero, 2023, The Journal of experimental medicine.

Interrogation of an Enzyme Library Reveals the Catalytic Plasticity of Naturally Evolved [4+2] Cyclases

M. W. van der Kamp, J. Mobarec, C. Willis, 2023, Chembiochem : a European journal of chemical biology.

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

M. W. van der Kamp, A. Mulholland, Wiktor Beker, 2017, Journal of chemical theory and computation.

Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl‐CoA enolization in citrate synthase

M. W. van der Kamp, A. Mulholland, F. Perruccio, 2007, Proteins.

Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution

N. Tokuriki, M. W. van der Kamp, A. Mulholland, 2023, bioRxiv.

Correction to "Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases".

M. W. van der Kamp, A. Hengge, S. C. Kamerlin, 2022, Journal of the American Chemical Society.

The consequences of pathogenic mutations to the human prion protein.

V. Daggett, M. W. van der Kamp, 2009, Protein engineering, design & selection : PEDS.

Pathogenic mutations in the hydrophobic core of the human prion protein can promote structural instability and misfolding.

M. W. van der Kamp, Valerie Daggett, 2010, Journal of molecular biology.

Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations.

V. Daggett, M. W. van der Kamp, 2011, Topics in current chemistry.

Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate.

Adrian J Mulholland, Miguel González, M. W. van der Kamp, 2007, The journal of physical chemistry. B.

Comment on: “Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme”

D. Hilvert, V. Arcus, M. W. van der Kamp, 2023, ACS Catalysis.

On the Temperature Dependence of Enzyme-Catalyzed Rates.

L. Schipper, E. Prentice, V. Arcus, 2016, Biochemistry.

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

M. W. van der Kamp, A. Mulholland, Wiktor Beker, 2017, Journal of chemical theory and computation.

Epistasis arises from shifting the rate-limiting step during enzyme evolution of a β-lactamase

N. Tokuriki, M. W. van der Kamp, A. Mulholland, 2024, Nature catalysis.

Influence of Wobbling Tryptophan and Mutations on PET Degradation Explored by QM/MM Free Energy Calculations

M. W. van der Kamp, B. Strodel, Kirill Zinovjev, 2024, bioRxiv.

High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase.

Adrian J Mulholland, Francesca Perruccio, Marc W van der Kamp, 2008, Chemical communications.

emle-engine: A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations

M. W. van der Kamp, I. Tuñón, Kirill Zinovjev, 2024, Journal of chemical theory and computation.

C. González‐Bello, M. W. van der Kamp, A. Mulholland, 2018, Organic & biomolecular chemistry.

Testing high-level QM/MM methods for modeling enzyme reactions: acetyl-CoA deprotonation in citrate synthase.

Adrian J Mulholland, Frederick R Manby, Marc W van der Kamp, 2010, The journal of physical chemistry. B.