Department of Chemistry

Peter J Bond Publications

2012

The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule.
Cross BC, Bond PJ, Sadowski PG, Jha BK, Zak J, Goodman JM, Silverman RH, Neubert TA, Baxendale IR, Ron D, Harding HP
Animals, Binding Sites, Coumarins, DNA-Binding Proteins, Endoplasmic Reticulum Stress, Endoribonucleases, Humans, Lysine, Membrane Proteins, Mice, Protein Binding, Protein-Serine-Threonine Kinases, Proteolysis, RNA Splicing, RNA, Messenger, Ribonucleases, Schiff Bases, Secretory Pathway, Transcription Factors 2012, 109, E869-E878. DOI: 10.1073/pnas.1115623109

Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms.
Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC
J Chem Inf Model 2012, 52, 617-648. DOI: 10.1021/ci200542m

Increased endothelial cell selectivity of triazole-bridged dihalogenated A-ring analogues of combretastatin A-1.
Beale TM, Bond PJ, Brenton JD, Charnock-Jones DS, Ley SV, Myers RM
Bioorg Med Chem 2012, 20, 1749-1759. DOI: 10.1016/j.bmc.2012.01.010

Minor pseudopilin self-assembly primes type II secretion pseudopilus elongation
Cisneros DA, Bond PJ, Pugsley AP, Campos M, Francetic O
EMBO Journal 2012, 0, 1041-1053.

Increased endothelial cell selectivity of triazole-bridged dihalogenated A-ring analogues of combretastatin A-1
Beale TM, Bond PJ, Brenton JD, Charnock-Jones DS, Ley SV, Myers RM
Bioorganic and Medicinal Chemistry 2012, 1749-1759.

A-ring dihalogenation increases the cellular activity of combretastatin-templated tetrazoles
Beale TM, Allwood DM, Bender A, Bond PJ, Brenton JD, Charnock-Jones DS, Ley SV, Myers RM, Shearman JW, Temple J, Unger J, Watts CA, Xian J
ACS Medicinal Chemistry Letters 2012, 177-181.

Computational prediction of metabolism: Sites, products, SAR, P450 enzyme dynamics, and mechanisms
Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC
Journal of Chemical Information and Modeling 2012, 617-648.

2011

From in silico target prediction to multi-target drug design: current databases, methods and applications.
Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, Young MP, Jenkins JL, Glick M, Glen RC, Bender A
J Proteomics 2011, 74, 2554-2574. DOI: 10.1016/j.jprot.2011.05.011

Molecular mechanism of selective recruitment of Syk kinases by the membrane antigen-receptor complex.
Bond PJ, Faraldo-Gómez JD
J Biol Chem 2011, 286, 25872-25881. DOI: 10.1074/jbc.M111.223321

Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation.
Bond PJ, Guy AT, Heron AJ, Bayley H, Khalid S
Biochemistry 2011, 50, 3777-3783. DOI: 10.1021/bi101404n

Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study
Piñeiro A, Bond PJ, Khalid S
Biochimica et Biophysica Acta - Biomembranes 2011, 1746-1752.

From in silico target prediction to multi-target drug design: Current databases, methods and applications
Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, Young MP, Jenkins JL, Glick M, Glen RC, Bender A
Journal of Proteomics 2011, 2554-2574.

2010

Antimicrobial and cell-penetrating peptides: structure, assembly and mechanisms of membrane lysis via atomistic and coarse-grained molecular dynamics simulations.
Bond PJ, Khalid S
Animals, Antimicrobial Cationic Peptides, Cell Membrane, Cell-Penetrating Peptides, Humans, Molecular Dynamics Simulation 2010, 17, 1313-1327.

Structural basis for the ion selectivity of F-ATP-synthase c-ring rotors
Krah A, Pogoryelov D, Langer J, Bond PJ, Meier T, Faraldo-Gomez JD
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010, 1797, 35-35. DOI: 10.1016/j.bbabio.2010.04.122

Structural and energetic basis for H+ versus Na+ binding selectivity in ATP synthase Fo rotors.
Krah A, Pogoryelov D, Langer JD, Bond PJ, Meier T, Faraldo-Gómez JD
Amino Acid Substitution, Bacterial Proton-Translocating ATPases, Binding Sites, Fusobacteria, Models, Molecular, Molecular Dynamics Simulation, Mutagenesis, Site-Directed, Mutant Proteins, Protein Conformation, Spectrometry, Mass, Electrospray Ionization, Spirulina, Thermodynamics 2010, 1797, 763-772. DOI: 10.1016/j.bbabio.2010.04.014

2009

Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens.
Garzón D, Bond PJ, Faraldo-Gómez JD
Amino Acid Sequence, Antigen Presentation, Antigens, CD1, Evolution, Molecular, Humans, Lipopeptides, Macrolides, Models, Molecular, Molecular Dynamics Simulation, Molecular Sequence Data, Mycobacterium, Phosphorylation, Protein Stability, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Analysis, Protein, Structural Homology, Protein 2009, 4, 253-260. DOI: 10.1016/j.molimm.2009.09.029

Complete ion-coordination structure in the rotor ring of Na+-dependent F-ATP synthases.
Meier T, Krah A, Bond PJ, Pogoryelov D, Diederichs K, Faraldo-Gómez JD
Bacterial Proton-Translocating ATPases, Binding Sites, Crystallography, X-Ray, Fusobacteria, Protein Conformation, Sodium 2009, 19, 498-507. DOI: 10.1016/j.jmb.2009.05.082

Coarse-Grain Simulations of the R-SNARE Fusion Protein in its Membrane Environment Detect Long-Lived Conformational Sub-States
Durrieu MP, Bond PJ, Sansom MSR, Lavery R, Baaden M
CHEMPHYSCHEM 2009, 10, 1548-1552. DOI: 10.1002/cphc.200900216

Interaction of monotopic membrane enzymes with a lipid bilayer: a coarse-grained MD simulation study.
Balali-Mood K, Bond PJ, Sansom MS
Animals, Binding Sites, Computer Simulation, Databases, Protein, Enzymes, Humans, Hydrolases, Hydrophobic and Hydrophilic Interactions, Isomerases, Lipid Bilayers, Membrane Proteins, Models, Molecular, Oxidoreductases, Phospholipids, Protein Binding, Protein Conformation, Protein Structure, Secondary, Static Electricity, Transferases 2009, 10, 2135-2145. DOI: 10.1021/bi8017398

2008

DNA and lipid bilayers: self-assembly and insertion
Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP
J R SOC INTERFACE 2008, 14, S241-S250. DOI: 10.1098/rsif.2008.0239.focus

Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer.
Bond PJ, Wee CL, Sansom MS
1,2-Dipalmitoylphosphatidylcholine, Amino Acids, Chlorides, Computer Simulation, Hydrophobic and Hydrophilic Interactions, Ions, Lipid Bilayers, Molecular Conformation, Protein Structure, Secondary, Sodium, Thermodynamics, Water 2008, 36, 11321-11331. DOI: 10.1021/bi800642m

Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization.
Psachoulia E, Fowler PW, Bond PJ, Sansom MS
Computer Simulation, Dimerization, Glycophorin, Membrane Proteins, Models, Molecular, Protein Structure, Secondary 2008, 27, 10503-10512. DOI: 10.1021/bi800678t

Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.
Carpenter T, Bond PJ, Khalid S, Sansom MS
1,2-Dipalmitoylphosphatidylcholine, Computer Simulation, Histidine, Influenza A virus, Ion Channels, Lipid Bilayers, Membrane Proteins, Models, Molecular, Protein Structure, Quaternary, Protein Structure, Secondary, Viral Matrix Proteins 2008, 25, 3790-3801. DOI: 10.1529/biophysj.108.131078

Coarse-grained simulations of the membrane-active antimicrobial Peptide maculatin 1.1.
Bond PJ, Parton DL, Clark JF, Sansom MS
Amphibian Proteins, Animals, Antimicrobial Cationic Peptides, Anura, Computer Simulation, Lipid Bilayers, Liposomes, Models, Molecular 2008, 14, 3802-3815. DOI: 10.1529/biophysj.108.128686

OmpA: gating and dynamics via molecular dynamics simulations.
Khalid S, Bond PJ, Carpenter T, Sansom MS
Bacterial Outer Membrane Proteins, Computer Simulation, Escherichia coli, Ion Channel Gating, Kinetics, Models, Biological, Models, Molecular, Pasteurella multocida, Protein Conformation, Pseudomonas aeruginosa, Sequence Homology, Static Electricity 2008, 13, 1871-1880. DOI: 10.1016/j.bbamem.2007.05.024

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.
Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, Sansom MS
1,2-Dipalmitoylphosphatidylcholine, Amino Acids, Computer Simulation, Lipid Bilayers, Membrane Proteins, Models, Molecular 2008, 61, 621-630. DOI: 10.1016/j.str.2008.01.014

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.
Cox K, Bond PJ, Grottesi A, Baaden M, Sansom MS
Bacterial Outer Membrane Proteins, Crystallography, X-Ray, Dimyristoylphosphatidylcholine, Lipid Bilayers, Magnetic Resonance Spectroscopy, Models, Molecular, Porosity, Principal Component Analysis, Protein Structure, Secondary 2008, 3, 131-141. DOI: 10.1007/s00249-007-0185-8

Coarse-grained simulation: a high-throughput computational approach to membrane proteins.
Sansom MS, Scott KA, Bond PJ
Computer Simulation, Lipid Bilayers, Membrane Proteins, Membrane Transport Proteins, Models, Molecular, Potassium Channels 2008, 33, 27-32. DOI: 10.1042/BST0360027

Molecular dynamics simulations of membrane proteins.
Biggin PC, Bond PJ
Computer Simulation, Kinetics, Lipid Bilayers, Membrane Proteins, Models, Molecular 2008, 147-160. DOI: 10.1007/978-1-59745-177-2_8

2007

Coarse-grained molecular dynamics simulations of membrane proteins and peptides.
Bond PJ, Holyoake J, Ivetac A, Khalid S, Sansom MS
Amino Acid Sequence, Animals, Cell Membrane, Computer Simulation, Cystic Fibrosis Transmembrane Conductance Regulator, Human Immunodeficiency Virus Proteins, Humans, Membrane Proteins, Membrane Transport Proteins, Molecular Sequence Data, Peptides, Viral Regulatory and Accessory Proteins 2007, 118, 593-605. DOI: 10.1016/j.jsb.2006.10.004

Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations.
Bond PJ, Sansom MS
Archaea, Computer Simulation, Lipid Bilayers, Membrane Proteins, Models, Molecular, Potassium Channels, Protein Structure, Quaternary, Protein Structure, Tertiary, Water 2007, 64, 2631-2636. DOI: 10.1073/pnas.0606822104

Membrane simulations of OpcA: Gating in the loops?
Bond PJ, Derrick JP, Sansom MSP
BIOPHYS J 2007, 13, L23-L25. DOI: 10.1529/biophysj.106.097311

Bilayer deformation around voltage-dependent potassium channels revealed by self-assembly coarse-grained simulations
Bond PJ, Sansom MSP
BIOPHYSICAL JOURNAL 2007, 0, 617A-617A.

Bacteriorhodopsin in the purple membrane
D'Rozario RS, Bond PJ, Sansom MSP
BIOPHYSICAL JOURNAL 2007, 0, 556A-556A.

2006

Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer.
Cuthbertson JM, Bond PJ, Sansom MS
Cell Membrane, Computer Simulation, Dimerization, Glycophorin, Hydrogen Bonding, Magnetic Resonance Spectroscopy, Micelles, Models, Molecular, Pliability, Protein Binding, Protein Structure, Quaternary, Protein Structure, Secondary, Protein Structure, Tertiary 2006, 45, 14298-14310. DOI: 10.1021/bi0610911

Cysteine-scanning mutagenesis and disulfide mapping studies of the conserved domain of the twin-arginine translocase TatB component
Lee PA, Orriss GL, Buchanan G, Greene NP, Bond PJ, Punginelli C, Jack RL, Sansom MSP, Berks BC, Palmer T
SEC-INDEPENDENT PROTEIN, ESCHERICHIA-COLI, TRANSPORT SYSTEM, EXPORT PATHWAY, SIGNAL PEPTIDE, MEMBRANE, COMPLEXES, RESIDUES, BINDING, ASSOCIATION 2006, 281, 34072-34085. DOI: 10.1074/jbc.M607295200

MD simulations of Mistic: conformational stability in detergent micelles and water.
Psachoulia E, Bond PJ, Sansom MS
Bacillus subtilis, Bacterial Proteins, Computer Simulation, Detergents, Membrane Proteins, Micelles, Models, Molecular, Molecular Chaperones, Protein Conformation, Protein Folding, Protein Structure, Secondary, Thermodynamics, Water 2006, 45, 9053-9058. DOI: 10.1021/bi0608818

Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.
Bond PJ, Faraldo-Gómez JD, Deol SS, Sansom MS
Bacterial Outer Membrane Proteins, Computer Simulation, Crystallization, Detergents, Models, Molecular, Protein Structure, Quaternary 2006, 103, 9518-9523. DOI: 10.1073/pnas.0600398103

Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa.
Khalid S, Bond PJ, Deol SS, Sansom MS
Bacteria, Bacterial Outer Membrane Proteins, Biophysical Phenomena, Biophysics, Cell Membrane, Computational Biology, Computer Simulation, Crystallography, X-Ray, Dimyristoylphosphatidylcholine, Escherichia coli, Ions, Lipid Bilayers, Lipids, Models, Biological, Models, Molecular, Molecular Conformation, Porins, Protein Binding, Protein Conformation, Protein Structure, Tertiary, Proteomics, Pseudomonas aeruginosa, Water 2006, 63, 6-15. DOI: 10.1002/prot.20845

Molecular simulations of membrane proteins: Protein/membrane interactions
Sansom M, Bond PJ, Khalid S, Balali-Mood K
2006, 231, -.

Insertion and assembly of membrane proteins via simulation.
Bond PJ, Sansom MS
Bacterial Outer Membrane Proteins, Computer Simulation, Glycophorin, Kinetics, Lipid Bilayers, Micelles, Models, Chemical, Models, Molecular, Protein Structure, Secondary 2006, 128, 2697-2704. DOI: 10.1021/ja0569104

Anionic phospholipid interactions with the potassium channel KcsA: simulation studies.
Deol SS, Domene C, Bond PJ, Sansom MS
Anions, Bacterial Proteins, Binding Sites, Cell Membrane, Computer Simulation, Crystallography, X-Ray, Databases, Protein, Escherichia coli Proteins, Hydrogen Bonding, Ions, Lipid Bilayers, Lipids, Models, Biological, Models, Molecular, Molecular Conformation, Mutation, Oxygen, Phosphates, Phosphatidic Acids, Phosphatidylethanolamines, Phosphatidylglycerols, Phospholipids, Potassium Channels, Potassium Channels, Voltage-Gated, Pressure, Protein Folding, Streptomyces lividans, Temperature, Time Factors 2006, 90, 822-830. DOI: 10.1529/biophysj.105.071407

2005

Simulation studies of the interactions between membrane proteins and detergents.
Bond PJ, Cuthbertson J, Sansom MS
Biochem Soc Trans 2005, 33, 910-912. DOI: 10.1042/BST20050910

Molecular simulations and lipid-protein interactions: potassium channels and other membrane proteins.
Sansom MS, Bond PJ, Deol SS, Grottesi A, Haider S, Sands ZA
Biochem Soc Trans 2005, 33, 916-920. DOI: 10.1042/BST20050916

Membrane protein structure quality in molecular dynamics simulation.
Law RJ, Capener C, Baaden M, Bond PJ, Campbell J, Patargias G, Arinaminpathy Y, Sansom MS
J Mol Graph Model 2005, 24, 157-165. DOI: 10.1016/j.jmgm.2005.05.006

Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment.
Patargias G, Bond PJ, Deol SS, Sansom MS
J Phys Chem B 2005, 109, 575-582. DOI: 10.1021/jp046727h

On the convergence of the conformational sampling in molecular dynamics simulations of membrane proteins
Faraldo-Gomez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Mark SPS
BIOPHYSICAL JOURNAL 2005, 88, 150A-150A.

Molecular Dynamics simulations of spontaneous micelle formation around membrane proteins.
Bond PJ, Sansom MSP
BIOPHYSICAL JOURNAL 2005, 88, 356A-356A.

2004

MD simulations of spontaneous membrane protein/detergent micelle formation.
Bond PJ, Cuthbertson JM, Deol SS, Sansom MS
Bacterial Outer Membrane Proteins, Computer Simulation, Escherichia coli Proteins, Glycophorin, Kinetics, Micelles, Phosphorylcholine, Protein Structure, Secondary, Thermodynamics 2004, 43, 15948-15949. DOI: 10.1021/ja044819e

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations
Faraldo-Gomez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Sansom MSP
PROTEINS 2004, 56, 783-791. DOI: 10.1002/prot.20257

Lipid-protein interactions of integral membrane proteins: a comparative simulation study.
Deol SS, Bond PJ, Domene C, Sansom MS
Bacterial Outer Membrane Proteins, Bacterial Proteins, Computer Simulation, Diffusion, Dimyristoylphosphatidylcholine, Lipid Bilayers, Membrane Fluidity, Membrane Proteins, Membranes, Artificial, Models, Chemical, Models, Molecular, Motion, Phosphatidylcholines, Potassium Channels, Protein Binding, Protein Conformation 2004, 49, 3737-3749. DOI: 10.1529/biophysj.104.048397

The simulation approach to bacterial outer membrane proteins.
Bond PJ, Sansom MS
Bacterial Outer Membrane Proteins, Computer Simulation, Lipids, Models, Molecular, Protein Conformation 2004, 33, 151-161. DOI: 10.1080/0968760410001699169

Conformational dynamics of OmpA: MD simulations of a bacterial outer membrane protein
Bond PJ, Sansom MSP
BIOPHYSICAL JOURNAL 2004, 0, 257A-257A.

2003

Lipid/protein interactions and the membrane/water interfacial region.
Domene C, Bond PJ, Deol SS, Sansom MS
Bacterial Outer Membrane Proteins, Bacterial Proteins, Computer Simulation, Dimyristoylphosphatidylcholine, Lipid Bilayers, Models, Molecular, Phosphatidylcholines, Potassium Channels, Water 2003, 35, 14966-14967. DOI: 10.1021/ja0364874

Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.
Bond PJ, Sansom MS
Bacterial Outer Membrane Proteins, Computer Simulation, Detergents, Dimyristoylphosphatidylcholine, Lipid Bilayers, Magnetic Resonance Spectroscopy, Membrane Proteins, Micelles, Models, Chemical, Models, Molecular, Phospholipids, Protein Conformation, Water 2003, 80, 1035-1053.

Membrane protein simulations: ion channels and bacterial outer membrane proteins.
Domene C, Bond PJ, Sansom MS
Anisotropy, Bacterial Outer Membrane Proteins, Bacterial Proteins, Cell Membrane, Computer Simulation, Ions, Lipid Bilayers, Models, Molecular, Porins, Potassium Channels, Protein Transport, Time Factors 2003, 30, 159-193.

2002

OmpA: a pore or not a pore? Simulation and modeling studies.
Bond PJ, Faraldo-Gómez JD, Sansom MS
Biophys J 2002, 83, 763-775. DOI: 10.1016/S0006-3495(02)75207-7