Department of Chemistry

Peter J Bond Publications


2014


Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories:trj_cavity
Teresa Paramo, Alexandra East, Diana Garzón, Martin B Ulmschneider, and Peter J Bond
Journal_of_Chemical_Theory_and_Computation DOI: 10.1021/ct401098b

2013


The structural basis for endotoxin-induced allosteric regulation of the Toll-like receptor 4 (TLR4) innate immune receptor.
Paramo T, Piggot TJ, Bryant CE, Bond PJ
J Biol Chem, 2013, 51, 36215-36225. DOI: 10.1074/jbc.M113.501957


Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes.
Watts CA, Richards FM, Bender A, Bond PJ, Korb O, Kern O, Riddick M, Owen P, Myers RM, Raff J, Gergely F, Jodrell DI, Ley SV
Chem Biol, 2013, 11, 1399-1410. DOI: 10.1016/j.chembiol.2013.09.012


Selective inhibition of the unfolded protein response: targeting catalytic sites for Schiff base modification.
Tomasio SM, Harding HP, Ron D, Cross BC, Bond PJ
Mol Biosyst, 2013-10, 10, 2408-2416. DOI: 10.1039/C3MB70234K


Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state.
Garzón D, Anselmi C, Bond PJ, Faraldo-Gómez JD
J Biol Chem, 2013, 27, 19528-19536. DOI: 10.1074/jbc.M113.470179


Structural and Thermodynamic Insights into Bacterial Outer Membrane Lipid Signaling by the Innate Immune System
Paramo T, Tomasio S, Bond PJ
BIOPHYSICAL JOURNAL, 2013, 2, 611A-611A.


A Zoom on Membrane Fusion through Coarse-Grained, Atomistic and Hybrid Molecular Dynamics of SNARE Proteins
Tek A, Darre L, Bond PJ, Sansom MSP, Pantano S, Baaden M
BIOPHYSICAL JOURNAL, 2013, 2, 32A-32A.


A Simulation Approach to Molecular Transport in Bacterial Reaction Chambers
Roessler F, Cebo T, Heffernan S, Bond PJ
BIOPHYSICAL JOURNAL, 2013, 2, 633A-633A.


The simulation approach to lipid-protein interactions.
Paramo T, Garzón D, Holdbrook DA, Khalid S, Bond PJ
Methods Mol Biol, 2013, 435-455. DOI: 10.1007/978-1-62703-275-9_19


Atomistic and Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins
Piggot TJ, Bond PJ, Khalid S
Proteins in Solution and at Interfaces: Methods and Applications in Biotechnology and Materials Science, 2013, 193-206.

2012


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, 3, 617-648. DOI: 10.1021/ci200542m


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
Proc Natl Acad Sci U S A, 2012, 15, E869-E878. DOI: 10.1073/pnas.1115623109


The Molecular Basis for Lipid Recognition and Signaling in the Toll-Like Receptor Complex and a Family of Lipid-Binding Proteins
Paramo T, Higson S, Piggot TJ, Bond PJ
BIOPHYSICAL JOURNAL, 2012, 3, 664A-664A.


Insights into Membrane Fusion from Molecular Dynamics Simulations of SNARE Proteins
Tek A, Bond PJ, Sansom MSP, Baaden M
BIOPHYSICAL JOURNAL, 2012, 3, 499A-499A.


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, 5, 1749-1759. DOI: 10.1016/j.bmc.2012.01.010


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, 5, 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, 3, 177-181.


Minor pseudopilin self-assembly primes type II secretion pseudopilus elongation
Cisneros DA, Bond PJ, Pugsley AP, Campos M, Francetic O
EMBO Journal, 2012, 4, 1041-1053.


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, 3, 617-648.

2011


Molecular mechanism of selective recruitment of Syk kinases by the membrane antigen-receptor complex.
Bond PJ, Faraldo-Gómez JD
J Biol Chem, 2011, 29, 25872-25881. DOI: 10.1074/jbc.M111.223321


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, 12, 2554-2574. DOI: 10.1016/j.jprot.2011.05.011


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, 18, 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, 6, 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, 12, 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
Protein Pept Lett, 2010-11, 11, 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, 2010-07, 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
Biochim Biophys Acta, 2010-06, 06-Jul, 763-772. DOI: 10.1016/j.bbabio.2010.04.014


Structural Basis for Regulation Specificity in Syk-Family Kinases
Bond PJ, Faraldo-Gomez JD
BIOPHYSICAL JOURNAL, 2010-01, 3, 442A-442A.


Nanopores as Biosensors: DNA Sequencing and Chiral Discrimination
Guy AT, Bond PJ, Khalid S
BIOPHYSICAL JOURNAL, 2010-01, 3, 597A-597A.


Multiscale Simulations of RNase E From E. coli: A Membrane Binding Protein
Khalid S, Bond PJ, Luisi BF
BIOPHYSICAL JOURNAL, 2010-01, 3, 81A-81A.


Mechanisms of Selective Sodium/proton Binding and Coupled Rotation in F1fo ATP Synthases: Insights from Quantitative Computer Simulations
Krah A, Bond PJ, Faraldo-Gomez JD
BIOPHYSICAL JOURNAL, 2010-01, 3, 434A-434A.

2009


Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens.
Garzón D, Bond PJ, Faraldo-Gómez JD
Mol Immunol, 2009-12, 02-Mar, 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
J Mol Biol, 2009, 2, 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, 09-Oct, 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
Biochemistry, 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, 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
Biochemistry, 2008, 43, 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
Biochemistry, 2008, 40, 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
Biophys J, 2008-10, 8, 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
Biophys J, 2008-10, 8, 3802-3815. DOI: 10.1529/biophysj.108.128686


OmpA: gating and dynamics via molecular dynamics simulations.
Khalid S, Bond PJ, Carpenter T, Sansom MS
Biochim Biophys Acta, 2008-09, 9, 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
Structure, 2008-04, 4, 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
Eur Biophys J, 2008-02, 2, 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
Biochem Soc Trans, 2008-02, Pt 1, 27-32. DOI: 10.1042/BST0360027


Molecular dynamics simulations of membrane proteins.
Biggin PC, Bond PJ
Methods Mol Biol, 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
J Struct Biol, 2007-03, 3, 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
Proc Natl Acad Sci U S A, 2007, 8, 2631-2636. DOI: 10.1073/pnas.0606822104


Membrane simulations of OpcA: Gating in the loops?
Bond PJ, Derrick JP, Sansom MSP
BIOPHYS J, 2007-01, 2, 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, 2007-01, 617A-617A.


Bacteriorhodopsin in the purple membrane
D'Rozario RS, Bond PJ, Sansom MSP
BIOPHYSICAL JOURNAL, 2007-01, 556A-556A.

2006


Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer.
Cuthbertson JM, Bond PJ, Sansom MS
Biochemistry, 2006, 48, 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
J BIOL CHEM, 2006, 45, 34072-34085. DOI: 10.1074/jbc.M607295200


MD simulations of Mistic: conformational stability in detergent micelles and water.
Psachoulia E, Bond PJ, Sansom MS
Biochemistry, 2006, 30, 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
Proc Natl Acad Sci U S A, 2006, 25, 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
Proteins, 2006, 1, 6-15. DOI: 10.1002/prot.20845


Molecular simulations of membrane proteins: Protein/membrane interactions
Sansom M, Bond PJ, Khalid S, Balali-Mood K
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2006, -.


Insertion and assembly of membrane proteins via simulation.
Bond PJ, Sansom MS
J Am Chem Soc, 2006, 8, 2697-2704. DOI: 10.1021/ja0569104


Anionic phospholipid interactions with the potassium channel KcsA: simulation studies.
Deol SS, Domene C, Bond PJ, Sansom MS
Biophys J, 2006, 3, 822-830. DOI: 10.1529/biophysj.105.071407


Membrane Protein Simulations: Modelling a Complex Environment
Bond PJ, Cuthbertson J, Deol SS, Forrest LR, Johnston J, Patargias G, Sansom MSP
Lecture Notes in Computational Science and Engineering, 2006, 1-20.

2005


Simulation studies of the interactions between membrane proteins and detergents.
Bond PJ, Cuthbertson J, Sansom MS
Biochem Soc Trans, 2005-11, Pt 5, 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, 2005-11, Pt 5, 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, 2005-10, 2, 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, 1, 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, 2005-01, 1, 150A-150A.


Molecular Dynamics simulations of spontaneous micelle formation around membrane proteins.
Bond PJ, Sansom MSP
BIOPHYSICAL JOURNAL, 2005-01, 1, 356A-356A.

2004


MD simulations of spontaneous membrane protein/detergent micelle formation.
Bond PJ, Cuthbertson JM, Deol SS, Sansom MS
J Am Chem Soc, 2004, 49, 15948-15949. DOI: 10.1021/ja044819e


Lipid-protein interactions of integral membrane proteins: a comparative simulation study.
Deol SS, Bond PJ, Domene C, Sansom MS
Biophys J, 2004-12, 6, 3737-3749. DOI: 10.1529/biophysj.104.048397


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, 4, 783-791. DOI: 10.1002/prot.20257


The simulation approach to bacterial outer membrane proteins.
Bond PJ, Sansom MS
Mol Membr Biol, 2004-05, 3, 151-161. DOI: 10.1080/0968760410001699169


Conformational dynamics of OmpA: MD simulations of a bacterial outer membrane protein
Bond PJ, Sansom MSP
BIOPHYSICAL JOURNAL, 2004-01, 1, 257A-257A.

2003


Lipid/protein interactions and the membrane/water interfacial region.
Domene C, Bond PJ, Deol SS, Sansom MS
J Am Chem Soc, 2003, 49, 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
J Mol Biol, 2003, 5, 1035-1053.


Membrane protein simulations: ion channels and bacterial outer membrane proteins.
Domene C, Bond PJ, Sansom MS
Adv Protein Chem, 2003, 159-193.

2002


OmpA: a pore or not a pore? Simulation and modeling studies.
Bond PJ, Faraldo-Gómez JD, Sansom MS
Biophys J, 2002-08, 2, 763-775. DOI: 10.1016/S0006-3495(02)75207-7