Biography Details
 
Dr. BOND Peter John
Principal Investigator
 

Areas of Research Interest

Peter J. Bond is Principal Investigator at the Bioinformatics Institute A*STAR. He has ~12 years of experience in the development and application of multiscale modelling and simulation approaches to understand biomolecular recognition and assembly. As well as gaining fundamental insights into the mechanisms of action of biomolecules, for example in the areas of immunological signalling or membrane transport, he helps to develop new approaches for pharmaceutical intervention in disease states and new applications in (bio)nanotechnology.

Biography

Following his graduation in Biochemistry at the University of Oxford, UK in 2001, Peter moved to the Laboratory of Molecular Biophysics to read for a D. Phil., supported by a Wellcome Trust Prize Studentship. He was awarded an EMBO Long-Term Fellowship in 2007 to carry out research at the Max Planck Institute of Biophysics in Frankfurt, Germany. In 2010, he became a University Lecturer and Group Leader in the Department of Chemistry, University of Cambridge, UK, before being appointed as Principal Investigator at the Bioinformatics Institute A*STAR from October 2013.

Selected Publications

  1. Lea-Smith DJ, Ortiz-Suarez ML, Lenn T, Nurnberg DJ, Baers LL, Davey MP, Parolini L, Huber RG, Cotton CA, Mastroianni G, Bombelli P, Ungerer P, Stevens TJ, Smith AG, Bond PJ, Mullineaux CW, Howe CJ.
    Hydrocarbons are essential for optimal cell size, division and growth of cyanobacteria.
    Plant Physiol. 2016 Oct 5. pii: pp.01205.2016.

  2. Huber RG, Kulemzina I, Ang K, Chavda AP, Suranthran S, Teh JT, Kenanov D, Liu G, Rancati G, Szmyd R, Kaldis P, Bond PJ, Ivanov D.
    Impairing Cohesin Smc1/3 Head Engagement Compensates for the Lack of Eco1 Function.
    Structure. 2016 Sep 27. pii: S0969-2126(16)30265-9. doi: 10.1016/j.str.2016.09.001.

  3. Fukuda Y, Cheong PL, Lynch J, Brighton C, Frase S, Kargas V, Rampersaud E, Wang Y, Sankaran VG, Yu B, Ney PA, Weiss MJ, Vogel P, Bond PJ, Ford RC, Trent RJ, Schuetz JD.
    The severity of hereditary porphyria is modulated by the porphyrin exporter and Lan antigen ABCB6.
    Nat Commun. 2016 Aug 10;7:12353. doi: 10.1038/ncomms12353.

  4. Marzinek JK, Holdbrook DA, Huber RG, Verma C, Bond PJ.
    Pushing the Envelope: Dengue Viral Membrane Coaxed into Shape by Molecular Simulations.
    Structure. 2016 Aug 2;24(8):1410-20. doi: 10.1016/j.str.2016.05.014. Epub 2016 Jul 7.

  5. Holdbrook DA, Huber RG, Piggot TJ, Bond PJ, Khalid S.
    Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition.
    PLoS One. 2016 Jun 16;11(6):e0156963. doi: 10.1371/journal.pone.0156963. eCollection 2016.

  6. Cording A, Gormally M, Bond PJ, Carrington M, Balasubramanian S, Miska EA, Thomas B.
    Selective inhibitors of trypanosomal uridylyl transferase RET1 establish druggability of RNA post-transcriptional modifications.
    RNA Biol. 2016 Jan 20:1-9. [Epub ahead of print]

  7. Marzinek JK, Lakshminarayanan R, Goh E, Huber RG, Panzade S, Verma C, Bond PJ.
    Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment.
    Sci Rep. 2016 Jan 20;6:19160. doi: 10.1038/srep19160.

  8. East A, Mechaly AE, Huysmans GH, Bernarde C, Tello-Manigne D, Nadeau N, Pugsley AP, Buschiazzo A, Alzari PM, Bond PJ, Francetic O.
    Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis.
    Structure. 2016 Jan 5;24(1):92-104. doi: 10.1016/j.str.2015.10.023. Epub 2015 Dec 10.

  9. Ortiz-Suarez ML, Bond PJ.
    The Structural Basis for Lipid and Endotoxin Binding in RP105-MD-1, and Consequences for Regulation of Host Lipopolysaccharide Sensitivity.
    Structure. 2016 Jan 5;24(1):200-11. doi: 10.1016/j.str.2015.10.021. Epub 2015 Dec 3.

  10. Paramo T, Tomasio SM, Irvine KL, Bryant CE, Bond PJ.
    Energetics of Endotoxin Recognition in the Toll-Like Receptor 4 Innate Immune Response.
    Sci Rep. 2015 Dec 9;5:17997. doi: 10.1038/srep17997.

  11. Huber RG, Fan H, Bond PJ.
    The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain.
    PLoS Comput Biol. 2015 Oct 16;11(10):e1004560. doi: 10.1371/journal.pcbi.1004560. eCollection 2015 Oct.

  12. Berglund NA, Kargas V, Ortiz-Suarez ML, Bond PJ.
    The role of protein-protein interactions in Toll-like receptor function.
    Prog Biophys Mol Biol. 2015 Oct;119(1):72-83. doi: 10.1016/j.pbiomolbio.2015.06.021. Epub 2015 Jul 2.

  13. Berglund NA, Piggot TJ, Jefferies D, Sessions RB, Bond PJ, Khalid S.
    Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study.
    PLoS Comput Biol. 2015 Apr 17;11(4):e1004180. doi: 10.1371/journal.pcbi.1004180. eCollection 2015 Apr.

  14. Burmann BM, Holdbrook DA, Callon M, Bond PJ, Hiller S.
    Revisiting the Interaction between the Chaperone Skp and Lipopolysaccharide.
    Biophys J. 2015 Mar 24;108(6):1516-26. doi: 10.1016/j.bpj.2015.01.029.

  15. Strahl H, Turlan C, Khalid S, Bond PJ, Kebalo JM, Peyron P, Poljak L, Bouvier M, Hamoen L, Luisi BF, Carpousis AJ.
    Membrane recognition and dynamics of the RNA degradosome.
    PLoS Genet. 2015 Feb 3;11(2):e1004961. doi: 10.1371/journal.pgen.1004961. eCollection 2015 Feb.

  16. Faustino AF, Guerra GM, Huber RG, Hollmann A, Domingues MM, Barbosa GM, Enguita FJ, Bond PJ, Castanho MA, Da Poian AT, Almeida FC, Santos NC, Martins IC.
    Understanding dengue virus capsid protein disordered N-Terminus and pep14-23-based inhibition.
    ACS Chem Biol. 2015 Feb 20;10(2):517-26. doi: 10.1021/cb500640t. Epub 2014 Nov 20.

  17. Biggin PC, Bond PJ.
    Molecular dynamics simulations of membrane proteins.
    Methods Mol Biol. 2015;1215:91-108. doi: 10.1007/978-1-4939-1465-4_5.

  18. Marzinek JK, Bond PJ, Lian G, Zhao Y, Han L, Noro MG, Pistikopoulos EN, Mantalaris A.
    Free energy predictions of ligand binding to an a-helix using steered molecular dynamics and umbrella sampling simulations.
    J Chem Inf Model. 2014 Jul 28;54(7):2093-104. doi: 10.1021/ci500164q. Epub 2014 Jul 17.

  19. Zhao Y, Marzinek JK, Bond PJ, Chen L, Li Q, Mantalaris A, Pistikopoulos EN, Noro MG, Han L, Lian G.
    A study on Fe(2+) - a-helical-rich keratin complex formation using isothermal titration calorimetry and molecular dynamics simulation.
    J Pharm Sci. 2014 Apr;103(4):1224-32. doi: 10.1002/jps.23895. Epub 2014 Feb 11.

  20. 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.
    Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes.
    Chem Biol. 2013 Nov 21;20(11):1399-410. doi: 10.1016/j.chembiol.2013.09.012. Epub 2013 Oct 24.

  21. Paramo T, Piggot TJ, Bryant CE, Bond PJ.
    The structural basis for endotoxin-induced allosteric regulation of the Toll-like receptor 4 (TLR4) innate immune receptor.
    J Biol Chem. 2013 Dec 20;288(51):36215-25. doi: 10.1074/jbc.M113.501957. Epub 2013 Oct 30.

  22. Tomasio SM, Harding HP, Ron D, Cross BC, Bond PJ.
    Selective inhibition of the unfolded protein response: targeting catalytic sites for Schiff base modification.
    Mol Biosyst. 2013 Oct;9(10):2408-16. doi: 10.1039/c3mb70234k. Review.

  23. Garzón D, Anselmi C, Bond PJ, Faraldo-Gómez JD.
    Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state.
    J Biol Chem. 2013 Jul 5;288(27):19528-36. doi: 10.1074/jbc.M113.470179. Epub 2013 May 15.

  24. Paramo T, Garzón D, Holdbrook DA, Khalid S, Bond PJ.
    The simulation approach to lipid-protein interactions.
    Methods Mol Biol. 2013;974:435-55. doi: 10.1007/978-1-62703-275-9_19.

  25. Khalid S, Bond PJ.
    Multiscale molecular dynamics simulations of membrane proteins.
    Methods Mol Biol. 2013;924:635-57. doi: 10.1007/978-1-62703-017-5_25. Review.

  26. 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.
    A-ring dihalogenation increases the cellular activity of combretastatin-templated tetrazoles.
    ACS Med Chem Lett. 2012 Jan 19;3(3):177-81. doi: 10.1021/ml200149g. eCollection 2012 Mar 8.

  27. Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC.
    Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms.
    J Chem Inf Model. 2012 Mar 26;52(3):617-48. doi: 10.1021/ci200542m. Epub 2012 Feb 17. Review.

  28. Cross BC, Bond PJ, Sadowski PG, Jha BK, Zak J, Goodman JM, Silverman RH, Neubert TA, Baxendale IR, Ron D, Harding HP.
    The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule.
    Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):E869-78. doi: 10.1073/pnas.1115623109. Epub 2012 Feb 6.

  29. Beale TM, Bond PJ, Brenton JD, Charnock-Jones DS, Ley SV, Myers RM.
    Increased endothelial cell selectivity of triazole-bridged dihalogenated A-ring analogues of combretastatin A-1.
    Bioorg Med Chem. 2012 Mar 1;20(5):1749-59. doi: 10.1016/j.bmc.2012.01.010. Epub 2012 Jan 18.

  30. Cisneros DA, Bond PJ, Pugsley AP, Campos M, Francetic O.
    Minor pseudopilin self-assembly primes type II secretion pseudopilus elongation.
    EMBO J. 2012 Feb 15;31(4):1041-53. doi: 10.1038/emboj.2011.454. Epub 2011 Dec 9.

  31. Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, Young MP, Jenkins JL, Glick M, Glen RC, Bender A.
    From in silico target prediction to multi-target drug design: current databases, methods and applications.
    J Proteomics. 2011 Nov 18;74(12):2554-74. doi: 10.1016/j.jprot.2011.05.011. Epub 2011 May 18. Review.

  32. Bond PJ, Faraldo-Gómez JD.
    Molecular mechanism of selective recruitment of Syk kinases by the membrane antigen-receptor complex.
    J Biol Chem. 2011 Jul 22;286(29):25872-81. doi: 10.1074/jbc.M111.223321. Epub 2011 May 21.

  33. Bond PJ, Guy AT, Heron AJ, Bayley H, Khalid S.
    Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation.
    Biochemistry. 2011 May 10;50(18):3777-83. doi: 10.1021/bi101404n. Epub 2011 Apr 13.

  34. Piñeiro Á, Bond PJ, Khalid S.
    Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: a multi-scale molecular dynamics simulation study.
    Biochim Biophys Acta. 2011 Jun;1808(6):1746-52. doi: 10.1016/j.bbamem.2011.02.015. Epub 2011 Feb 24.

  35. Bond PJ, Khalid S.
    Antimicrobial and cell-penetrating peptides: structure, assembly and mechanisms of membrane lysis via atomistic and coarse-grained molecular dynamics simulations.
    Protein Pept Lett. 2010 Nov;17(11):1313-27. Review.

  36. Krah A, Pogoryelov D, Langer JD, Bond PJ, Meier T, Faraldo-Gómez JD.
    Structural and energetic basis for H+ versus Na+ binding selectivity in ATP synthase Fo rotors.
    Biochim Biophys Acta. 2010 Jun-Jul;1797(6-7):763-72. doi: 10.1016/j.bbabio.2010.04.014. Epub 2010 Apr 21.

  37. Garzón D, Bond PJ, Faraldo-Gómez JD.
    Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens.
    Mol Immunol. 2009 Dec;47(2-3):253-60. doi: 10.1016/j.molimm.2009.09.029. Epub 2009 Oct 13.

  38. Meier T, Krah A, Bond PJ, Pogoryelov D, Diederichs K, Faraldo-Gómez JD.
    Complete ion-coordination structure in the rotor ring of Na+-dependent F-ATP synthases.
    J Mol Biol. 2009 Aug 14;391(2):498-507. doi: 10.1016/j.jmb.2009.05.082. Epub 2009 Jun 3.

  39. Durrieu MP, Bond PJ, Sansom MS, Lavery R, Baaden M.
    Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.
    Chemphyschem. 2009 Jul 13;10(9-10):1548-52. doi: 10.1002/cphc.200900216.

  40. Balali-Mood K, Bond PJ, Sansom MS.
    Interaction of monotopic membrane enzymes with a lipid bilayer: a coarse-grained MD simulation study.
    Biochemistry. 2009 Mar 17;48(10):2135-45. doi: 10.1021/bi8017398.

  41. Bond PJ, Wee CL, Sansom MS.
    Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer.
    Biochemistry. 2008 Oct 28;47(43):11321-31. doi: 10.1021/bi800642m. Epub 2008 Oct 2.

  42. Psachoulia E, Fowler PW, Bond PJ, Sansom MS.
    Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization.
    Biochemistry. 2008 Oct 7;47(40):10503-12. doi: 10.1021/bi800678t. Epub 2008 Sep 11.

  43. Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MS.
    DNA and lipid bilayers: self-assembly and insertion.
    J R Soc Interface. 2008 Dec 6;5 Suppl 3:S241-50. doi: 10.1098/rsif.2008.0239.focus.

  44. Bond PJ, Parton DL, Clark JF, Sansom MS.
    Coarse-grained simulations of the membrane-active antimicrobial Peptide maculatin 1.1.
    Biophys J. 2008 Oct;95(8):3802-15. doi: 10.1529/biophysj.108.128686. Epub 2008 Jul 18.

  45. Carpenter T, Bond PJ, Khalid S, Sansom MS.
    Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.
    Biophys J. 2008 Oct;95(8):3790-801. doi: 10.1529/biophysj.108.131078. Epub 2008 Jul 11.

  46. Biggin PC, Bond PJ.
    Molecular dynamics simulations of membrane proteins.
    Methods Mol Biol. 2008;443:147-60. doi: 10.1007/978-1-59745-177-2_8.

  47. Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, Sansom MS.
    Coarse-grained MD simulations of membrane protein-bilayer self-assembly.
    Structure. 2008 Apr;16(4):621-30. doi: 10.1016/j.str.2008.01.014.

  48. Sansom MS, Scott KA, Bond PJ.
    Coarse-grained simulation: a high-throughput computational approach to membrane proteins.
    Biochem Soc Trans. 2008 Feb;36(Pt 1):27-32. doi: 10.1042/BST0360027. Review.

  49. Khalid S, Bond PJ, Carpenter T, Sansom MS.
    OmpA: gating and dynamics via molecular dynamics simulations.
    Biochim Biophys Acta. 2008 Sep;1778(9):1871-80. Epub 2007 Jun 2. Review.

  50. Cox K, Bond PJ, Grottesi A, Baaden M, Sansom MS.
    Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.
    Eur Biophys J. 2008 Feb;37(2):131-41. Epub 2007 Jun 6.

  51. Bond PJ, Sansom MS.
    Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations.
    Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2631-6. Epub 2007 Feb 14.

  52. Cuthbertson JM, Bond PJ, Sansom MS.
    Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer.
    Biochemistry. 2006 Dec 5;45(48):14298-310.

  53. Bond PJ, Holyoake J, Ivetac A, Khalid S, Sansom MS.
    Coarse-grained molecular dynamics simulations of membrane proteins and peptides.
    J Struct Biol. 2007 Mar;157(3):593-605. Epub 2006 Oct 20.

  54. Bond PJ, Derrick JP, Sansom MS.
    Membrane simulations of OpcA: gating in the loops?
    Biophys J. 2007 Jan 15;92(2):L23-5. Epub 2006 Nov 17.

  55. Lee PA, Orriss GL, Buchanan G, Greene NP, Bond PJ, Punginelli C, Jack RL, Sansom MS, Berks BC, Palmer T.
    Cysteine-scanning mutagenesis and disulfide mapping studies of the conserved domain of the twin-arginine translocase TatB component.
    J Biol Chem. 2006 Nov 10;281(45):34072-85. Epub 2006 Sep 13.

  56. Psachoulia E, Bond PJ, Sansom MS.
    MD simulations of Mistic: conformational stability in detergent micelles and water.
    Biochemistry. 2006 Aug 1;45(30):9053-8.

  57. Patargias G, Bond PJ, Deol SS, Sansom MS.
    Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment.
    J Phys Chem B. 2005 Jan 13;109(1):575-82.

  58. Bond PJ, Faraldo-Gómez JD, Deol SS, Sansom MS.
    Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.
    Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9518-23. Epub 2006 Jun 9.

  59. Bond PJ, Sansom MS.
    Insertion and assembly of membrane proteins via simulation.
    J Am Chem Soc. 2006 Mar 1;128(8):2697-704.

  60. Khalid S, Bond PJ, Deol SS, Sansom MS.
    Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa.
    Proteins. 2006 Apr 1;63(1):6-15.

  61. Deol SS, Domene C, Bond PJ, Sansom MS.
    Anionic phospholipid interactions with the potassium channel KcsA: simulation studies.
    Biophys J. 2006 Feb 1;90(3):822-30. Epub 2005 Nov 4.

  62. Sansom MS, Bond PJ, Deol SS, Grottesi A, Haider S, Sands ZA.
    Molecular simulations and lipid-protein interactions: potassium channels and other membrane proteins.
    Biochem Soc Trans. 2005 Nov;33(Pt 5):916-20.

  63. Bond PJ, Cuthbertson J, Sansom MS.
    Simulation studies of the interactions between membrane proteins and detergents.
    Biochem Soc Trans. 2005 Nov;33(Pt 5):910-2.

  64. Law RJ, Capener C, Baaden M, Bond PJ, Campbell J, Patargias G, Arinaminpathy Y, Sansom MS.
    Membrane protein structure quality in molecular dynamics simulation.
    J Mol Graph Model. 2005 Oct;24(2):157-65.

  65. Bond PJ, Cuthbertson JM, Deol SS, Sansom MS.
    MD simulations of spontaneous membrane protein/detergent micelle formation.
    J Am Chem Soc. 2004 Dec 15;126(49):15948-9.

  66. Deol SS, Bond PJ, Domene C, Sansom MS.
    Lipid-protein interactions of integral membrane proteins: a comparative simulation study.
    Biophys J. 2004 Dec;87(6):3737-49. Epub 2004 Oct 1.

  67. Faraldo-Gómez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Sansom MS.
    Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.
    Proteins. 2004 Dec 1;57(4):783-91.

  68. Bond PJ, Sansom MS.
    The simulation approach to bacterial outer membrane proteins.
    Mol Membr Biol. 2004 May-Jun;21(3):151-61. Review.

  69. Domene C, Bond PJ, Deol SS, Sansom MS.
    Lipid/protein interactions and the membrane/water interfacial region.
    J Am Chem Soc. 2003 Dec 10;125(49):14966-7.

  70. Domene C, Bond PJ, Sansom MS.
    Membrane protein simulations: ion channels and bacterial outer membrane proteins.
    Adv Protein Chem. 2003;66:159-93. Review. No abstract available.

  71. Beckstein O, Biggin PC, Bond P, Bright JN, Domene C, Grottesi A, Holyoake J, Sansom MS.
    Ion channel gating: insights via molecular simulations.
    FEBS Lett. 2003 Nov 27;555(1):85-90. Review.

  72. Bond PJ, Sansom MS.
    Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.
    J Mol Biol. 2003 Jun 20;329(5):1035-53.

  73. Bond PJ, Faraldo-Gómez JD, Sansom MS.
    OmpA: a pore or not a pore? Simulation and modeling studies.
    Biophys J. 2002 Aug;83(2):763-75.

  74. Sansom MS, Bond P, Beckstein O, Biggin PC, Faraldo-Gómez J, Law RJ, Patargias G, Tieleman DP.
    Water in ion channels and pores--simulation studies.
    Novartis Found Symp. 2002;245:66-78; discussion 79-83, 165-8. Review.

 

 
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