Multiscale Simulation, Modelling, and Design in Biological Chemistry and Biophysics
Dr. BOND Peter John
Principal Investigator

Group Members
Dr. BOND Peter JohnPrincipal Investigator
Dr. HOLDBROOK DanielPostdoctoral Fellow
Dr. HUBER RolandPostdoctoral Fellow
Dr. MARZINEK JanPostdoctoral Fellow
Ms. BOON Li Shan Priscilla PhD student
Mr. SHIVGAN Aishwary Tukaram PhD student
Ms. WEETMAN Samantha PhD student
Research Overview

The overall aim of our research is to understand the structural basis for key macromolecular recognition and assembly processes associated with essential biochemical functions, including signal transduction, transport, and folding. A particular focus is on the receptor complexes of the innate and adaptive branches of the mammalian immune system. We also have an ongoing interest in biomembranes, and their roles both in carrying information and in compartmentalization. Our main method of choice is molecular simulation, which provides a theoretical basis for studying the structure and dynamics of biomolecules in unprecedented detail. This yields information complementary to data obtained via other biochemical and biophysical approaches, and enables us to formulate and experimentally test new hypotheses with our collaborators.

As well as gaining fundamental insights into the mechanisms of action of biomolecules, we help to develop new approaches for pharmaceutical intervention in disease states, and where possible, to extend our observations to underlying principles applicable to (bio)nanotechnology. Our work encompasses several "flavours" of simulation, which enhance the nature and breadth of information we can obtain. On the one hand, we recognize the importance of the thermodynamic landscape, and use rigorous sampling approaches to quantitatively characterize macromolecular conformational changes and assembly processes in atomic detail. On the other, we take advantage of simplified, coarse-grained models to explore biological phenomena over extended time and length scales, enabling us to "fill the gap" between high-resolution structures and low-resolution biophysical data.

Scholarship Opportunities

We are currently offering PhD projects to Singaporeans and other nationals intending to take up Singapore citizenship, as part of the A*STAR Graduate Scholarship (Overseas) programme, in collaboration with groups at the University of Cambridge, University of Oxford, and Imperial College London. Project details »

Selected Publications

  1. Ivanov SM, Cawley A, Huber RG, Bond PJ, Warwicker J.
    Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold.
    PLoS One. 2017 Oct 10;12(10):e0185928. doi: 10.1371/journal.pone.0185928. eCollection 2017.
    PubMed PMID: 29016650; PubMed Central PMCID: PMC5634604.

  2. Bond PJ, Verma CS.
    Prog Biophys Mol Biol. 2017 Sep;128:1-2. doi: 10.1016/j.pbiomolbio.2017.07.005.
    PubMed PMID: 28743422.

  3. Kargas V, Marzinek JK, Holdbrook DA, Yin H, Ford RC, Bond PJ.
    A polar SxxS motif drives assembly of the transmembrane domains of Toll-like receptor 4.
    Biochim Biophys Acta. 2017 Oct;1859(10):2086-2095. doi: 10.1016/j.bbamem.2017.07.010. Epub 2017 Jul 22.
    PubMed PMID: 28739292.

  4. Chang HH, Huber RG, Bond PJ, Grad YH, Camerini D, Maurer-Stroh S, Lipsitch M.
    Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses.
    Bull World Health Organ. 2017 Jul 1;95(7):517-525I. doi: 10.2471/BLT.16.182105. Epub 2016 Jul 18.
    PubMed PMID: 28670016; PubMed Central PMCID: PMC5487971.

  5. Holdbrook DA, Burmann BM, Huber RG, Petoukhov MV, Svergun DI, Hiller S, Bond PJ.
    A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone.
    Structure. 2017 Jul 5;25(7):1079-1088.e3. doi:10.1016/j.str.2017.05.018. Epub 2017 Jun 22.
    PubMed PMID: 28648612.

  6. Petrlova J, Hansen FC, van der Plas MJA, Huber RG, Mörgelin M, Malmsten M, Bond PJ, Schmidtchen A.
    Aggregation of thrombin-derived C-terminal fragments as a previously undisclosed host defense mechanism.
    Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4213-E4222. doi: 10.1073/pnas.1619609114. Epub 2017 May 4.
    PubMed PMID: 28473418; PubMed Central PMCID: PMC5448181.

  7. Boags A, Hsu PC, Samsudin F, Bond PJ, Khalid S.
    Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes.
    J Phys Chem Lett. 2017 Jun 1;8(11):2513-2518. doi: 10.1021/acs.jpclett.7b00473. Epub 2017 May 22.
    PubMed PMID: 28467715.

  8. Collins RF, Kargas V, Clarke BR, Siebert CA, Clare DK, Bond PJ, Whitfield C, Ford RC.
    Full-length, Oligomeric Structure of Wzz Determined by Cryoelectron Microscopy Reveals Insights into Membrane-Bound States.
    Structure. 2017 May 2;25(5):806-815.e3. doi: 10.1016/j.str.2017.03.017. Epub 2017 Apr 20.
    PubMed PMID: 28434914.

  9. Santos-Moreno J, East A, Guilvout I, Nadeau N, Bond PJ, Tran Van Nhieu G, Francetic O.
    Polar N-terminal Residues Conserved in Type 2 Secretion Pseudopilins Determine Subunit Targeting and Membrane Extraction Steps during Fibre Assembly.
    J Mol Biol. 2017 Jun 2;429(11):1746-1765. doi: 10.1016/j.jmb.2017.04.005. Epub 2017 Apr 17.
    PubMed PMID: 28427876.

  10. Schönbach C, Verma C, Bond PJ, Ranganathan S.
    Bioinformatics and systems biology research update from the 15(th) International Conference on Bioinformatics (InCoB2016).
    BMC Bioinformatics. 2016 Dec 22;17(Suppl 19):524. doi: 10.1186/s12859-016-1409-7.
    PubMed PMID: 28155668; PubMed Central PMCID: PMC5259976.

For full publication list »

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