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

Group Members
Dr. BOND Peter JohnPrincipal Investigator
Dr. HUBER RolandPostdoctoral Fellow
Ms. BOON Li Shan Priscilla PhD student
Mr. Damien Francis Mohamed JEFFERIES 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. 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.

For full publication list »

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