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Research project

OMSys: Towards a systems model of a bacterial outer membrane

  • Research funder:
    Biotechnology & Biological Sciences Research Council
  • Status:
    Not active

Project overview

Many bacteria have an outer membrane which is the interface between the cell and its environment. The components of this membrane are well studied at an individual level, but there is a need to model and understand the outer membrane as a whole. In this project we aim to develop such a model of a bacterial outer membrane, linking computer simulations of the component molecules through to a more 'systems biology' approach to modelling the outer membrane as a whole. Such an approach to modelling an OM must be multi-scale i.e. it must embrace a number of levels ranging from atomistic level modelling of e.g. the component proteins through to higher level 'agent-based' modelling of the interplay of multiple components within the outer membrane as a whole. The different levels of description will be integrated to enable predictive modelling in order to explore the roles of outer membrane changes in e.g. antibiotic resistance.

Research outputs

Atomistic molecular-dynamics simulations enable prediction of the Arginine Permeation Pathway through OccD1/OprD from pseudomonas aeruginosa
2014, Biophysical Journal, 107(8), 1853-1861
DOI: 10.1016/j.bpj.2014.08.035
Type: article
Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study
2013, Biochimica et Biophysica Acta (BBA) - Biomembranes, 1828(2), 284-293
DOI: 10.1016/j.bbamem.2012.08.021
Type: article
Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment
2013, Biochimica et Biophysica Acta (BBA) - Biomembranes, 1828(2), 715-723
DOI: 10.1016/j.bbamem.2012.09.002
Type: article
Single-stranded DNA within nanopores: conformational dynamics and implications for sequencing; a molecular dynamics simulation study
2012, Biophysical Journal, 103(5), 1028-1036
DOI: 10.1016/j.bpj.2012.08.012
Type: article
Molecular dynamics simulations of phosphatidylcholine membranes: a comparative force field study
2012, Journal of Chemical Theory and Computation, 8(11), 4593-4609
DOI: 10.1021/ct3003157
Type: article
Electroporation of the E. coli and S. Aureus membranes: molecular dynamics simulations of complex bacterial membranes
2011, The Journal of Physical Chemistry B, 115(45), 13381-13388
DOI: 10.1021/jp207013v
Type: article
Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: a multi-scale molecular dynamics simulation study
2011, Biochimica et Biophysica Acta (BBA) - Biomembranes
DOI: 10.1016/j.bbamem.2011.02.015
Type: article