Oxford University, Structural Bioinformatics & Computational Biochemistry Unit

Welcome to the Structural Bioinformatics and Computational Biochemistry Unit

We are interested in using computational methods to explore the relationship between structure and function in membrane proteins. This is important, as membrane proteins account for ~25% of all genes, and play key roles in the physiology of cells. Indeed, membrane proteins are targets for ~50% of drugs, and mutations in membrane proteins may result in diseases ranging from diabetes to cystic fibrosis.

Computer simulations allow membrane proteins to 'come alive' - that is, we can simulate the motions of membrane proteins and use this to explore the relationship between (static) structure and dynamic function. This is relevant to a number of areas ranging from biomedicine to nanotechnology.

Follow the links above to find out more about who we are and the work that we do.

Upcoming Events

Latest Publications:

Hedger, G.; Sansom, M.S.P.(2016)
Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations
BBA Biomembranes(paper, open access)

Vogeley, L.; El Arnaout, T; Bailey J; Stansfeld, P.J.; Boland, C; Caffrey, M. (2016)
Structural basis of lipoprotein signal peptidase II action and inhibition by the antibiotic globomycin
Science. (paper, open access)

Gu Y; Li, H; Dong, H; Wang, Z; Zeng Y; Paterson NG; Stansfeld, P.J.; Wang, W, Dong, C (2016)
Structural basis of outer membrane protein insertion by the BAM complex
Nature (paper, open access)

Li, D.; Stansfeld, P.J.; Sansom, M.S.P.; et al.; Caffrey, M. (2015)
Ternary structure reveals mechanism of a membrane diacylglycerol kinase.
Nature Communications. (paper, open access)

Hanson, S.M.; Sansom, M.S.P.; Becker, E.B.E. (2015)
Modeling Suggests TRPC3 Hydrogen Bonding and Not Phosphorylation Contributes to the Ataxia Phenotype of the Moonwalker Mouse.
Structure (paper, open access)

Stansfeld, P.J.;Goose, J.E.;Caffrey, M.; Carpenter, E.P.; Parker, J.L,; Newstead, S.; Sansom, M.S.P. (2015)
MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes.
Structure (paper, open access)

Jefferys, E.; Sands, Z.A.; Shi, J.; Sansom, M.S.P.; Fowler, P.W. (2015)
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries.
JCTC (paper, open access)

Hedger, G..; Sansom, M.S.P.; Koldsoe, H. (2015)
The juxtamembrane regions of human receptor tyrosine kinases exhibit conserved interaction sites with anionic lipids.
Nature Scientific Reports (paper, open access)

Hanson, S.M.; Newstead, S.; Swartz, K.J., Sansom, M.S.P. (2015)
Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation.
Biophysical Journal (paper, open access)

Kalli, A.C.; Sansom, M.S.P.; Reithmeier, R.A.F. (2015)
Molecular Dynamics Simulations of the Bacterial UraA H+-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin.
PlOS Comp. Biol. (paper, open access)

Benoist Laurent, Chavent, M.; Cragnolini, T.; Dahl, A.C.E.; Pasquali, S.; Derreumaux, P.; Sansom, M.S.P.; Baaden, M. (2014)
Epock: rapid analysis of protein pocket dynamics.
Bioinformatics (paper, open access)

Aryal, P.; Abd-Wahab, F.; Bucci, G; Sansom, M.S.P.; Tucker, Stephen J. (2014)
Influence of Lipids on the Hydrophobic Barrier within the Pore of the TWIK-1 K2P Channel.
Channels (paper, open access)

Koldsoe, H.K.; Shorthouse,D.; Helie,J.; Sansom, M.S.P. (2014)
Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers.
PLoS Comp Biol. (paper, open access)

Trick, J.L.; Wallace, E.J.; Bayley, H.; Sansom, M.S.P. (2014)
Designing a Hydrophobic Barrier within Biomimetic Nanopores.
ACS Nano (paper, open access)

Rouse, S.L.; Sansom, M.S.P. (2014)
Interactions of Lipids and Detergents with a Viral Ion Channel Protein: Molecular Dynamics Simulation Studies.
J. Phys. Chem. B (paper, open access)

Chavent, M.; Chetwynd, A.P.; Stansfeld,P.J.; Sansom, M.S.P. (2014)
Dimerization of the EphA1 Receptor Tyrosine Kinase Transmembrane Domain: Insights into the Mechanism of Receptor Activation.
Biochemistry (paper, open access)

Fowler, P.W.;Bollepalli, M.K.; Rapedius, M.; Nematian, E.; Shang, L; Sansom, M.S.P. ; Tucker, S.J; Baukrowitz, T. (2014)
Insights into the structural nature of the transition state in the Kir channel gating pathway.
Channels (paper, open access)

Kalli, A.C.; Sansom, M.S.P. (2014)
Interactions of peripheral proteins with model membranes as viewed by molecular dynamics simulations.
Biochemical Society Transactions (paper, open access)

Halim, K.B.; Koldso, H.K. ; Sansom, M.S.P. (2014)
Interactions of the EGFR juxtamembrane domain with PIP2-containing lipid bilayers: Insights from multiscale molecular dynamics simulations.
Biochimica et biophysica acta (paper, open access)

Aryal, P.; Abd-Wahab F; Bucci G; Sansom, M.S.P. and Tucker, S.J. (2014)
A hydrophobic barrier deep within the inner pore of the TWIK-1 K2P potassium channel.
Nature Communications (paper, open access)

Aryal, P.; Sansom, M.S.P. and Tucker, S.J. (2014)
Hydrophobic Gating in Ion Channels.
Journal of Molecular Biology (paper, open access)

J. Tan,Rouse, S.L.; Li, D.; Pye, V.D; Vogeley; L.,Brinth, A.R.; El Arnaout, T.; Whitney, J.C.; Howell, P.L.; Sansom, M.S.P. and Caffrey, M. (2014)
A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa.
Biological Crystallography (paper, open access)

Lonsdale, R.Rouse, S.L.; Sansom, M.S.P. and Mulholland, A.J. (2014)
A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes.
PLOS Comp. Biol. (paper, open access)

Bollepalli, Fowler, P.W.; Rapedius, M.; Shang, L.; Sansom, M.S.P. Tucker, S.J.; and Baukrowitz, T. (2014)
State-Dependent Network Connectivity Determines Gating in a K+ Channel.
Structure (paper, open access)

Hall,B.A.H;Abd Halim, K.;Buyan, A.; Emmanouil, B. and Sansom, M.S.P.. (2014)
A Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices.
JCTC (paper, open access)

Kalli, A.C.; Devaney, I. and Sansom, M.S.P.. (2014)
Interactions of Phosphatase and Tensin Homologue (PTEN) Proteins with Phosphatidylinositol Phosphates: Insights from Molecular Dynamics Simulations of PTEN and Voltage Sensitive Phosphatase.
Biochemistry (paper, PubMed)

Dunton, T.A.; Goose, J.E.; Gavaghan, D.J.; Sansom, M.S.P. and Osborne, J.M.(2014)
The Free Energy Landscape of Dimerization of a Membrane Protein, NanC
PLoS Comp. Bio. (paper, open access)

Reddy, T.; Manrique, S.; Buyan, A.; Hall, B.; Chetwynd, A. and Sansom, M.S.P.. (2014)
Primary and Secondary Dimer Interfaces of the FGFR3 Transmembrane Domain: Characterization via Multiscale Molecular Dynamics Simulations.
Biochemistry (paper, open access)

Zubcevic, L.; Bavro, V.N.; Muniz, J.R.C.; Schmidt, M.R.; Wang, S.; De Zorzi, R.; Venien-Bryan, C.; Sansom, M.S.P.; Nichols, C.G. and Tucker, S.J.(2014)
Control of KirBac3. 1 potassium channel gating at the interface between cytoplasmic domains
JBC (paper, open access)

Jefferys,E.; Sansom, M.S.P. and Fowler, P.W.(2014)
FD169: NRas slows the rate at which a model lipid bilayer phase separates
Faraday Discussion (paper, open access)

Chavent, M.; Reddy, T.; Goose, J.E.; Dahl, A.C.E.; Stone, J.E.; Jobard, B.J. and Sansom, M.S.P. and Osborne, J.M.(2014)
The Free Energy Landscape of Dimerization of a Membrane Protein, NanC
Faraday Discussion (paper, open access)

Roussel, G.; Rouse, S.L.; Sansom, M.S.P.; Michaux, C. and Perpete, E.A. (2014)
The role of 2-methyl-2, 4-pentanediol in sodium dodecyl sulfate micelle dissociation unveiled by dynamic light scattering and molecular dynamics simulations
Colloids and Surfaces B: Biointerfaces

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Last updated 22 October 2014