Research
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Our research is focused on studying and computationally modeling the protein machinery that drives membrane biology. Lipid bilayer membranes are bi-molecular lipid sheets, roughly 3-6 nanometers thick, that protect and compartmentalize the cellular machinery. Communication and transport across lipid bilayers is achieved by proteins associated with or embedded into the bilayer.


There are open Ph.D. positions and post-doctoral positions

Come and join an international group of students and post-docs working at the forefront of bioscience simulation and modeling, with extensive international collaboration in China, the USA, and Europe.

We collaborate with the experimental and computational lab of Martin Ulmschneider at Johns Hopkins University, Baltimore, MD, USA.

SJTU students will be encouraged to travel and partly do their Ph.D. projects in the USA.

For information please contact

 

Computer resources

MARCC
Maryland Advanced Research Computing Center
Xeon E5-2680v3 24 cores/node
Speed = 300 ns/day

ANTON
D.E. Shaw Anton at PSC (via NSF)
Speed = 4 us/day

 

Voltage-gated sodium channels (NaV)

This project is in collaboration with the X-ray crystallography group of B.A.Wallace, U. London, Birkbeck

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Voltage-gated sodium channel NaVMs. Conducting Na+ ions are shown as blue beads. 50 MB avi

Calculated I-V curves for Na+ (red) and K+ (blue) used for calculation of single-channel conductances.

NaVMs ion binding sites in the selectivity filter, as determined from MD simulations (A) and overlayed to the experimental (crystallographic) electron density map (F)

     

Martin B. Ulmschneider, Claire Bagnéris, Emily C. McCusker, Paul G. DeCaen, Markus Delling, David E. Clapham,
Jakob P. Ulmschneider, and B. A. Wallace
Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel
PNAS 2013, 110, 16, p.6364–6369

McCusker, E.C., Bagnéris, C., Naylor, C.E., Cole, A., D’Avanzo, N., Nichols, C.G., Wallace, B.A.
Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing.
Nature Communications 2012, 3, 1102


Membrane active peptides

MD Simulation of spontaneous insertion of the antimicrobial peptide PGLa into a DMPC lipid bilayer.

Mechanism of antimicrobial peptides. The peptides adsorb to the membrane and form surface aggregates. Subsequently, they kill the bacterium either through pore formation or membrane lysis.

M. B.Ulmschneider, J. P. Ulmschneider, N. Schiller, B.A. Wallace, G. von Heijne & S. H. White
Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion
Nature Communications 2014, 5:4863

 

Group photos

The 1st Shanghai Symposium on Membrane Active Peptides and Proteins, November 14th-15th, 2015

 

Group at Paulaner Shanghai 2014 - Jakob's favorite place

 

At the Shanghai Synchrotron 2014

 

 

 

 
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