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Professor Mark Sansom, Head of Department
A new home for membrane proteins
Membrane proteins in bilayers. There are now over 2000 membrane protein structures embedded within lipid membranes and housed within the MemProtMD database (Click to enlarge)
A new database that will help researchers understand the structure of proteins in a membrane is announced in the journal Structure.
Phill Stansfeld, with Mark Sansom, Jo Parker and Simon Newstead in the department, and collaborators in Oxford and Dublin, describe their pipeline 'MemProtMD' and its importance to the research community (1, 2).
The new resource is an automated simulation pipeline for predicting the location of a membrane protein structure in a lipid bilayer. It will give researchers greater insight into how a protein functions within its local membrane environment.
As Dr Stansfeld explains, the group was aiming to create a resource like the Protein Data Bank (PDB), specifically for membrane proteins. 'Whilst there have been methods which take a protein structure and insert it into a lipid bilayer, this has only been done manually up to now. With MemProtMD we have automated this process.'
Another novel feature of the tool is that it uses an 'explicit lipid membrane', doing more than simply inserting the protein into an artificial 'slab' membrane representation. MemProtMD determines the dynamic behaviour of protein in the membrane, taking into account how the protein may deform the lipid and where the protein-lipid interactions might be.