MemProtMD: A Database of Membrane Proteins Embedded in Lipid Bilayers
Thomas D. Newport, Mark S.P. Sansom, and Phillip J. Stansfeld
Many biophysical studies indicate interactions with lipid/detergent molecules are critical to the folding/stability of membrane proteins, but only limited structural data are available on these interactions. In principle, atomistic molecular dynamics (MD) simulations may be used to follow the self-assembly of proteins with lipid/detergent. However, MD studies are limited to system sizes of up to ~100,000 atoms and time lengths of up to ~100 ns. Coarse grained (CG) models, in which small groups of atoms are treated collectively as large particles, provide a method for increasing timescales and system dimensions.
Setup
Membrane protein structures are automatically identified in the PDB and converted to Coarse Grained (CG) representation. Membrane lipids and solvent are then added and a 1000 ns Coarse-Grained Molecular Dynamics simulation is performed to allow a lipid bilayer to self-assemble. The final 800 ns simulation is analysed to study the dynamics of the assembled membrane. Simulations are then converted to atomistic resolution.
Citing MemProtMD
Except where indicated otherwise, all data provided through the MemProtMD web server and database is licenced under a Creative Commons Attribution 4.0 International License. You are free to use, share, adapt and redistribute data shown here, as long as it is properly attributed.
The MemProtMD Database and Server
The MemProtMD Database was published in Nucleic Acids Research. Please cite:
Newport, Thomas D. et al. The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions. Nucleic Acids Research (2019) Web. 12 Nov. 2018.
The MemProtMD Pipeline
The MemProtMD pipeline is a tool used to set up and run Coarse-Grained Self-Assembly simulations. The paper was published in Structure. Please cite:
Stansfeld, Phillip J. et al. Memprotmd: Automated Insertion Of Membrane Protein Structures Into Explicit Lipid Membranes. Structure 23.7 (2015): 1350-1361. Web. 2 Feb. 2015.
Contact the MemProtMD Team
By email
We're always interested to hear from users - send suggestions, bugs or requests to phillip.stansfeld@warwick.ac.uk.
On twitter
MemProtMD has an official Twitter feed - follow us or start a conversation with @MemProtMD.
In Person
MemProtMD is based in the Department of Biochemistry at Oxford University.
Meet the team
Phill Stansfeld
Phill's research focuses on using molecular dynamics simulations to study the properties of membrane proteins. After using coarse-grained simulations extensively to study membrane-bound proteins, as a PostDoc in Mark Sansom's group Phill built the MemProtMD pipeline to automate the process of assembling lipid bilayers around membrane-bound proteins, funded by the BBSRC. Phill is now a full Professor at the University of Warwick (see: https://stansfeldresearchgroup.wordpress.com).
Charlotte Lynch
With a background in materials science, Charlotte applied her skills to biological problems, first as a PostDoc within Mark Sansom's group, in Biochemistry, Oxford, and then within Philip Fowler's group in Modernising Molecular Microbiology. Charlotte joined the MemProtMD team as part of an ERC proposal to develop a Molecular Dynamics Database (MDDB).
Philip Biggin
Phil leads a group within the Structural Bioinformatics and Computational Biochemistry Unit (SBCB) specialising in using molecular dynamics simulations to study the structure and function of membrane proteins, specialising in receptor dynamics, conformational changes and ligand-binding (see: https://sbcb.bioch.ox.ac.uk/biggin.php).
Meet the Original team
Tom Newport
With a background in biological sciences and experience using a broad range of web technologies, Tom developed the MemProtMD pipeline and web interface. Tom was a DPhil Student on the EPSRC's Systems Biology Doctoral Training Centre between 2014 and 2018. Tom currently works at Oxford Nanopore Technologies.
Mark Sansom
Mark is now retired. Prior to retirement, Mark established and led a group within the Structural Bioinformatics and Computational Biochemistry Unit (SBCB) specialising in using molecular dynamics simulations to study the structure and function of membrane proteins. He was also Head of the Department of Biochemistry between 2011 and 2018.
External Collections in MemProtMD
MPStruc
Steve White's hand-curated collection of Membrane Proteins of Known Function, grouped by protein, structure, publication and function. http://blanco.biomol.uci.edu/mpstruc/
Transporter Classification Database (TCDB)
Milton Saier's collection of Transporters and Channels. http://www.tcdb.org
Protein Data Bank (PDB)
A Structural View of Biology containing 3D shapes of proteins, nucleic acids, and complex assemblies. https://www.rcsb.org
UniProtKB
A comprehensive, high-quality and freely accessible resource of protein sequence and functional information. https://www.uniprot.org
PFAM
A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). https://pfam.xfam.org
Gene Ontology
The GO defines concepts/classes used to describe gene function, and relationships. Split by molecular function, cellular component and biological process. http://geneontology.org