Membrane proteins

From Proteopedia

Proteopedia Articles

• Receptor#Transmembrane (cell surface) receptors
• Photosystem II
• Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, 2ic8.
• Ion channels
• Pore forming toxin, α-hemolysin
• Urea transporter
• Glutamate receptor
• G protein-coupled receptors
• A Physical Model of the β2-Adrenergic Receptor

Technical Issues

• Representing membranes in Jmol/Proteopedia

See Also

• Secondary structure
• Ligand Binding N-Terminal of Metabotropic Glutamate Receptors

External Resources

• Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem. 2021 Jan-Jun;296:100557. doi: 10.1016/j.jbc.2021.100557. Epub 2021, Mar 18. PMID:33744283 doi:http://dx.doi.org/10.1016/j.jbc.2021.100557

• Membrane Proteins of Known 3D Structure (from the Stephen White laboratory at Univ. California, Irvine, USA).
• Membrane Proteins of Known Structure (from Max Planck Institute in Frankfurt, Germany) not updated since 2006 but useful for tabulation of crystallization conditions.
• Orientations of Proteins in Membranes (OPM) database (University of Michigan, USA) features calculated membrane boundaries for all membrane proteins in the PDB.
• MemProtMD - A database of membrane proteins embedded in lipid bilayers features a database of over 5000 intrinsic membrane protein structures identified in the Protein Data Bank, inserted into simulated lipid bilayers using Coarse-Grained Self Assembly Molecular Dynamics simulations. A few of the MemProtMD workflows have been put together as a set of Google Colab notebooks for establishing membrane protein structures in bilayers, see here.
• The PSIPRED Protein Structure Prediction Server has a highly accurate method for protein secondary structure prediction for proteins without an empirically-determined 3D structure and features also a widely used transmembrane topology prediction method where the output includes a Kyte-Doolittle Hydropathy Plot.

• von Heijne G. Membrane-protein topology. Nat Rev Mol Cell Biol. 2006 Dec;7(12):909-18. PMID:17139331 doi:10.1038/nrm2063