Membrane proteins: Difference between revisions
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==Proteopedia Articles== | ==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]]. | *Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, [[2ic8]]. | ||
*[[Ion channels]] | *[[Ion channels]] | ||
*[[Pore forming toxin, α- | *[[Pore forming toxin, α-hemolysin]] | ||
*[[Urea transporter]] | *[[Urea transporter]] | ||
*[[Glutamate receptor | *[[Ionotropic Glutamate Receptor|Glutamate receptor]] | ||
*[[G protein-coupled receptor|G protein-coupled receptors]] | |||
*[[A Physical Model of the β2-Adrenergic Receptor ]] | |||
==Technical Issues== | |||
*[[Jmol/Visualizing membrane position|Representing membranes in Jmol/Proteopedia]] | |||
==See Also== | |||
* [[Secondary structure]] | |||
* [[Ligand Binding N-Terminal of Metabotropic Glutamate Receptors]] | |||
==External Resources== | ==External Resources== | ||
<ref group="xtra">PMID: 33744283</ref><references group="xtra"/> | |||
*[http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html Membrane Proteins of Known 3D Structure] (from the Stephen White laboratory at Univ. California, Irvine, USA). | *[http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html Membrane Proteins of Known 3D Structure] (from the Stephen White laboratory at Univ. California, Irvine, USA). | ||
*[http://www.mpibp-frankfurt.mpg.de/michel/public/memprotstruct.html Membrane Proteins of Known Structure] (from Max Planck Institute in Frankfurt, Germany) not updated since 2006 but useful for tabulation of crystallization conditions. | *[http://www.mpibp-frankfurt.mpg.de/michel/public/memprotstruct.html Membrane Proteins of Known Structure] (from Max Planck Institute in Frankfurt, Germany) not updated since 2006 but useful for tabulation of crystallization conditions. | ||
*[http://opm.phar.umich.edu/ Orientations of Proteins in Membranes (OPM) database] (University of Michigan, USA) features calculated membrane boundaries for all membrane proteins in the PDB. | *[http://opm.phar.umich.edu/ Orientations of Proteins in Membranes (OPM) database] (University of Michigan, USA) features calculated membrane boundaries for all membrane proteins in the PDB. | ||
* [http://bioinf.cs.ucl.ac.uk/psipred/ The PSIPRED Protein Structure Prediction Server] has a highly accurate method for protein secondary structure prediction and features also a widely used transmembrane topology prediction method. | * [http://memprotmd.bioch.ox.ac.uk/ 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 [https://github.com/pstansfeld/MemProtMD/ here]. | ||
* [http://bioinf.cs.ucl.ac.uk/psipred/ 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. | |||
<ref group="xtra">PMID: 17139331</ref><references group="xtra"/> | <ref group="xtra">PMID: 17139331</ref><references group="xtra"/> | ||
Latest revision as of 22:32, 14 April 2022
Proteopedia ArticlesProteopedia 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 IssuesTechnical Issues
See AlsoSee Also
External ResourcesExternal 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