Membrane proteins: Difference between revisions
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==Technical Issues== | ==Technical Issues== | ||
===How To Show The Membrane In Proteopedia=== | |||
*[[Jmol/Visualizing membrane position|Representing membranes in Jmol/Proteopedia]] | *[[Jmol/Visualizing membrane position|Representing membranes in Jmol/Proteopedia]] | ||
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*[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://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. | * [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. | * [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 21:04, 29 March 2025
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
How To Show The Membrane In Proteopedia
See Also
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:https://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
Proteopedia Page Contributors and Editors (what is this?)
Wayne Decatur, Eric Martz, Nikki Hunter, Alexander Berchansky, Jaime Prilusky, David Canner
