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Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)
Published on: April 20, 2015
OPM: orientations of proteins in membranes database
Mikhail A Lomize1, Andrei L Lomize, Irina D Pogozheva
1College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI 48109-1065, USA.
Bioinformatics (Oxford, England)
|January 7, 2006
Summary
The Orientations of Proteins in Membranes (OPM) database offers a curated collection of membrane proteins with calculated positions within lipid bilayers. This resource facilitates the analysis and download of protein structures and their membrane boundaries.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Membrane proteins play crucial roles in cellular functions.
- Understanding their spatial arrangement in lipid bilayers is essential for deciphering biological mechanisms.
- The Protein Data Bank (PDB) contains structural information for many proteins, but their membrane orientations require specific calculation.
Purpose of the Study:
- To create a comprehensive database of membrane protein orientations.
- To provide a resource for analyzing and comparing protein structures within the lipid bilayer context.
- To make calculated protein structures and membrane boundaries readily accessible for research.
Main Methods:
- The Orientations of Proteins in Membranes (OPM) database compiles data from the Protein Data Bank.
- Spatial arrangements of transmembrane, monotopic, and peripheral proteins in lipid bilayers were theoretically calculated.
- Calculated orientations were compared with available experimental data.
Main Results:
- The OPM database includes a diverse collection of membrane proteins.
- Detailed structural classifications, species information, destination membranes, and segment counts are provided.
- Calculated parameters such as hydrophobic thickness and tilt angle are available for each protein.
Conclusions:
- The OPM database serves as a valuable resource for studying membrane protein structures and their interactions with lipid bilayers.
- It enables detailed analysis, sorting, and searching based on various structural and biological properties.
- All coordinate files and calculated membrane boundaries are available for download, facilitating further research and computational studies.
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