General features of the database
MPtopo is divided into three data sets. The 3D_Helix set contains helix-bundle membrane proteins whose three-dimentional structures have been determined using x-ray diffraction or NMR methods. The TM segments are known precisely.
The 1D_Helix set contains helix-bundle membrane proteins whose TM helices have been identified by experimental techniques such as gene fusion, proteolytic degradation, and amino acid deletion. We have examined carefully the publications related to the topologies of the proteins before including them in the database. No proteins have been included whose topologies are based solely on hydropathy plots. While we are reasonably certain of the number of TM segments of each protein included in 1D_Helix, the exact locations and lengths of the segments are less certain.
The 3D_Other set contains beta-barrel and montopic membrane proteins whose three-dimentional structures have been determined crystallographically. TM segments of the beta-barrel proteins are, of course, beta-strands. The monotopic proteins have no TM segments, and are bound to the membrane surface by hydrophobic alpha-helices running parallel to the membrane plane.
MPtopo is freely available. Records can be downloaded individually from a list, or as a composite text file.
MPtopo currently contains a total of 185 proteins with 1089 TM segments. We maintain a list of proteins included in the database, which is updated regularly as new proteins are added. The table given below lists several general characteristics of the database. Even though the database is modest in size, it is extremely useful because curation greatly reduces the possibility of incorrect TM assignments.
MPtopo was last updated Thursday, August 30, 2007
| MPtopo Data Set | |||
|---|---|---|---|
| Characteristic | 3D_Helix | 1D_Helix | 3D_Other |
| *Not included in this table (but included in the database) are monotopic proteins and proteins with complex topologies, such as chloride channels, whose TM segments are not easily classified. A list of these proteins is available here. | |||
| Number of Proteins/Protein Subunits | 119 | 41 | 25 |
| Number of total residues | 27431 | 17431 | 10319 |
| Number of residues in TM segments | 11848 | 6635 | 4207 |
| Number of total TM segments | 455 | 300 | 334 |
| Average TM segment length | 26±5 | 22±3 | 12±3 |
| TM segment length range | 10-48 | 11-46 | 6-23 |
General Features of MPtopo Querier
MPtopo Querier is a java applet developed for the purpose of searching/querying the MPtopo database. Querier can be activated by clicking on the 'Search MPtopo' button at the top of this page. MPtopo can be searched by the protein name, author name, number of TM segments, PIR number, PDB number, Swiss-Prot number, Swiss-Prot entry, Swiss-Prot name, and other fields. One can also do a full-text search using any word, phrase, or partial phrase. A search can be performed on either the complete database or on any one of the three subsets. The results of a search are returned within the 'MPtopoQuerier Results' window and represent the complete database record of each matched entry.
All matched database records are returned. Using the results window, each returned result can be viewed individually. The amino acid sequence of any one of the results can be sent to MPEx in order to generate and view its hydropathy profile using the 'to MPEx' button within the results window.
Using MPTopoQuerier
From 'Choose MPtopo database set', select the section of the database to be searched using the pull-down menu.
From 'Search Criterion' pull-down menus, select the field you wish to search, and then enter the term to search for in the 'Search Data' box. There are thirteen search fields:
- Protein Name. Official PDB and Swiss-Prot names are included in the records.
- PDB Number
- Full Text. Search data may consist of any word or partial word appearing in the database. Please do NOT use any boolean operators (AND, OR, etc.), or quotes( " ).
- Swiss-Prot number
- Swiss-Prot entry
- Swiss-Prot name
- Author last name
- Number of TM segments = . Enter a specific number of protein segments.
- Number of TM segments < . Number of TM segments less than a chosen value.
- Number of TM segments > . Number of TM segments greater than a chosen value.
- Nterm in
- Nterm out
Press the 'Reset' button to remove any selections and reset the form.
MPtopo will be expanded as new 3D structures are reported and as new 1D structures of high reliability are uncovered. Suggestions for 1D proteins to include in MPtopo are welcome! Send suggestions and comments to .
