Featured Technology Archive

Membrane Proteins of Known 3D Structure Database:
The Go-To Resource for Membrane Protein Structures and Hydropathy Information

mpstrucProfessor Stephen White began the Membrane Proteins of Known 3D Structure Database (mpstruc) in 1998. As someone who has a deep interest in membrane proteins, he simply thought that it would be a useful resource. White, a Professor of Physiology and Biophysics at the University of California-Irvine, started the web site as a fairly rudimentary HTML page that has progressed to the current searchable version through the expertise of software engineer Craig Snider. As the graph illustrates, there is an exponential growth in the number of membrane protein crystal structures being solved. In order to keep up with this trend, Snider has developed sophisticated software based on Groovy/Grails mpstruc graphto make it easy to keep the pages up to date. The dynamic user interface seen in the web browser is written in Javascript.

“Initially,” White said, “only unique structures (basically the first structure in each class) were included in the database, but over the years, as the site began to be used for teaching, there was demand to include all qualifying membrane protein structures, not just the first-of-class structures.” This is a challenge as the numbers of structures increases and articles describing new structures have progressed from the covers of top-tier journals to follow-up articles in many different biochemically oriented journals. Then, as now, White's group kept a sharp eye on the literature to ensure addition of qualified structures. Over the years, however, maintenance of the pages has become more of a community effort, as authors want their structures listed in mpstruc and consequently make sure they are included. One of the newest features of the web site is a bulletin board that allows authors to post structure information before publication if the structures have been released by the PDB. The pre-publication notes include a link to the PDB entry, as well as the tentative title and author list for the publication.

In addition to mpstruc, users have access to other membrane protein-related tools developed by the White Lab: MPtopo and MPEx. MPtopo (Membrane Protein Topology Database) is a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. This database contains 185 proteins with 1089 TM segments and can be searched by text or queried using information such as protein name, author name, PDB name, number of TM segments, etc. All results from MPtopo can be sent to MPEx (Membrane Protein Explorer), a tool for exploring the topology and other features of membrane proteins by means of hydropathy plots based upon thermodynamic and biological principles. Eventually MPtopo will contain the topologies of all of the first-of-class structures and will be tied to mpstruc. “But that is a very demanding task that will take lots of time and effort to complete,” White said.

Read more about:


Looking for more membrane protein-related resources? Mpstruc is just one of the resources that can be accessed through the PSI SBKB Membrane Proteins Hub. Browse research highlights, get acquainted with the PSI:Biology Membrane Protein Centers, follow PSI:Biology coverage of the Human TM Proteome, and more.

share on Facebook Tweet This share on LinkedIn add Google Bookmark add to delicious Share on reddit share on StumbleUpon Digg this