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Technology Topics Modeling

Spot the pore

PSI-SGKB [doi:10.1038/th_psisgkb.2009.61]
Technical Highlight - January 2010
Short description: Straightforward web-based software pinpoints the central channel of any transmembrane protein.

The pore of the bacterial MscS voltage-modulated mechanosensitive channel (PDB 2OAU), as seen by PoreWalker. Atoms and residues that line the walls of the channel are colored orange and blue, respectively, and the rest of the protein is shown in green. The red spheres indicate the ‘path’ of the cavity from the periplasm (bottom) to the cytoplasm (top). The size of the spheres specifies the

Transmembrane channels usually have a cavity that spans the whole protein, although this is not always easy to identify. Janet Thornton and colleagues have developed an easy-to-use, automated method to visualize and describe the path followed by ions or molecules crossing the membrane.

Channel proteins control the transport of ions and some small molecules across biological membranes. They are essential to the cell — the maintenance of homeostasis, responsiveness to stimuli, and the electrochemical gradient across the cell membrane are just a few of their roles.

Until now, only one program, called HOLE, was available to visualize channels in transmembrane proteins. This was developed in 1993 and has proved very popular. But a new program, PoreWalker, looks to be more reliable and requires no user information.

PoreWalker uses a stepwise procedure to identify the channel of a known three-dimensional structure. First it identifies the pore center, which it assumes is the biggest and longest cavity through the channel. Then it optimizes geometric criteria to define the pore's diameter, lining residues, shape and size and displays this information.

The team tested their algorithm against several structures of transmembrane channel proteins from the Membrane Proteins of Known 3D Structure resource, which includes both ion and small-molecule channels. It seems that PoreWalker is able to locate correctly the pore axis and the pore centers in most of theses examples, although it struggled with two channels — Amt-B and Amt-1 — which are shaped like an hour-glass and have multiple exits.

Overall, PoreWalker is a robust, simple to use, web-available method for interpreting and analyzing coordinate data from PDB files. This algorithm will help provide a deeper understanding of membrane protein structures.

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  1. M. Pellegrini, T. Maiwald & J. M. Thornton. PoreWalker: A novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
    PLoS Comput. Biol. 5, e1000440 (2009). doi:10.1371/journal.pcbi.1000440

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