********************************************************************* ********************************************************************* PORE WALKER 1.0 M. Pellegrini-Calace, T. Maiwald & J.M. Thornton EMBL/EBI, The Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Contacts: Dr. Marialuisa Pellegrini-Calace marial@ebi.ac.uk Tim Maiwald maiwald@ebi.ac.uk ********************************************************************* ********************************************************************* PoreWalker is a novel fully-automated method for the detection and characterisation of transmembrane protein channels from their 3D structure. It includes four consecutive steps: (1) identification of the protein main axis; (2) identification and optimization of the centre of the pore; (3) detection of the best cavity and optimization of the pore axis; (4) analysis of pore features: size, shape, regularity and straightness of the pore and pore- lining atoms and residues. PoreWalker is available as web-server at the following URL address: http://wwwdev.ebi.ac.uk/thornton-srv/software/PoreWalker/ ========= Inputs ========= PoreWalker only input is the 3D structure of the protein to analyse in PDB format. Since the program identifies the longest and widest cavity across the protein, i.e. the pore, it is advisable to submit a PDB file including coordinates of one functioning channel. For instance, for functional oligomers in which all chains contribute to make the pore, like potassium channels, the oligomeric structures should be submitted; for functional oligomers showing one pore per monomer, like in the case of aquaporins, a single monomer should be submitted. ========= Outputs ========= Pore Walkers outputs are shown in the following sections: 1) PORE SHAPE: The section shows the prediction of the shape of the pore. Conical frustums and cylinders and the shape prediction string represent a 2D projection of the 3D shape of the pore as calculated by variations of diameter values along the pore. In the diagram, the bottom of the pore axis (i.e. the lowest x-coordinate) correspond to the bottom of the stack. 'D' indicates a conical frustum generated by decreasing pore diameter values, i.e. the diameter of the lower base of the frustum is bigger than the diameter of its upper circle. 'U' indicates the opposite conical frustum, i.e. lower base diameter smaller than upper base diameter. 'S' indicates a cylinder. The pore diameter profile shows the variation of pore diameters along the pore from the lowest to the highest x-coordinate at 3 Angstrom steps. 2) PORE VISUALIZATION: Pore and estimated way through it are visualized by eight pictures, four for the whole structure and four to the pore only. Pictures are taken by cutting the protein structure along the pore axis, i.e. the x-axis, along the xy and xz planes and should be seen as sandwich-like complementary pairs. The lowest coordinate along the pore-axis corresponds to the bottom of any picture. Red sphere indicate the centre of the pore at 3 Angstrom steps along the pore axis, and their sizes are proportional to the pore diameter measured at that point. Identified pore- lining atoms and the corresponding pore-lining residues are coloured in orange and blue, respectively. The remaining portions of the proteins are shown in green. The PDB file used to derive the images, coloured accordingly in the temperature column, can be downloaded in the 'Downloads' section. 3) SLIDESHOW OF CROSS SECTIONS OF THE PORE: Two slideshows of sequential images show pore sections perpendicular to the pore axis at 5 Angstrom steps. Slideshows contain snapshots corresponding to pore slices of X Angstrom and taken from the lowest to the highest x-coordinates. Slices a seen from the lowest x- coordinates and from the highest x-coordinates as shown in the left and right slideshows, respectively. 4) FEATURES OF THE CAVITY Centres of the pore at 1 Angstrom slices and the smallest diameter per slice are shown in this section. Images of the structure are generated as in the PORE VISUALIZATION section. Protein surface is shown in green, pore centres are displayed as red spheres of constant diameter. The regularity of the pore cavity is shown by a pore diameter profile (1Ang) and by a diagram of consecutive straight and curve lines representing pore sections whose centres can or cannot be fitted on a line, respectively. Vertical straight lines indicate pore sections for which linear fitting produces parallel lines. In addition, the number of all slice pore centres that could be fitted on a line as percentage, the total number of lines and the RMSD from the best line that can be generated by linear fitting of all slice centres are shown. 5) DOWNLOADS Downloadable Pore Walker results file include: (a) a text file listing results from all calculations: pore shape prediction (3 Angstrom steps) as shape string (see PORE FEATURES section) and diameters along the channel; cavity properties at (1 Angstrom steps) as diameters along the channel and number of lines found list with corresponding RMSDs; list of pore lining residues and corresponding position along the pore axis (z-coordinate). (b) the submitted PDB structure as rotated and translated so that the predicted optimal pore axis corresponds to the x-axis and without hetero-atoms, in which predicted pore-lining atoms and residues are colored in blue and orange, respectively, and pore centres at 3 Angstrom slice are indicated as water molecules; (c) a text file including a list of the identified pore-lining residues with their beta-carbon coordinates along the pore axis (i.e. x-coordinates). =========== Citations =========== When publishing results obtained by PoreWalker, please cite: Pellegrini-Calace M, Maiwald T and Thornton JM (2009) "Pore-Walker: a novel tool for the identification and characterization of transmembrane protein channels from their three-dimensional structure", PLOS Comp. Biol., 5(7), 1-16.