BACKGROUND: The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. RESULTS: The algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. The fully functional program is available as a stand-alone version and as plug-in for the molecular modeling program PyMol. Additionally, selected functions are accessible in an online version. CONCLUSION: The algorithm developed automatically finds the path from a starting point located within the interior of a protein. The algorithm is sufficiently rapid and robust to enable routine analysis of molecular dynamics trajectories containing thousands of snapshots. The algorithm is based on reciprocal metrics and provides an easy method to find a centerline, i.e. the spine, of complicated objects such as a protein tunnel. It can also be applied to many other molecules. CAVER is freely available from the web site http://loschmidt.chemi.muni.cz/caver/.

National Center for Biomolecular Research Masaryk University Kamenice 5 A4 625 00 Brno Czech Republic

Zobrazit více v PubMed

Kleywegt GJ, Jones TA. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallographica Section D. 1994;50:178–185. PubMed

Lesk AM. Molecular speleology – the exploration of crevices in proteins for prediction of binding-sites, design of drugs and analysis of surface recognition. Acta Crystallographica Section A. 1986;42:83–85.

Laurie ATR, Jackson RM. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics. 2005;21:1908–1916. doi: 10.1093/bioinformatics/bti315. PubMed DOI

Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science. 1998;7:1884–1897. PubMed PMC

Chaloupkova R, Sykorova J, Prokop Z, Jesenska A, Monincovaa M, Pavlova M, Tsuda M, Nagata Y, Damborsky J. Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel. Journal of Biological Chemistry. 2003;278:52622–52628. doi: 10.1074/jbc.M306762200. PubMed DOI

Bui JM, Tai K, McCammon JA. Acetylcholinesterase: Enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2. Journal of the American Chemical Society. 2004;126:7198–7205. doi: 10.1021/ja0485715. PubMed DOI

Tara S, Helms V, Straatsma TP, McCammon JA. Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A. Biopolymers. 1999;50:347–359. doi: 10.1002/(SICI)1097-0282(19991005)50:4<347::AID-BIP1>3.0.CO;2-R. PubMed DOI

Bitter I, Sato M, Bender MA, Kaufman A, Wan M, Wax MR. Automatic, accurate and robust colon centerline algorithm. Radiology. 2000;217:370–370.

Bitter I, Kaufman AE, Sato M. Penalized-distance volumetric skeleton algorithm. Transactions on Visualization and Computer Graphics. 2001;7:195–206. doi: 10.1109/2945.942688. DOI

Wan M, Liang ZR, Ke Q, Hong LC, Bitter I, Kaufman A. Automatic centerline extraction for virtual colonoscopy. Transactions on Medical Imaging. 2002;21:1450–1460. doi: 10.1109/TMI.2002.806409. PubMed DOI

Kaufman AE, Lakare S, Kreeger K, Bitter I. Virtual colonoscopy. Communications of the ACM. 2005;48:37–41. doi: 10.1145/1042091.1042117. DOI

Barber CB, Dobkin DP, Huhdanpaa H. The Quickhull algorithm for convex hulls. ACM Transactions on Mathematical Software. 1996;22:469–483. doi: 10.1145/235815.235821. DOI

Dijkstra EW. A note on two problems in connection with graphs. Numeriskche Mathematik. 1959;1:83–89.

Ford LR, Fulkerson DR. Flows in Networks. Princeton University Press; 1962.

Bellman R. On a Routing Problem. Quarterly of Applied Mathematic. 1958;16:87–90.

Floyd RW. Algorithm 97: Shortest path. Communications of the ACM. 1962;5:345. doi: 10.1145/367766.368168. DOI

DeLano WL. The case for open-source software in drug discovery. Drug Discovery Today. 2005;10:213–217. doi: 10.1016/S1359-6446(04)03363-X. PubMed DOI

Damborsky J, Rorije E, Jesenska A, Nagata Y, Klopman G, Peijnenburg WJGM. Structure-specificity relationships for haloalkane dehalogenases. Environmental Toxicology and Chemistry. 2001;20:2681–2689. doi: 10.1897/1551-5028(2001)020<2681:SSRFHD>2.0.CO;2. PubMed DOI

Franken SM, Rozeboom HJ, Kalk KH, Dijkstra BW. Crystal-structure of haloalkane dehalogenase – an enzyme to detoxify halogenated alkanes. EMBO Journal. 1991;10:1297–1302. PubMed PMC

Verschueren KHG, Kingma J, Rozeboom HJ, Kalk KH, Janssen DB, Dijkstra BW. Crystallographic and fluorescence studies of the interaction of haloalkane dehalogenase with halide-ions – studies with halide compounds reveal a halide binding-site in the active-site. Biochemistry. 1993;32:9031–9037. doi: 10.1021/bi00086a008. PubMed DOI

Verschueren KHG, Franken SM, Rozeboom HJ, Kalk KH, Dijkstra BW. Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction-mechanism. Journal of Molecular Biology. 1993;232:856–872. doi: 10.1006/jmbi.1993.1436. PubMed DOI

Verschueren KHG, Seljee F, Rozeboom HJ, Kalk KH, Dijkstra BW. Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase. Nature. 1993;363:693–698. doi: 10.1038/363693a0. PubMed DOI

Krooshof GH, Ridder IS, Tepper AWJW, Vos GJ, Rozeboom HJ, Kalk KH, Dijkstra BW, Janssen DB. Kinetic analysis and X-ray structure of haloalkane dehalogenase with a modified halide-binding site. Biochemistry. 1998;37:15013–15023. doi: 10.1021/bi9815187. PubMed DOI

Pikkemaat MG, Ridder IS, Rozeboom HJ, Kalk KH, Dijkstra BW, Janssen DB. Crystallographic and kinetic evidence of a collision complex formed during halide import in haloalkane dehalogenase. Biochemistry. 1999;38:12052–12061. doi: 10.1021/bi990849w. PubMed DOI

Ridder IS, Rozeboom HJ, Dijkstra BW. Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 Angstrom resolution. Acta Crystallographica Section D. 1999;55:1273–1290. PubMed

Schanstra JP, Ridder IS, Heimeriks GJ, Rink R, Poelarends GJ, Kalk KH, Dijkstra BW, Janssen DB. Kinetic characterization and X-ray structure of a mutant of haloalkane dehalogenase with higher catalytic activity and modified substrate range. Biochemistry. 1996;35:13186–13195. doi: 10.1021/bi961151a. PubMed DOI

Newman J, Peat TS, Richard R, Kan L, Swanson PE, Affholter JA, Holmes IH, Schindler JF, Unkefer CJ, Terwilliger TC. Haloalkane dehalogenases: Structure of a Rhodococcus enzyme. Biochemistry. 1999;38:16105–16114. doi: 10.1021/bi9913855. PubMed DOI

Marek J, Vevodova J, Smatanova IK, Nagata Y, Svensson LA, Newman J, Takagi M, Damborsky J. Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry. 2000;39:14082–14086. doi: 10.1021/bi001539c. PubMed DOI

Oakley AJ, Prokop Z, Bohac M, Kmunicek J, Jedlicka T, Monincova M, Kuta-Smatanova I, Nagata Y, Damborsky J, Wilce MCJ. Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: Evidence for product- and water-mediated inhibition. Biochemistry. 2002;41:4847–4855. doi: 10.1021/bi015734i. PubMed DOI

Oakley AJ, Klvana M, Otyepka M, Nagata Y, Wilce MCJ, Damborsky J. Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 Angstrom resolution: Dynamics of catalytic residues. Biochemistry. 2004;43:870–878. PubMed

Streltsov VA, Prokop Z, Damborsky J, Nagata Y, Oakley A, Wilce MCJ. Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates. Biochemistry. 2003;42:10104–10112. doi: 10.1021/bi027280a. PubMed DOI

Otyepka M, Damborsky J. Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains. Protein Science. 2002;11:1206–1217. doi: 10.1110/ps.ps3830102. PubMed DOI PMC

Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst

Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site

ChannelsDB: database of biomacromolecular tunnels and pores

Membrane cholesterol access into a G-protein-coupled receptor

The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

HotSpot Wizard: a web server for identification of hot spots in protein engineering

Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling