Nucleic Acids Research

This Article Abstract Print PDF (711K) Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal Add to My Personal Archive Download to citation manager Search for citing articles in: ISI Web of Science (135) Request Permissions Commercial Re-use Guidelines for Open Access NAR Content Google Scholar Articles by Binkowski, T. A. Articles by Liang, J. Search for Related Content PubMed PubMed Citation Articles by Binkowski, T. A. Articles by Liang, J. Social Bookmarking          What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 13 3352-3355
© 2003 Oxford University Press

CASTp: Computed Atlas of Surface Topography of proteins

T. Andrew Binkowski, Shapor Naghibzadeh and Jie Liang^*

Department of Bioengineering, MC-063, University of Illinois at Chicago, 851 S. Morgan Street, Chicago, IL 60607, USA

*To whom correspondence should be addressed. Tel: +1 3123551789; Fax: +1 3129965921; Email: jliang{at}uic.edu

Received February 14, 2003; Accepted March 6, 2003

	ABSTRACT

TOP ABSTRACT INTRODUCTION CASTp SERVER: VOIDS AND... USING CASTp AVAILABILITY REFERENCES

 
Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These include pockets located on protein surfaces and voids buried in the interior of proteins. The measurement includes the area and volume of pocket or void by solvent accessible surface model (Richards' surface) and by molecular surface model (Connolly's surface), all calculated analytically. CASTp can be used to study surface features and functional regions of proteins. CASTp includes a graphical user interface, flexible interactive visualization, as well as on-the-fly calculation for user uploaded structures. CASTp is updated daily and can be accessed at http://cast.engr.uic.edu.

	INTRODUCTION

TOP ABSTRACT INTRODUCTION CASTp SERVER: VOIDS AND... USING CASTp AVAILABILITY REFERENCES

 
Protein performs its function through interaction with other molecules such as substrate, ligand, DNA and other domains of proteins. The three-dimensional structure of protein provides the necessary shape and physicochemical texture to facilitate these interactions. Structural information of protein surface regions enables detailed studies of the relationship of protein structure and function. Specifically, characterization of protein surface regions helps to analyze enzyme mechanism, to determine binding specificity and to plan mutation studies. It can also help to identify the biological roles of newly solved protein structures with an unknown function.

	CASTp SERVER: VOIDS AND POCKETS OF PROTEINS

TOP ABSTRACT INTRODUCTION CASTp SERVER: VOIDS AND... USING CASTp AVAILABILITY REFERENCES

 
The CASTp web server aims to provide a comprehensive and detailed quantitative characterization of interior voids and surface pockets of proteins, which are prominent concave regions of proteins that are frequently associated with binding events (1,2). CASTp is based on the alpha shape and the pocket algorithm developed in computational geometry (2,3). In CASTp, voids are defined as buried unfilled empty space inside proteins after removing all hetero atoms that are inaccessible to water molecules (modeled as a spherical probe of 1.4 Å) from outside (4). Pockets are defined as concave caverns with constrictions at the opening on the surface regions of proteins. Unlike voids, pockets allow easy access of water probes from the outside.

CASTp identifies all pockets and voids on a protein structure and provides detailed delineation of all atoms participating in their formation. It also measures the volume and area of each pocket and void analytically, using both the solvent accessible surface model (Richards' surface) and molecular surface model (Connolly's surface). In addition, it measures the size of mouth openings of individual pockets, which helps to assess the accessibility of binding sites to various ligands and substrates. CASTp computation has been shown to be useful in a number of biological studies (5–10). The underlying algorithm and example of applications have been described elsewhere (2,3).

The CASTp server, in its most current release, was updated in January 2003. The previous version was launched in 1998 at the University of Minnesota. It is listed in the Research Consortium of Structural Bioinformatics PDB website at the San Diego Supercomputing Center (http://www.rcsb.org/pdb/), a central portal of structural bioinformatics worldwide. CASTp allows access to information of computed pockets and voids for structures in the Protein Data Bank (PDB). The server currently contains characterization of 1 322 538 pockets and voids that have been computed from 19 161 protein structures from the PDB. The CASTp server is updated nightly with new PDB entries.

	USING CASTp

TOP ABSTRACT INTRODUCTION CASTp SERVER: VOIDS AND... USING CASTp AVAILABILITY REFERENCES

 
An intuitive graphic user interface allows querying of the CASTp server by typing the four letter PDB name of a protein structure, by keyword searching or by submitting their own molecular structure in the PDB format. Figure 1 shows the form for requesting a CASTp calculation. When querying by keyword, a list of relevant PDB structures are returned as obtained by redirecting to RCSB's PDB query site.

View larger version (60K): [in this window] [in a new window]   Figure 1. An intuitive graphic user interface allows users to request a CASTp calculation by typing the four letter PDB name of a protein structure, by keyword searching or by submitting their own molecular structure in the PDB format. For visualization, the user has the choice of using MDL's Chime plug-in (Windows, MacOS and IRIX only) or Mage (11) java applet. In addition, users may also elect to have results emailed back as files.

 
For visualization, the user has the choice of using Chime plug-in developed by MDL Information Systems or Mage developed in the Richardson laboratory at Duke University (http://kinemage.biochem.duke.edu) (11). Chime is a browser plug-in that runs under Windows, MacOS and IRIX. This is a good choice for Windows 95/98/NT/2000 or IRIX. Mage is a Java applet that requires only a Java-enabled browser. This is a good choice for Linux platforms.

Figure 2 shows the binding site pocket on the catalytic domain of protein kinase A (pdb 2cpk [PDB] ) that is automatically identified by CASTp. Protein kinase A is an important enzyme in the signal transduction of vertebrates, participating in the regulation of glycogen synthesis, fatty acid synthesis, the oxidation of pyruvate to acteyl-CoA, mobilization of triacylglycerols and other processes. Many functionally important residues in the catalytic domain are located in this pocket, including the whole of the glycine rich loop (GTGSFGAV) starting from residue 50 that anchors ATP to the protein, the invariant K72 important to the optimum activity of the enzyme, the stabilizing E91 which forms a salt bridge with K72, residue E127 known to bind to the pseudosubstrate synthetic inhibitor, residue K168 in the catalytic loop which neutralizes the local negative charge of the gamma phosphate of the ATP, residue N171 which stabilizes the catalytic loop through hydrogen bonding to the backbone carbonyl of D166 (which is also identified) and residues D184 and G186 in the well-conserved triplet of DFG, where D184 is an invariant residue for orienting the gamma phosphate of MgATP for transfer to the substrate (12). Additional recent examples showing how CASTp computations have been used can be found in the literature (13–17).

View larger version (104K): [in this window] [in a new window]   Figure 2. Visualization of ATP binding pocket automatically identified on the structure of the catalytic subunit of protein kinase A (pdb 2cpk [PDB] ). It is the largest pocket and contains the following residues: L49, G50, T51, G52, S53, F54, G55, R56, V57, A70, K72, L74, V79, N84, H87, T88, E91, L95, V104, M120, E121, Y122, V123, E127, D166, K168, E170, N171, L173, T183, D184, G186, F187, G200, T201 and F327. A large number of these residues are known to be functionally important (see http://www.sdsc.edu/kinases/) (12).

 
Once a protein is loaded in the browser, the user can interactively interrogate the protein structure. In addition to the simple manipulations built in to Chime plug-in and Mage applet (i.e. rotation, translation, zoom in/out), the user interface also allows selective highlighting of individual pockets. Summary information of measurement of individual pocket and void is conveniently displayed in a scrolling menu. Selection of a specific pocket from this menu also reveals the wall atoms comprising the pocket in a separate small window. By typing in the name and number of a residue, the user can easily identify the pocket or void that contains a particular residue.

Users may also choose the ‘Email only’ option to obtain results via email attachment. These include the following files: summary information of pockets and voids, summary information of mouth openings of pockets, atomic delineation of pocket walls, atomic delineation of mouth rims and a RasMol (18) and a kinemage (11) visualization script.

CASTp also supports on-the-fly calculations of voids and pockets on a structure uploaded by user. The user only needs to submit the coordinate file of a structure in the PDB format. When the calculation is finished, a visualization window will be opened. The results will also be emailed as an attachment to the user if requested. An added feature for the calculation of uploaded structures is that the user can adjust the probe radius to any values between 0.0 and 10.0 Å.

	AVAILABILITY

TOP ABSTRACT INTRODUCTION CASTp SERVER: VOIDS AND... USING CASTp AVAILABILITY REFERENCES

 
CASTp can be freely accessed on the World Wide Web at http://cast.engr.uic.edu.

	ACKNOWLEDGEMENTS

 
We thank Drs Herbert Edelsbrunner and Mike Facello for the alpha shape API library upon which the geometry engine of CASTp is implemented. We thank Dr Clare K. Woodward for encouragement. This work is supported by research grants from the National Science Foundation (CAREER DBI0133856 and DBI0078270).

	REFERENCES

TOP ABSTRACT INTRODUCTION CASTp SERVER: VOIDS AND... USING CASTp AVAILABILITY REFERENCES

 

1. Lakowski,R.A., Luscombe,N.M., Swindells,M.B. and Thornton,J.M. (1996) Protein clefts in molecular recognition and function. Protein Sci., 5, 2438–2452.[Web of Science][Medline]

2. Liang,J., Edelsbrunner,H. and Woodward,C. (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci., 7, 1884–1897.[Web of Science][Medline]

3. Edeslbrunner,H., Facello,M. and Liang,J. (1998) On the definition and the construction of pockets in macromolecules. Disc. Appl. Math., 88, 18–29.

4. Lee,B. and Richards,F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55, 379–400.[CrossRef][Web of Science][Medline]

5. Paetzel,M. and Strynadka,N. (1999) Common protein architecture and binding sites in proteases utilizing a Ser/Lys dyad mechanism. Protein Sci., 8, 2533–2536.[Web of Science][Medline]

6. Kim,S., Liang,J. and Barry,B. (1997) Chemical complementation identifies a proton acceptor for redox-active tyrosin D in photosystem II. Proc. Natl Acad. Sci. USA, 94, 14406–14411.[Abstract/Free Full Text]

7. LiCata,V.J. and Bernlohr,D.A. (1998) Surface properties of adipocyte lipid-binding protein: Response to lipid binding, and comparison with homologous proteins. Proteins, 33, 577–589.[CrossRef][Web of Science][Medline]

8. Ory,J.J. and Banaszak,L.J. (1999) Studies of the ligand binding reaction of adipocyte lipid binding protein using the fluorescent probe 1,8-anilinonaphthalene-8-sulfonate. Biophys. J., 77, 1107–1116.[Web of Science][Medline]

9. Li,H., Raman,C., Glaser,C., Blasko,E., Young,T., Parkinson,J., Whitlow,M. and Poulos,T. (1999) Crystal structures of zinc-free and -bound heme domain of human inducible nitric-oxide synthase. J. Biol. Chem., 274, 21276–21284.[Abstract/Free Full Text]

10. Thompson,J., Reese-Wagoner,A. and Banaszak,L. (1999) Liver fatty acid binding protein: species variation and the accommodation of different ligands. Biochim. Biophys. Acta, 1441, 117–130.[Medline]

11. Richardson,D.C. and Richardson,J.S. (1994) Kinemages-simple macromolecular graphics for interactive teaching and publication. Trends Biochem. Sci., 3, 135–138.

12. Smith,C., Shindyalov,I., Veretnik,S., Gribskov,M., Taylor,S., Ten Eyck,L. and Bourne,P. (1997) Development of Internet-based multimedia applications. Trends Biochem. Sci., 22, 444–446.[CrossRef][Web of Science][Medline]

13. Liu,R., Pidikiti,R., Ha,C.E., Petersen,C.E., Bhagavan,N.V. and Eckenhoff,R.G. (2002) The role of electrostatic interactions in human serum albumin binding and stabilization by halothane. J. Biol. Chem., 277, 36373–36379.[Abstract/Free Full Text]

14. Thompson,J.R. and Banaszak,L.J. (2002) Lipid-protein interactions in lipovitellin. Biochemistry, 41, 9398–9409.[CrossRef][Medline]

15. Paetzel,M., Dalbey,R.E. and Strynadka,N.C.J. (2002) Crystal structure of a bacterial signal peptidase apoenzyme—implications for signal peptide binding and the Ser-Lys dyad mechanism. J. Biol. Chem., 277, 9512–9519.[Abstract/Free Full Text]

16. Regni,C., Tipton,P.A. and Beamer,L.J. (2002) Crystal structure of PMM/PGM: an enzyme in the biosynthetic pathway of P.aeruginosa virulence factors. Structure, 10, 269–279.[Medline]

17. Hilgers,M.T. and Ludwig,M.L. (2001) Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site. Proc. Natl Acad. Sci. USA, 98, 11169–11174.[Abstract/Free Full Text]

18. Sayle,R.A. and Milner-White,E.J. (1995) RASMOL: biomolecular graphics for all. Trends Biochem. Sci., 20, 374.[CrossRef][Web of Science][Medline]

CiteULike    Connotea    Del.icio.us    What's this?

This article has been cited by other articles:

				V. Sauve, P. Roversi, K. J. Leath, E. F. Garman, R. Antrobus, S. M. Lea, and B. C. Berks Mechanism for the Hydrolysis of a Sulfur-Sulfur Bond Based on the Crystal Structure of the Thiosulfohydrolase SoxB J. Biol. Chem., August 7, 2009; 284(32): 21707 - 21718. [Abstract] [Full Text] [PDF]

				S. Sonavane and P. Chakrabarti Cavities in protein-DNA and protein-RNA interfaces Nucleic Acids Res., August 1, 2009; 37(14): 4613 - 4620. [Abstract] [Full Text] [PDF]

				K. Rother, P. W. Hildebrand, A. Goede, B. Gruening, and R. Preissner Voronoia: analyzing packing in protein structures Nucleic Acids Res., January 1, 2009; 37(suppl_1): D393 - D395. [Abstract] [Full Text] [PDF]

				M. H. Kim, Y. Kim, H.-J. Park, J. S. Lee, S.-N. Kwak, W.-H. Jung, S.-G. Lee, D. Kim, Y.-C. Lee, and T.-K. Oh Structural Insight into Bioremediation of Triphenylmethane Dyes by Citrobacter sp. Triphenylmethane Reductase J. Biol. Chem., November 14, 2008; 283(46): 31981 - 31990. [Abstract] [Full Text] [PDF]

				W. C. Lee, M. L. Reniere, E. P. Skaar, and M. E. P. Murphy Ruffling of Metalloporphyrins Bound to IsdG and IsdI, Two Heme-degrading Enzymes in Staphylococcus aureus J. Biol. Chem., November 7, 2008; 283(45): 30957 - 30963. [Abstract] [Full Text] [PDF]

				C. Walsh, M. Gangloff, T. Monie, T. Smyth, B. Wei, T. J. McKinley, D. Maskell, N. Gay, and C. Bryant Elucidation of the MD-2/TLR4 Interface Required for Signaling by Lipid IVa J. Immunol., July 15, 2008; 181(2): 1245 - 1254. [Abstract] [Full Text] [PDF]

				T.-L. Chiu, Z. Wen, S. G. Rupasinghe, and M. A. Schuler Comparative molecular modeling of Anopheles gambiae CYP6Z1, a mosquito P450 capable of metabolizing DDT PNAS, July 1, 2008; 105(26): 8855 - 8860. [Abstract] [Full Text] [PDF]

				I. Sanchez-Moreno, R. Coral-Vazquez, J.P. Mendez, and P. Canto Full-length SRY protein is essential for DNA binding Mol. Hum. Reprod., June 1, 2008; 14(6): 325 - 330. [Abstract] [Full Text] [PDF]

				J. A. Gavira, A. Camara-Artigas, W. De Jesus-Bonilla, J. Lopez-Garriga, A. Lewis, R. Pietri, S.-R. Yeh, C. L. Cadilla, and J. M. Garcia-Ruiz Structure and Ligand Selection of Hemoglobin II from Lucina pectinata J. Biol. Chem., April 4, 2008; 283(14): 9414 - 9423. [Abstract] [Full Text] [PDF]

				N. Shen, M. Zhou, B. Yang, Y. Yu, X. Dong, and J. Ding Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states Nucleic Acids Res., March 27, 2008; 36(4): 1288 - 1299. [Abstract] [Full Text] [PDF]

				E. Ploskon, C. J. Arthur, S. E. Evans, C. Williams, J. Crosby, T. J. Simpson, and M. P. Crump A Mammalian Type I Fatty Acid Synthase Acyl Carrier Protein Domain Does Not Sequester Acyl Chains J. Biol. Chem., January 4, 2008; 283(1): 518 - 528. [Abstract] [Full Text] [PDF]

				J. Fort, L. R. de la Ballina, H. E. Burghardt, C. Ferrer-Costa, J. Turnay, C. Ferrer-Orta, I. Uson, A. Zorzano, J. Fernandez-Recio, M. Orozco, et al. The Structure of Human 4F2hc Ectodomain Provides a Model for Homodimerization and Electrostatic Interaction with Plasma Membrane J. Biol. Chem., October 26, 2007; 282(43): 31444 - 31452. [Abstract] [Full Text] [PDF]

				G. Cacciapuoti, M. Porcelli, M. A. Moretti, F. Sorrentino, L. Concilio, V. Zappia, Z.-J. Liu, W. Tempel, F. Schubot, J. P. Rose, et al. The First Agmatine/Cadaverine Aminopropyl Transferase: Biochemical and Structural Characterization of an Enzyme Involved in Polyamine Biosynthesis in the Hyperthermophilic Archaeon Pyrococcus furiosus J. Bacteriol., August 15, 2007; 189(16): 6057 - 6067. [Abstract] [Full Text] [PDF]

				Y. Xue, L. B. Moore, J. Orans, L. Peng, S. Bencharit, S. A. Kliewer, and M. R. Redinbo Crystal Structure of the Pregnane X Receptor-Estradiol Complex Provides Insights into Endobiotic Recognition Mol. Endocrinol., May 1, 2007; 21(5): 1028 - 1038. [Abstract] [Full Text] [PDF]

				B. Campanini, F. Schiaretti, S. Abbruzzetti, D. Kessler, and A. Mozzarelli Sulfur Mobilization in Cyanobacteria: THE CATALYTIC MECHANISM OF L-CYSTINE C-S LYASE (C-DES) FROM SYNECHOCYSTIS J. Biol. Chem., December 15, 2006; 281(50): 38769 - 38780. [Abstract] [Full Text] [PDF]

				H. Matsumura, K. Izui, and K. Mizuguchi A novel mechanism of allosteric regulation of archaeal phosphoenolpyruvate carboxylase: a combined approach to structure-based alignment and model assessment Protein Eng. Des. Sel., September 1, 2006; 19(9): 409 - 419. [Abstract] [Full Text] [PDF]

				J. Dundas, Z. Ouyang, J. Tseng, A. Binkowski, Y. Turpaz, and J. Liang CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W116 - W118. [Abstract] [Full Text] [PDF]

				C. L. Lawson, B. H. Yung, A. G. Barbour, and W. R. Zuckert Crystal Structure of Neurotropism-Associated Variable Surface Protein 1 (Vsp1) of Borrelia turicatae. J. Bacteriol., June 1, 2006; 188(12): 4522 - 4530. [Abstract] [Full Text] [PDF]

				A. Borgia, D. Bonivento, C. Travaglini-Allocatelli, A. Di Matteo, and M. Brunori Unveiling a Hidden Folding Intermediate in c-Type Cytochromes by Protein Engineering J. Biol. Chem., April 7, 2006; 281(14): 9331 - 9336. [Abstract] [Full Text] [PDF]

				Y. Y. Tseng and J. Liang Estimation of Amino Acid Residue Substitution Rates at Local Spatial Regions and Application in Protein Function Inference: A Bayesian Monte Carlo Approach Mol. Biol. Evol., February 1, 2006; 23(2): 421 - 436. [Abstract] [Full Text] [PDF]

				R. Khayat, L. Tang, E. T. Larson, C. M. Lawrence, M. Young, and J. E. Johnson From the Cover: Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses PNAS, December 27, 2005; 102(52): 18944 - 18949. [Abstract] [Full Text] [PDF]

				T. A. Binkowski, P. Freeman, and J. Liang pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins Nucleic Acids Res., July 1, 2004; 32(suppl_2): W555 - W558. [Abstract] [Full Text] [PDF]

This Article Abstract Print PDF (711K) Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal Add to My Personal Archive Download to citation manager Search for citing articles in: ISI Web of Science (135) Request Permissions Commercial Re-use Guidelines for Open Access NAR Content Google Scholar Articles by Binkowski, T. A. Articles by Liang, J. Search for Related Content PubMed PubMed Citation Articles by Binkowski, T. A. Articles by Liang, J. Social Bookmarking          What's this?

Online ISSN 1362-4962 - Print ISSN 0305-1048

Copyright © 2009 Oxford University Press

Oxford Journals Oxford University Press

• Site Map
• Privacy Policy
• Frequently Asked Questions

Other Oxford University Press sites: Oxford University Press Oxford Journals China Oxford Journals Japan American National Biography Booksellers' Information Service Children's Fiction and Poetry Children's Reference Corporate & Special Sales Dictionaries Dictionary of National Biography Digital Reference English Language Teaching Higher Education Textbooks Humanities International Education Unit Law Medicine Music Online Products Oxford English Dictionary Reference Rights and Permissions Science School Books Social Sciences Very Short Introductions World's Classics