Identification and analysis of conserved pockets on protein surfaces

BMC Bioinformatics

Volumn 14, Issue SUPPL7, 2013, Pages

  Cammisa, Marco ^a,b   Correra, Antonella ^a,b   Andreotti, Giuseppina ^b   Cubellis, Maria Vittoria ^a,c  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b CNR Consiglio Nazionale delle Ricerche   (Italy)

^c CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE POCKET; FRAGMENT-BASED SCREENINGS; FUNDAMENTAL PRINCIPLES; LIGAND-BINDING SITES; LOW MOLECULAR WEIGHT DRUGS; RECURSIVE ALGORITHMS; SEQUENCE CONSERVATION; STATISTICAL SIGNIFICANCE;

AMINO ACIDS; LIGANDS; OPTIMIZATION; THREE DIMENSIONAL; TOOLS;

PROTEINS;

LIGAND; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYME ACTIVE SITE; HUMAN; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION;

ALGORITHMS; AMINO ACID SEQUENCE; BINDING SITES; CATALYTIC DOMAIN; COMPUTER SIMULATION; CONSERVED SEQUENCE; HUMANS; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 84881182670     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S7-S9     Document Type: Article

References (26)

1. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic acids research 2006, (34 Web Server):W116-118.
2. Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci 1998, 7(9):1884-1897. 10.1002/pro.5560070905, 2144175, 9761470.
3. Laskowski RA. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. Journal of molecular graphics 1995, 13(5):323-330. 307-328, 10.1016/0263-7855(95)00073-9, 8603061.
4. Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G. Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. BMC Bioinformatics 2012, 13(Suppl 4):S17. 10.1186/1471-2105-13-S4-S17, 3521384, 23282238.
5. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic acids research 2010, (38 Web Server):W529-533.
6. Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS computational biology 2009, 5(12):e1000585. 10.1371/journal.pcbi.1000585, 2777313, 19997483.
7. Huang B, Schroeder M. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC structural biology 2006, 6:19. 10.1186/1472-6807-6-19, 1601958, 16995956.
8. Chelliah V, Chen L, Blundell TL, Lovell SC. Distinguishing structural and functional restraints in evolution in order to identify interaction sites. J Mol Biol 2004, 342(5):1487-1504. 10.1016/j.jmb.2004.08.022, 15364576.
9. Goldenberg O, Erez E, Nimrod G, Ben-Tal N. The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic acids research 2009, (37 Database):D323-327.
10. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
11. Andreotti G, Citro V, De Crescenzo A, Orlando P, Cammisa M, Correra A, Cubellis MV. Therapy of Fabry disease with pharmacological chaperones: from in silico predictions to in vitro tests. Orphanet journal of rare diseases 2011, 6(1):66. 10.1186/1750-1172-6-66, 3216245, 22004918.
12. DesJarlais RL, Sheridan RP, Seibel GL, Dixon JS, Kuntz ID, Venkataraghavan R. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. Journal of medicinal chemistry 1988, 31(4):722-729. 10.1021/jm00399a006, 3127588.
13. Laskowski RA, Luscombe NM, Swindells MB, Thornton JM. Protein clefts in molecular recognition and function. Protein Sci 1996, 5(12):2438-2452. 2143314, 8976552.
14. Capra JA, Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics (Oxford, England) 2007, 23(15):1875-1882.
15. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic acids research 2005, (33 Web Server):W299-302.
16. Fan JQ. A counterintuitive approach to treat enzyme deficiencies: use of enzyme inhibitors for restoring mutant enzyme activity. Biol Chem 2008, 389(1):1-11.
17. Bradford TM, Litjens T, Parkinson EJ, Hopwood JJ, Brooks DA. Mucopolysaccharidosis type VI (Maroteaux-Lamy syndrome): a Y210C mutation causes either altered protein handling or altered protein function of N-acetylgalactosamine 4-sulfatase at multiple points in the vacuolar network. Biochemistry 2002, 41(15):4962-4971. 10.1021/bi0121149, 11939792.
18. Litjens T, Hopwood JJ. Mucopolysaccharidosis type VI: Structural and clinical implications of mutations in N-acetylgalactosamine-4-sulfatase. Hum Mutat 2001, 18(4):282-295. 10.1002/humu.1190, 11668612.
19. Sigrist CJ, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N. PROSITE, a protein domain database for functional characterization and annotation. Nucleic acids research 2010, (38 Database):D161-166.
20. Mizuguchi K, Sele M, Cubellis MV. Environment specific substitution tables for thermophilic proteins. BMC Bioinformatics 2007, 8(Suppl 1):S15. 10.1186/1471-2105-8-S1-S15, 2099483, 18047714.
21. Waters ML. Aromatic interactions in model systems. Current opinion in chemical biology 2002, 6(6):736-741. 10.1016/S1367-5931(02)00359-9, 12470725.
22. Koide S, Sidhu SS. The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. ACS chemical biology 2009, 4(5):325-334. 10.1021/cb800314v, 2829252, 19298050.
23. Birtalan S, Fisher RD, Sidhu SS. The functional capacity of the natural amino acids for molecular recognition. Molecular bioSystems 2010, 6(7):1186-1194. 10.1039/b927393j, 20383388.
24. Landon MR, Lancia DR, Yu J, Thiel SC, Vajda S. Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. Journal of medicinal chemistry 2007, 50(6):1231-1240. 10.1021/jm061134b, 17305325.
25. Martin JL, Begun J, McLeish MJ, Caine JM, Grunewald GL. Getting the adrenaline going: crystal structure of the adrenaline-synthesizing enzyme PNMT. Structure 2001, 9(10):977-985. 10.1016/S0969-2126(01)00662-1, 11591352.
26. Cubellis MV, Cailliez F, Lovell SC. Secondary structure assignment that accurately reflects physical and evolutionary characteristics. BMC Bioinformatics 2005, 6(Suppl 4):S8. 10.1186/1471-2105-6-S4-S8, 1866377, 16351757.