Automated scaffold selection for enzyme design

Proteins: Structure, Function and Bioinformatics

Volumn 77, Issue 1, 2009, Pages 74-83

  Malisi, Christoph ^a,b   Kohlbacher, Oliver ^b   Höcker, Birte ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^b UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

Active site recapitulation; Computational biology; Motif search; Protein design; Structural bioinformatics

Indexed keywords

SCAFFOLD PROTEIN;

ARTICLE; CHEMICAL REACTION; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN STRUCTURE;

ALGORITHMS; AMINO ACID MOTIFS; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; ENZYMES; PROTEIN CONFORMATION; PROTEIN ENGINEERING;

EID: 70349330137     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22418     Document Type: Article

References (32)

1. Tanaka F. Catalytic antibodies as designer proteases and esterases. Chem Rev 2002;102:4885-4906.
2. Bloom JD, Meyer MM, Meinhold P, Otey CR, MacMillan D, Arnold FH. Evolving strategies for enzyme engineering. Curr Opin Struct Biol 2005;15:447-452.
3. Benson DE, Haddy AE, Hellinga HW. Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. Biochemistry 2002;41:3262-3269.
4. Benson DE, Wisz MS, Hellinga HW. Rational design of nascent metalloenzymes. Proc Natl Acad Sci USA 2000;97:6292-6297.
5. Pinto AL, Hellinga HW, Caradonna JP. Construction of a catalytically active iron superoxide dismutase by rational protein design. Proc Natl Acad Sci USA 1997;94:5562-5567.
6. Bolon DN, Mayo SL. Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 2001;98:14274-14279.
7. Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, III, Hilvert D, Houk KN, Stoddard BL, Baker D. De novo computational design of retro-aldol enzymes. Science 2008;319:1387-1391. (Pubitemid 351354873)
8. Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D. Kemp elimination catalysts by computational enzyme design. Nature 2008;453:190-195. (Pubitemid 351667979)
9. Hellinga HW, Caradonna JP, Richards FM. Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin J Mol Biol 1991;222:787-803.
10. Hellinga HW, Richards FM. Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry J Mol Biol 1991;222:763-785.
11. Dahiyat BI, Mayo SL. Protein design automation. Protein Sci 1996;5:895-903.
12. Hearst DP, Cohen FE. GRAFTER: a computational aid for the design of novel proteins. Protein Eng 1994;7:1411-1421.
13. Hornischer K, Blöcker H. Grafting of discontinuous sites: a protein modeling strategy. Protein Eng 1996;9:931-939. (Pubitemid 26402296)
14. Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Rothlisberger D, Baker D. New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 2006;15:2785-2794. (Pubitemid 44833759)
15. Nussinov R, Wolfson HJ. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc Natl Acad Sci USA 1991;88:10495-10499. (Pubitemid 21915862)
16. Stark A, Russell RB. Annotation in three dimensions. PINTS: patterns in non-homologous tertiary structures. Nucleic Acids Res 2003; 31:3341-3344.
17. Wallace AC, Borkakoti N, Thornton JM. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci 1997;6:2308-2323.
18. Dechancie J, Clemente FR, Smith AJ, Gunaydin H, Zhao YL, Zhang X, Houk KN. How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design. Protein Sci 2007;16:1851-1866. (Pubitemid 47367108)
19. Zhang X, DeChancie J, Gunaydin H, Chowdry AB, Clemente FR, Smith AJ, Handel TM, Houk KN. Quantum mechanical design of enzyme active sites. J Org Chem 2008;73:889-899. (Pubitemid 351198732)
20. Carter P, Wells JA. Dissecting the catalytic triad of a serine protease. Nature 1988;332:564-568.
21. Lassila JK, Keeffe JR, Oelschlaeger P, Mayo SL. Computationally designed variants of Escherichia coli chorismate mutase show altered catalytic activity. Protein Eng Des Sel 2005;18:161-163. (Pubitemid 40695120)
22. Woycechowsky KJ, Hilvert D. Deciphering enzymes. Genetic selection as a probe of structure and mechanism. Eur J Biochem 2004;271:1630-1637. (Pubitemid 38586296)
23. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542. (Pubitemid 8109216)
24. Wang Y, Anderson JB, Chen J, Geer LY, He S, Hurwitz DI, Liebert CA, Madej T, Marchler GH, Marchler-Bauer A, Panchenko AR, Shoemaker BA, Song JS, Thiessen PA, Yamashita RA, Bryant SH. MMDB: Entrez's 3D-structure database. Nucleic Acids Res 2002;30:249-252.
25. Dunbrack RL, Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
26. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
27. Huang B, Schroeder M. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol 2006;6:19. (Pubitemid 44570436)
28. Bron C, Kerbosch J. Algorithm 457: finding all cliques of an undirected graph. Commun ACM 1973;16:575-577.
29. Coutsias EA, Seok C, Dill KA. Using quaternions to calculate RMSD. J Comput Chem 2004;25:1849-1857.
30. Kohlbacher O, Lenhof HP. BALL-rapid software prototyping in computational molecular biology. Biochemicals algorithms library. Bioinformatics 2000;16:815-824.
31. Cazals F, Karande C. A note on the problem of reporting maximal cliques. Theor Comput Sci 2008;407:564-568.
32. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.