MAP2.03D: A sequence/structure based server for protein engineering

ACS Synthetic Biology

Volumn 1, Issue 4, 2012, Pages 139-150

  Verma, Rajni ^a,b   Schwaneberg, Ulrich ^b   Roccatano, Danilo ^a  

^a JACOBS UNIVERSITY BREMEN   (Germany)

^b RWTH AACHEN UNIVERSITY   (Germany)

Author keywords

Bioinformatics tools; Directed evolution; Mutagenesis assistant program; Mutational bias indicator; Protein engineering; Random mutagenesis methods

Indexed keywords

DEXTRO AMINO OXIDASE; FRUCTOSE BISPHOSPHATE ALDOLASE; N ACETYLNEURAMINATE LYASE; OXIDOREDUCTASE; PHYTASE; UNCLASSIFIED DRUG; DEXTRO AMINO ACID OXIDASE; LYASE; N-ACETYLNEURAMINATE LYASE; RECOMBINANT PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; COMPUTER PROGRAM; CRYSTALLOGRAPHY; HYDROGEN BOND; HYDROPHOBICITY; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; CHEMICAL STRUCTURE; CHEMISTRY; DIRECTED MOLECULAR EVOLUTION; GENETICS; INTERNET; PROCEDURES; PROTEIN CONFORMATION; STATISTICS AND NUMERICAL DATA; SYNTHETIC BIOLOGY; THREE DIMENSIONAL IMAGING; METHODOLOGY; STATISTICS;

6-PHYTASE; AMINO ACID SUBSTITUTION; D-AMINO-ACID OXIDASE; DIRECTED MOLECULAR EVOLUTION; IMAGING, THREE-DIMENSIONAL; INTERNET; MODELS, MOLECULAR; MUTAGENESIS; OXO-ACID-LYASES; PROTEIN CONFORMATION; PROTEIN ENGINEERING; RECOMBINANT PROTEINS; SOFTWARE; SYNTHETIC BIOLOGY;

EID: 84868216091     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb200019x     Document Type: Article

References (54)

1. Bornscheuer, U. T., and Pohl, M. (2001) Improved biocatalysts by directed evolution and rational protein design. Curr. Opin. Chem. Biol. 5, 137-143. (Pubitemid 32245673)
2. Brakmann, S. (2001) Discovery of superior enzymes by directed molecular evolution. ChemBioChem 2, 865-871. (Pubitemid 33722699)
3. Wong, T. S., Arnold, F. H., and Schwaneberg, U. (2004) Laboratory evolution of cytochrome p450 BM-3 monooxygenase for organic cosolvents. Biotechnol. Bioeng. 85, 351-358. (Pubitemid 38182228)
4. Roccatano, D., Wong, T. S., Schwaneberg, U., and Zacharias, M. (2006) Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: A molecular dynamics simulation study. Biopolymers 83, 467-476. (Pubitemid 44851660)
5. Wong, T. S., Zhurina, D., and Schwaneberg, U. (2006) The diversity challenge in directed protein evolution. Comb. Chem. High Throughput Screening 9, 271-288. (Pubitemid 43800252)
6. Wong, T. S., Roccatano, D., and Schwaneberg, U. (2007) Steering directed protein evolution: Strategies to manage combinatorial complexity of mutant libraries. Environ. Microbiol. 9, 2645-2659. (Pubitemid 47547556)
7. Smith, J. M. (1970) Natural selection and concept of a protein space. Nature 225, 563-564.
8. Olsen, M., Iverson, B., and Georgiou, G. (2000) High-throughput screening of enzyme libraries. Curr. Opin. Biotechnol. 11, 331-337. (Pubitemid 30598926)
9. Tawfik, D. S., and Bershtein, S. (2008) Advances in laboratory evolution of enzymes. Curr. Opin. Chem. Biol. 12, 151-158.
10. Shivange, A. V., Marienhagen, J., Mundhada, H., Schenk, A., and Schwaneberg, U. (2009) Advances in generating functional diversity for directed protein evolution. Curr. Opin. Chem. Biol. 13, 19-25.
11. Turner, N. J. (2009) Directed evolution drives the next generation of biocatalysts. Nat. Chem. Biol. 5, 567-573.
12. Wong, T. S., Roccatano, D., Loakes, D., Tee, K. L., Schenk, A., Hauer, B., and Schwaneberg, U. (2008) Transversion-enriched sequence saturation mutagenesis (SeSaM-Tv+): A random mutagenesis method with consecutive nucleotide exchanges that complements the bias of error-prone PCR. Biotechnol. J. 3, 74-82. (Pubitemid 351200933)
13. Dennig, A., Shivange, A. V., Marienhagen, J., and Schwaneberg, U. (2011) OmniChange: The sequence independent method for simultaneous site-saturation of five codons. PLoS ONE 6, e26222.
14. Chica, R. A., Doucet, N., and Pelletier, J. N. (2005) Semirational approaches to engineering enzyme activity: Combining the benefits of directed evolution and rational design. Curr. Opin. Biotechnol. 16, 378-384. (Pubitemid 41111523)
15. Zumarraga, M., Camarero, S., Shleev, S., Martinez-Arias, A., Ballesteros, A., Plou, F. J., and Alcalde, M. (2008) Altering the laccase functionality by in vivo assembly of mutant libraries with different mutational spectra. Proteins 71, 250-260. (Pubitemid 351358608)
16. Vanhercke, T., Ampe, C., Tirry, L., and Denolf, P. (2005) Reducing mutational bias in random protein libraries. Anal. Biochem. 339, 9-14. (Pubitemid 40342672)
17. Wong, T. S., Roccatano, D., Zacharias, M., and Schwaneberg, U. (2006) A statistical analysis of random mutagenesis methods used for directed protein evolution. J. Mol. Biol. 355, 858-871. (Pubitemid 41817641)
18. Wong, T. S., Roccatano, D., and Schwaneberg, U. (2007) Are transversion mutations better? A Mutagenesis Assistant Program analysis on P450 BM-3 heme domain. Biotechnol. J. 2, 133-142. (Pubitemid 46738895)
19. Rasila, T. S., Pajunen, M. I., and Savilahti, H. (2009) Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment. Anal. Biochem. 388, 71-80.
20. Ditursi, M. K., Kwon, S. J., Reeder, P. J., and Dordick, J. S. (2006) Bioinformatics-driven, rational engineering of protein thermostability. Protein Eng., Des. Sel. 19, 517-524. (Pubitemid 44627325)
21. Shoichet, B. K., and Beadle, B. M. (2002) Structural bases of stability-function tradeoffs in enzymes. J. Mol. Biol. 321, 285-296.
22. Berman, H., Henrick, K., and Nakamura, H. (2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10, 980-980.
23. Zhang, H., Zhang, T., Chen, K., Shen, S., Ruan, J., and Kurgan, L. (2009) On the relation between residue flexibility and local solvent accessibility in proteins. Proteins 76, 617-636.
24. Teilum, K., Olsen, J. G., and Kragelund, B. B. (2009) Functional aspects of protein flexibility. Cell. Mol. Life Sci. 66, 2231-2247.
25. Gromiha, M. M., Oobatake, M., Kono, H., Uedaira, H., and Sarai, A. (1999) Role of structural and sequence information in the prediction of protein stability changes: Comparison between buried and partially buried mutations. Protein Eng., Des. Sel. 12, 549-555. (Pubitemid 29368961)
26. Pilone, M. S. (2000) D-Amino acid oxidase: New findings. Cell. Mol. Life Sci. 57, 1732-1747.
27. Pollegioni, L., and Molla, G. (2011) New biotech applications from evolved D-Amino acid oxidases. Trends Biotechnol. 29, 276-283.
28. Lin-Goerke, J. L., Robbins, D. J., and Burczak, J. D. (1997) PCRbased random mutagenesis using manganese and reduced dNTP concentration. Biotechniques 23, 409-412. (Pubitemid 27398185)
29. Vartanian, J. P., Henry, M., and Wain-Hobson, S. (1996) Hypermutagenic PCR involving all four transitions and a sizeable proportion of transversions. Nucleic Acids Res. 24, 2627-2631. (Pubitemid 26239725)
30. Jmol: An open-source Java viewer for chemical structures in 3D. http://www.jmol.org/
31. Pollegioni, L., Diederichs, K., Molla, G., Umhau, S., Welte, W., Ghisla, S., and Pilone, M. S. (2002) Yeast D-Amino acid oxidase: Structural basis of its catalytic properties. J. Mol. Biol. 324, 535-546. (Pubitemid 35430517)
32. Sacchi, S., Rosini, E., Molla, G., Pilone, M. S., and Pollegioni, L. (2004) Modulating D-Amino acid oxidase substrate specificity: Production of an enzyme for analytical determination of all D-Amino acids by directed evolution. Protein Eng. Des. Sel. 17, 517-525. (Pubitemid 39487531)
33. Rao, D. E., Rao, K. V., Reddy, T. P., and Reddy, V. D. (2009) Molecular characterization, physicochemical properties, known and potential applications of phytases: An overview. Crit. Rev. Biotechnol. 29, 182-198.
34. Garrett, J. B., Kretz, K. A., O'Donoghue, E., Kerovuo, J., Kim, W., Barton, N. R., Hazlewood, G. P., Short, J. M., Robertson, D. E., and Gray, K. A. (2004) Enhancing the thermal tolerance and gastric performance of a microbial phytase for use as a phosphate-mobilizing monogastric-feed supplement. Appl. Environ. Microb. 70, 3041-3046. (Pubitemid 38657822)
35. Fields, P. A. (2001) Review: Protein function at thermal extremes: Balancing stability and flexibility. Comp. Biochem. Phys. A 129, 417-431. (Pubitemid 32553917)
36. Kim, M. S., and Lei, X. G. (2008) Enhancing thermostability of Escherichia coli phytase AppA2 by error-prone PCR. Appl. Microbiol. Biotechnol. 79, 69-75.
37. Wada, M., Hsu, C. C., Franke, D., Mitchell, M., Heine, A., Wilson, I., and Wong, C. H. (2003) Directed evolution of Nacetylneuraminic acid aldolase to catalyze enantiomeric aldol reactions. Bioorg. Med. Chem. 11, 2091-2098. (Pubitemid 36379026)
38. Gromiha, M. M., and Selvaraj, S. (2004) Inter-residue interactions in protein folding and stability. Prog. Biophys. Mol. Biol. 86, 235-277. (Pubitemid 39027234)
39. Kabsch, W., and Sander, C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
40. Chothia, C. (1976) The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105, 1-12.
41. Peisajovich, S. G., and Tawfik, D. S. (2007) Protein engineers turned evolutionists. Nat. Methods 4, 991-994. (Pubitemid 350201764)
42. Karplus, P. A., and Schulz, G. E. (1985) Prediction of chain flexibility in proteins-A tool for the selection of peptide antigens. Naturwissenschaften 72, 212-213. (Pubitemid 15094544)
43. Yuan, Z., Zhao, J., and Wang, Z. X. (2003) Flexibility analysis of enzyme active sites by crystallographic temperature factors. Protein Eng., Des. Sel. 16, 109-114. (Pubitemid 36458649)
44. Kumar, S., and Nussinov, R. (2002) Close-range electrostatic interactions in proteins. ChemBioChem 3, 604-617. (Pubitemid 36004524)
45. Kyte, J., and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
46. Burley, S. K., and Petsko, G. A. (1985) Aromatic-Aromatic interaction: A mechanism of protein structure stabilization. Science 229, 23-28.
47. Overington, J., Johnson, M. S., Sali, A., and Blundell, T. L. (1990) Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction. Proc. R. Soc. London, Ser. B 241, 132-145. (Pubitemid 20327859)
48. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242. (Pubitemid 30047768)
49. Smith, T. F., and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
50. Liao, G. J., Lee, Y. J., Lee, Y. H., Chen, L. L., and Chu, W. S. (1998) Structure and expression of the D-Amino-Acid oxidase gene from the yeast Rhodosporidium toruloides. Biotechnol. Appl. Biochem. 27, 55-61.
51. Rodriguez, E., Han, Y., and Lei, X. G. (1999) Cloning, sequencing, and expression of an Escherichia coli acid phosphatase/ phytase gene (appA2) isolated from pig colon. Biochem. Biophys. Res. Commun. 257, 117-123. (Pubitemid 29299057)
52. Lim, D., Golovan, S., Forsberg, C. W., and Jia, Z. (2000) Crystal structures of Escherichia coli phytase and its complex with phytate. Nat. Struct. Biol. 7, 108-113. (Pubitemid 30082506)
53. Ohta, Y., Watanabe, K., and Kimura, A. (1985) Complete nucleotide sequence of the E. coli N-Acetylneuraminate lyase. Nucleic Acids Res. 13, 8843-8852.
54. Izard, T., Lawrence, M. C., Malby, R. L., Lilley, G. G., and Colman, P. M. (1994) The three-dimensional structure of Nacetylneuraminate lyase from Escherichia coli. Structure 2, 361-369.