Erratum: Computational structure-based redesign of en-zyme activity (Proceedings of the National Academy of Sciences of the United States of America (2009) 106 (3764-3769) DOI:10.1073/pnas.0900266106);Computational structure-based redesign of enzyme activity

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 10, 2009, Pages 3764-3769

  Chen, Cheng Yu ^a   Georgiev, Ivelin ^b   Anderson, Amy C ^c   Donald, Bruce R ^a,b  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b Duke University   (United States)

^c UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Biophysical algorithms; Gramicidin S synthetase; Nonribosomal peptide synthetase; Protein design

Indexed keywords

GRAMICIDIN S SYNTHETASE; PEPTIDE SYNTHASE; PHENYLALANINE;

ADENYLATION; ARTICLE; COMPUTER AIDED DESIGN; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME SUBSTRATE; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; VALIDATION STUDY; WILD TYPE;

EID: 62649153772     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0902117106     Document Type: Erratum

References (37)

1. Bolon D, Mayo S (2001) Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 98:14274-14279.
2. Korkegian A, Black ME, Baker D, Stoddard BL (2005) Computational thermostabilization of an enzyme. Science 308:857-860.
3. Stevens B, Lilien R, Georgiev I, Donald BR, Anderson A (2006) Redesigning the PheA domain of gramicidin synthetase leads to a new understanding of the enzyme's mechanism and selectivity. Biochemistry 45:15495-15504.
4. Kuchner O, Arnold FH (1997) Directed evolution of enzyme catalysts. Trends Biotechnol 15:523-530.
5. Chica RA, Doucet N, Pelletier JN (2005) Semi-rational approaches to engineering enzyme activity: Combining the benefits of directed evolution and rational design. Curr Opin Biotechnol 16:378-384.
6. Fox RJ, et al. (2007) Improving catalytic function by ProSAR-driven enzyme evolution. Nat Biotechnol 25:338-344.
7. Fischbach MA, Lai JR, Roche ED, Walsh CT, Liu DR (2007) Directed evolution can rapidly improve the activity of chimeric assembly line enzymes. Proc Natl Acad Sci USA 104:11951-11956.
8. Jiang L, et al. (2008) De novo computational design of retro-aldol enzymes. Science 319:1387-1391.
9. Röthlisberger D, et al. (2008) Kemp elimination catalysts by computational enzyme design. Nature 453:190-195.
10. Ponder J, Richards F (1987) Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes. JMol Biol 193:775-791.
11. Lovell SC, Word J, Richardson J, Richardson D (2000) The penultimate rotamer library. Proteins 40:389-408.
12. Gordon DB, Marshall SA, Mayo SL (1999) Energy functions for protein design. Curr Opin Struct Biol 9:509-513.
13. Vizcarra CL, Mayo SL (2005) Electrostatics in computational protein design. Curr Opin Chem Biol 9:622-626.
14. Georgiev I, Lilien R, Donald BR (2008) The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. J Comput Chem 29:1527-1542.
15. Georgiev I, Donald BR (2007) Dead-end elimination with backbone flexibility. Bioinformatics 23:i185-i194.
16. Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR (2008) Algorithm for backrub motions in protein design. Bioinformatics 24:i196 -il204.
17. Smith CA, Kortemme T (2008) Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol 380:742-756.
18. Lippow SM, Wittrup KD, Tidor B (2007) Computational design of antibody-affinity improvement beyond in vivo maturation. Nat Biotechnol 25:1171-1176.
19. Dahiyat B, Mayo S (1997) De novo protein design: Fully automated sequence selection. Science 278:82-87.
20. Looger L, Dwyer M, Smith J, Hellinga H (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423:185-190.
21. Kuhlman B, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364-1368.
22. Sieber SA, Marahiel MA (2003) Learning from nature's drug factories: Nonribosomal synthesis of macrocyclic peptides. J Bacteriol 185:7036-7043.
23. Conti E, Stachelhaus T, Marahiel M, Brick P (1997) Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. EMBO J 16:4174-4183.
24. Stachelhaus T, Mootz H, Marahiel M (1999) The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem Biol 6:493-505.
25. Challis G, Ravel J, Townsend C (2000) Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. Chem Biol 7:211-224.
26. Lilien R, Stevens B, Anderson A, Donald BR (2005) A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase A phenylalanine adenylation enzyme. J Comp Biol 12:740-761.
27. Georgiev I, Lilien R, Donald BR (2006) Improved pruning algorithms and divide-and-conquer strategies for dead-end elimination, with application to protein design. Bioinformatics 22:e174-e183.
28. Voigt CA, Mayo SL, Arnold FH, Wang ZG (2001) Computational method to reduce the search space for directed protein evolution. Proc Natl Acad Sci USA 98:3778-3783.
29. Pelt JEV, Northrop DB (1984) Purification and properties of gentamicin nucleotidyl-transferase from Escherichia coli: Nucleotide specificity, pH optimum, and the separation of two electrophoretic variants. Arch Biochem Biophys 230:250-263.
30. Luo L, Burkart MD, Stachelhaus T, Walsh CT (2001) Substrate recognition and selection by the initiation module PheATE of gramicidin S synthetase. J Am Chem Soc 123:11208-11218.
31. Eppelmann K, Stachelhaus T, Marahiel M (2002) Exploitation of the selectivity-conferring code of nonribosomal peptide synthetases for the rational design of novel peptide antibiotics. Biochemistry 41:9718-9726.
32. Wong KF, Selzer T, Benkovic SJ, Hammes-Schiffer S (2005) Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. Proc Natl Acad Sci USA 102:6807-6812.
33. Leach A, Lemon A (1998) Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm. Proteins 33:227-239.
34. Desmet J, De Maeyer M, Hazes B, Lasters I (1992) The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356:539-542.
35. Pierce N, Spriet J, Desmet J, Mayo S (2000) Conformational splitting: A more powerful criterion for dead-end elimination. J Comput Chem 21:999-1009.
36. Cornell W, et al. (1995) A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J Am Chem Soc 117:5179-5197.
37. Lazaridis T, Karplus M (1999) Effective energy function for proteins in solution. Proteins Struct Funct Genet 35:133-152.