Strategies and computational tools for improving randomized protein libraries

Biomolecular Engineering

Volumn 22, Issue 4, 2005, Pages 105-112

  Patrick, Wayne M ^a   Firth, Andrew E ^b  

^a EMORY UNIVERSITY   (United States)

^b UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

Directed evolution; Library; Molecular diversity; Random mutagenesis; Redundancy

Indexed keywords

COMPUTATIONAL METHODS; FUNCTIONS; REDUNDANCY; STRUCTURAL ANALYSIS;

DIRECTED EVOLUTION; LIBRARY; MOLECULAR DIVERSITY; RANDOM MUTAGENESIS;

PROTEINS;

OLIGONUCLEOTIDE;

ALGORITHM; CODON; ERROR; GENOMICS; INFORMATION; METHODOLOGY; MOLECULAR EVOLUTION; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; RANDOMIZATION; REDUNDANCY ANALYSIS; REVIEW; SEQUENCE HOMOLOGY; STATISTICS;

ALGORITHMS; ANIMALS; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; DIRECTED MOLECULAR EVOLUTION; FUNGAL PROTEINS; GENE LIBRARY; HUMANS; INTERNET; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MUTAGENESIS; MUTATION; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; PROTEIN ENGINEERING; PROTEIN KINASE INHIBITORS; PROTEINS; PROTEOMICS; RECOMBINATION, GENETIC; SOFTWARE; VARIATION (GENETICS);

EID: 23944525846     PISSN: 13890344     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bioeng.2005.06.001     Document Type: Review

References (58)

1. F.H. Arnold When blind is better: protein design by evolution Nat Biotechnol 16 1998 617 618
2. S. Lutz, and W.M. Patrick Novel methods for directed evolution of enzymes: quality, not quantity Curr Opin Biotechnol 15 2004 291 297
3. C. Neylon Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution Nucleic Acids Res 32 2004 1448 1459
4. G.J. Williams, A.S. Nelson, and A. Berry Directed evolution of enzymes for biocatalysis and the life sciences Cell Mol Life Sci 61 2004 3034 3046
5. R.W. Roberts, and W.W. Ja In vitro selection of nucleic acids and proteins: what are we learning? Curr Opin Struct Biol 9 1999 521 529
6. R.C. Cadwell, and G.F. Joyce Randomization of genes by PCR mutagenesis PCR Methods Appl 2 1992 28 33
7. J.D. Hermes, S.M. Parekh, S.C. Blacklow, H. Koster, and J.R. Knowles A reliable method for random mutagenesis: the generation of mutant libraries using spiked oligodeoxyribonucleotide primers Gene 84 1989 143 151
8. W.P. Stemmer DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution Proc Natl Acad Sci USA 91 1994 10747 10751
9. W.P. Stemmer Rapid evolution of a protein in vitro by DNA shuffling Nature 370 1994 389 391
10. G.L. Moore, and C.D. Maranas Computational challenges in combinatorial library design for protein engineering AIChE J 50 2004 262 272
11. S.E. Brenner A tour of structural genomics Nat Rev Genet 2 2001 801 809
12. J. Minshull, J.E. Ness, C. Gustafsson, and S. Govindarajan Predicting enzyme function from protein sequence Curr Opin Chem Biol 9 2005 202 209
13. M. Wiederstein, and M.J. Sippl Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials J Mol Biol 345 2005 1199 1212
14. F. Glaser, Y. Rosenberg, A. Kessel, T. Pupko, and N. Ben-Tal The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures Proteins 58 2005 610 617
15. L. Holm, and C. Sander Protein folds and families: sequence and structure alignments Nucleic Acids Res 27 1999 244 247
16. S.J. Williams, and S.G. Withers Glycosynthases: mutant glycosidases for glycoside synthesis Aust J Chem 55 2002 3 12
17. K.L. Morley, and R.J. Kazlauskas Improving enzyme properties: when are closer mutations better? Trends Biotechnol 23 2005 231 237
18. M.C. Orencia, J.S. Yoon, J.E. Ness, W.P. Stemmer, and R.C. Stevens Predicting the emergence of antibiotic resistance by directed evolution and structural analysis Nat Struct Biol 8 2001 238 242
19. S. Park, K.L. Morley, G.P. Horsman, M. Holmquist, K. Hult, and R.J. Kazlauskas Focusing mutations into the P. fluorescens esterase binding site increases enantioselectivity more effectively than distant mutations Chem Biol 12 2005 45 54
20. C.A. Voigt, C. Martinez, Z.G. Wang, S.L. Mayo, and F.H. Arnold Protein building blocks preserved by recombination Nat Struct Biol 9 2002 553 558
21. M.M. Meyer, J.J. Silberg, C.A. Voigt, J.B. Endelman, S.L. Mayo, and Z.G. Wang Library analysis of SCHEMA-guided protein recombination Protein Sci 12 2003 1686 1693
22. K. Hiraga, and F.H. Arnold General method for sequence-independent site-directed chimeragenesis J Mol Biol 330 2003 287 296
23. C.R. Otey, J.J. Silberg, C.A. Voigt, J.B. Endelman, G. Bandara, and F.H. Arnold Functional evolution and structural conservation in chimeric cytochromes p450: calibrating a structure-guided approach Chem Biol 11 2004 309 318
24. G.L. Moore, and C.D. Maranas Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach Proc Natl Acad Sci USA 100 2003 5091 5096
25. M.C. Saraf, G.L. Moore, and C.D. Maranas Using multiple sequence correlation analysis to characterize functionally important protein regions Protein Eng 16 2003 397 406
26. M.C. Saraf, A.R. Horswill, S.J. Benkovic, and C.D. Maranas FamClash: a method for ranking the activity of engineered enzymes Proc Natl Acad Sci USA 101 2004 4142 4147
27. S. Govindarajan, J.E. Ness, S. Kim, E.C. Mundorff, J. Minshull, and C. Gustafsson Systematic variation of amino acid substitutions for stringent assessment of pairwise covariation J Mol Biol 328 2003 1061 1069
28. P. Acharya, E. Rajakumara, R. Sankaranarayanan, and N.M. Rao Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase J Mol Biol 341 2004 1271 1281
29. M.D. Hughes, D.A. Nagel, A.F. Santos, A.J. Sutherland, and A.V. Hine Removing the redundancy from randomised gene libraries J Mol Biol 331 2003 973 979
30. M.J. Dufton The significance of redundancy in the genetic code J Theor Biol 102 1983 521 526
31. M.D. Hughes, Z.R. Zhang, A.J. Sutherland, A.F. Santos, and A.V. Hine Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing: identification of novel zinc finger proteins Nucleic Acids Res 33 2005 e32
32. S. Shafikhani, R.A. Siegel, E. Ferrari, and V. Schellenberger Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization Biotechniques 23 1997 304 310
33. W.M. Patrick, A.E. Firth, and J.M. Blackburn User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries Protein Eng 16 2003 451 457
34. L.A. Rowe, M.L. Geddie, O.B. Alexander, and I. Matsumura A comparison of directed evolution approaches using the β-glucuronidase model system J Mol Biol 332 2003 851 860
35. T. Vanhercke, C. Ampe, L. Tirry, and P. Denolf Reducing mutational bias in random protein libraries Anal Biochem 339 2005 9 14
36. B.D. Biles, and B.A. Connolly Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR Nucleic Acids Res 32 2004 e176
37. J.D. Hermes, S.C. Blacklow, and J.R. Knowles Searching sequence space by definably random mutagenesis: improving the catalytic potency of an enzyme Proc Natl Acad Sci USA 87 1990 696 700
38. J.T. Wong Role of minimization of chemical distances between amino acids in the evolution of the genetic code Proc Natl Acad Sci USA 77 1980 1083 1086
39. T. Tan, L.D. Bogarad, and M.W. Deem Modulation of base-specific mutation and recombination rates enables functional adaptation within the context of the genetic code J Mol Evol 59 2004 385 399
40. D.A. Drummond, B.L. Iverson, G. Georgiou, and F.H. Arnold Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins J Mol Biol 350 2005 806 816
41. A.E. Firth, and W.M. Patrick Statistics of protein library construction Bioinformatics 21 2005 3314 3315
42. H. Zhao, L. Giver, Z. Shao, J.A. Affholter, and F.H. Arnold Molecular evolution by staggered extension process (StEP) in vitro recombination Nat Biotechnol 16 1998 258 261
43. G.L. Moore, C.D. Maranas, S. Lutz, and S.J. Benkovic Predicting crossover generation in DNA shuffling Proc Natl Acad Sci USA 98 2001 3226 3231
44. G.L. Moore, and C.D. Maranas Predicting out-of-sequence reassembly in DNA shuffling J Theor Biol 219 2002 9 17
45. N. Maheshri, and D.V. Schaffer Computational and experimental analysis of DNA shuffling Proc Natl Acad Sci USA 100 2003 3071 3076
46. W.M. Coco, L.P. Encell, W.E. Levinson, M.J. Crist, A.K. Loomis, and L.L. Licato Growth factor engineering by degenerate homoduplex gene family recombination Nat Biotechnol 20 2002 1246 1250
47. J.E. Ness, S. Kim, A. Gottman, R. Pak, A. Krebber, and T.V. Borchert Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently Nat Biotechnol 20 2002 1251 1255
48. D. Zha, A. Eipper, and M.T. Reetz Assembly of designed oligonucleotides as an efficient method for gene recombination: a new tool in directed evolution ChemBioChem 4 2003 34 39
49. M. Ostermeier, J.H. Shim, and S.J. Benkovic A combinatorial approach to hybrid enzymes independent of DNA homology Nat Biotechnol 17 1999 1205 1209
50. S. Lutz, M. Ostermeier, and S.J. Benkovic Rapid generation of incremental truncation libraries for protein engineering using α-phosphothioate nucleotides Nucleic Acids Res 29 2001 e16
51. V. Sieber, C.A. Martinez, and F.H. Arnold Libraries of hybrid proteins from distantly related sequences Nat Biotechnol 19 2001 456 460
52. S. Lutz, M. Ostermeier, G.L. Moore, C.D. Maranas, and S.J. Benkovic Creating multiple-crossover DNA libraries independent of sequence identity Proc Natl Acad Sci USA 98 2001 11248 11253
53. M.L. Gerth, W.M. Patrick, and S. Lutz A second-generation system for unbiased reading frame selection Protein Eng Des Sel 17 2004 595 602
54. F. Sun The polymerase chain reaction and branching processes J Comput Biol 2 1995 63 86
55. L.J. Schwimmer, P. Rohatgi, B. Azizi, K.L. Seley, and D.F. Doyle Creation and discovery of ligand-receptor pairs for transcriptional control with small molecules Proc Natl Acad Sci USA 101 2004 14707 14712
56. A.D. Bosley, and M. Ostermeier Mathematical expressions useful in the construction, description and evaluation of protein libraries Biomol Eng 22 2005 57 61
57. C. Jelsch, L. Mourey, J.M. Masson, and J.P. Samama Crystal structure of Escherichia coli TEM1 β-lactamase at 1.8 Å resolution Proteins 16 1993 364 383
58. D. Lim, F. Sanschagrin, L. Passmore, L. De Castro, R.C. Levesque, and N.C. Strynadka Insights into the molecular basis for the carbenicillinase activity of PSE-4 β-lactamase from crystallographic and kinetic studies Biochemistry 40 2001 395 402