Engineering proteinase K using machine learning and synthetic genes

BMC Biotechnology

Volumn 7, Issue , 2007, Pages

  Liao, Jun ^a   Warmuth, Manfred K ^a   Govindarajan, Sridhar ^b   Ness, Jon E ^b   Wang, Rebecca P ^b   Gustafsson, Claes ^b   Minshull, Jeremy ^b  

^a University of California Santa Cruz   (United States)

^b DNA20 Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; GENES; HYDROLYSIS; LEARNING SYSTEMS; PROTEINS;

FUNCTIONAL IMPROVEMENTS; PROTEIN ENGINEERING; PROTEINASE; SYNTHETIC GENES;

ENZYMES;

PROTEINASE K; SYNTHETIC DNA; TETRAPEPTIDE; RECOMBINANT PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; CHEMICAL REACTION; CONTROLLED STUDY; CORRELATION ANALYSIS; ENZYME ACTIVITY; ENZYME SYNTHESIS; GENE SYNTHESIS; HIGH THROUGHPUT SCREENING; HYDROLYSIS; LEARNING ALGORITHM; MACHINE LEARNING; PREDICTION; PROTEIN ENGINEERING; PROTEIN EXPRESSION; PROTEIN FUNCTION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; ALGORITHM; AMINO ACID SEQUENCE; ARTIFICIAL INTELLIGENCE; CHEMISTRY; DRUG DESIGN; ESCHERICHIA COLI; EVALUATION; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; MUTATION; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; AMINO ACID SEQUENCE; ARTIFICIAL INTELLIGENCE; DRUG DESIGN; ENDOPEPTIDASE K; ESCHERICHIA COLI; GENES, SYNTHETIC; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROTEIN ENGINEERING; RECOMBINANT PROTEINS; SEQUENCE ANALYSIS, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 34147184400     PISSN: None     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-7-16     Document Type: Article

References (64)

1. van Regenmortel MH Are there two distinct research strategies for developing biologically active molecules: Rational design and empirical selection? J Mol Recognit 2000 13 1 1-4 10.1002/(SICI)1099-1352(200001/ 02)13:1<1::AID-JMR490>3.0.CO;2-W 10679890
2. Ryu DD Nam DH Recent progress in biomolecular engineering Biotechnol Prog 2000 16 2-16 10.1021/bp088059d 10662483
3. Tobin MB Gustafsson C Huisman GW Directed evolution: The 'rational' basis for 'irrational' design Curr Opinion on Structural Biology 2000 10 421-427 10.1016/S0959-440X(00)00109-3
4. Korkegian A Black ME Baker D Stoddard BL Computational thermostabilization of an enzyme Science 2005 308 5723 857-860 10.1126/ science.1107387 15879217
5. Dwyer MA Looger LL Hellinga HW Computational design of a biologically active enzyme Science 2004 304 5679 1967-1971 10.1126/science.1098432 15218149
6. Roberts RW Totally in vitro protein selection using mRNA-protein fusions and ribosome display Curr Opin Chem Biol 1999 3 3 268-273 10.1016/ S1367-5931(99)80042-8 10359713
7. Crameri A Raillard SA Bermudez E Stemmer WPC DNA shuffling of a family of genes from diverse species accelerates directed evolution Nature 1998 391 288-291 10.1038/34663 9440693
8. Ness JE Kim S Gottman A Pak R Krebber A Borchert TV Govindarajan S Mundorff EC Minshull J Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently Nat Biotechnol 2002 20 12 1251-1255 10.1038/nbt754 12426575
9. Atkinson AC Donev AN Optimum Experimental Designs Oxford Statistical Science Series Oxford, Clarendon Press 1992
10. Eriksson L Jonsson J Hellberg S Lindgren F Skagerberg B Sjostrom M Wold S Peptide QSAR on substance P analogues, enkephalins and bradykinins containing L- and D-amino acids Acta Chem Scand 1990 44 50-55 1698414
11. Hellberg S Sjostrom M Skagerberg B Wold S Peptide quantitative structure-activity relationships, a multivariate approach J Med Chem 1987 30 7 1126-1135 10.1021/jm00390a003 3599020
12. Hellberg S Sjöström M Wold S The prediction of bradykinin potentiating potency of pentapeptides. An example of a peptide quantitative structure-activity relationship. Acta Chem Scand B 1986 40 135-140 3705868
13. Mee RP Auton TR Morgan PJ Design of active analogues of a 15-residue peptide using D-optimal design, QSAR and a combinatorial search algorithm. J Pept Res 1997 49 89-102 9128105
14. Norinder U Rivera C Unden A A quantitative structure-activity relationship study of some substance P-related peptides. A multivariate approach using PLS and variable selection J Pept Res 1997 49 2 155-162 9147311
15. Sandberg M Deceiphering sequence data, a multivariate approach Dept Organic Chemistry Umea, Umea University 1997
16. Strom MB Haug BE Rekdal O Skar ML Stensen W Svendsen JS Important structural features of 15-residue lactoferricin derivatives and methods for improvement of antimicrobial activity Biochem Cell Biol 2002 80 1 65-74 10.1139/o01-236 11908644
17. Nambiar KP Stackhouse J Stauffer DM Kennedy WP Eldredge JK Benner SA Total synthesis and cloning of a gene coding for the ribonuclease S protein Science 1984 223 4642 1299-1301 10.1126/science.6322300 6322300
18. Jonsson J Norberg T Carlsson L Gustafsson C Wold S Quantitative sequence-activity models (QSAM) - tools for sequence design Nucleic Acids Res 1993 21 733-739 309176 8441682 10.1093/nar/21.3.733
19. Bucht G Wikstrom P Hjalmarsson K Optimising the signal peptide for glycosyl phosphatidylinositol modification of human acetylcholinesterase using mutational analysis and peptide-quantitative structure-activity relationships Biochim Biophys Acta 1999 1431 2 471-482 10350622
20. Aita T Hamamatsu N Nomiya Y Uchiyama H Shibanaka Y Husimi Y Surveying a local fitness landscape of a protein with epistatic sites for the study of directed evolution Biopolymers 2002 64 2 95-105 10.1002/bip.10126 11979520
21. Aita T Iwakura M Husimi Y A cross-section of the fitness landscape of dihydrofolate reductase Protein Eng 2001 14 9 633-638 10.1093/protein/ 14.9.633 11707608
22. Aita T Uchiyama H Inaoka T Nakajima M Kokubo T Husimi Y Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: Application to prolyl endopeptidase and thermolysin Biopolymers 2000 54 1 64-79 10.1002/ (SICI)1097-0282(200007)54:1<64::AID-BIP70>3.0.CO;2-R 10799982
23. Tian J Gong H Sheng N Zhou X Gulari E Gao X Church G Accurate multiplex gene synthesis from programmable DNA microchips Nature 2004 432 7020 1050-1054 10.1038/nature03151 15616567
24. Kodumal SJ Patel KG Reid R Menzella HG Welch M Santi DV Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster Proc Natl Acad Sci U S A 2004 101 44 15573-15578 524854 15496466 10.1073/pnas.0406911101
25. Xiong AS Yao QH Peng RH Li X Fan HQ Cheng ZM Li Y A simple, rapid, high-fidelity and cost-effective PCR-based two-step DNA synthesis method for long gene sequences Nucleic Acids Res 2004 32 12 e98 484193 15240836 10.1093/nar/gnh094
26. Young L Dong Q Two-step total gene synthesis method Nucleic Acids Res 2004 32 7 e59 407838 15087491 10.1093/nar/gnh058
27. Chen KQ Arnold FH Enzyme engineering for nonaqueous solvents: Random mutagenesis to enhance activity of subtilisin E in polar organic media Biotechnology (N Y) 1991 9 11 1073-1077 10.1038/nbt1191-1073 1367624
28. Stemmer WP DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution Proc Natl Acad Sci U S A 1994 91 22 10747-10751 45099 7938023 10.1073/pnas.91.22.10747
29. Gunkel FA Gassen HG Proteinase K from Tritirachium album Limber. Eur J Biochem 1989 179 185-194 10.1111/j.1432-1033.1989.tb14539.x 2645134
30. Gustafsson C Govindarajan S Minshull J Codon bias and heterologous protein expression Trends Biotechnol 2004 22 7 346-353 10.1016/ j.tibtech.2004.04.006 15245907
31. Henaut A Danchin A Analysis and predictions from Escherichia coli sequences. Escherichia coli and Salmonella typhimurium cellular and molecular biology Washington, D.C, ASM press Neidhardt F C, Curtiss RIII, Ingraham J, Lin E, Brooks Low K, Magasanik B, Reznikoff W, Riley M, M. S, Umbarger H 1996 2 2047-2066
32. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994 22 22 4673-4680 308517 7984417 10.1093/nar/22.22.4673
33. Ness JE Cox AJ Govindarajan S Gustafsson C Gross RA Minshull J Empirical biocatalyst engineering: Escaping the tyranny of high throughput screening ACS Symposium Series 900Polymer Biocatalysis and Biomaterials Washington, DC, American Chemical Society Cheng HA, Gross RA 2005 900 37-50
34. Almog O Gallagher DT Ladner JE Strausberg S Alexander P Bryan P Gilliland GL Structural basis of thermostability. Analysis of stabilizing mutations in subtilisin BPN' J Biol Chem 2002 277 30 27553-27558 10.1074/jbc.M111777200 12011071
35. Bryan PN Protein engineering of subtilisin Biochim Biophys Acta 2000 1543 2 203-222 11150607
36. Dayhoff MO Eck FV A Model of Evolutionary Change in Proteins Atlas of Protein Sequence and Structure 1968 3 33-41
37. Casari G Sander C Valencia A A method to predict functional residues in proteins. Nat Struct Biol 1995 2 171-178 10.1038/nsb0295-171 7749921
38. Schoch GA Attias R Le Ret M Werck-Reichhart D Key substrate recognition residues in the active site of a plant cytochrome P450, CYP73A1. Homology guided site-directed mutagenesis Eur J Biochem 2003 270 18 3684-3695 10.1046/j.1432-1033.2003.03739.x 12950252
39. Lehmann M Kostrewa D Wyss M Brugger R D'Arcy A Pasamontes L van Loon AP From DNA sequence to improved functionality: Using protein sequence comparisons to rapidly design a thermostable consensus phytase Protein Eng 2000 13 1 49-57 10.1093/protein/13.1.49 10679530
40. Minshull J Ness JE Gustafsson C Govindarajan S Predicting enzyme function from protein sequence Curr Opin Chem Biol 2005 9 2 202-209 10.1016/j.cbpa.2005.02.003 15811806
41. Hoerl AE Kennard RW Ridge regression: Biased estimation for nonorthogonal problems. Technometrics 1970 12 55-67 10.2307/1267351
42. Tibshirani R Regression selection and shrinkage via the lasso J Royal Statist Soc B 1996 58 267-288
43. Wold H Estimation of principal components and related models by iterative least squares. Multivariate Analysis New York, Academic Press Krishnaiaah PR 1966 391-420
44. Drucker H Burges C Kaufman L Smola A Vapnik V Support Vector Regression Machines. Neural Information Processing Systems MIT Press Moser M, Jordan J, Petsche T 1997 9 155-161
45. Smola AJ Schölkopf B A Tutorial on Support Vector Regression. Technical Report Series in Neural and Computational Learning London, Royal Holloway College, University of London, UK, 1998
46. Demiriz A Bennett KP Shawe-Taylor J Linear Programming Boosting via Column Generation. Machine Learning 2001 46 225-254 10.1023/ A:1012470815092
47. Helmbold DP Kivinen J Warmuth MK Worst-case loss bounds for single neurons. Advances in Neural Information Processing Systems Cambridge, MA, MIT Press Touretzky DS, Mozer M, Hasselmo ME 1995 8 309-315
48. Liao J Santa Cruz, University of Santa Cruz 2005 PhD
49. Govindarajan S Ness JE Kim S Mundorff EC Minshull J Gustafsson C Systematic variation of amino Acid substitutions for stringent assessment of pairwise covariation J Mol Biol 2003 328 5 1061-1069 10.1016/S0022-2836(03)00357-7 12729741
50. Taguchi G Introduction to quality engineering. Dearborn, MI, Asian Productivity Organization (Distributed by American Supplier Institute Inc) 1986
51. Taguchi G Chowdhury S Wu Y Taguchi's Quality Rngineering Handbook John Wiley & Sons Inc 2004
52. Mitra P Murthy CA Pal SK A probabilistic active support vector learning algorithm IEEE Trans Pattern Anal Mach Intell 2004 26 3 413-418 10.1109/ TPAMI.2004.1262340 15376888
53. Warmuth MK Liao J Ratsch G Mathieson M Putta S Lemmen C Active learning with support vector machines in the drug discovery process J Chem Inf Comput Sci 2003 43 2 667-673 10.1021/ci025620t 12653536
54. Lam RL Welch WJ Comparison of methods based on diversity and similarity for molecule selection and the analysis of drug discovery data Methods Mol Biol 2004 275 301-316 15141118
55. Fang J Dong Y Lushington GH Ye QZ Georg GI Support vector machines in HTS data mining: Type I MetAPs inhibition study J Biomol Screen 2006 11 2 138-144 10.1177/1087057105284334 16418315
56. Kretz KA Richardson TH Gray KA Robertson DE Tan X Short JM Gene site saturation mutagenesis: A comprehensive mutagenesis approach Methods Enzymol 2004 388 3 11 15289056
57. Goldberg SM Johnson J Busam D Feldblyum T Ferriera S Friedman R Halpern A Khouri H Kravitz SA Lauro FM Li K Rogers YH Strausberg R Sutton G Tallon L Thomas T Venter E Frazier M Venter JC A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes Proc Natl Acad Sci U S A 2006 103 30 11240-11245 1544072 16840556 10.1073/pnas.0604351103
58. Venter JC Remington K Heidelberg JF Halpern AL Rusch D Eisen JA Wu D Paulsen I Nelson KE Nelson W Fouts DE Levy S Knap AH Lomas MW Nealson K White O Peterson J Hoffman J Parsons R Baden-Tillson H Pfannkoch C Rogers YH Smith HO Environmental genome shotgun sequencing of the Sargasso Sea Science 2004 304 5667 66-74 10.1126/science.1093857 15001713
59. Cello J Paul AV Wimmer E Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template Science 2002 297 1016-1018 10.1126/science.1072266 12114528
60. Ciccarelli RB Gunyuzlu P Huang J Scott C Oakes FT Construction of synthetic genes using PCR after automated DNA synthesis of their entire top and bottom strands Nucleic Acids Res 1991 19 21 6007-6013 329059 1945885 10.1093/nar/19.21.6007
61. Del Mar EG Largman C Brodrick JW Fassett M Geokas MC Substrate specificity of human pancreatic elastase 2 Biochemistry 1980 19 3 468-472 10.1021/bi00544a011 6898442
62. Kasafirek E Fric P Slaby J Malis F p-Nitroanilides of 3-carboxypropionyl-peptides. Their cleavage by elastase, trypsin, and chymotrypsin Eur J Biochem 1976 69 1 1-13 10.1111/ j.1432-1033.1976.tb10852.x 991849
63. Santos CF Paula CA Salgado MC Oliveira EB Kinetic characterization and inhibition of the rat MAB elastase-2, an angiotensin I-converting serine protease Can J Physiol Pharmacol 2002 80 1 42-47 10.1139/y02-004 11911225
64. Swiss Protein Data Bank Viewer http://swissmodel.expasy.org/spdbv/