Synthesizing non-natural parts from natural genomic template

Journal of Biological Engineering

Volumn 3, Issue , 2009, Pages

  Dhar, Pawan K ^a   Thwin, Chaw Su ^a   Tun, Kyaw ^a   Tsumoto, Yuko ^a   Maurer Stroh, Sebastian ^b   Eisenhaber, Frank ^b   Surana, Uttam ^c  

^a RIKEN   (Japan)

^b BIOINFORMATICS INSTITUTE   (Singapore)

^c INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEIN EKA1; PROTEIN EKA2; PROTEIN EKA3; PROTEIN EKA4; PROTEIN EKA5; PROTEIN EKA6; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CELL GROWTH; CONTROLLED STUDY; DNA TEMPLATE; ESCHERICHIA COLI; GROWTH INHIBITION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; WESTERN BLOTTING; WILD TYPE;

EID: 61349088767     PISSN: None     EISSN: None     Source Type: Journal    
DOI: 10.1186/1754-1611-3-2     Document Type: Article

References (28)

1. Cook PR Nongenic transcription, gene regulation and action at a distance J Cell Sci 2003, 116:4483-91 14576342
2. Bejerano G Haussler D Blanchette M Into the heart of darkness: large-scale clustering of human non-coding DNA Bioinformatics 2004, 20:i40-8 15262779
3. Shabalina SA Spiridonov NA The mammalian transcriptome and the function of non-coding DNA sequences Genome Biol 2004, 5:105 395773 15059247
4. Taft RJ Pheasant M Mattick JS The relationship between non-protein-coding DNA and eukaryotic complexity Bioessays 2007, 29:288-99 17295292
5. Dawson PE Muir TW Clark-Lewis I Kent SB Synthesis of proteins by native chemical ligation Science 1994, 266:776-9 7973629
6. Nilsson BL Soellner MB Raines RT Chemical synthesis of proteins Annu Rev Biophys Biomol Struct 2005, 34:91-118 15869385
7. Brian Kuhlman Baker D Exploring folding free energy landscapes using computational protein design Curr Opin Struct Biol 2004, 14:89-95 15102454
8. Riechmann L Winter G Novel folded protein domains generated by combinatorial shuffling of polypeptide segments Proc Natl Acad Sci USA 2000, 97:10068-73 27691 10954734
9. Sen S Venkata Dasu V Mandal B Developments in directed evolution for improving enzyme functions Appl Biochem Biotechnol 2007, 143:212-23 18057449
10. Blattner FR Plunkett G 3rd Bloch CA Perna NT Burland V et al The complete genome sequence of Escherichia coli K-12 Science 1997, 277:1453-74 9278503
11. Lokanath NK Shiromizu I Ohshima N Nodake Y Sugahara M Yokoyama S Kuramitsu S Miyano M Kunishima N Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability Acta Crystallogr D Biol Crystallogr 2004, 60(Pt 10):1816-23 15388928
12. Jackson CJ Carr PD Liu JW Watt SJ Beck JL Ollis DL The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes J Mol Biol 2007, 367:1047-62 17306828
13. Shenoy AR Capuder M Draskovic P Lamba D Visweswariah SS Podobnik M Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis J Mol Biol 2007, 365:211-25 17059828
14. Ginalski K Elofsson A Fischer D Rychlewski L 3D-Jury: A simple approach to improve protein structure predictions Bioinformatics 2003, 19:1015-8 12761065
15. Russell RJ Haire LF Stevens DJ Collins PJ Lin YP Blackburn GM Hay AJ Gamblin SJ Skehel JJ The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design Nature 2006, 443:45-9 16915235
16. Eswar N Eramian D Webb B Shen MY Sali A Protein structure modeling with MODELLER Methods Mol Biol 2008, 426:145-159 18542861
17. Kaján L Rychlewski L Evaluation of 3D-Jury on CASP7 models BMC Bioinformatics 2007, 8:304 2040163 17711571
18. Wootton JC Non-globular domains in protein sequences: Automated segmentation using complexity measures Comput Chem 1994, 18:269-85 7952898
19. Tjaden B Saxena RM Stolyar S Haynor DR Kolker E Rosenow C Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays Nucleic Acids Res 2002, 30:3732-8 137427 12202758
20. Nurminsky DI Nurminskaya MV De Aguiar D Hartl DL Selective sweep of a newly evolved sperm-specific gene in Drosophila Nature 1998, 396:572-575 9859991
21. Cai J Zhao R Huifeng J Wang W De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae Genetics 2008, 179:487-496 2390625 18493065
22. Giacomelli MG Hancock AS Masel J The conversion of 3'UTRs into coding regions Mol Biol Evol 2007, 24:457 1808353 17099057
23. Levine MT Jones CD Kern AD Lindfors HA Begun DJ Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression Proc Natl Acad Sci USA 2006, 103:9935-9939 1502557 16777968
24. Long M Betran E Thornton K Wang W The origin of new genes: Glimpses from the young and old Nat Rev Genet 2003, 4:865-875 14634634
25. Altschul SF Madden TL Schaffer AA Zhang J Zheng Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25:3389-3402 146917 9254694
26. Ausubel FM Brent R Kingston RE Moore DD Seidman JG Smith JA Struhl K Current Protocols in Molecular Biology Green/Wiley-Interscience New York 1990
27. McGuffin LJ Jones DT Improvement of the GenTHREADER method for genomic fold recognition Bioinformatics 2003, 19:874-81 12724298
28. Krieger E Koraimann G Vriend G Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field Proteins 2002, 47:393-402 11948792