MolCraft: A hierarchical approach to the synthesis of artificial proteins

Journal of Molecular Catalysis B: Enzymatic

Volumn 28, Issue 4-6, 2004, Pages 145-153

  Shiba, Kiyotaka ^a  

^a CANCER INSTITUTE   (Japan)

Author keywords

Combinatorial bioengineering; Evolutionary molecular engineering; Functional motifs; In vitro evolution; Protein engineering

Indexed keywords

GENES; MUTAGENESIS; PERTURBATION TECHNIQUES; POLYMERIZATION; POLYMERS; PROTEINS; SYNTHESIS (CHEMICAL);

BIOLOGICAL ACTIVITY; JUNCTIONAL PERTURBATIONS; MODULAR STRUCTURES; MOLECULAR DIVERSE;

CATALYSIS;

PEPTIDE; POLYMER;

DELETION MUTANT; GENE ACTIVITY; INSTRUMENTATION; MOLECULAR EVOLUTION; NANOTECHNOLOGY; OPEN READING FRAME; POLYMERIZATION; PROTEIN ENGINEERING; PROTEIN PROCESSING; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; REVIEW;

INSERTION SEQUENCES;

EID: 2442583681     PISSN: 13811177     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcatb.2003.12.027     Document Type: Review

References (106)

1. Tyers M., Mann M. Nature. 422:2003;193
2. Collins F.S., Morgan M., Patrinos A. Science. 300:2003;286
3. Collins F.S., Green E.D., Guttmacher A.E., Guyer M.S. Nature. 422:2003;835
4. Ulmer K.M. Science. 219:1983;666
5. Pabo C. Nature. 301:1983;200
6. Dahiyat B.I., Mayo S.L. Science. 278:1997;82
7. Regan L., DeGrado W.F. Science. 241:1988;976
8. Hecht M.H., Richardson J.S., Richardson D.C., Ogden R.C. Science. 249:1990;884
9. Ramirez-Alvarado M., Blanco F.J., Serrano L. Nat. Struct. Biol. 3:1996;604
10. Kortemme T., RamirezAlvarado M., Serrano L. Science. 281:1998;253
11. Harbury P.B., Plecs J.J., Tidor B., Alber T., Kim P.S. Science. 282:1998;1462
12. Kraemer-Pecore C.M., Wollacott A.M., Desjarlais J.R. Curr. Opin. Chem. Biol. 5:2001;690
13. Joyce G.F. Gene. 82:1989;83
14. Szostak J.W. Trends Biochem. Sci. 17:1992;89
15. Marks J.D., Hoogenboom H.R., Griffiths A.D., Winter G. J. Biol. Chem. 267:1992;16007
16. Kauffman S.A. J. Theor. Biol. 157:1992;1
17. Gallop M.A., Barrett R.W., Dower W.J., Fodor S.P.A., Gordon E.M. J. Med. Chem. 37:1994;1233
18. Kenan D.J., Tsai D.E., Keene J.D. Trends Biochem. Sci. 19:1994;57
19. Zwick M.B., Shen J.Q., Scott J. Curr. Opin. Biotechnol. 9:1998;427
20. Lorsch J.R., Szostak J.W. Biochemistry. 33:1994;973
21. Prudent J.R., Uno T., Schultz P.G. Science. 264:1994;1924
22. Ekland E.H., Szostak J.W., Bartel D.P. Science. 269:1995;364
23. Illangasekare M., Sanchez G., Nickles T., Yarus M. Science. 267:1995;643
24. Dai X., De Mesmaeker A., Joyce G.F. Science. 267:1995;237
25. Wilson C., Szostak J.W. Nature. 374:1995;777
26. Lee N., Bessho Y., Wei K., Szostak J.W., Suga H. Nat. Struct. Biol. 7:2000;28
27. Saito H., Kourouklis D., Suga H. EMBO J. 20:2001;1797
28. Ellington A.D., Szostak J.W. Nature. 346:1990;818
29. Sassanfar M., Szostak J.W. Nature. 364:1993;550
30. Bock L.C., Griffin L.C., Latham J.A., Vermaas E.H., Toole J.J. Nature. 355:1992;564
31. Scott J.K., Smith G.P. Science. 249:1990;386
32. Harada K., Martin S.S., Frankel A.D. Nature. 380:1996;175
33. Pasqualini R., Ruoslahti E. Nature. 380:1996;364
34. Colas P., Cohen B., Jessen T., Grishina I., Mccoy J., Brent R. Nature. 380:1996;548
35. Frugier M., Schimmel P. Proc. Natl. Acad. Sci. U.S.A. 94:1997;11291
36. Keefe A.D., Szostak J.W. Nature. 410:2001;715
37. Ptitsyn O.B., Volkenstein M.V. J. Biomol. Struct. Dyn. 4:1986;137
38. White S.H., Jacobs R.E. J. Mol. Evol. 36:1993;79
39. Rossmann M.G., Moras D., Olsen K.W. Nature. 250:1974;194
40. Go M. Nature. 291:1981;90
41. Jasin M., Regan L., Schimmel P. Nature. 306:1983;441
42. Patthy L. Curr. Opin. Struct. Biol. 1:1991;351
43. Baron M., Norman D.G., Campbell I.D. Trends Biochem. Sci. 16:1991;13
44. Doolittle R.F. Annu. Rev. Biochem. 64:1995;287
45. Gilbert W. Cold Spring Harbor Symp. Quant. Biol. 52:1987;901
46. Logsdon J.M., Tyshenko M.G., Dixon C., Jafari J.D., Walker V.K., Palmer J.D. Proc. Natl. Acad. Sci. U.S.A. 92:1995;8507
47. de Souza S.J., Long M., Klein R.J., Roy S., Lin S., Gilbert W. Proc. Natl. Acad. Sci. U.S.A. 95:1998;5094
48. Patthy L. Gene. 238:1999;103
49. Long M. Curr. Opin. Genet. Dev. 11:2001;673
50. Bogarad L.D., Deem M.W. Proc. Natl. Acad. Sci. U.S.A. 96:1999;2591
51. Mikheeva S., Jarrell K.A. Proc. Natl. Acad. Sci. U.S.A. 93:1996;7486
52. Fisch I., Kontermann R.E., Finnern R., Hartley O., Solergonzalez A.S., Griffiths A.D., Winter G. Proc. Natl. Acad. Sci. U.S.A. 93:1996;7761
53. Crameri A., Cwirla S., Stemmer W.P.C. Nat. Med. 2:1996;100
54. Nishigaki K., Taguchi K., Kinoshita Y., Aita T., Husimi Y. Mol. Divers. 4:1998;187
55. Ostermeier M., Shim J.H., Benkovic S.J. Nat. Biotech. 17:1999;1205
56. Tsuji T., Kobayashi K., Yanagawa H. FEBS Lett. 453:1999;145
57. Tsuji T., Onimaru M., Yanagawa H. Nucleic Acids Res. 29:2001;E97
58. Kolkman J.A., Stemmer W.P. Nat. Biotech. 19:2001;423
59. Lutz S., Ostermeier M., Moore G.L., Maranas C.D., Benkovic S.J. Proc. Natl. Acad. Sci. U.S.A. 98:2001;11248
60. Sieber V., Martinez C.A., Arnold F.H. Nat. Biotech. 19:2001;456
61. Shiba K., Hatada T., Takahashi Y., Noda T. J. Biochem. (Tokyo). 132:2002;689
62. Kitamura K., Kinoshita Y., Narasaki S., Nemoto N., Husimi Y., Nishigaki K. Protein Eng. 15:2002;843
63. K. Kashiwagi, K. Shiba, J. Mol. Catal. B (2003) xxx.
64. Stemmer W.P.C. Nature. 370:1994;389
65. Stemmer W.P.C. BioTechnology. 13:1995;549
66. Crameri A., Raillard S.A., Bermudez E., Stemmer W.P.C. Nature. 391:1998;288
67. Ohno S. Proc. Natl. Acad. Sci. U.S.A. 78:1981;7657
68. Ohno S., Epplen J.T. Proc. Natl. Acad. Sci. U.S.A. 80:1983;3391
69. Ohno S. J. Mol. Evol. 20:1984;313
70. Ohno S. J. Mol. Evol. 25:1987;325
71. Krejchi M.T., Atkins E.D.T., Waddon A.J., Fournier M.J., Mason T.L., Tirrell D.A. Science. 265:1994;1427
72. McGrath K.P., Fournier M.J., Mason T.L., Tirrell D.A. J. Am. Chem. Soc. 114:1992;727
73. Sutherland G.R., Richards R.I. Proc. Natl. Acad. Sci. U.S.A. 92:1995;3636
74. Wolfe K.H., Shields D.C. Nature. 387:1997;708
75. Bailey J.A., Gu Z., Clark R.A., Reinert K., Samonte R.V., Schwartz S., Adams M.D., Myers E.W., Li P.W., Eichler E.E. Science. 297:2002;1003
76. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al. Nature. 409:2001;860
77. Kobe B., Deisenhofer J. Nature. 366:1993;751
78. Shiba K., Takahashi Y., Noda T. J. Mol. Biol. 320:2002;833
79. Shiba K., Shirai T., Honma T., Noda T. Protein Eng. 16:2003;57
80. Rohlfing D.L., Fox S.W. Adv. Catal. 20:1969;373
81. Kumagai I., Takeda S., Miura K.-i. Proc. Natl. Acad. Sci. U.S.A. 89:1992;5887
82. Wakasugi K., Ishimori K., Imai K., Wada Y., Morishima I. J. Biol. Chem. 269:1994;18750
83. K. Shiba, in: M. Go, P. Schimmel (Eds.), Tracing Biological Evolution in Protein and Gene Structures, Elsevier, Amsterdam, 1995, p. 11.
84. Inaba K., Wakasugi K., Ishimori K., Konno T., Kataoka M., Morishima I. J. Biol. Chem. 272:1997;30054
85. Tsuji T., Yoshida K., Satoh A., Kohno T., Kobayashi K., Yanagawa H. J. Mol. Biol. 286:1999;1581
86. Shiba K., Schimmel P. Proc. Natl. Acad. Sci. U.S.A. 89:1992;1880
87. Shiba K., Schimmel P. J. Biol. Chem. 267:1992;22703
88. Schultz J., Milpetz F., Bork P., Ponting C.P. Proc. Natl. Acad. Sci. U.S.A. 95:1998;5857
89. Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J., Hofmann K., Bairoch A. Nucleic Acids Res. 30:2002;235
90. Adman E.T. Curr. Opin. Struct. Biol. 1:1991;895
91. Shiba K., Takahashi T., Noda T. Proc. Natl. Acad. Sci. U.S.A. 94:1997;3805
92. K. Shiba, in preparation.
93. Whaley S.R., English D.S., Hu E.L., Barbara P.F., Belcher A.M. Nature. 405:2000;665
94. Lee S.W., Mao C., Flynn C.E., Belcher A.M. Science. 296:2002;892
95. Naik R.R., Stringer S.J., Agarwal G., Jones S.E., Stone M.O. Nat. Mater. 1:2002;169
96. Wang S., Humphreys E.S., Chung S.Y., Delduco D.F., Lustig S.R., Wang H., Parker K.N., Rizzo N.W., Subramoney S., Chiang Y.M., Jagota A. Nat. Mater. 2:2003;196
97. Zhu J., Kase D., Shiba K., Kasuya D., Yudasaka M., Iijima S. Nano Lett. 3:2003;1033
98. Sano K., Shiba K. J. Am. Chem. Soc. 125:2003;14234
99. Sarikaya M., Tamerler C., Jen A.K., Schulten K., Baneyx F. Nat. Mater. 2:2003;577
100. Sykaras N., Iacopino A.M., Marker V.A., Triplett R.G., Woody R.D. Int. J. Oral Maxillofac. Implants. 15:2000;675
101. Puleo D.A., Nanci A. Biomaterials. 20:1999;2311
102. Suzuki Y., Tanihara M., Suzuki K., Saitou A., Sufan W., Nishimura Y. J. Biomed. Mater. Res. 50:2000;405
103. Shiba K., Honma T., Minamisawa T., Nishiguchi K., Noda T. EMBO Rep. 4:2003;148
104. Shiba K. J. Biochem. Mol. Biol. 31:1998;209
105. Benner S.A. Nature. 421:2003;118
106. H. Saito, T. Honma, T. Minamisawa, K. Yamazaki, T. Noda, T. Yamori, K. Shiba, Chem. Biol. (2004) in press.