Protein engineering methods applied to membrane protein targets

Protein Engineering, Design and Selection

Volumn 26, Issue 2, 2013, Pages 91-100

  Lluis, M W ^a   Godfroy III, J I ^b   Yin, H ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b University of Colorado at Boulder   (United States)

Author keywords

computational design; directed evolution; membrane proteins; protein engineering

Indexed keywords

BIOCHEMICAL INFORMATION; CELLULAR REGULATION; COMPUTATIONAL DESIGN; COMPUTATIONAL MODELING; DIRECTED EVOLUTION; DRUG DESIGN; GENES ENCODING; GLOBULAR PROTEINS; HIGH RESOLUTION; HUMAN GENOMES; ION CHANNEL; MEMBRANE PROTEINS; NATURAL SELECTION; PROTEIN ENGINEERING; PROTEIN THERAPEUTICS; SIGNALING RECEPTOR; STRUCTURE-FUNCTION RELATIONSHIP; TRANS-MEMBRANE DOMAINS; TRANS-MEMBRANE PROTEINS;

ACTIVATION ANALYSIS; BIOCHEMICAL ENGINEERING; BIOLOGICAL MEMBRANES; CRYSTAL STRUCTURE; GENETIC ENGINEERING; ION EXCHANGE; MOLECULAR BIOLOGY;

PROTEINS;

G PROTEIN COUPLED RECEPTOR; MEMBRANE PROTEIN; MUTANT PROTEIN;

AMINO ACID SEQUENCE; CRYSTAL STRUCTURE; CRYSTALLIZATION; DIRECTED MOLECULAR EVOLUTION; HUMAN; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN TARGETING; REVIEW; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; ANIMALS; COMPUTER SIMULATION; CRYSTALLIZATION; DIRECTED MOLECULAR EVOLUTION; HUMANS; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN ENGINEERING; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN TRANSPORT; RECOMBINANT PROTEINS;

EID: 84872356936     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzs079     Document Type: Review

References (78)

1. Ahram,M., Litou,Z.I., Fang,R. and Al-Tawallbeh,G. (2006) In Silico Biol., 6, 379-386
2. Arnold,F.H. (1998) Acc. Chem. Res., 31, 125-131
3. Barth,P., Wallner,B. and Baker,D. (2009) Proc. Natl Acad. Sci. USA, 106, 1409-1414
4. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) Nucleic Acids Res., 28, 235-242
5. Binz,H.K., Stumpp,M.T., Forrer,P., Amstutz,P. and Plückthun,A. (2003) J. Mol. Biol., 332, 489-503
6. Burkhardt,A., Willingham,M., Gay,C., Jeang,K.T. and Schlegel,R. (1989) Virology, 170, 334-339
7. Call,M.E., Schnell,J.R., Xu,C., Lutz,R.A., Chou,J.J. and Wucherpfennig,K.W. (2006) Cell, 127, 355-368
8. Cammett,T.J., Jun,S.J., Cohen,E.B., Barrera,F.N., Engelman,D.M. and DiMaio,D. (2010) Proc. Natl Acad. Sci. USA, 107, 3447-3452
9. Cantor,J.R., Panayiotou,V., Agnello,G., Georgiou,G. and Stone,E.M. (2012) Methods Enzymol., 502, 291-319
10. Caputo,G.A., Litvinov,R.I., Li,W., Bennett,J.S., DeGrado,W.F. and Yin,H. (2008) Biochemistry, 47, 8600-8606
11. Cherezov,V., Abola,E. and Stevens,R.C. (2010) Methods Mol. Biol., 654, 141-168
12. Chin,C.N., Sachs,J.N. and Engelman,D.M. (2005) FEBS Lett., 579, 3855-3858
13. Cui,T., Mowrey,D., Bondarenko,V., et al. (2012) Biochim. Biophys. Acta, 1818, 617-626
14. Dodevski,I. and Plückthun,A. (2011) J. Mol. Biol., 408, 599-615
15. Duong,M.T., Jaszewski,T.M., Fleming,K.G. and MacKenzie,K.R. (2007) J. Mol. Biol., 371, 422-434
16. Finger,C., Escher,C. and Schneider,D. (2009) Sci. Signal., 2, ra56
17. Forrer,P., Stumpp,M.T., Binz,H.K. and Plückthun,A. (2003) FEBS Lett., 539, 2-6
18. Gimpl,G., Klein,U., Reiländer,H. and Fahrenholz,F. (1995) Biochemistry, 34, 13794-13801
19. Godfroy,J.I., III, Roostan,M., Moroz,Y.S., Korendovych,I.V. and Yin,H. (2012) PLoS ONE. Accepted for publication October 1, 2012
20. Grossfield,A. (2011) Biochim. Biophys. Acta, 1808, 1868-1878
21. Hackel,B.J., Neil,J.R., White,F.M. and Wittrup,K.D. (2011) Protein Eng. Des. Sel., 25, 47-57
22. Hajduczki,A., Majumdar,S., Fricke,M., Brown,I.A.M. and Weiss,G.A. (2011) ACS Chem. Biol., 6, 301-307
23. Harrison,P.M., Kumar,A., Lang,N., Snyder,M. and Gerstein,M. (2002 Nucleic Acids Res., 30, 1083-1090
24. Huber,T., Steiner,D., Rothlisberger,D. and Plückthun,A. (2007) J. Struct. Biol., 159, 206-221
25. Hunte,C. and Michel,H. (2002) Curr. Opin. Struct. Biol., 12, 503-508
26. Jin,M.S., Kim,S.E., Heo,J.Y., Lee,M.E., Kim,H.M., Paik,S.G., Lee,H. and Lee,J.O. (2007) Cell, 130, 1071-1082
27. Kang,J.Y., Nan,X., Jin,M.S., Youn,S.J., Ryu,Y.H., Mah,S., Han,S.H., Lee,H., Paik,S.G. and Lee,J.O. (2009) Immunity, 31, 873-884
28. Katzen,F., Peterson,T.C. and Kudlicki,W. (2009) Trends Biotechnol., 27, 455-460
29. Kohl,A., Binz,H.K., Forrer,P., Stumpp,M.T., Plückthun,A. and Grutter,M.G. (2003) Proc. Natl Acad. Sci. USA, 100, 1700-1705
30. Korendovych,I.V., Senes,A., Kim,Y.H., Lear,J.D., Fry,H.C., Therien,M.J., Blasie,J.K., Walker,F.A. and DeGrado,W.F. (2010) J. Am. Chem. Soc., 132, 15516-15518
31. Lagane,B., Gaibelet,G., Meilhoc,E., Masson,J.M., Ce'zanne,L. and Lopez,A. (2000) J. Biol. Chem., 275, 33197-33200
32. Langosch,D. and Arkin,I.T. (2009) Protein Sci., 18, 1343-1358
33. Langosch,D., Brosig,B., Kolmar,H. and Fritz,H.-J. (1996) J. Mol. Biol., 263, 525-530
34. Lappano,R. and Maggiolini,M. (2011) Nat. Rev. Drug Discov., 10, 47-60
35. Lemmon,M.A., Flanagan,J.M., Treutlein,H.R., Zhang,J. and Engelman,D.M. (1992) Biochemistry, 31, 12719-12725
36. Li,R., Gorelik,R., Nanda,V., Law,P.B., Lear,J.D., DeGrado,W.F. and Bennett,J.S. (2004) J. Biol. Chem., 279, 26666-26673
37. Lundstrom,K. (2005) Trends Biotechnol., 23, 103-108
38. MacKenzie,K.R. (2006) Chem. Rev., 106, 1931-1977
39. MacKenzie,K.R., Prestegard,J.H. and Engelman,D.M. (1997) Science, 276, 131-133
40. Marlatt,S.A., Kong,Y., Cammett,T.J., Korbel,G., Noonan,J.P. and DiMaio,D. (2011) Protein Eng. Des. Sel., 24, 311-320
41. McCusker,E.C., Bane,S.E., O'Malley,M.A. and Robinson,A.S. (2007 Biotechnol. Prog., 23, 540-547
42. Milovnik,P., Ferrari,D., Sarkar,C.A. and Plückthun,A. (2009) Protein Eng. Des. Sel., 22, 357-366
43. Moore,D.T., Berger,B.W. and DeGrado,W.F. (2008) Structure, 16, 991-1001
44. Murakami,S., Nakashima,R., Yamashita,E. and Yamaguchi,A. (2002) Nature, 419, 587-593
45. Nemoto,W. and Toh,H. (2006) Curr. Protein Pept. Sci., 7, 561-575
46. Overington,J.P., Al-Lazikani,B. and Hopkins,A.L. (2006) Nat. Rev. Drug Discov., 5, 993-996
47. Park,B.S., Song,D.H., Kim,H.M., Choi,B.S., Lee,H. and Lee,J.O. (2009) Nature, 458, 1191-1195
48. Perez-Aguilar,J.M. and Saven,J.G. (2012) Structure, 20, 5-14
49. Petti,L., Nilson,L.A. and DiMaio,D. (1991) Embo J., 10, 845-855
50. Pogson,M., Georgiou,G. and Iverson,B.L. (2009) Curr. Opin. Biotechnol., 20, 390-397
51. Pos,K.M., Schiefner,A., Seeger,M.A. and Diederichs,K. (2004) FEBS Lett., 564, 333-339
52. Salom,D., Cao,P., Sun,W., Kramp,K., Jastrzebska,B., Jin,H., Feng,Z. and Palczewski,K. (2012) Faseb J., 26, 492-502
53. Sammond,D.W., Joce,C., Takeshita,R., McQuate,S.E., Ghosh,N., Martin,J.M. and Yin,H. (2011) Biopolymers, 95, 772-784
54. Sanders,C.R., Kuhn Hoffmann,A., Gray,D.N., Keyes,M.H. and Ellis,C.D. (2004) Chembiochem, 5, 423-426
55. Sarkar,C.A., Dodevski,I., Kenig,M., Dudli,S., Mohr,A., Hermans,E. and Plückthun,A. (2008) Proc. Natl Acad. Sci. USA, 105, 14808-14813
56. Scheideman,E.H., Marlatt,S.A., Xie,Y., Hu,Y., Sutton,R.E. and DiMaio,D. (2012) J. Virol, 86, 10281-10292
57. Schlegel,R., Wade-Glass,M., Rabson,M.S. and Yang,Y.C. (1986) Science, 233, 464-467
58. Seddon,A.M., Curnow,P. and Booth,P.J. (2004) Biochim Biophys Acta, 1666, 105-117
59. Senes,A., Gerstein,M. and Engelman,D.M. (2000) Journal of Molecular Biology, 296, 921-936
60. Sennhauser,G., Amstutz,P., Briand,C., Storchenegger,O. and Grutter,M.G. (2007) PLoS. Biol., 5, e7
61. Shapiro,M.G., Westmeyer,G.G., Romero,P.A., et al. (2010) Nat. Biotechnol., 28, 264-270
62. Slovic,A.M., Kono,H., Lear,J.D., Saven,J.G. and DeGrado,W.F. (2004) Proc. Natl. Acad. Sci. USA, 101, 1828-1833
63. Stevens,T.J. and Arkin,I.T. (2000) Proteins, 39, 417-420
64. Stewart,C.R., Stuart,L.M., Wilkinson,K., et al. (2009) Nat. Immunol., 11, 155-161
65. Surti,T., Klein,O., Aschheim,K., DiMaio,D. and Smith,S.O. (1998) Proteins, 33, 601-612
66. Talbert-Slagle,K. and DiMaio,D. (2009) Virology, 384, 345-351
67. Talbert-Slagle,K., Marlatt,S., Barrera,F.N., Khurana,E., Oates,J., Gerstein,M., Engelman,D.M., Dixon,A.M. and DiMaio,D. (2009) J. Virol., 83, 9773-9785
68. Topiol,S. and Sabio,M. (2009) Biochem. Pharmacol., 78, 11-20
69. Van Arnam,E.B., Lester,H.A. and Dougherty,D.A. (2011) ACS Chem. Biol., 6, 1063-1068
70. Vithayathil,R., Hooy,R.M., Cocco,M.J. and Weiss,G.A. (2011) J. Mol. Biol., 414, 499-510
71. von Heijne,G. (2007) J. Intern. Med., 261, 543-557
72. Walters,R.F. and DeGrado,W.F. (2006) Proc. Natl Acad. Sci. USA, 103, 13658-13663
73. White,S.H. (2004) Protein Sci., 13, 1948-1949
74. Yarnitzky,T., Levit,A. and Niv,M.Y. (2010) Curr. Opin. Drug Discov. Devel., 13, 317-325
75. Yildirim,M.A., Goh,K.I., Cusick,M.E., Barabasi,A.L. and Vidal,M. (2007) Nat. Biotechnol., 25, 1119-1126
76. Yin,H., Slusky,J.S., Berger,B.W., et al. (2007) Science, 315, 1817-1822
77. Zhang,H., Tay,P.N., Cao,W., Li,W. and Lu,J. (2002) FEBS Lett., 532, 171-176
78. Zhu,H., Metcalf,D.G., Streu,C.N., Billings,P.C., DeGrado,W.F. and Bennett,J.S. (2010) J. Mol. Biol., 401, 882-891