Consensus protein design

Protein Engineering, Design and Selection

Volumn 29, Issue 7, 2016, Pages 245-251

  Porebski, Benjamin T ^a,b   Buckle, Ashley M ^a  

^a MONASH UNIVERSITY   (Australia)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

consensus design; multiple sequence alignment; protein stability; semi rational design; statistical sequence analysis; thermostability

Indexed keywords

AMINO ACIDS; DESIGN;

MULTIPLE SEQUENCE ALIGNMENTS; PROTEIN STABILITY; RATIONAL DESIGN; SEQUENCE ANALYSIS; THERMOSTABILITY;

PROTEINS;

CONSENSUS DEVELOPMENT; GENE MUTATION; IMMUNOGENICITY; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STABILITY; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIGNAL NOISE RATIO; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; GENETICS; HUMAN; INFORMATION SCIENCE; PROCEDURES; TEMPERATURE; THERMODYNAMICS;

PROTEIN;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; INFORMATICS; PROTEIN ENGINEERING; PROTEIN STABILITY; PROTEINS; SEQUENCE ALIGNMENT; TEMPERATURE; THERMODYNAMICS;

EID: 84977104386     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzw015     Document Type: Review

References (108)

1. Alton, K., Stabinsky, Y., Richards, R., Ferguson, B., Goldstein, L., Altrock, B., Miller, L. and Stebbing, N. (1983) The Biology of Interferon System. 2nd ed. Amsterdam: Elsevier Science Publishers, pp. 119-128.
2. Amin, N., Liu, A.D., Ramer, S., Aehle, W., Meijer, D., Metin, M., Wong, S., Gualfetti, P. and Schellenberger, V. (2004) Protein Eng., Des. Sel., 17, 787-793.
3. Arnold, F.H. and Volkov, A.A. (1999) Curr. Opin. Chem. Biol., 3, 54-59.
4. Atchley, W.R., Wollenberg, K.R., Fitch, W.M., Terhalle, W. and Dress, A.W. (2000) Mol. Biol. Evol., 17, 164-178.
5. Barrick, D., Ferreiro, D.U. and Komives, E.A. (2008) Curr. Opin. Struct. Biol., 18, 27-34.
6. Bartlett, G.J., Porter, C.T., Borkakoti, N. and Thornton, J.M. (2002) J. Mol. Biol., 324, 105-121.
7. Bauer, F., Schweimer, K., Klüver, E., Conejo-Garcia, J.R., Forssmann, W.G., Rösch, P., Adermann, K. and Sticht, H. (2001) Protein Sci., 10, 2470-2479.
8. Bershtein, S., Goldin, K. and Tawfik, D.S. (2008) J. Mol. Biol., 379, 1029-1044.
9. Blatt, L.M., Davis, J.M., Klein, S.B. and Taylor, M.W. (1996) J. Interferon Cytokine Res., 16, 489-499.
10. Bloom, J.D. and Glassman, M.J. (2009) PLoS Comput. Biol., 5, e1000349.
11. Bloom, J.D., Silberg, J.J., Wilke, C.O., Drummond, D.A., Adami, C. and Arnold, F.H. (2005) Proc. Natl. Acad. Sci., 102, 606-611.
12. Bloom, J.D., Labthavikul, S.T., Otey, C.R. and Arnold, F.H. (2006) Proc. Natl. Acad. Sci., 103, 5869-5874.
13. Bornscheuer, U.T., Huisman, G.W., Kazlauskas, R.J., Lutz, S., Moore, J.C. and Robins, K. (2012) Nature, 485, 185-194.
14. Brown, N.G., Pennington, J.M., Huang, W., Ayvaz, T. and Palzkill, T. (2010) J. Mol. Biol., 404, 832-846.
15. Brustad, E.M. and Arnold, F.H. (2011) Curr. Opin. Chem. Biol., 15, 201-210.
16. Case, B.A. and Hackel, B.J. (2016) Biotechnol. Bioeng., doi:10.1002/bit.25931.
17. Chen, J. and Stites, W.E. (2001) Biochemistry, 40, 14012-14019.
18. Chirino, A.J., Ary, M.L. and Marshall, S.A. (2004) Drug Discov. Today, 9, 82-90.
19. Dai, M., Fisher, H.E., Temirov, J., Kiss, C., Phipps, M.E., Pavlik, P., Werner, J.H. and Bradbury, A.R.M. (2007) Protein Eng. Des. Sel., 20, 69-79.
20. De Groot, A.S. and Scott, D.W. (2007) Trends Immunol., 28, 482-490.
21. Dinner, A.R., Sali, A., Smith, L.J., Dobson, C.M. and Karplus, M. (2000) Trends Biochem. Sci., 25, 331-339.
22. Dobson, C.M. (2003) Nature, 426, 884-890.
23. Durani, V. and Magliery, T.J. (2013) Methods Enzymol., 523, 237-256.
24. Ferreiro, D.U., Cervantes, C.F., Truhlar, S.M.E., Cho, S.S., Wolynes, P.G. and Komives, E.A. (2007a) J. Mol. Biol., 365, 1201-1216.
25. Ferreiro, D.U., Hegler, J.A., Komives, E.A. and Wolynes, P.G. (2007b) Proc. Natl. Acad. Sci. USA, 104, 19819-19824.
26. Finn, R.D., Clements, J. and Eddy, S.R. (2011) Nucleic Acids Res., 39, W29-W37.
27. Finn, R.D., Coggill, P., Eberhardt, R.Y., et al. (2016) Nucleic Acids Res., 44, D279-D285.
28. Gershenson, A., Gierasch, L.M., Pastore, A. and Radford, S.E. (2014) Nat. Chem. Biol., 10, 884-891.
29. Gettins, P.G.W. (2002) Chem. Rev., 102, 4751-4804.
30. Gianni, S., Camilloni, C., Giri, R., Toto, A., Bonetti, D., Morrone, A., Sormanni, P., Brunori, M. and Vendruscolo, M. (2014) Proc. Natl. Acad. Sci. USA, 111, 14141-14146.
31. Göbel, U., Sander, C., Schneider, R. and Valencia, A. (1994) Proteins, 18, 309-317.
32. Horovitz, A. and Fersht, A.R. (1992) J. Mol. Biol., 224, 733-740.
33. Huang, Y., Niu, B., Gao, Y., Fu, L. and Li, W. (2010) Bioinformatics, 26, 680-682.
34. Huntington, J.A., Read, R.J. and Carrell, R.W. (2000) Nature, 407, 923-926.
35. Jäckel, C., Bloom, J.D., Kast, P., Arnold, F.H. and Hilvert, D. (2010) J. Mol. Biol., 399, 541-546.
36. Jacobs, S.A., Diem, M.D., Luo, J., Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.L. and O'Neil, K.T. (2012) Protein Eng. Des. Sel., 25, 107-117.
37. Jawa, V., Cousens, L.P., Awwad, M., Wakshull, E., Kropshofer, H. and De Groot, A.S. (2013) Clin. Immunol., 149, 534-555.
38. Jiang, X., Kowalski, J. and Kelly, J.W. (2001) Protein Sci., 10, 1454-1465.
39. Jiang, L., Althoff, E.A., Clemente, F.R., et al. (2008) Science, 319, 1387-1391.
40. Joh, N.H., Wang, T., Bhate, M.P., Acharya, R., Wu, Y., Grabe, M., Hong, M., Grigoryan, G. and DeGrado, W.F. (2014) Science, 346, 1520-1524.
41. Kemena, C. and Notredame, C. (2009) Bioinformatics, 25, 2455-2465.
42. Khersonsky, O., Kiss, G., Röthlisberger, D., Dym, O., Albeck, S., Houk, K.N., Baker, D. and Tawfik, D.S. (2012) Proc. Natl. Acad. Sci. USA, 109, 10358-10363.
43. Krishnan, B. and Gierasch, L.M. (2011) Nat. Struct. Mol. Biol., 18, 222-226.
44. Law, R.H.P., Zhang, Q., McGowan, S., et al. (2006) Genome Biol., 7, 216.
45. Lehmann, M., Kostrewa, D., Wyss, M., Brugger, R., D'Arcy, A., Pasamontes, L. and van Loon, A.P. (2000) Protein Eng., 13, 49-57.
46. Lehmann, M., Loch, C., Middendorf, A., Studer, D., Lassen, S.F., Pasamontes, L., van Loon, A.P.G.M. and Wyss, M. (2002) Protein Eng., 15, 403-411.
47. Lehmann, M. and Wyss, M. (2001) Curr. Opin. Biotechnol., 12, 371-375.
48. Letunic, I., Doerks, T. and Bork, P. (2015) Nucleic Acids Res., 43, D257-D260.
49. LiCata, V.J. and Ackers, G.K. (1995) Biochemistry, 34, 3133-3139.
50. Lockless, S.W. and Ranganathan, R. (1999) Science, 286, 295-299.
51. Lomas, D.A. and Carrell, R.W. (2002) Nat. Rev. Genet., 3, 759-768.
52. Luque, I., Leavitt, S.A. and Freire, E. (2002) Annu. Rev. Biophys. Biomol. Struct., 31, 235-256.
53. Lutz, S. (2010) Curr. Opin. Biotechnol., 21, 734-743.
54. Macias, M.J., Gervais, V., Civera, C. and Oschkinat, H. (2000) Nat. Struct. Biol., 7, 375-379.
55. Magliery, T.J. (2015) Curr. Opin. Struct. Biol., 33, 161-168.
56. Magliery, T.J., Lavinder, J.J. and Sullivan, B.J. (2011) Curr. Opin. Chem. Biol., 15, 443-451.
57. Magliery, T.J. and Regan, L. (2004) J. Mol. Biol., 343, 731-745.
58. Main, E.R.G., Xiong, Y., Cocco, M.J., D'Andrea, L. and Regan, L. (2003) Structure, 11, 497-508.
59. Matthews, B.W. (1993) Annu. Rev. Biochem., 62, 139-160.
60. Morrison, D.A. (2015) Syst. Bot., 40, 14-26.
61. Mosavi, L.K., Minor, D.L. and Peng, Z.Y. (2002) Proc. Natl. Acad. Sci., 99, 16029-16034.
62. NCBI Resource Coordinators (2014) Nucleic Acids Res., 42, D7-17.
63. Nikolova, P.V., Henckel, J., Lane, D.P. and Fersht, A.R. (1998) Proc. Natl. Acad. Sci. USA, 95, 14675-14680.
64. Nikolova, P.V., Wong, K.B., DeDecker, B., Henckel, J. and Fersht, A.R. (2000) Embo J., 19, 370-378.
65. Nuin, P.A.S., Wang, Z. and Tillier, E.R.M. (2006) BMC Bioinf., 7, 471.
66. Ozer, H.G. and Ray, W.C. (2006) Nucleic Acids Res., 34, W133-W136.
67. Paatero, A., Rosti, K., Shkumatov, A.V., et al. (2016) Biochemistry, 55, 914-926.
68. Pantoliano, M.W., Whitlow, M., Wood, J.F., Dodd, S.W., Hardman, K.D., Rollence, M.L. and Bryan, P.N. (1989) Biochemistry, 28, 7205-7213.
69. Parker, R., Mercedes-Camacho, A. and Grove, T.Z. (2014) Protein Sci., 23, 790-800.
70. Parmeggiani, F., Pellarin, R., Larsen, A.P., Varadamsetty, G., Stumpp, M.T., Zerbe, O., Caflisch, A. and Plückthun, A. (2008) J. Mol. Biol., 376, 1282-1304.
71. Patrick, W.M. and Firth, A.E. (2005) Biomol. Eng., 22, 105-112.
72. Pauling, L., Zuckerkandl, E., Henriksen, T. and Lövstad, R. (1963) Acta Chem. Scand., 17(suppl.), 9-16.
73. Pearson, W.R. (2013) Curr Protoc Bioinformatics, 42, 3.1:3.1.1-3.1.8.
74. Polizzi, K.M., Chaparro-Riggers, J.F., Vazquez-Figueroa, E. and Bommarius, A.S. (2006) Biotechnol. J., 1, 531-536.
75. Porebski, B.T., Nickson, A.A., Hoke, D.E., Hunter, M.R., Zhu, L., McGowan, S., Webb, G.I. and Buckle, A.M. (2015) Protein Eng. Des. Sel., 28, 67-78.
76. Poteete, A.R., Rennell, D., Bouvier, S.E. and Hardy, L.W. (1997) Protein Sci., 6, 2418-2425.
77. Risso, V.A., Gavira, J.A., Gaucher, E.A. and Sanchez-Ruiz, J.M. (2014) Proteins, 82, 887-896.
78. Rost, B. (1999) Protein Eng., 12, 85-94.
79. Sanchez-Ruiz, J.M. (2010) Biophys. Chem., 148, 1-15.
80. Schreiber, G., Buckle, A.M. and Fersht, A.R. (1994) Structure, 2, 945-951.
81. Shoichet, B.K., Baase, W.A., Kuroki, R. and Matthews, B.W. (1995) Proc. Natl. Acad. Sci., 92, 452-456.
82. Sigrist, C.J.A., Cerutti, L., Hulo, N., Gattiker, A., Falquet, L., Pagni, M., Bairoch, A. and Bucher, P. (2002) Briefings Bioinf., 3, 265-274.
83. Sigrist, C.J.A., de Castro, E., Cerutti, L., Cuche, B.A., Hulo, N., Bridge, A., Bougueleret, L. and Xenarios, I. (2013) Nucleic Acids Res., 41, D344-D347.
84. Socolich, M., Lockless, S.W., Russ, W.P., Lee, H., Gardner, K.H. and Ranganathan, R. (2005) Nature, 437, 512-518.
85. Sonnhammer, E.L., Eddy, S.R., Birney, E., Bateman, A. and Durbin, R. (1998) Nucleic Acids Res., 26, 320-322.
86. Steipe, B. (1999) Curr. Top. Microbiol. Immunol., 243, 55-86.
87. Steipe, B., Schiller, B., Plückthun, A. and Steinbacher, S. (1994) J. Mol. Biol., 240, 188-192.
88. Stevens, A.J., Brown, Z.Z., Shah, N.H., Sekar, G., Cowburn, D. and Muir, T.W. (2016) J. Am. Chem. Soc., 138, 2162-2165.
89. Sullivan, B.J., Durani, V. and Magliery, T.J. (2011) J. Mol. Biol., 413, 195-208.
90. Sullivan, B.J., Nguyen, T., Durani, V., Mathur, D., Rojas, S., Thomas, M., Syu, T. and Magliery, T.J. (2012) J. Mol. Biol., 420, 384-399.
91. Talavera, D., Lovell, S.C. and Whelan, S. (2015) Mol. Biol. Evol., 32, 2456-2468.
92. Thornton, J.W. (2004) Nat. Rev. Genet., 5, 366-375.
93. Thornton, J.W., Need, E. and Crews, D. (2003) Science, 301, 1714-1717.
94. Tokuriki, N., Stricher, F., Schymkowitz, J., Serrano, L. and Tawfik, D.S. (2007) J. Mol. Biol., 369, 1318-1332.
95. Tokuriki, N., Stricher, F., Serrano, L. and Tawfik, D.S. (2008) PLoS Comput. Biol., 4, e1000002.
96. Tokuriki, N. and Tawfik, D.S. (2009a) Curr. Opin. Struct. Biol., 19, 596-604.
97. Tokuriki, N. and Tawfik, D.S. (2009b) Science, 324, 203-207.
98. UniProt Consortium (2008) Nucleic Acids Res., 36, D190-D195.
99. Vazquez-Figueroa, E., Yeh, V., Broering, J.M., Chaparro-Riggers, J.F. and Bommarius, A.S. (2008) Protein Eng., Des. Sel., 21, 673-680.
100. Wang, Q., Buckle, A.M., Foster, N.W., Johnson, C.M. and Fersht, A.R. (1999) Protein Sci., 8, 2186-2193.
101. Wijma, H.J., Floor, R.J. and Janssen, D.B. (2013) Curr. Opin. Struct. Biol., 23, 588-594.
102. Wijma, H.J., Floor, R.J., Jekel, P.A., Baker, D., Marrink, S.J. and Janssen, D.B. (2014) Protein Eng. Des. Sel., 27, 49-58.
103. Wilson, D., Pethica, R., Zhou, Y., Talbot, C., Vogel, C., Madera, M., Chothia, C. and Gough, J. (2009) Nucleic Acids Res., 37, D380-D386.
104. Wirtz, P. and Steipe, B. (1999) Protein Sci., 8, 2245-2250.
105. Woolfson, D.N., Bartlett, G.J., Burton, A.J., Heal, J.W., Niitsu, A., Thomson, A.R. and Wood, C.W. (2015) Curr. Opin. Struct. Biol., 33, 16-26.
106. Yang, Z., Kumar, S. and Nei, M. (1995) Genetics, 141, 1641-1650.
107. Zahnd, C., Wyler, E., Schwenk, J.M., et al. (2007) J. Mol. Biol., 369, 1015-1028.
108. Zvelebil, M.J., Barton, G.J., Taylor, W.R. and Sternberg, M.J. (1987) J. Mol. Biol., 195, 957-961.