Towards the computational design of protein post-translational regulation

Bioorganic and Medicinal Chemistry

Volumn 23, Issue 12, 2015, Pages 2877-2882

  Strumillo, Marta ^a   Beltrao, Pedro ^a,b  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF AVEIRO   (Portugal)

Author keywords

Allosteric; Bioinformatics; PTMs

Indexed keywords

ALLOSTERISM; ARTICLE; HUMAN; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; AMINO ACID SEQUENCE; ANIMAL; METABOLISM; MOLECULAR GENETICS; MOLECULAR MODEL;

PROTEIN;

ALLOSTERIC REGULATION; AMINO ACID SEQUENCE; ANIMALS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN INTERACTION MAPS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOLYSIS;

EID: 84930225507     PISSN: 09680896     EISSN: 14643391     Source Type: Journal    
DOI: 10.1016/j.bmc.2015.04.056     Document Type: Article

References (78)

1. C. Choudhary, and M. Mann Nat. Rev. Mol. Cell Biol. 2010
2. J.V. Olsen, and M. Mann Mol. Cell. Proteomics 12 2013 3444
3. B.T. Weinert, V. Iesmantavicius, S.A. Wagner, C. Schölz, B. Gummesson, P. Beli, T. Nyström, and C. Choudhary Mol. Cell 51 2013 265
4. H. Nishi, K. Hashimoto, and A.R. Panchenko Structure 19 2011 1807
5. J.D. Nardozzi, K. Lott, and G. Cingolani Cell Commun. Signalling 8 2010 32
6. H. Nishi, A. Shaytan, and A.R. Panchenko Front. Genet. 5 2014 270
7. E.S. Groban, A. Narayanan, and M.P. Jacobson PLoS Comput. Biol. 2 2006 e32
8. J. Soroka, S.K. Wandinger, N. Mäusbacher, T. Schreiber, K. Richter, H. Daub, and J. Buchner Mol. Cell 45 2012 517
9. K. Sharma, R.C.J. D'Souza, S. Tyanova, C. Schaab, J.R. Wis̈niewski, J. Cox, and M. Mann Cell Rep. 2014 1
10. P. Beltrao, J.C. Trinidad, D. Fiedler, A. Roguev, W.A. Lim, K.M. Shokat, A.L. Burlingame, and N.J. Krogan PLoS Biol. 7 2009 e1000134
11. L.J. Holt, B.B. Tuch, J. Villén, A.D. Johnson, S.P. Gygi, and D.O. Morgan Science 325 2009 1682
12. C.R. Landry, E.D. Levy, and S.W. Michnick Trends Genet. 25 2009 193
13. C.S.H. Tan, B. Bodenmiller, A. Pasculescu, M. Jovanovic, M.O. Hengartner, C. Jørgensen, G.D. Bader, R. Aebersold, T. Pawson, R. Linding, C. Soon, and H. Tan Sci. Signalling 2 2009 9
14. A.M. Moses, and C.R. Landry Trends Genet. 26 2010 462
15. P. Beltrao, V. Albanèse, L.R. Kenner, D.L. Swaney, A. Burlingame, J. Villén, W.A. Lim, J.S. Fraser, J. Frydman, and N.J. Krogan Cell 150 2012 413
16. A.P. Oliveira, C. Ludwig, P. Picotti, M. Kogadeeva, R. Aebersold, and U. Sauer Mol. Syst. Biol. 8 2012 623
17. E. Kanshin, L.-P. Bergeron-Sandoval, S.S. Isik, P. Thibault, and S.W. Michnick Cell Rep. 10 2015 1202
18. P. Beltrao, P. Bork, N.J. Krogan, and V. van Noort Mol. Syst. Biol. 9 2013 714
19. O. Schueler-Furman, C. Wang, P. Bradley, K. Misura, and D. Baker Science 310 2005 638
20. T. Kortemme, M. Ramírez-Alvarado, and L. Serrano Science 281 1998 253
21. B.I. Dahiyat, C. Sarisky, and S.L. Mayo J. Mol. Biol. 273 1997 789
22. B. Kuhlman, G. Dantas, G.C. Ireton, G. Varani, B.L. Stoddard, and D. Baker Science 302 2003 1364
23. G.T. Kapp, S. Liu, A. Stein, D.T. Wong, A. Remenyi, B.J. Yeh, J.S. Fraser, J. Taunton, W.A. Lim, and T. Kortemme Proc. Natl. Acad. Sci. U.S.A 109 2012 5277
24. T. Kortemme, L.A. Joachimiak, A.N. Bullock, A.D. Schuler, B.L. Stoddard, and D. Baker Nat. Struct. Mol. Biol. 11 2004 371
25. D.J. Mandell, and T. Kortemme Nat. Chem. Biol. 5 2009 797
26. G. Kiss, N. Çelebi-Ölçüm, R. Moretti, D. Baker, and K.N. Houk Angew. Chem., Int. Ed. 52 2013 5700
27. B.T. Seet, I. Dikic, M.-M. Zhou, and T. Pawson Nat. Rev. Mol. Cell Biol. 7 2006 473
28. B.A. Liu, B.W. Engelmann, and P.D. Nash Proteomics 12 2012 1527
29. M. Tinti, L. Kiemer, S. Costa, M.L. Miller, F. Sacco, J.V. Olsen, M. Carducci, S. Paoluzi, F. Langone, C.T. Workman, N. Blom, K. Machida, C.M. Thompson, M. Schutkowski, S. Brunak, M. Mann, B.J. Mayer, L. Castagnoli, and G. Cesareni Cell Rep. 3 2013 1293
30. A.E.H. Elia, P. Rellos, L.F. Haire, J.W. Chao, F.J. Ivins, K. Hoepker, D. Mohammad, L.C. Cantley, S.J. Smerdon, and M.B. Yaffe Cell 115 2003 83
31. K.E. Moore, S.M. Carlson, N.D. Camp, P. Cheung, R.G. James, K.F. Chua, A. Wolf-Yadlin, and O. Gozani Mol. Cell 50 2013 444
32. B.D. Bryson, A.M. Del Rosario, J.S. Gootenberg, M.B. Yaffe, and F.M. White Proteomics 2015
33. M.L. Miller, L.J. Jensen, F. Diella, C. Jørgensen, M. Tinti, L. Li, M. Hsiung, S.A. Parker, J. Bordeaux, T. Sicheritz-Ponten, M. Olhovsky, A. Pasculescu, J. Alexander, S. Knapp, N. Blom, P. Bork, S. Li, G. Cesareni, T. Pawson, B.E. Turk, M.B. Yaffe, S. Brunak, and R. Linding Sci. Signal. 1 2008 2
34. G. Barnea, W. Strapps, G. Herrada, Y. Berman, J. Ong, B. Kloss, R. Axel, and K.J. Lee Proc. Natl. Acad. Sci. U.S.A. 105 2008 64
35. P.L. Howard, M.C. Chia, S. Del Rizzo, F.-F. Liu, and T. Pawson Proc. Natl. Acad. Sci. U.S.A. 100 2003 11267
36. K. Kurokawa, N. Mochizuki, Y. Ohba, H. Mizuno, A. Miyawaki, and M. Matsuda J. Biol. Chem. 276 2001 31305
37. J. Zhang, Y. Ma, S.S. Taylor, and R.Y. Tsien Proc. Natl. Acad. Sci. U.S.A. 98 2001 14997
38. A.Y. Ting, K.H. Kain, R.L. Klemke, and R.Y. Tsien Proc. Natl. Acad. Sci. U.S.A. 98 2001 15003
39. M. Sato, T. Ozawa, K. Inukai, T. Asano, and Y. Umezawa Nat. Biotechnol. 20 2002 287
40. V. Van Noort, J. Seebacher, S. Bader, S. Mohammed, I. Vonkova, M.J. Betts, S. Kühner, R. Kumar, T. Maier, M. O'Flaherty, V. Rybin, A. Schmeisky, E. Yus, J. Stülke, L. Serrano, R.B. Russell, A.J.R. Heck, P. Bork, and A.-C. Gavin Mol. Syst. Biol. 8 2012 571
41. J. Karanicolas, J.E. Corn, I. Chen, L.A. Joachimiak, O. Dym, S.H. Peck, S. Albeck, T. Unger, W. Hu, G. Liu, and S. Delbecq Mol. Cell 42 2011 250
42. L. Szilák, J. Moitra, D. Krylov, and C. Vinson Nat. Struct. Biol. 4 1997 112
43. L. Szilák, J. Moitra, and C. Vinson Protein Sci. 6 1997 1273
44. R.S. Signarvic, and W.F. DeGrado J. Mol. Biol. 334 2003 1
45. C.A. Smith, C.A. Shi, M.K. Chroust, T.E. Bliska, M.J.S. Kelly, M.P. Jacobson, and T. Kortemme Structure 21 2013 54
46. X. Ye, G. Nalepa, M. Welcker, B.M. Kessler, E. Spooner, J. Qin, S.J. Elledge, B.E. Clurman, and J.W. Harper J. Biol. Chem. 279 2004 50110
47. B. Hao, S. Oehlmann, M.E. Sowa, J.W. Harper, and N.P. Pavletich Mol. Cell 26 2007 131
48. M. Kõivomägi, E. Valk, R. Venta, A. Iofik, M. Lepiku, E.R.M. Balog, S.M. Rubin, D.O. Morgan, and M. Loog Nature 480 2011 128
49. T. Komatsu, and T. Inoue Methods Mol. Biol. 1174 2014 231
50. S.D.M. Santos, R. Wollman, T. Meyer, and J.E. Ferrell Cell 149 2012 1500
51. X. Yang, A.P.-T. Jost, O.D. Weiner, and C. Tang Mol. Biol. Cell 24 2013 2419
52. D. Niopek, D. Benzinger, J. Roensch, T. Draebing, P. Wehler, R. Eils, and B. Di Ventura Nat. Commun. 5 2014 4404
53. W. Lim Rev. Mol. Cell Biol. 11 2010 393
54. E.G. Krebs, and E.H. Fischer Biochim. Biophys. Acta 1000 1989 302
55. L.N. Johnson FASEB J. 6 1992 2274
56. S. Kim, H. Sun, H.L. Ball, K. Wassmann, X. Luo, and H. Yu Proc. Natl. Acad. Sci. U.S.A. 107 2010 19772
57. H. Dou, L. Buetow, A. Hock, G.J. Sibbet, K.H. Vousden, and D.T. Huang Nat. Struct. Mol. Biol. 19 2012 184
58. L. Cui, H.M. Neoh, M. Shoji, and K. Hiramatsu Antimicrob. Agents Chemother. 53 2009 1231
59. P.G. Leonard, D. Golemi-Kotra, and A.M. Stock Proc. Natl. Acad. Sci. U.S.A. 110 2013 8525
60. L.M. Espinoza-Fonseca, D. Kast, and D.D. Thomas Biophys. J. 93 2007 2083
61. W.D. Nelson, S.E. Blakely, Y.E. Nesmelov, and D.D. Thomas Proc. Natl. Acad. Sci. U.S.A. 102 2005 4000
62. M.G.S. Costa, P.R. Batista, C.S. Shida, C.H. Robert, P.M. Bisch, and P.G. Pascutti BMC Genomics 11 2010 S5
63. O. Quraishi, D.K. Nägler, T. Fox, J. Sivaraman, M. Cygler, J.S. Mort, and A.C. Storer Biochemistry 38 1999 5017
64. S. Mitternacht, and I.N. Berezovsky PLoS Comput. Biol. 2011 7
65. E. Cilia, G.W. Vuister, and T. Lenaerts PLoS Comput. Biol. 2012 8
66. G.M. Süel, S.W. Lockless, M. Wall, and R. Ranganathan Nat. Struct. Biol. 10 2003 59
67. R.N. McLaughlin, F.J. Poelwijk, A. Raman, W.S. Gosal, and R. Ranganathan Nature 491 2012 138
68. K.A. Reynolds, R.N. McLaughlin, and R. Ranganathan Cell 147 2011 1564
69. R.G. Smock, O. Rivoire, W.P. Russ, J.F. Swain, S. Leibler, R. Ranganathan, and L.M. Gierasch Mol. Syst. Biol. 6 2010 414
70. W.P. Russ, D.M. Lowery, P. Mishra, M.B. Yaffe, and R. Ranganathan Nature 437 2005 579
71. M. Novinec, M. Korenč, A. Caflisch, R. Ranganathan, B. Lenarčič, and A. Baici Nat. Commun. 5 2014 3287
72. A.J. Riemen, and M.L. Waters J. Am. Chem. Soc. 131 2009 14081
73. A.J. Riemen, and M.L. Waters J. Am. Chem. Soc. 132 2010 9007
74. S. Balakrishnan, and N.J. Zondlo J. Am. Chem. Soc. 128 2006 5590
75. S.C. Zondlo, F. Gao, and N.J. Zondlo J. Am. Chem. Soc. 132 2010 5619
76. M. Kaern, W.J. Blake, and J.J. Collins Annu. Rev. Biomed. Eng. 5 2003 179
77. A.S. Khalil, and J.J. Collins Nat. Rev. Genet. 11 2010 367
78. M.A. Fischbach, J.A. Bluestone, and W.A. Lim Sci. Transl. Med. 5 2013 s7