Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates

Cell

Volumn 163, Issue 3, 2015, Pages 594-606

  Aakre, Christopher D ^a   Herrou, Julien ^b   Phung, Tuyen N ^a   Perchuk, Barrett S ^a   Crosson, Sean ^b   Laub, Michael T ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTITOXIN; TOXIN; BACTERIAL PROTEIN; BACTERIAL TOXIN; DNA BINDING PROTEIN; PARD PROTEIN, BACTERIA;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL CHROMOSOME; CHIMERA; COEVOLUTION; EPISTASIS; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION; SCANNING ELECTRON MICROSCOPY; SEQUENCE ALIGNMENT; BACTERIUM; CHEMISTRY; CLASSIFICATION; MESORHIZOBIUM; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOLECULAR MODEL;

AMINO ACID SEQUENCE; ANTITOXINS; BACTERIA; BACTERIAL PROTEINS; BACTERIAL TOXINS; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; MESORHIZOBIUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN INTERACTION MAPS;

EID: 84959155451     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.09.055     Document Type: Article

References (26)

1. A. Aharoni, L. Gaidukov, O. Khersonsky, S. McQ Gould, C. Roodveldt, and D.S. Tawfik The 'evolvability' of promiscuous protein functions Nat. Genet. 37 2005 73 76
2. D.W. Anderson, A.N. McKeown, and J.W. Thornton Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites eLife 4 2015 e07864
3. J.D. Bloom, and F.H. Arnold In the light of directed evolution: pathways of adaptive protein evolution Proc. Natl. Acad. Sci. USA 106 Suppl 1 2009 9995 10000
4. E.J. Capra, B.S. Perchuk, J.M. Skerker, and M.T. Laub Adaptive mutations that prevent crosstalk enable the expansion of paralogous signaling protein families Cell 150 2012 222 232
5. K.M. Dalton, and S. Crosson A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex Biochemistry 49 2010 2205 2215
6. M.A. DePristo, D.M. Weinreich, and D.L. Hartl Missense meanderings in sequence space: a biophysical view of protein evolution Nat. Rev. Genet. 6 2005 678 687
7. A. Fiebig, C.M. Castro Rojas, D. Siegal-Gaskins, and S. Crosson Interaction specificity, toxicity and regulation of a paralogous set of ParE/RelE-family toxin-antitoxin systems Mol. Microbiol. 77 2010 236 251
8. D.M. Fowler, and S. Fields Deep mutational scanning: a new style of protein science Nat. Methods 11 2014 801 807
9. R. Hallez, D. Geeraerts, Y. Sterckx, N. Mine, R. Loris, and L. Van Melderen New toxins homologous to ParE belonging to three-component toxin-antitoxin systems in Escherichia coli O157:H7 Mol. Microbiol. 76 2010 719 732
10. H. Kamisetty, S. Ovchinnikov, and D. Baker Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era Proc. Natl. Acad. Sci. USA 110 2013 15674 15679
11. D.A. Kondrashov, and F.A. Kondrashov Topological features of rugged fitness landscapes in sequence space Trends Genet. 31 2015 24 33
12. J. Kuriyan, and D. Eisenberg The origin of protein interactions and allostery in colocalization Nature 450 2007 983 990
13. B. Lehner Molecular mechanisms of epistasis within and between genes Trends Genet. 27 2011 323 331
14. R. Leplae, D. Geeraerts, R. Hallez, J. Guglielmini, P. Drèze, and L. Van Melderen Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families Nucleic Acids Res. 39 2011 5513 5525
15. R.N. McLaughlin Jr., F.J. Poelwijk, A. Raman, W.S. Gosal, and R. Ranganathan The spatial architecture of protein function and adaptation Nature 491 2012 138 142
16. D. Melamed, D.L. Young, C.E. Gamble, C.R. Miller, and S. Fields Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein RNA 19 2013 1537 1551
17. J.R. Newman, and A.E. Keating Comprehensive identification of human bZIP interactions with coiled-coil arrays Science 300 2003 2097 2101
18. S. Ovchinnikov, H. Kamisetty, and D. Baker Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information eLife 3 2014 e02030
19. A.I. Podgornaia, and M.T. Laub Protein evolution. Pervasive degeneracy and epistasis in a protein-protein interface Science 347 2015 673 677
20. H.R. Ramage, L.E. Connolly, and J.S. Cox Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution PLoS Genet. 5 2009 e1000767
21. J.M. Skerker, B.S. Perchuk, A. Siryaporn, E.A. Lubin, O. Ashenberg, M. Goulian, and M.T. Laub Rewiring the specificity of two-component signal transduction systems Cell 133 2008 1043 1054
22. M.A. Stiffler, J.R. Chen, V.P. Grantcharova, Y. Lei, D. Fuchs, J.E. Allen, L.A. Zaslavskaia, and G. MacBeath PDZ domain binding selectivity is optimized across the mouse proteome Science 317 2007 364 369
23. Y. Yamaguchi, J.H. Park, and M. Inouye Toxin-antitoxin systems in bacteria and archaea Annu. Rev. Genet. 45 2011 61 79
24. M. Yang, C. Gao, Y. Wang, H. Zhang, and Z.G. He Characterization of the interaction and cross-regulation of three Mycobacterium tuberculosis RelBE modules PLoS ONE 5 2010 e10672
25. A. Zarrinpar, S.H. Park, and W.A. Lim Optimization of specificity in a cellular protein interaction network by negative selection Nature 426 2003 676 680
26. L. Zhu, J.D. Sharp, H. Kobayashi, N.A. Woychik, and M. Inouye Noncognate Mycobacterium tuberculosis toxin-antitoxins can physically and functionally interact J. Biol. Chem. 285 2010 39732 39738