Mapping of Protein-Protein Interaction Sites by the 'Absence of Interference' Approach

Journal of Molecular Biology

Volumn 376, Issue 4, 2008, Pages 1091-1099

  Dhayalan, Arunkumar ^a   Jurkowski, Tomasz P ^a   Laser, Heike ^a   Reinhardt, Richard ^b   Jia, Da ^c   Cheng, Xiaodong ^c   Jeltsch, Albert ^a  

^a JACOBS UNIVERSITY BREMEN   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

directed evolution; protein protein interaction; random mutagenesis; structure prediction; yeast two hybrid

Indexed keywords

DNA METHYLTRANSFERASE 3A;

ABSENCE OF INTERFERENCE APPROACH; ARTICLE; CONTROLLED STUDY; MUTAGENESIS; MUTATION; MUTATION RATE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; STRUCTURE ANALYSIS; TWO HYBRID SYSTEM;

EID: 39049093111     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.12.032     Document Type: Article

References (36)

1. Kumar A., and Snyder M. Protein complexes take the bait. Nature 415 (2002) 123-124
2. von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., and Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417 (2002) 399-403
3. Russell R.B., Alber F., Aloy P., Davis F.P., Korkin D., Pichaud M., et al. A structural perspective on protein-protein interactions. Curr. Opin. Struct. Biol. 14 (2004) 313-324
4. Fry D.C. Protein-protein interactions as targets for small molecule drug discovery. Biopolymers 84 (2006) 535-552
5. Henrick K., and Thornton J.M. PQS: a protein quaternary structure file server. Trends Biochem. Sci. 23 (1998) 358-361
6. Gray J.J. High-resolution protein-protein docking. Curr. Opin. Struct. Biol. 16 (2006) 183-193
7. Schueler-Furman O., Wang C., Bradley P., Misura K., and Baker D. Progress in modeling of protein structures and interactions. Science 310 (2005) 638-642
8. Vasilescu J., and Figeys D. Mapping protein-protein interactions by mass spectrometry. Curr. Opin. Biotechnol. 17 (2006) 394-399
9. Landgraf C., Panni S., Montecchi-Palazzi L., Castagnoli L., Schneider-Mergener J., Volkmer-Engert R., and Cesareni G. Protein interaction networks by proteome peptide scanning. PLoS Biol. 2 (2004) E14
10. Legrain P., and Selig L. Genome-wide protein interaction maps using two-hybrid systems. FEBS Lett. 480 (2000) 32-36
11. Uetz P. Two-hybrid arrays. Curr. Opin. Chem. Biol. 6 (2002) 57-62
12. Stelzl U., and Wanker E.E. The value of high quality protein-protein interaction networks for systems biology. Curr. Opin. Chem. Biol. 10 (2006) 551-558
13. Parrish J.R., Gulyas K.D., and Finley Jr. R.L. Yeast two-hybrid contributions to interactome mapping. Curr. Opin. Biotechnol. 17 (2006) 387-393
14. Vidal M., Braun P., Chen E., Boeke J.D., and Harlow E. Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system. Proc. Natl. Acad. Sci. USA 93 (1996) 10321-10326
15. Valdar W.S., and Thornton J.M. Conservation helps to identify biologically relevant crystal contacts. J. Mol. Biol. 313 (2001) 399-416
16. Glaser F., Pupko T., Paz I., Bell R.E., Bechor-Shental D., Martz E., and Ben-Tal N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19 (2003) 163-164
17. Hermann A., Gowher H., and Jeltsch A. Biochemistry and biology of mammalian DNA methyltransferases. Cell. Mol. Life Sci. 61 (2004) 2571-2587
18. Klose R.J., and Bird A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31 (2006) 89-97
19. Okano M., Bell D.W., Haber D.A., and Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99 (1999) 247-257
20. Gowher H., and Jeltsch A. Molecular enzymology of the catalytic domains of the Dnmt3a and Dnmt3b DNA methyltransferases. J. Biol. Chem. 277 (2002) 20409-20414
21. Reither S., Li F., Gowher H., and Jeltsch A. Catalytic mechanism of DNA-(cytosine-C5)-methyltransferases revisited: covalent intermediate formation is not essential for methyl group transfer by the murine Dnmt3a enzyme. J. Mol. Biol. 329 (2003) 675-684
22. Gowher H., Liebert K., Hermann A., Xu G., and Jeltsch A. Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J. Biol. Chem. 280 (2005) 13341-13348
23. Margot J.B., Ehrenhofer-Murray A.E., and Leonhardt H. Interactions within the mammalian DNA methyltransferase family. BMC Mol. Biol. 4 (2003) 7
24. Hata K., Okano M., Lei H., and Li E. Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. Development 129 (2002) 1983-1993
25. Bourc'his D., Xu G.L., Lin C.S., Bollman B., and Bestor T.H. Dnmt3L and the establishment of maternal genomic imprints. Science 294 (2001) 2536-2539
26. Bloom J.D., Meyer M.M., Meinhold P., Otey C.R., MacMillan D., and Arnold F.H. Evolving strategies for enzyme engineering. Curr. Opin. Struct. Biol. 15 (2005) 447-452
27. Yuan L., Kurek I., English J., and Keenan R. Laboratory-directed protein evolution. Microbiol. Mol. Biol. Rev. 69 (2005) 373-392
28. Cadwell R.C., and Joyce G.F. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2 (1992) 28-33
29. Gowher H., Loutchanwoot P., Vorobjeva O., Handa V., Jurkowska R.Z., Jurkowski T.P., and Jeltsch A. Mutational analysis of the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase. J. Mol. Biol. 357 (2006) 928-941
30. Jia D., Jurkowska R.Z., Zhang X., Jeltsch A., and Cheng X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449 (2007) 248-251
31. Kim P.M., Lu L.J., Xia Y., and Gerstein M.B. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314 (2006) 1938-1941
32. Bentley D.R. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16 (2006) 545-552
33. Staudinger J., Perry M., Elledge S.J., and Olson E.N. Interactions among vertebrate helix-loop-helix proteins in yeast using the two-hybrid system. J. Biol. Chem. 268 (1993) 4608-4611
34. Jeltsch A., and Lanio T. Site-directed mutagenesis by polymerase chain reaction. Methods Mol. Biol. 182 (2002) 85-94
35. Guex N., and Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18 (1997) 2714-2723
36. Sayle R.A., and Milner-White E.J. RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20 (1995) 374