Recognition rules for binding of Zn-Cys2His2 transcription factors to operator DNA

References

• Andreini, C., Banci, L., Bertini, I., & Rosato, A. (2006). Zinc through the three domains of life. Journal of Proteome Research, 5, 3173–3178.10.1021/pr0603699
   PubMed Web of Science ®Google Scholar
• Auld, D. S. (2001). Zinc coordination sphere in biochemical zinc sites. Biometals, 14, 271–313.10.1023/A:1012976615056
   PubMed Web of Science ®Google Scholar
• Benos, P. V., Lapedes, A. S., & Stormo, G. D. (2002). Is there a code for protein DNA recognition? Probabilistically. Bioessays, 24, 466–475.
   PubMed Web of Science ®Google Scholar
• Berg, J. M., & Shi, Y. (1996). The galvanization of biology: A growing appreciation for the roles of zinc. Science, 271, 1081–1085.10.1126/science.271.5252.1081
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., … Zardecki, C. (2002). The protein data bank. Acta Crystallographica, D58, 899–907.
   Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The RCSB protein data bank. Nucleic Acids Research, 28, 235–242.10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Chirgadze, N. Yu., Sivozhelezov, V. S., Polozov, R. V., Stepanenko, V. A., & Ivanov, V. V. (2012). Recognition rules for binding of homeodomains to operator DNA. Journal of Biomolecular Structure & Dynamics, 29, 715–731.
   PubMed Web of Science ®Google Scholar
• Chirgadze, N. Yu., Zheltukhin, E. I., Polozov, R. V., Sivozhelezov, V. S., & Ivanov, V. V. (2009). Binding regularities in complexes of transcription factors with operator DNA: Homeodomain family. Journal of Biomolecular Structure & Dynamics, 26, 687–700.
   PubMed Web of Science ®Google Scholar
• Choo, Y., & Klug, A. (1997). Physical basis of a protein-DNA recognition code. Current Opinion in Structural Biology, 7, 117–125.10.1016/S0959-440X(97)80015-2
   PubMed Web of Science ®Google Scholar
• Christianson, D. W. (1991). Structural biology of zinc. Advances in Protein Chemistry, 42, 281–355.10.1016/S0065-3233(08)60538-0
   PubMedGoogle Scholar
• Condit, C. M., & Railsback, L. B. (2007). Generalization through similarity: Motif discourse in the discovery and elaboration of zinc finger proteins, BioMed Central, Journal of Biomedical Discovery and Collaboration, 2, 5. doi:10.1186/1747-5333-2-5
   PubMedGoogle Scholar
• Desjarlais, J. R., & Berg, J. M. (1992). Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proceedings of the National Academy of Sciences, 89, 7345–7349.10.1073/pnas.89.16.7345
   PubMed Web of Science ®Google Scholar
• Elrod-Erickson, M., Benson, T. E., & Pabo, C. O. (1998). High resolution structures of variant Zif268-DNA complexes: Implications for understanding zinc finger-DNA recognition. Structure, 6, 451–464.10.1016/S0969-2126(98)00047-1
   PubMed Web of Science ®Google Scholar
• Elrod-Erickson, M., Rould, M. A., Nekludova, L., & Pabo, C. O. (1996). Zif268 protein-DNA complexes refined at 1.6A: A model system for understanding zinc finger-DNA interactions. Structure, 4, 1171–1180.10.1016/S0969-2126(96)00125-6
   PubMed Web of Science ®Google Scholar
• Engelke, D. R., Ng, S. Y., Shastry, B. S., & Roeder, R. G. (1980). Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes. Cell, 19, 717–728.
   PubMed Web of Science ®Google Scholar
• Finn, R. D., Tate, J., Mistry, J., Coggill, P. C., Sammut, S. J., Hotz, H. R., … Bateman, A. (2008). The Pfam protein families database. Nucleic Acids Research, 36, D281–D288.
   PubMed Web of Science ®Google Scholar
• Freemont, P. S., Lane, A. N., & Sanderson, M. R. (1991). Structure aspects of protein-DNA recognition. Biochemical Journal, 278, 1–23.
   PubMed Web of Science ®Google Scholar
• Gamsjaeger, R., Liew, C. K., Loughlin, F. E., Crossley, M., & Mackay, J. P. (2007). Sticky fingers: Zinc-fingers as protein-recognition motifs. Trends in Biochemical Sciences, 32, 63–70.10.1016/j.tibs.2006.12.007
   PubMed Web of Science ®Google Scholar
• Jones, S., Heyningen, P., Berman, H. M., & Thornton, J. M. (1999). Protein-DNA interactions: A structural analysis. Journal of Molecular Biology, 287, 877–896.10.1006/jmbi.1999.2659
   PubMed Web of Science ®Google Scholar
• Klug, A. (2010). The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annual Review of Biochemistry, 79, 213–231.10.1146/annurev-biochem-010909-095056
   PubMed Web of Science ®Google Scholar
• Krishna, S. S., Majumdar, I., & Grishin, N. V. (2003). Structural classification of zinc fingers; survey and summary. Nucleic Acids Research, 31, 532–550.10.1093/nar/gkg161
   PubMed Web of Science ®Google Scholar
• Laity, J. H., Lee, B. M., & Wright, P. E. (2001). Zinc finger proteins: New insights into structural and functional diversity. Current Opinion in Structural Biology, 11, 39–46.10.1016/S0959-440X(00)00167-6
   PubMed Web of Science ®Google Scholar
• Matthews, B. W. (1988). Protein-DNA interaction. No code for recognition. Nature, 335, 294–295.10.1038/335294a0
   PubMed Web of Science ®Google Scholar
• McCammon, J. A. (1998). Theory of biomolecular recognition. Current Opinion in Structural Biology, 8, 245–249.10.1016/S0959-440X(98)80046-8
   PubMed Web of Science ®Google Scholar
• Miller, J., McLachlan, A. D., & Klug, A. (1985). Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO Journal, 4, 1609–1614.
   PubMed Web of Science ®Google Scholar
• Murzin, A. G., Brenner, S. E., Hubbard, T., & Chothia, C. (1995). SCOP: A structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology, 247, 536–540.
   PubMed Web of Science ®Google Scholar
• Nakama, T., Kubota, Y., & Sarai, A. (1998). 3DinSight: An integrated relational database and search tool for the structure, function and properties of biomolecules. Bioinformatics, 14, 188–195.
   PubMed Web of Science ®Google Scholar
• Nolte, R. T., Conlin, R. M., Harrison, S. C., & Brown, R. S. (1998). Differing roles for zinc fingers in DNA recognition: Structure of a six-finger transcription factor IIIA complex. Proceedings of National Academy of Sciences of USA, 17, 2938–2943.10.1073/pnas.95.6.2938
   Web of Science ®Google Scholar
• Norambuena, T., & Melo, F. (2010). The protein-DNA interface database. BioMed Central, Bioinformatics, 11, 262–274.
   PubMedGoogle Scholar
• Paillard, G., & Lavery, R. (2004). Analyzing protein-DNA recognition mechanisms. Structure, 12, 113–122.10.1016/j.str.2003.11.022
   PubMed Web of Science ®Google Scholar
• Patel, K., Kumar, A., & Durani, S. (2007). Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures. Biochimica et Biophysica Acta, Protein and Proteomics, 1774, 1247–1253.10.1016/j.bbapap.2007.07.010
   Web of Science ®Google Scholar
• Pavletich, N. P., & Pabo, C. O. (1991). Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1Å. Science, 252, 809–817.10.1126/science.2028256
   PubMed Web of Science ®Google Scholar
• Pavletich, N. P., & Pabo, C. O. (1993). Crystal structure of a five – finger GLI-DNA complex: New perspectives on Zn fingers. Science, 261, 1701–1707.10.1126/science.8378770
   PubMed Web of Science ®Google Scholar
• Ponomarenko, J. V., Ponomarenko, M. P., Frolov, A. S., Vorobyev, D. G., Overton, G. C., & Kolchanov, N. A. (1999). Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinformatics, 15, 654–668.10.1093/bioinformatics/15.7.654
   PubMed Web of Science ®Google Scholar
• Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., … Finn, R. D. (2012). The Pfam protein families’ database. Nucleic Acids Research, 40, D290–301.
   Google Scholar
• Reddy, C. K., Das, A., & Jayaram, B. (2001). Do water molecules mediate protein-DNA recognition? Journal of Molecular Biology, 314, 619–632.10.1006/jmbi.2001.5154
   PubMed Web of Science ®Google Scholar
• Rhodes, D., Schwabe, J. W., Chapman, L., & Fairall, L. (1996). Towards an understanding of protein-DNA recognition. Philosophical Transactions of the Royal Society, London B, 351, 501–509.10.1098/rstb.1996.0048
   PubMed Web of Science ®Google Scholar
• Rohs, R., Jin, X., West, S. M., Joshi, R., Honig, B., & Mann, R. S. (2010). Origins of specificity in protein-DNA recognition. Annual Review of Biochemistry, 79, 233–269.10.1146/annurev-biochem-060408-091030
   PubMed Web of Science ®Google Scholar
• Shoemaker, B. A., Zhang, D., Tyagi, M., Thangudu, R. R., Fong, J. H., Marchler-Bauer, A., … Panchenko, A. R. (2012). IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Research, 40, D834–D840.10.1093/nar/gkr997
   PubMed Web of Science ®Google Scholar
• Steffen, N. R., Murphy, S. D., Tolleri, L., Hatfield, G. W., & Lathrop, R. H. (2002). DNA sequence and structure: Direct and indirect recognition in protein-DNA binding. Bioinformatics, 18, S22–S30.10.1093/bioinformatics/18.suppl_1.S22
   Google Scholar
• Surai, A., & Kono, H. (2005). Protein-DNA recognition patterns and prediction. Annual Review of Biophysics: Biomolecular Structures, 34, 379–395.
   PubMedGoogle Scholar
• Suzuki, M., Brenner, S. E., Gerstein, M., & Yagi, N. (1995). DNA recognition code of transcription factors. Protein Engineering, 8, 319–328.10.1093/protein/8.4.319
   PubMedGoogle Scholar
• Suzuki, M., Gerstein, M., & Yagi, N. (1994). Stereochemical basis of DNA recognition by Zn finger. Nucleic Acids Research, 22, 3397–3405.10.1093/nar/22.16.3397
   PubMed Web of Science ®Google Scholar
• Wolfe, S. A., Nekludova, L., & Pabo, C. O. (2000). DNA recognition by Cys2His2 zinc finger proteins. Annual Review of Biophysics and Biomolecular Structure, 29, 183–212.10.1146/annurev.biophys.29.1.183
   PubMedGoogle Scholar
• Wuttke, D. S., Foster, M. P., Case, D. A., Gottesfeld, J. M., & Wright, P. E. (1997). Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: Determinants of affinity and sequence specificity. Journal of Molecular Biology, 17, 183–206.10.1006/jmbi.1997.1291
   Web of Science ®Google Scholar