269
Views
12
CrossRef citations to date
0
Altmetric
Articles

Investigation of arc repressor DNA-binding specificity by comparative molecular dynamics simulations

&
Pages 2083-2093 | Received 24 Nov 2014, Accepted 08 Dec 2014, Published online: 14 Jan 2015

References

  • Andreeva, A. , Howorth, D. , Brenner, S. E. , Hubbard, T. J. , Chothia, C. , & Murzin, A. G. (2004). SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Research , 32 , D226–229.10.1093/nar/gkh039
  • Ashworth, J. , Havranek, J. J. , Duarte, C. M. , Sussman, D. , Monnat, R. J., Jr , Stoddard, B. L. , & Baker, D. (2006). Computational redesign of endonuclease DNA binding and cleavage specificity. Nature , 441 , 656–659.10.1038/nature04818
  • Baker, C. R. , Tuch, B. B. , & Johnson, A. D. (2011). Extensive DNA-binding specificity divergence of a conserved transcription regulator. Proceedings of the National Academy of Sciences , 108 , 7493–7498.10.1073/pnas.1019177108
  • Berendsen, H. J. C. , Postma, J. P. M. , van Gunsteren, W. F. , DiNola, A. , & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics , 81 , 3684–3690.10.1063/1.448118
  • Berman, H. M. , Westbrook, J. , Feng, Z. , Gilliland, G. , Bhat, T. N. , Weissig, H. , … Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research , 28 , 235–242.10.1093/nar/28.1.235
  • Burgering, M. J. , Hald, M. , Boelens, R. , Breg, J. N. , & Kaptein, R. (1995). Hydrogen exchange studies of the Arc repressor: Evidence for a monomeric folding intermediate. Biopolymers , 35 , 217–226.10.1002/(ISSN)1097-0282
  • Chène, P. (1999). Mutations at position 277 modify the DNA-binding specificity of human p53 in vitro . Biochemical and Biophysical Research Communications , 263 (1), 1–5.10.1006/bbrc.1999.1294
  • Crooks, G. E. , Hon, G. , Chandonia, J. M. , & Brenner, S. E. (2004). WebLogo: A sequence logo generator. Genome Research , 14 , 1188–1190.10.1101/gr.849004
  • Csermely, P. , Palotai, R. , & Nussinov, R. (2010). Induced fit, conformational selection and independent dynamic segments: An extended view of binding events. Trends in Biochemical Sciences , 35 , 539–546.10.1016/j.tibs.2010.04.009
  • Darden, T. , York, D. , & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics , 98 , 10089–11009.10.1063/1.464397
  • Filippova, G. N. , Qi, C. F. , Ulmer, J. E. , Moore, J. M. , Ward, M. D. , Hu, Y. J. , … Lobanenkov, V. V. (2002). Tumor-associated zinc finger mutations in the CTCF transcription factor selectively alter tts DNA-binding specificity. Cancer Research , 62 , 48–52.
  • Fuxreiter, M. , Simon, I. , & Bondos, S. (2011). Dynamic protein-DNA recognition: Beyond what can be seen. Trends in Biochemical Sciences , 36 , 415–423.10.1016/j.tibs.2011.04.006
  • Gohler, T. , Jager, S. , Warnecke, G. , Yasuda, H. , Kim, E. , & Deppert, W. (2005). Mutant p53 proteins bind DNA in a DNA structure-selective mode. Nucleic Acids Research , 33 , 1087–1100.10.1093/nar/gki252
  • Gordon J. C. , Myers J. B. , Folta T. , Shoja V. , Heath L. S. , & Onufriev, A . (2005). H++: A server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Research , 33 , W368–W371.10.1093/nar/gki464
  • Grünberg, R. , Leckner, J. , & Nilges, M. (2004). Complementarity of structure ensembles in protein-protein binding. Structure , 12 , 2125–2136.10.1016/j.str.2004.09.014
  • Gu, J. , Gribskov, M. , & Bourne, P. E. (2006). Wiggle-predicting functionally flexible regions from primary sequence. PLoS Computational Biology , 2 , e90.10.1371/journal.pcbi.0020090
  • Hess, B. (2008). P-LINCS: A parallel linear constraint solver for molecular simulation. Journal of Chemical Theory & Computation , 4 , 116–122.10.1021/ct700200b
  • Humphrey, W. , Dalke, A. , & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics , 14 , 33–38.10.1016/0263-7855(96)00018-5
  • Janin J. , Sternberg M. J . (2013). Protein flexibility, not disorder, is intrinsic to molecular recognition. F1000 Biology Reports , 5 : 2. doi:10.3410/B5-2
  • Jorgensen, W. L. , Chandrasekhar, J. , Madura, J. D. , Impey, R. W. , & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics , 79 , 926–935.10.1063/1.445869
  • Kalodimos, C. G. , Biris, N. , Bonvin, A. M. , Levandoski, M. M. , Guennuegues, M. , Boelens, R. , & Kaptein, R. (2004). Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science , 305 , 386–389.10.1126/science.1097064
  • Latchman, D. S. (1996). Transcription-factor mutations and disease. New England Journal of Medicine , 334 , 28–33.
  • Luscombe, N. M. , Laskowski, R. A. , & Thornton, J. M. (2001). Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Research , 29 , 2860–2874.10.1093/nar/29.13.2860
  • Luscombe, N. M. , & Thornton, J. M. (2002). Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity. Journal of Molecular Biology , 320 , 991–1009.10.1016/S0022-2836(02)00571-5
  • MacKerell, A. D., Jr , Banavali, N. , & Foloppe, N. (2000). Development and current status of the CHARMM force field for nucleic acids. Biopolymers , 56 , 257–265.10.1002/(ISSN)1097-0282
  • Marcovitz, A. , & Levy, Y. (2009). Arc-repressor dimerization on DNA: Folding rate enhancement by colocalization. Biophysical Journal , 96 , 4212–4220.10.1016/j.bpj.2009.01.057
  • Mathelier, A. , Zhao, X. , Zhang, A. W. , Parcy, F. , Worsley-Hunt, R. , Arenillas, D. J. , … Wasserman, W. W. (2014). JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Research , 42 , D142–D147.
  • Matthews, B. W. (1988). Protein-DNA interaction. No code for recognition. Nature , 335 , 294–295.
  • Michael Gromiha, M. , Siebers, J. G. , Selvaraj, S. , Kono, H. , & Sarai, A. (2004). Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. Journal of Molecular Biology , 337 , 285–294.10.1016/j.jmb.2004.01.033
  • Pabo, C. O. , & Nekludova, L. (2000). Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition? Journal of Molecular Biology , 301 , 597–624.10.1006/jmbi.2000.3918
  • Peng, X. , Jonas, J. , & Silva, J. L. (1993). Molten-globule conformation of Arc repressor monomers determined by high-pressure 1H NMR spectroscopy. Proceedings of the National Academy of Sciences , 90 , 1776–1780.10.1073/pnas.90.5.1776
  • Porteus, M. H. , & Baltimore, D. (2003). Chimeric nucleases stimulate gene targeting in human cells. Science , 300 , 763.10.1126/science.1078395
  • Raumann, B. E. , Knight, K. L. , & Sauer, R. T. (1995). Dramatic changes in DNA-binding specificity caused by single residue substitutions in an Arc/Mnt hybrid repressor. Nature Structural Biology , 2 , 1115–1122.10.1038/nsb1295-1115
  • Raumann, B. E. , Rould, M. A. , Pabo, C. O. , & Sauer, R. T. (1994). DNA recognition by β-sheets in the Arc represser–operator crystal structure. Nature , 367 , 754–757.10.1038/367754a0
  • 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
  • Rohs, R. , West, S. M. , Liu, P. , & Honig, B. (2009). Nuance in the double-helix and its role in protein-DNA recognition. Current Opinion in Structural Biology , 19 , 171–177.10.1016/j.sbi.2009.03.002
  • Rohs, R. , West, S. M. , Sosinsky, A. , Liu, P. , Mann, R. S. , & Honig, B. (2009). The role of DNA shape in protein-DNA recognition. Nature , 461 , 1248–1253.10.1038/nature08473
  • Šali, A. , & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology , 234 , 779–815.10.1006/jmbi.1993.1626
  • Schildbach, J. F. , Karzai, A. W. , Raumann, B. E. , & Sauer, R. T. (1999). Origins of DNA-binding specificity: Role of protein contacts with the DNA backbone. Proceedings of the National Academy of Sciences , 96 , 811–817.10.1073/pnas.96.3.811
  • Schott, J. J. , Benson, D. W. , Basson, C. T. , Pease, W. , Silberbach, G. M. , Moak, J. P. , … Seidman, J. G. (1998). Congenital heart disease caused by mutations in the transcription factor NKX2-5. Science , 281 , 108–111.10.1126/science.281.5373.108
  • Schulz G. E. (1979). Nucleotide binding proteins. In M. Balaban (Ed.), Molecular mechanisms of biological recognition (pp. 79–94). North-Holland: Elsevier/North-Holland Biomedical Press.
  • Thukral, S. K. , Lu, Y. , Blain, G. C. , Harvey, T. S. , & Jacobsen, V. L. (1995). Discrimination of DNA binding sites by mutant p53 proteins. Molecular & Cellular Biology , 15 , 5196–5202.
  • Tsai, C. J. , del Sol, A. , & Nussinov, R. (2008). Allostery: Absence of a change in shape does not imply that allostery is not at play. Journal of Molecular Biology , 378 (1), 1–11.10.1016/j.jmb.2008.02.034
  • Uil, T. G. , Haisma, H. J. , & Rots, M. G. (2003). Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities. Nucleic Acids Research , 31 , 6064–6078.10.1093/nar/gkg815
  • Urnov, F. D. , Miller, J. C. , Lee, Y. L. , Beausejour, C. M. , Rock, J. M. , Augustus, S. , … Holmes, M. C. (2005). Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature , 435 , 646–651.10.1038/nature03556
  • Uversky V. N. , Dunker A. K. (2013). The case for intrinsically disordered proteins playing contributory roles in molecular recognition without a stable 3D structure. F1000 Biology Reports , 5 : 1. doi:10.3410/B5-1
  • Van Der Spoel, D. , Lindahl, E. , Hess, B. , Groenhof, G. , Mark, A. E. , & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry , 26 , 1701–1718.10.1002/(ISSN)1096-987X
  • Vuzman, D. , & Levy, Y. (2012). Intrinsically disordered regions as affinity tuners in protein-DNA interactions. Molecular BioSystems , 8 , 47–57.10.1039/c1mb05273j
  • Wlodarski, T. , & Zagrovic, B. (2009). Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin. Proceedings of the National Academy of Sciences , 106 , 19346–19351.10.1073/pnas.0906966106
  • Zhou, H. X. (2012). Intrinsic disorder: Signaling via highly specific but short-lived association. Trends in Biochemical Sciences , 37 , 43–48.10.1016/j.tibs.2011.11.002

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.