Join for Free!
112322 members
table of contents table of contents

A simple physical energy function, which uses electrostatics, solvation, hydrogen bonds and …

Biology Articles » Biophysics » Molecular Biophysics » Protein–DNA binding specificity predictions with structural models » References

- Protein–DNA binding specificity predictions with structural models

Bulyk, M. (2003) Computational prediction of transcription-factor binding site locations Genome Biol., 5, 201. Stormo, G.D. (2000) DNA binding sites: representation and discovery Bioinformatics, 16, 16–23. Siggia, E.D. (2005) Computational methods for transcriptional regulation Curr. Opin. Genet. Dev., 15, 214–221. Seeman, N.C., Rosenberg, J.M., Rich, A. (1976) Sequence-specific recognition of double helical nucleic acids by proteins Proc. Natl Acad. Sci. USA, 73, 804–808. Suzuki, M. and Yagi, N. (1994) DNA recognition code of transcription factors in the helix–turn–helix, probe helix, hormone receptor, and zinc finger families Proc. Natl Acad. Sci. USA, 91, 12357–12361. Matthews, B.W. (1988) Protein–DNA interaction. No code for recognition Nature, 335, 294–295. 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 Res., 29, 2860–2874. Luscombe, N.M. and Thornton, J.M. (2002) Protein–DNA interactions: amino acid conservation and the effects of mutations on binding specificity J. Mol. Biol., 320, 991–1009. Pabo, C.O. and Sauer, R.T. (1992) Transcription factors: structural families and principles of DNA recognition Annu. Rev. Biochem., 61, 1053–1095. Pabo, C.O. and Nekludova, L. (2000) Geometric analysis and comparison of protein–DNA interfaces: Why is there no simple code for recognition? J. Mol. Biol., 301, 597–624. Benos, P.V., Lapedes, A.S., Stormo, G.D. (2002) Is there a code for protein–DNA recognition? Probab(ilistical)ly Bioessays, 24, 466–475. Mandel-Gutfreund, Y. and Margalit, H. (1998) Quantitative parameters for amino acid–base interaction: implications for prediction of protein–DNA binding sites Nucleic Acids Res., 26, 2306–2312. Kono, H. and Sarai, A. (1999) Structure-based prediction of DNA target sites by regulatory proteins Proteins, 35, 114–131. Sandelin, A. and Wasserman, W.W. (2004) Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics J. Mol. Biol., 338, 207–215. Benos, P.V., Lapedes, A.S., Stormo, G.D. (2002) Probabilistic code for DNA recognition by proteins of the EGR family J. Mol. Biol., 323, 701–727. Kaplan, T., Friedman, N., Margalit, H. (2005) ab initio prediction of transcription factor targets using structural knowledge PLoS Comput. Biol., 1, e1 . Endres, R.G., Schulthess, T.C., Wingreen, N.S. (2004) Toward an atomistic model for predicting transcription-factor binding sites Proteins, 57, 262–268. Paillard, G. and Lavery, R. (2004) Analyzing protein–DNA recognition mechanisms Structure, 12, 113–122. Paillard, G., Deremble, C., Lavery, R. (2004) Looking into DNA recognition: zinc finger binding specificity Nucleic Acids Res., 32, 6673–6682. Havranek, J.J., Duarte, C.M., Baker, D. (2004) A simple physical model for the prediction and design of protein–DNA interactions J. Mol. Biol., 344, 59–70. Kortemme, T., Morozov, A.V., Baker, D. (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein–protein complexes J. Mol. Biol., 326, 1239–1259. Onufriev, A., Bashford, S.D., Case, D.A. (2004) Exploring protein native states and large-scale conformational changes with a modified generalized Born model Proteins, 55, 383–394. Lazaridis, T. and Karplus, M. (1999) Effective energy function for proteins in solution Proteins, 35, 133–152. Wang, J., Cieplak, P., Kollman, P.A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem., 21, 1049–1074. Olson, W.K., Gorin, A.A., Lu, X., Hock, L.M., Zhurkin, V.B. (1998) DNA sequence-dependent deformability deduced from protein–DNA crystal complexes Proc. Natl Acad. Sci. USA, 95, 11163–11168. Lu, X. and Olson, W.K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structure Nucleic Acids Res., 31, 5108–5121. Lu, X., El Hassan, M.A., Hunter, C.A. (1997) Structure and conformation of helical nucleic acids: analysis program (SCHNAaP) J. Mol. Biol., 273, 668–680. Gromiha, M.M., Siebers, J.G., Selvaraj, S., Kono, H., Sarai, A. (2004) Intermolecular and intramolecular readout mechanisms in protein–DNA recognition J. Mol. Biol., 337, 285–294. Berg, O.G. and von Hippel, P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters J. Mol. Biol., 193, 723–750. Jin, Y., Zhong, H., Vershon, A.K. (1999) The yeast a1 and 2 homeodomain proteins do not contribute equally to heterodimeric DNA binding Mol. Cell. Biol., 19, 585–593. Swirnoff, A.H. and Milbrandt, J. (1995) DNA-binding specificity of NGFI-A and related zinc finger transcription factors Mol. Cell. Biol., 15, 2275–2287. Robison, K., McGuire, A., Church, G. (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome J. Mol. Biol., 284, 241–254. Salgado, H., Gama-Castro, S., Martínez-Antonio, A., Díaz-Peredo, E., Sánchez-Solano, F., Peralta-Gil, M., Garcia-Alonso, D., Jimenez-Jacinto, V., Santos-Zavaleta, A., Bonavides-Martinez, C., et al. (2004) RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 Nucleic Acids Res., 32, D303–D306. Pierce, M., Benjamin, K.R., Montano, S.P., Georgiadis, M.M., Winter, E., Vershon, A.K. (2003) Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression Mol. Cell. Biol., 23, 4814–4825. Natarajan, K., Meyer, M.R., Jackson, B.M., Slade, D., Roberts, C., Hinnebusch, A.G., Marton, M.J. (2001) Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast Mol. Cell. Biol., 21, 4347–4368. Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhauser, R., et al. (2001) The TRANSFAC system on gene expression regulation Nucleic Acids Res., 29, 281–283. Wilson, D.S., Guenther, B., Desplan, C., Kuriyan, J. (1995) High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA Cell, 82, 709–719. Jaynes, E.T. Probability Theory: The Logic of Science, (2003) Cambridge, UK Cambridge University Press . Dunbrack, R.L., Jr and Cohen, F.E. (1997) Bayesian statistical analysis of protein side-chain rotamer preferences Protein Sci., 6, 1661–1681. Kuhlman, B. and Baker, D. (2000) Native protein sequences are close to optimal for their structures Proc. Natl Acad. Sci. USA, 97, 10383–10388. Lesser, D.R., Kurpiewski, M.R., Jen-Jacobson, L. (1990) The energetic basis of specificity in the EcoRI endonuclease–DNA interaction Science, 250, 776–786. Hamilton, T.B., Borel, F., Romaniuk, P.J. (1998) Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1 Biochemistry, 37, 2051–2058. Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O., Herskowitz, I. (1998) The transcriptional program of sporulation in budding yeast Science, 282, 699–705. Dranginis, A.M. (1990) Binding of yeast a1 and 2 as a heterodimer to the operator DNA of a haploid-specific gene Nature, 347, 682–685. Hao, D., Ohme-Takagi, M., Sarai, A. (1998) Unique mode of GCC box recognition by the DNA-binding domain of ethylene-responsive element-binding factor (ERF domain) in plant J. Biol. Chem., 273, 26857–26861. Lipsick, J.S. and Wang, D.-M. (1999) Transformation by v-Myb Oncogene, 18, 3047–3055. Tanikawa, J., Yasukawa, T., Enari, M., Ogata, K., Nishimura, Y., Ishii, S., Sarai, A. (1993) Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain Proc. Natl Acad. Sci. USA, 90, 9320–9324. Lee, M.R. and Kollman, P.A. (2001) Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction Structure, 9, 905–916. Engler, L.E., Sapienza, P., Dorner, L.F., Kucera, R., Schildkraut, I., Jen-Jacobson, L. (2001) The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC J. Mol. Biol., 307, 619–636. Poon, G.M.K. and Macgregor, R.B., Jr. (2003) Base coupling in sequence-specific site recognition by the ETS domain of murine PU.1 J. Mol. Biol., 328, 805–819. Sarai, A. and Takeda, Y. (1989) Repressor recognizes the 2-fold symmetric half-operator sequences asymmetrically Proc. Natl Acad. Sci. USA, 86, 6513–6517. Takeda, Y., Sarai, A., Rivera, V.M. (1989) Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments Proc. Natl Acad. Sci USA, 86, 439–443 . Fields, D.N., He, Y., Al-Uzri, A.Y., Stormo, G.D. (1997) Quantitative specificity of the Mnt repressor J. Mol. Biol., 271, 178–194. Man, T.-K. and Stormo, G.D. (2001) Non-independence of Mnt repressor–operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay Nucleic Acids Res., 15, 2471–2478 . Bulyk, M.L., Johnson, P., Church, G. (2002) Nucleotides of transcription factor binding sites exert inter-dependent effects on the binding affinities of transcription factors Nucleic Acids Res., 30, 1255–1261. Benos, P.V., Bulyk, M.L., Stormo, G.D. (2002) Additivity in protein–DNA interactions: how good an approximation is it? Nucleic Acids Res., 30, 4442–4451. Vogtli, M., Elke, C., Imhof, M.O., Lezzi, M. (1998) High level transactivation by the ecdysone receptor complex at the core recognition motif Nucleic Acids Res., 26, 2407–2414. Schneider, T.D. and Stephens, R.M. (1990) Sequence logos: a new way to display consensus sequences Nucleic Acids Res., 18, 6097–6100. Kortemme, T. and Baker, D. (2002) A simple physical model for binding energy hot spots in protein–protein complexes Proc. Natl Acad. Sci. USA, 99, 14116–14121. Kim, D.E., Chivian, D., Baker, D. (2004) Protein structure prediction and analysis using the Robetta server Nucleic Acids Res., 32, W526–W531. Thompson, J.D., Higgins, D.G., Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res., 22, 4673–4680. Rajewsky, N., Vergassola, M., Gaul, U., Siggia, E.D. (2002) Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo BMC Bioinformatics, 3, 30. Schroeder, D., Pearce, M., Fak, J., Fan, H., Unnerstall, U., Emberly, E., Rajewsky, N., Siggia, E.D., Gaul, U. (2004) Transcriptional control in the segmentation gene network of Drosophila PLoS Biol., 2, 1396–1410 . Fraenkel, E., Rould, M.A., Chambers, K.A., Pabo, C.O. (1998) Engrailed homeodomain–DNA complex at 2.2 Å resolution: a detailed view of the interface and comparison with other Engrailed structures J. Mol. Biol., 284, 351–361. Tucker-Kellogg, L., Rould, M.A., Chambers, K.A., Ades, S.E., Sauer, R.T., Pabo, C.O. (1997) Engrailed (Gln50->Lys) homeodomain–DNA complex at 1.9 Å resolution: structural basis for enhanced affinity and altered specificity Structure, 5, 1047–1054. Nekludova, L. and Pabo, C.O. (1994) Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein–DNA complexes Proc. Natl Acad. Sci. USA, 91, 6948–6952. Miller, J.C. and Pabo, C.O. (2001) Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition J. Mol. Biol., 313, 309–315. Coskun-Ari, F.F. and Hill, T.M. (1997) Sequence-specific interactions in the Tus–Ter complex and the effect of base pair substitutions on arrest of DNA replication in Escherichia. coli J. Biol. Chem., 272, 26448–26456. Frank, D.E., Saecker, R.M., Bond, J.P., Capp, M.W., Tsodikov, O.V., Melcher, S.E., Levandoski, M.M., Record, M.T., Jr. (1997) Thermodynamics of the interactions of Lac repressor with variants of the symmetric Lac operator: effects of converting a consensus site to a non-specific site J. Mol. Biol., 267, 1186–1206. Grillo, A.O., Brown, M.P., Royer, C.A. (1999) Probing the physical basis for trp repressor-operator recognition J. Mol. Biol., 287, 539–554. Boyer, M., Poujol, N., Margeat, E., Royer, C.A. (2000) Quantitative characterization of the interaction between purified human estrogen receptor and DNA using fluorescence anisotropy Nucleic Acids Res., 28, 2494–2502. Gunasekera, A., Ebright, Y.W., Ebright, R.H. (1992) DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein J. Biol. Chem., 267, 14713–14720.

rating: 3.00 from 2 votes | updated on: 7 Dec 2007 | views: 7975 |

Rate article: