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Aromatic hydrogen bond in sequence-specific protein DNA recognition.

Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X, Kunkel TA, Berman H, Ebright RH
Nat Struct Biol 3 837-41 (1996)
Cited: 55 times
EuropePMC logo PMID: 8836098

Reviews - 1run mentioned but not cited (2)

  1. Catabolite activator protein: DNA binding and transcription activation. Lawson CL, Swigon D, Murakami KS, Darst SA, Berman HM, Ebright RH. Curr Opin Struct Biol 14 10-20 (2004)
  2. Conservation of the three-dimensional structure in non-homologous or unrelated proteins. Sousounis K, Haney CE, Cao J, Sunchu B, Tsonis PA. Hum Genomics 6 10 (2012)

Articles - 1run mentioned but not cited (23)

  1. Probability-based protein secondary structure identification using combined NMR chemical-shift data. Wang Y, Jardetzky O. Protein Sci 11 852-861 (2002)
  2. Protein-DNA binding specificity predictions with structural models. Morozov AV, Havranek JJ, Baker D, Siggia ED. Nucleic Acids Res 33 5781-5798 (2005)
  3. DNA conformations and their sequence preferences. Svozil D, Kalina J, Omelka M, Schneider B. Nucleic Acids Res 36 3690-3706 (2008)
  4. Structural analysis of conserved base pairs in protein-DNA complexes. Mirny LA, Gelfand MS. Nucleic Acids Res 30 1704-1711 (2002)
  5. Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication. Guarnera E, Berezovsky IN. PLoS Comput Biol 12 e1004678 (2016)
  6. Energetics of protein-DNA interactions. Donald JE, Chen WW, Shakhnovich EI. Nucleic Acids Res 35 1039-1047 (2007)
  7. Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors. Rodgers TL, Townsend PD, Burnell D, Jones ML, Richards SA, McLeish TC, Pohl E, Wilson MR, Cann MJ. PLoS Biol 11 e1001651 (2013)
  8. Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Ahmad S, Ahmad S, Keskin O, Sarai A, Nussinov R. Nucleic Acids Res 36 5922-5932 (2008)
  9. On the use of DXMS to produce more crystallizable proteins: structures of the T. maritima proteins TM0160 and TM1171. Spraggon G, Pantazatos D, Klock HE, Wilson IA, Woods VL, Lesley SA. Protein Sci 13 3187-3199 (2004)
  10. Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps. Napoli AA, Lawson CL, Ebright RH, Berman HM. J Mol Biol 357 173-183 (2006)
  11. An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles. Xu B, Yang Y, Liang H, Zhou Y. Proteins 76 718-730 (2009)
  12. Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs. Marathe A, Karandur D, Bansal M. BMC Struct Biol 9 24 (2009)
  13. A structural-alphabet-based strategy for finding structural motifs across protein families. Wu CY, Chen YC, Lim C. Nucleic Acids Res 38 e150 (2010)
  14. Bioinformatic analysis of the protein/DNA interface. Schneider B, Cerný J, Svozil D, Cech P, Gelly JC, de Brevern AG. Nucleic Acids Res 42 3381-3394 (2014)
  15. Predicting target DNA sequences of DNA-binding proteins based on unbound structures. Chen CY, Chien TY, Lin CK, Lin CW, Weng YZ, Chang DT. PLoS One 7 e30446 (2012)
  16. Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces. Louet M, Seifert C, Hensen U, Gräter F. PLoS Comput Biol 11 e1004358 (2015)
  17. Exploring the evolution of protein function in Archaea. Goncearenco A, Berezovsky IN. BMC Evol Biol 12 75 (2012)
  18. PiDNA: Predicting protein-DNA interactions with structural models. Lin CK, Chen CY. Nucleic Acids Res 41 W523-30 (2013)
  19. Structure and effective charge characterization of proteins by a mobility capillary electrophoresis based method. Zhang W, Wu H, Zhang R, Fang X, Xu W. Chem Sci 10 7779-7787 (2019)
  20. Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Brylinski M. Front Genet 4 118 (2013)
  21. Structural features differentiate the mechanisms between 2S (2 state) and 3S (3 state) folding homodimers. Li L, Gunasekaran K, Gan JG, Zhanhua C, Shapshak P, Sakharkar MK, Kangueane P. Bioinformation 1 42-49 (2005)
  22. Knowledge-based three-body potential for transcription factor binding site prediction. Qin W, Zhao G, Carson M, Jia C, Lu H. IET Syst Biol 10 23-29 (2016)
  23. Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis. Chen Y, Lin YC, Luo Y, Cai X, Qiu P, Cui S, Wang Z, Huang HY, Huang HD. Brief Bioinform 24 bbad138 (2023)


Reviews citing this publication (3)

  1. Transcription activation by catabolite activator protein (CAP). Busby S, Ebright RH. J Mol Biol 293 199-213 (1999)
  2. Molecular and biological constraints on ligand-binding affinity and specificity. Szwajkajzer D, Carey J. Biopolymers 44 181-198 (1997)
  3. cAMP Activation of the cAMP Receptor Protein, a Model Bacterial Transcription Factor. Youn H, Carranza M. J Microbiol 61 277-287 (2023)

Articles citing this publication (27)

  1. WebLogo: a sequence logo generator. Crooks GE, Hon G, Chandonia JM, Brenner SE. Genome Res 14 1188-1190 (2004)
  2. DNA bending: the prevalence of kinkiness and the virtues of normality. Dickerson RE. Nucleic Acids Res 26 1906-1926 (1998)
  3. Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? Pabo CO, Nekludova L. J Mol Biol 301 597-624 (2000)
  4. NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Luscombe NM, Laskowski RA, Thornton JM. Nucleic Acids Res 25 4940-4945 (1997)
  5. Helix bending as a factor in protein/DNA recognition. Dickerson RE, Chiu TK. Biopolymers 44 361-403 (1997)
  6. Conformational flexibility of B-DNA at 0.74 A resolution: d(CCAGTACTGG)(2). Kielkopf CL, Ding S, Kuhn P, Rees DC. J Mol Biol 296 787-801 (2000)
  7. Crystal structure of the Vibrio cholerae quorum-sensing regulatory protein HapR. De Silva RS, Kovacikova G, Lin W, Taylor RK, Skorupski K, Kull FJ. J Bacteriol 189 5683-5691 (2007)
  8. Role of aromatic amino acids in protein-nucleic acid recognition. Baker CM, Grant GH. Biopolymers 85 456-470 (2007)
  9. An analysis of the relationship between hydration and protein-DNA interactions. Woda J, Schneider B, Patel K, Mistry K, Berman HM. Biophys J 75 2170-2177 (1998)
  10. Structural basis of bacterial transcription activation. Liu B, Hong C, Huang RK, Yu Z, Steitz TA. Science 358 947-951 (2017)
  11. NCI: A server to identify non-canonical interactions in protein structures. Babu MM. Nucleic Acids Res 31 3345-3348 (2003)
  12. Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: ab initio fragment molecular orbital study. Fukuzawa K, Komeiji Y, Mochizuki Y, Kato A, Nakano T, Tanaka S. J Comput Chem 27 948-960 (2006)
  13. Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution. Kapanidis AN, Ebright YW, Ludescher RD, Chan S, Ebright RH. J Mol Biol 312 453-468 (2001)
  14. Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan. Nanda V, Brand L. Proteins 40 112-125 (2000)
  15. A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR. Giardina G, Rinaldo S, Castiglione N, Caruso M, Cutruzzolà F. Proteins 77 174-180 (2009)
  16. The Pseudomonas aeruginosa DNR transcription factor: light and shade of nitric oxide-sensing mechanisms. Giardina G, Castiglione N, Caruso M, Cutruzzolà F, Rinaldo S. Biochem Soc Trans 39 294-298 (2011)
  17. Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins. Chakkaravarthi S, Babu MM, Gromiha MM, Jayaraman G, Sethumadhavan R. Proteins 65 75-86 (2006)
  18. Unusual heme binding properties of the dissimilative nitrate respiration regulator, a bacterial nitric oxide sensor. Rinaldo S, Castiglione N, Giardina G, Caruso M, Arcovito A, Longa SD, D'Angelo P, Cutruzzolà F. Antioxid Redox Signal 17 1178-1189 (2012)
  19. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO. PLoS One 13 e0197272 (2018)
  20. DNA binding properties of a chemically synthesized DNA binding domain of hRFX1. Cornille F, Emery P, Schüler W, Lenoir C, Mach B, Roques BP, Reith W. Nucleic Acids Res 26 2143-2149 (1998)
  21. Mechanism of DNA recognition by the restriction enzyme EcoRV. Zahran M, Daidone I, Smith JC, Imhof P. J Mol Biol 401 415-432 (2010)
  22. Non-canonical interactions of porphyrins in porphyrin-containing proteins. Stojanović SÐ, Isenović ER, Zarić BL. Amino Acids 43 1535-1546 (2012)
  23. Solvation of nucleosides in aqueous mixtures of organic solvents: relevance to DNA open basepairs. Ababneh AM, Large CC, Georghiou S. Biophys J 85 1111-1127 (2003)
  24. Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies. Stojanović SĐ, Isenović ER, Zarić BL. Mol Inform 30 430-442 (2011)
  25. A compact review on the comparison of conventional and non-conventional interactions on the structural stability of therapeutic proteins. Ramanathan K, Shanthi V, Sethumadhavan R. Interdiscip Sci 3 144-160 (2011)
  26. Oxygen-aromatic contacts in intra-strand base pairs: analysis of high-resolution DNA crystal structures and quantum chemical calculations. Jain A, Krishna Deepak RNV, Sankararamakrishnan R. J Struct Biol 187 49-57 (2014)
  27. Water-mediated interactions in the CRP-cAMP-DNA complex: does water mediate sequence-specific binding at the DNA primary-kink site? VanSchouwen BM, Gordon HL, Rothstein SM, Komeiji Y, Fukuzawa K, Tanaka S. Comput Biol Chem 32 149-158 (2008)


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