Advertisement

Molecular Biology Reports

, Volume 46, Issue 3, pp 3571–3596 | Cite as

DNA–protein interaction: identification, prediction and data analysis

  • Abbasali EmamjomehEmail author
  • Darush Choobineh
  • Behzad HajieghrariEmail author
  • Nafiseh MahdiNezhad
  • Amir Khodavirdipour
Review
  • 300 Downloads

Abstract

Life in living organisms is dependent on specific and purposeful interaction between other molecules. Such purposeful interactions make the various processes inside the cells and the bodies of living organisms possible. DNA–protein interactions, among all the types of interactions between different molecules, are of considerable importance. Currently, with the development of numerous experimental techniques, diverse methods are convenient for recognition and investigating such interactions. While the traditional experimental techniques to identify DNA–protein complexes are time-consuming and are unsuitable for genome-scale studies, the current high throughput approaches are more efficient in determining such interaction at a large-scale, but they are clearly too costly to be practice for daily applications. Hence, according to the availability of much information related to different biological sequences and clearing different dimensions of conditions in which such interactions are formed, with the developments related to the computer, mathematics, and statistics motivate scientists to develop bioinformatics tools for prediction the interaction site(s). Until now, there has been much progress in this field. In this review, the factors and conditions governing the interaction and the laboratory techniques for examining such interactions are addressed. In addition, developed bioinformatics tools are introduced and compared for this reason and, in the end, several suggestions are offered for the promotion of such tools in prediction with much more precision.

Keywords

DNA-binding protein DNA–protein interaction Experimental technique Prediction 

Notes

Acknowledgements

This work has been supported by University of Zabol in Grant code: UOZ-GR-9517-31.

Compliance with ethical standards

Conflict of interest

The authors declare that this article content has no conflict of interest.

References

  1. 1.
    Adams RL (1990) DNA methylation: The effect of minor bases on DNA-protein interactions. Biochem J 265(2):309–320Google Scholar
  2. 2.
    Ahmad S, Gromiha MM, Sarai A (2004) Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics 20(4):477–486Google Scholar
  3. 3.
    Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T, Wolberger C (2002) Hoogsteen base pair embedded in undistorted B-DNA. Nucleic Acids Res 30(23):5244–5252Google Scholar
  4. 4.
    Alibés A, Serrano L, Nadra AD (2010) Structure-based DNA-binding prediction and design. Methods Mol Biol 649:77–88Google Scholar
  5. 5.
    Anguly A, Rajdev P, Williams SM, Chatterji D (2012) Nonspecific interaction between DNA and protein allows for cooperativity: a case study with mycobacterium DNA binding protein. J Phys Chem B 116(1):621–632Google Scholar
  6. 6.
    Bailly C, Kluza J, Martin C et al (2005) DNase I footprinting of small molecule binding sites on DNA. Methods Mol Biol 288:319–342Google Scholar
  7. 7.
    Baker CM, Grant GH (2007) Role of aromatic amino acids in protein-nucleic acid recognition. Biopolymers 85(5–6):456–470Google Scholar
  8. 8.
    Brenowitz M, Senear DF, Shea MA, Ackers GK (1986) Quantitative DNase footprint titration: a method for studying protein-DNA interactions. Methods Enzymol 130:132–181Google Scholar
  9. 9.
    Bruckner A, Polge C, Lentze N, Auerbach D, Schlattner U (2009) Yeast two-hybrid, a powerful tool for systems biology. Int J Mol Sci 10(6):2763–2788Google Scholar
  10. 10.
    Bryne JC, Valen E, Tang M-HE et al (2008) JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 36(suppl 1):D102–D106Google Scholar
  11. 11.
    Cai YH, Huang H (2012) Advances in the study of protein–DNA interaction. Amino acids 43(3):1141–1146Google Scholar
  12. 12.
    Carey MF, Peterson CL, Smale ST (2009) Chromatin immunoprecipitation (ChIP). Cold Spring Harb Protoc.  https://doi.org/10.1101/pdb.prot5279 Google Scholar
  13. 13.
    Carey MF, Peterson CL, Smale ST (2013) DNaseI footprinting. Cold Spring Harb Protoc 5:469–478Google Scholar
  14. 14.
    Chen YC, Wright JD, Lim C (2012) DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res 40:W249–W256Google Scholar
  15. 15.
    Chien CT, Bartel PL, Sternglanz R, Fields S (1991) The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. Proc Natl Acad Sci USA 88(21):9578–9582Google Scholar
  16. 16.
    Chiu TP, Rao S, Mann RS et al (2017) Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding. Nucleic Acids Res 45(21):12565–12576Google Scholar
  17. 17.
    Cohen SX, Moulin M, Hashemolhosseini S et al (2002) Structure of the GCM domain–DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition. EMBO J 22(8):1835–1845Google Scholar
  18. 18.
    Collas P (2010) The current state of chromatin immunoprecipitation. Mol Biotechnol 45(1):87–100Google Scholar
  19. 19.
    Comeau SR, Gatchell DW, Vajda S, Camacho CJ (2004) ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 32:W96–W99Google Scholar
  20. 20.
    Contreras-Moreira B (2009) 3D-footprint: a database for the structural analysis of protein–DNA complexes. Nucleic Acids Res 38:D91–D97Google Scholar
  21. 21.
    Contreras-Moreira B, Branger PA, Collado-Vides J (2007) TFmodeller: comparative modelling of protein–DNA complexes. Bioinformatics 23(13):1694–1696Google Scholar
  22. 22.
    Cook KB, Kazan H, Zuberi K et al (2011) RBPDB: a database of RNA-binding specificities. Nucleic Acids Res 39(suppl 1):D301–D308Google Scholar
  23. 23.
    Coulocheri SA, Pigis DG, Papavassiliou KA, Papavassiliou AG (2007) Hydrogen bonds in protein–DNA complexes: where geometry meets plasticity. Biochimie 89(11):1291–1303Google Scholar
  24. 24.
    Damm K, Thompson C, Evans R (1989) Protein encoded by v-erbA functions as a thyroid-hormone receptor antagonist. Nature 339:593–597Google Scholar
  25. 25.
    Daniels DS, Woo TT, Luu KX et al (2004) DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol Biol 11(8):714–720Google Scholar
  26. 26.
    Dantas-Machado ACD, Zhou T, Rao S, Goel P et al (2015) Evolving insights on how cytosine methylation affects protein–DNA binding. Brief Funct Genomics 14(1):61–73Google Scholar
  27. 27.
    Das PM, Ramachandran K, Van-Wert J, Singal R (2004) Chromatin immunoprecipitation assay. Biotechniques 37:961–969Google Scholar
  28. 28.
    de Vries SJ, Schindler CE, Chauvot de Beauchene I, Zacharias M (2015) A web interface for easy flexible protein-protein docking with ATTRACT. Biophys J 108:462–465Google Scholar
  29. 29.
    de Vries SJ, van Dijk M, Bonvin AM (2010) The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 5:883–897Google Scholar
  30. 30.
    Dey B, Thukral S, Krishnan S et al (2012) DNA–protein interactions: methods for detection and analysis. Mol Cell Biochem 365:279–299.  https://doi.org/10.1007/s11010-012-1269-z Google Scholar
  31. 31.
    Ding XM, Pan XY, Xu C, Shen HB (2010) Computational prediction of DNA–protein interactions: a review. Curr Comput Aided Drug Des 6(3):197–206Google Scholar
  32. 32.
    Donald JE, Chen WW, Shakhnovich EI (2007) Energetics of protein–DNA interactions. Nucleic Acids Res 35(4):1039–1047Google Scholar
  33. 33.
    Ebert JC, Altman RB (2008) Robust recognition of zinc binding sites in proteins. Protein Sci 17(1):54–65Google Scholar
  34. 34.
    Etheve L, Martin J, Lavery R (2016) Dynamics and recognition within a protein–DNA complex: a molecular dynamics study of the SKN-1/DNA interaction. Nucleic Acids Res 44(3):1440–1448Google Scholar
  35. 35.
    Etheve L, Martin J, Lavery R (2016) Protein–DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors. Nucleic Acids Res 44(20):9990–10002Google Scholar
  36. 36.
    Etheve L, Martin J, Lavery R (2017) Decomposing protein–DNA binding and recognition using simplified protein models. Nucleic Acids Res 45(17):10270–10283Google Scholar
  37. 37.
    Fields S, Song OA (1989) A novel genetic system to detect protein-protein interactions. Nature 340(6230):245–246Google Scholar
  38. 38.
    Fried MG (1989) Measurement of protein–DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis 10:366–376Google Scholar
  39. 39.
    Furlan-Magaril M, Rincón-Arano H, Recillas-Targa F (2009) Sequential chromatin immunoprecipitation protocol: ChIP–reChIP. Methods Mol Biol 543:253–266Google Scholar
  40. 40.
    Gade P, Kalvakolanu DV (2012) Chromatin immunoprecipitation assay as a tool for analyzing transcription factor activity. Methods Mol Biol 809:85–104Google Scholar
  41. 41.
    Gajiwala KS, Chen H, Cornille F et al (2000) Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature 403(6772):916–921Google Scholar
  42. 42.
    Ganguly A, Rajdev P, Williams SM, Chatterji D (2012) Nonspecific interaction between DNA and protein allows for cooperativity: a case study with mycobacterium DNA binding protein. J Phys Chem B 116(1):621–632Google Scholar
  43. 43.
    Gao M, Skolnick J (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions. Nucleic Acids Res 36(12):3978–3992Google Scholar
  44. 44.
    Gao M, Skolnick J (2009) A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS Comput Biol 5(11):e1000567Google Scholar
  45. 45.
    Giesecke AV, Joung JK (2007) The bacterial two-hybrid system as a reporter system for analyzing protein–protein interactions. CSH Protoc.  https://doi.org/10.1101/pdb.prot4672 Google Scholar
  46. 46.
    Gilmour DS. Lis JT (1985) In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster. Mol Cell Biol 5:2009–2018Google Scholar
  47. 47.
    Glasfeld A, Schumacher MA, Choi KY et al (1996) A positively charged residue in the minor groove does not alter the bending of a DNA duplex. J Am Chem Soc 118:13073–13074Google Scholar
  48. 48.
    Gross DS, Garrard WT (1998) Nuclease hypersensitive sites in chromatin. Annu Rev Biochem 57:159–197Google Scholar
  49. 49.
    Hall James KB, Kranz K (1999) Nitrocellulose filter binding for determination of dissociation constants. RNA-Protein Interaction Protocols 118:105–114Google Scholar
  50. 50.
    Hampshire AJ, Rusling DA, Broughton-Head VJ, Fox KR (2007) Footprinting: a method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands. Methods 42(2):128–140Google Scholar
  51. 51.
    Harris LA, Williams LD, Koudelka BK (2014) Specific minor groove solvation is a crucial determinant of DNA binding site recognition. Nucleic Acids Res 42(22):14053–14059Google Scholar
  52. 52.
    Harteis S, Schneider S (2014) Making the bend: DNA tertiary structure and protein-DNA interactions. Int J Mol Sci 15(7):12335–12363Google Scholar
  53. 53.
    Hellman LM, Fried MG (2007) Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc 2(8):1849–1861Google Scholar
  54. 54.
    Hoffman MM, Khrapov MA, Cox JC, Yao J, Tong L, Ellington AD (2004) AANT: the amino acid–nucleotide interaction database. Nucleic Acids Res 32(suppl 1):D174–D181Google Scholar
  55. 55.
    Hu JS, Olson EN, Kingston RE (1992) HEB, a helix–loop–helix protein related to E2A and ITF2 that can modulate the DNA-binding ability of myogenic regulatory factors. Mol Cell Biol 12(3):1031–1042Google Scholar
  56. 56.
    Hudson WH, Ortlund EA (2014) The structure, function and evolution of proteins that bind DNA and RNA. Nat Rev Mol Cell Biol 15(11):749–760Google Scholar
  57. 57.
    Hwang S, Gou Z, Kuznetsov IB (2007) DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. Bioinformatics 23(5):634–636Google Scholar
  58. 58.
    Illergård K, Ardell DH, Elofsson A (2009) Structure is three to ten times more conserved than sequence-a study of structural response in protein cores. Proteins 77(3):499–508Google Scholar
  59. 59.
    Ji ZL, Chen X, Zhen CJ et al (2003) KDBI: kinetic data of bio-molecular Interactions database. Nucleic Acids Res 31(1):255–257Google Scholar
  60. 60.
    Jimenez-Garcia B, Pons C, Svergun DI, Bernado P, Fernandez-Recio J (2015) pyDockSAXS: protein-protein complex structure by SAXS and computational docking. Nucleic Acids Res 43:W356–W361Google Scholar
  61. 61.
    Joerger AC, Ang HC, Veprintsev DB et al (2005) Structures of p53 cancer mutants and mechanism of rescue by second-site suppressor mutations. J Biol Chem 280(16):16030–16037Google Scholar
  62. 62.
    Joerger DR (2007) Antimicrobial films for food applications: a quantitative analysis of their effectiveness. Packag Technol Sci 20:231–273Google Scholar
  63. 63.
    Johnson DS, Mortazavi A et al (2007) Genome-wide mapping of in vivo protein–DNA interactions. Science 316:1497–1502.  https://doi.org/10.1126/science.1141319 Google Scholar
  64. 64.
    Jones S, Shanahan HP, Berman HM, Thornton JM (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res 31(24):7189–7198Google Scholar
  65. 65.
    Jones S, Thornton JM (2003) Protein–DNA Interactions: The story so far and a new method for prediction. Comp Funct Genom 4(4):428–431Google Scholar
  66. 66.
    Jones S, van Heyningen P, Berman HM, Thornton JM (1999) Protein-DNA interactions: a structural analysis. J Mol Biol 287(5):877–896Google Scholar
  67. 67.
    Joung JK, Ramm EI, Pabo CO (2000) A bacterial two-hybrid selection system for studying protein–DNA and protein–protein interactions. Proc Natl Acad Sci USA 97(13):7382–7387Google Scholar
  68. 68.
    Joyce AP, Zhang C, Bradley P, Havranek JJ (2015) Structure-based modeling of protein: DNA specificity. Brief Funct Genom 14(1):39–49Google Scholar
  69. 69.
    Karimova G, Gauliard E, Davi M et al (2017) Protein–protein interaction: bacterial two-hybrid. In: Journet L, Cascales E (eds) Bacterial protein secretion systems. Methods in molecular biology, vol 1615. Humana Press, New YorkGoogle Scholar
  70. 70.
    Khabiri M, Freddolino PL (2017) Deficiencies in molecular dynamics simulation-based prediction of protein–DNA binding free energy landscapes. J Phys Chem 121:5151–5161Google Scholar
  71. 71.
    Khan A, Fornes O, Stigliani A et al (2018) JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res 46(D1):D260–D266Google Scholar
  72. 72.
    Kirsanov DD, Zanegina ON, Aksianov EA et al (2012) NPIDB: nucleic acid/protein interaction database. Nucleic Acids Res 41:D517–D523Google Scholar
  73. 73.
    Kochańczyk T, Drozd A, Krężel A (2015) Relationship between the architecture of zinc coordination and zinc binding affinity in proteins-insights into zinc regulation. Metallomics 7(2):244–257Google Scholar
  74. 74.
    Krężel A, Maret W (2014) The biological inorganic chemistry of zinc ions. Arch Biochem Biophys 611:3–19Google Scholar
  75. 75.
    Krishna SS, Majumdar I, Grishin NV (2003) Survey and summary: structural classification of zinc fingers. Nucleic Acids Res 31(2):532–550Google Scholar
  76. 76.
    Lawson CL, Berman HM (2008) Indirect readout of DNA sequence by proteins. In: Rice PA, Correll CC (eds) Protein nucleic acid interactions. Royal Society of Chemistry, Cambridge, pp 66–86Google Scholar
  77. 77.
    Lebrun A, Shakked Z, Lavery R (1997) Local DNA stretching mimics the distortion caused by the TATA box-binding protein. PNAS 94(7):2993–2998Google Scholar
  78. 78.
    Lee S, Blundell TL (2009) BIPA: a database for protein–nucleic acid interaction in 3D structures. Bioinformatics 25(12):1559–1560Google Scholar
  79. 79.
    Leon O, Roth M (2000) Zinc fingers: DNA binding and protein-protein interactions. Biol Res 33(1):21–30Google Scholar
  80. 80.
    Lesk VI, Sternberg MJ (2008) 3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. Bioinformatics 24:1137–1144Google Scholar
  81. 81.
    Lewis BA, Walia RR, Terribilini M et al (2011) PRIDB: a protein–RNA interface database. Nucleic Acids Res 39(suppl 1):D277–D282Google Scholar
  82. 82.
    Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28:327–334Google Scholar
  83. 83.
    Lin CK, Chen CY (2013) PiDNA: predicting protein–DNA interactions with structural models. Nucleic Acids Res 41(W1):W523–W530Google Scholar
  84. 84.
    Lin JS, Lai EM (2017) Protein–protein interactions: yeast two-hybrid system. Methods Mol Biol 1615:177–187Google Scholar
  85. 85.
    Lin WZ, Fang JA, Xiao X, Chou K-C (2011) iDNA-Prot: identification of DNA binding proteins using random forest with grey model. PLoS ONE 6(9):e24756Google Scholar
  86. 86.
    Liu B, Xu J, Lan X et al (2014) iDNA-Prot|dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition. PLoS ONE 9(9):e106691Google Scholar
  87. 87.
    Lou W, Wang X, Chen F et al (2014) Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes. PLoS ONE 9(1):e86703Google Scholar
  88. 88.
    Luscombe NM, Austin SE, Berman HM, Thornton JM (2000) An overview of the structures of protein–DNA complexes. Genome Biol 1:1–37Google Scholar
  89. 89.
    Luscombe NM, Laskowski RA, Thornton JM (2001) Amino acid-base interactions: a three-dimensional analysis of protein–DNA interactions at an atomic level. Nucleic Acids Res 29(13):2860–2874Google Scholar
  90. 90.
    Lyskov S, Gray JJ (2008) The RosettaDock server for local protein–protein docking. Nucleic Acids Res 36:W233–W238Google Scholar
  91. 91.
    Macindoe G, Mavridis L, Venkatraman V, Devignes MD, Ritchie DW (2010) HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Res 38:W445–W449Google Scholar
  92. 92.
    MacPherson S, Larochelle M, Turcotte B (2006) A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol Mol Biol Rev 70(3):583–604Google Scholar
  93. 93.
    Mahony S, Benos PV (2007) STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 35(suppl 2):W253–W258Google Scholar
  94. 94.
    Mangelsdorf DJ, Evans RM (1995) The RXR heterodimers and orphan receptors. Cell 83(6):841–850Google Scholar
  95. 95.
    Maple J, Møller SG (2007) Yeast two-hybrid screening. Methods Mol Biol 362:207–223Google Scholar
  96. 96.
    Mathelier A, Fornes O, Arenillas DJ et al (2015) JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res 44:D110–D115Google Scholar
  97. 97.
    Mathelier A, Zhao X, Zhang AW et al (2014) JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res 42(Database issue):D142–D147Google Scholar
  98. 98.
    Matys V, Fricke E, Geffers R et al (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31(1):374–378Google Scholar
  99. 99.
    Matys V, Kel-Margoulis OV, Fricke E et al (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34(Database issue):D108–D110Google Scholar
  100. 100.
    McEwan AR, Raab A, Kelly SM et al (2011) Zinc is essential for high-affinity DNA binding and recombinase activity of ΦC31 integrase. Nucleic Acids Res 39(14):6137–6147Google Scholar
  101. 101.
    Meng X, Brodsky MH, Wolfe SA (2005) A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nature Biotechnol 23(8):988–994Google Scholar
  102. 102.
    Meng X, Wolfe SA (2006) Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nat Protoc 1(1):30–45Google Scholar
  103. 103.
    Meng XY, Zhang HX, Mezei M, Cui M (2011) Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des 7(2):146–157Google Scholar
  104. 104.
    Michaleka JJ, Chester M, Jaramilloc P et al (2011) Valuation of plug-in vehicle life-cycle air emissions and oil displacement benefits. PNAS 108(40):16554–16558Google Scholar
  105. 105.
    Mikles DC, Bhat V, Schuchardt BJ et al (2013) pH modulates the binding of early growth response protein 1 transcription factor to DNA. FEBS 280:3669–3684Google Scholar
  106. 106.
    Miller J, Stagljar I (2004) Using the yeast two-hybrid system to identify interacting proteins. Methods Mol Biol 261:247–262Google Scholar
  107. 107.
    Milne TA, Zhao K, Hess JL (2009) Chromatin immunoprecipitation (ChIP) for analysis of histone modifications and chromatin-associated proteins. Methods Mol Biol 538:409–423Google Scholar
  108. 108.
    Molloy PL (2000) Electrophoretic mobility shift assays. Methods Mol Biol 130:235–246Google Scholar
  109. 109.
    Morozov AV, Havranek JJ, Baker D, Siggia ED (2005) Protein–DNA binding specificity predictions with structural models. Nucleic Acids Res 33(18):5781–5798Google Scholar
  110. 110.
    Murugan R (2010) Theory of site-specific DNA–protein interactions in the presence of conformational fluctuations of DNA binding domains. Biophysical J 99(2):353–359Google Scholar
  111. 111.
    Nelson JD, Denisenko O, Bomsztyk K (2006) Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nature Protocols-Electronic Edition 1(1):179Google Scholar
  112. 112.
    Newburger DE, Bulyk ML (2009) UniPROBE: an online database of protein binding microarray data on protein–DNA interactions. Nucleic Acids Res 37(suppl 1):D77–D82Google Scholar
  113. 113.
    Newton AL, Sharpe BK, Kwan A et al (2000) The transactivation domain within cysteine/histidine-rich region 1 of CBP comprises two novel zinc-binding modules. J Biol Chem 275(20):15128–15134Google Scholar
  114. 114.
    Nilkanta C, Angshuman B (2015) An overview of DNA–protein interactions. Curr Chem Biol 9(2):73–83Google Scholar
  115. 115.
    Nimrod G, Schushan M, Szilágyi A et al (2010) iDBPs: a web server for the identification of DNA binding proteins. Bioinformatics 26(5):692–693Google Scholar
  116. 116.
    Nimrod G, Szilagyi A, Leslie C, Ben-Tal N (2010) Identification of DNA–binding proteins using structural, electrostatic and evolutionary features. J Mol Biol 387:1040–1053Google Scholar
  117. 117.
    Norambuena T, Melo F (2010) The protein–DNA interface database. BMC Bioinformatics 11(1):262Google Scholar
  118. 118.
    Noy A, Sutthibutpong T, Harris SA (2016) Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophysical Reviews 8(3):233–243Google Scholar
  119. 119.
    Ofran Y, Rost B (2007) ISIS: interaction sites identified from sequence. Bioinformatics 23(2):e13–e16Google Scholar
  120. 120.
    Orlando V (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 25(3):99–104Google Scholar
  121. 121.
    Ozbek P, Soner S, Erman B, Haliloglu T (2010) DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. Nucleic Acids Res 38: W417–W423Google Scholar
  122. 122.
    Pace NJ, Weerapana E (2014) Zinc-binding cysteines: diverse functions and structural motifs. Biomolecules 4(2):419–434Google Scholar
  123. 123.
    Parisien M, Freed KF, Sosnick TR (2012) On docking, scoring and assessing protein-DNA complexes in a rigid-body framework. PLoS ONE 7(2):e32647.  https://doi.org/10.1371/journal.pone.0032647 Google Scholar
  124. 124.
    Park B, Kim H, Han K (2014) DBBP: database of binding pairs in protein-nucleic acid interactions. BMC Bioinformatics 15(Suppl 15):S5Google Scholar
  125. 125.
    Patikoglou GA, Joseph L. Kim JL et al (1999) TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev 13(24):3217–3230Google Scholar
  126. 126.
    Payvar F, DeFranco D, Firestone GL, Edgar B et al (1983) Sequence-specific binding of glucocorticoid receptor to MTV DNA at sites within and upstream of the transcribed region. Cell 35(2):381–392Google Scholar
  127. 127.
    Pellegrini-Calace M, Thornton JM (2005) Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information. Nucleic Acids Res 33(7):2129–2140Google Scholar
  128. 128.
    Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z (2014) ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics 30:1771–1773Google Scholar
  129. 129.
    Pogenberg V, Ogmundsdóttir MH, Bergsteinsdóttir K et al (2012) Restricted leucine zipper dimerization and specificity of DNA recognition of the melanocyte master regulator MITF. Genes Dev 26(23):2647–2658Google Scholar
  130. 130.
    Portales-Casamar E, Thongjuea S, Kwon AT et al (2009) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 38:D105–D110Google Scholar
  131. 131.
    Pourhassan-Moghaddam M, Rahmati-Yamchi M, Akbarzadeh A et al (2013) Protein detection through different platforms of immuno-loop-mediated isothermal amplification. Nanoscale Res Lett 8(1):485Google Scholar
  132. 132.
    Prabakaran P, An J, Gromiha MM et al (2001) Thermodynamic database for protein–nucleic acid interactions (ProNIT). Bioinformatics 17(11):1027–1034Google Scholar
  133. 133.
    Pradhan L, Nam HJ (2015) NuProPlot: nucleic acid and protein interaction analysis and plotting program. Acta Crystallogr D Biol Crystallogr 71(Pt 3):667–674Google Scholar
  134. 134.
    Propper K, Meindl K, Sammito M et al (2014) Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries. Acta Cryst D70:1743–1757Google Scholar
  135. 135.
    Pugh B (2012) Methods, systems and kits for detecting protein-nucleic acid interactions. United States Application Publication, United States PatentsGoogle Scholar
  136. 136.
    Rio DC (2014) Electrophoretic mobility shift assays for RNA–protein complexes. Cold Spring Harb Protoc (4):435–440Google Scholar
  137. 137.
    Rohs R, Dantas Machado AC, Yang L (2015) Exposing the secrets of sex determination. Nat Struct Mol Biol 22:437–438Google Scholar
  138. 138.
    Rohs R, Jin X, West SM et al (2010) Origins of specificity in protein–DNA recognition. Annu Rev Biochem 79:233Google Scholar
  139. 139.
    Rohs R, West S, Sosinsky A et al (2009) The role of DNA shape in protein–DNA recognition. Nature 461(7268):1248–1253Google Scholar
  140. 140.
    Rosinski JA, Atchley WR (1999) Molecular evolution of helix-turn-helix proteins. J Mol Evol 49(3):301–309Google Scholar
  141. 141.
    Sandelin A, Alkema W, Engström P et al (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32(suppl 1):D91–D94Google Scholar
  142. 142.
    Sapienza PJ, Niu T, Kurpiewski MR, Grigorescu A, Jen-Jacobson L (2013) Thermodynamic and structural basis for relaxation of specificity in protein–DNA recognition. Int J Mol Sci 15:12335–12363Google Scholar
  143. 143.
    Schindler C, Shuai K, Prezioso VR, Darnell JE Jr (1992) Interferon-dependent tyrosine phosphorylation of a latent cytoplasmic transcription factor. Science 257(5071):809–813Google Scholar
  144. 144.
    Schleif R (1988) DNA binding by proteins. Science 241(4870):1182–1187Google Scholar
  145. 145.
    Schneider B, Gelly JC, de-Brevern AG, Černý J (2014) Local dynamics of proteins and DNA evaluated from crystallographic B factors. Acta Crystallogr D Biol Crystallogr 70(Pt 9):2413–2419Google Scholar
  146. 146.
    Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 33:W363–W367Google Scholar
  147. 147.
    Setny P, Bahadur RP, Zacharias M (2012) Protein–DNA docking with a coarse-grained force field. BMC Bioinformatics 13:228.  https://doi.org/10.1186/1471-2105-13-228 Google Scholar
  148. 148.
    Si J, Zhang Z, Lin B, Schroeder M, Huang B (2011) MetaDBSite: a meta approach to improve protein DNA-binding sites prediction. BMC Syst Biol 5(Suppl 1):S7Google Scholar
  149. 149.
    Si J, Zhao R, Wu R (2015) An overview of the prediction of protein DNA-binding sites. Int J Mol Sci 16(3):5194–5215Google Scholar
  150. 150.
    Siggers T, Gordân R (2014) Protein–DNA binding: complexities and multi-protein codes. Nucleic Acids Res 42(4):2099–2111Google Scholar
  151. 151.
    Spirin S, Titov M, Karyagina A, Alexeevski A (2007) NPIDB: a database of nucleic acids–protein interactions. Bioinformatics 23(23):3247–3248Google Scholar
  152. 152.
    Spyrakis F, Cozzini P, Bertoli C et al (2007) Energetics of the protein–DNA–water interaction. BMC Struct Biol 7:4.  https://doi.org/10.1186/1472-6807-7-4 Google Scholar
  153. 153.
    Stormo GD, Zhao Y (2010) Determining the specificity of protein–DNA interactions. Nat Rev Genet 11:751–760Google Scholar
  154. 154.
    Tainer J, Cunningham RP (1993) Molecular recognition in DNA-binding proteins and enzymes. Curr Opin Biotechnol 4(4):474–483Google Scholar
  155. 155.
    Teichmann SA, Wigge PA, Charoensawan V (2012) Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes. Cell Cycle 11(24):4487–4488Google Scholar
  156. 156.
    Terribilini M, Sander JD, Lee J-H et al (2007) RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res 35(suppl 2):W578–W584Google Scholar
  157. 157.
    Torchala M, Moal IH, Chaleil RA, Fernandez-Recio J, Bates PA (2013) SwarmDock: a server for flexible protein–protein docking. Bioinformatics 29:807–809Google Scholar
  158. 158.
    Tovchigrechko A, Vakser IA (2006) GRAMM-X public web server for protein–protein docking. Nucleic Acids Res 34:W310–W314Google Scholar
  159. 159.
    Tran NTL, Huang C-H (2014) A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data. Biol Direct 9(1):4Google Scholar
  160. 160.
    Tuszynska I, Magnus M, Jonak K, Dawson W, Bujnicki JM (2015) NPDock: a web server for protein–nucleic acid docking. Nucleic Acids Res 43:W425–W430Google Scholar
  161. 161.
    Umesono K, Murakami K, Thompson C, Evans RM (1991) Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3 receptors. Cell 65(7):1255–1266Google Scholar
  162. 162.
    Vidal M, Brachmann RK, Fattaey A et al (1996) Reverse two-hybrid and one-hybrid systems to detect dissociation of protein–protein and DNA–protein interactions. Proc Natl Acad Sci USA 93:10315–10320Google Scholar
  163. 163.
    Vinckevicius A, Chakravarti D (2012) Chromatin immunoprecipitation: advancing analysis of nuclear hormone signaling. J Mol Endocrinol 49(2):R113–R123Google Scholar
  164. 164.
    Vlieghe D, Sandelin A, De Bleser PJ et al (2006) A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res 34:D95–D97Google Scholar
  165. 165.
    Von-Hippel PH (2007) From “Simple” DNA–protein interactions to the macromolecular machines of gene expression. Annu Rev Biophys Biomol Struct 36:79–105Google Scholar
  166. 166.
    Wang HC, Ho CH, Hsu KC et al (2014) DNA mimic proteins: functions, structures, and bioinformatic analysis. Biochemistry 53(18):2865–2874Google Scholar
  167. 167.
    Wang L, Brown SJ (2006) BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res 34(suppl 2):W243–W248Google Scholar
  168. 168.
    Wang L, Huang C, Yang MQ, Yang JY (2010) BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC systems biol 4(Suppl 1):S3Google Scholar
  169. 169.
    Wang L, Yang MQ, Yang JY (2009) Prediction of DNA-binding residues from protein sequence information using random forests. BMC Genom 10(Suppl 1):S1Google Scholar
  170. 170.
    Wilson KA, Holland DJ, Wetmore SD (2016) Topology of RNA–protein nucleobase-amino acid π–π interactions and comparison to analogous DNA–protein π–π contacts. RNA 22(5):696–708Google Scholar
  171. 171.
    Wilson KA, Rachael AW, Minette NA et al (2015) Landscape of π–π and sugar–π contacts in DNA–protein interactions. J Biomol Struct Dyn 34(1)Google Scholar
  172. 172.
    Wingender E, Dietze P, Karas H, Knüppel R (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 24(1):238–241Google Scholar
  173. 173.
    Wong E, Wei CL (2009) ChIP’ing the mammalian genome: technical advances and insights into functional elements. Genome Med 1(9):89Google Scholar
  174. 174.
    Wu G, Yustein JT, McCall MN et al (2013) ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics 29(9):1182–1189Google Scholar
  175. 175.
    Wu J, Liu H, Duan X et al (2009) Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics 25(1):30–35Google Scholar
  176. 176.
    Xie Z, Hu S, Blackshaw S, Zhu H, Qian J (2010) hPDI: a database of experimental human protein–DNA interactions. Bioinformatics 26(2):287–289Google Scholar
  177. 177.
    Yan Y, Zhang D, Zhou P, Li B, Huang S (2017) HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res 45:W365–W373Google Scholar
  178. 178.
    Yesudhas D, Batool M, Anwar MA et al (2017) Proteins recognizing DNA: structural uniqueness and versatility of DNA-binding domains in stem cell transcription factors. Genes 8(8):192Google Scholar
  179. 179.
    Yu J, Vavrusa M, Andreani J, Rey J, Tuffery P, Guerois R (2016) InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information. Nucleic Acids Res 44:W542–W549Google Scholar
  180. 180.
    Zanegina O, Kirsanov D, Baulin E, Karyagina A, Alexeevski A, Spirin S (2016) An updated version of NPIDB includes new classifications of DNA–protein complexes and their families. Nucleic Acids Res 44:144–153Google Scholar
  181. 181.
    Zhang Y, Xu J, Zheng W et al (2014) newDNA–Prot: prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation. Comput Biol Chem 52:51–59Google Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB)University of ZabolZabolIran
  2. 2.Agricultural Biotechnology, Department of Plant Breeding and Biotechnology (PBB), Faculty of AgricultureUniversity of ZabolZabolIran
  3. 3.Department of Agricultural Biotechnology, College of AgricultureJahrom UniversityJahromIran
  4. 4.Division of Human Genetics, Department of AnatomySt. John’s hospitalBangaloreIndia

Personalised recommendations