Skip to main content
SpringerLink
Log in

DNA–protein interaction: identification, prediction and data analysis

  • Review
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Adams RL (1990) DNA methylation: The effect of minor bases on DNA-protein interactions. Biochem J 265(2):309–320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):477–486

    Article  CAS  PubMed  Google Scholar 

  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):5244–5252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Alibés A, Serrano L, Nadra AD (2010) Structure-based DNA-binding prediction and design. Methods Mol Biol 649:77–88

    Article  CAS  PubMed  Google Scholar 

  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):621–632

    Article  CAS  Google Scholar 

  6. Bailly C, Kluza J, Martin C et al (2005) DNase I footprinting of small molecule binding sites on DNA. Methods Mol Biol 288:319–342

    CAS  PubMed  Google Scholar 

  7. Baker CM, Grant GH (2007) Role of aromatic amino acids in protein-nucleic acid recognition. Biopolymers 85(5–6):456–470

    Article  CAS  PubMed  Google Scholar 

  8. Brenowitz M, Senear DF, Shea MA, Ackers GK (1986) Quantitative DNase footprint titration: a method for studying protein-DNA interactions. Methods Enzymol 130:132–181

    Article  CAS  PubMed  Google Scholar 

  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):2763–2788

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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–D106

    CAS  PubMed  Google Scholar 

  11. Cai YH, Huang H (2012) Advances in the study of protein–DNA interaction. Amino acids 43(3):1141–1146

    Article  CAS  PubMed  Google Scholar 

  12. Carey MF, Peterson CL, Smale ST (2009) Chromatin immunoprecipitation (ChIP). Cold Spring Harb Protoc. https://doi.org/10.1101/pdb.prot5279

    Article  PubMed  Google Scholar 

  13. Carey MF, Peterson CL, Smale ST (2013) DNaseI footprinting. Cold Spring Harb Protoc 5:469–478

    Google Scholar 

  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–W256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):9578–9582

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):12565–12576

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):1835–1845

    Article  Google Scholar 

  18. Collas P (2010) The current state of chromatin immunoprecipitation. Mol Biotechnol 45(1):87–100

    Article  CAS  PubMed  Google Scholar 

  19. Comeau SR, Gatchell DW, Vajda S, Camacho CJ (2004) ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 32:W96–W99

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Contreras-Moreira B (2009) 3D-footprint: a database for the structural analysis of protein–DNA complexes. Nucleic Acids Res 38:D91–D97

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Contreras-Moreira B, Branger PA, Collado-Vides J (2007) TFmodeller: comparative modelling of protein–DNA complexes. Bioinformatics 23(13):1694–1696

    Article  CAS  PubMed  Google Scholar 

  22. Cook KB, Kazan H, Zuberi K et al (2011) RBPDB: a database of RNA-binding specificities. Nucleic Acids Res 39(suppl 1):D301–D308

    Article  CAS  PubMed  Google Scholar 

  23. Coulocheri SA, Pigis DG, Papavassiliou KA, Papavassiliou AG (2007) Hydrogen bonds in protein–DNA complexes: where geometry meets plasticity. Biochimie 89(11):1291–1303

    Article  CAS  PubMed  Google Scholar 

  24. Damm K, Thompson C, Evans R (1989) Protein encoded by v-erbA functions as a thyroid-hormone receptor antagonist. Nature 339:593–597

    Article  CAS  PubMed  Google Scholar 

  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):714–720

    Article  CAS  PubMed  Google Scholar 

  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):61–73

    Article  CAS  PubMed  Google Scholar 

  27. Das PM, Ramachandran K, Van-Wert J, Singal R (2004) Chromatin immunoprecipitation assay. Biotechniques 37:961–969

    Article  CAS  PubMed  Google Scholar 

  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 108:462–465

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. de Vries SJ, van Dijk M, Bonvin AM (2010) The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 5:883–897

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  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):197–206

    Article  CAS  PubMed  Google Scholar 

  32. Donald JE, Chen WW, Shakhnovich EI (2007) Energetics of protein–DNA interactions. Nucleic Acids Res 35(4):1039–1047

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Ebert JC, Altman RB (2008) Robust recognition of zinc binding sites in proteins. Protein Sci 17(1):54–65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):1440–1448

    Article  CAS  PubMed  Google Scholar 

  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):9990–10002

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Etheve L, Martin J, Lavery R (2017) Decomposing protein–DNA binding and recognition using simplified protein models. Nucleic Acids Res 45(17):10270–10283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Fields S, Song OA (1989) A novel genetic system to detect protein-protein interactions. Nature 340(6230):245–246

    Article  CAS  PubMed  Google Scholar 

  38. Fried MG (1989) Measurement of protein–DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis 10:366–376

    Article  CAS  PubMed  Google Scholar 

  39. Furlan-Magaril M, Rincón-Arano H, Recillas-Targa F (2009) Sequential chromatin immunoprecipitation protocol: ChIP–reChIP. Methods Mol Biol 543:253–266

    Article  CAS  PubMed  Google Scholar 

  40. Gade P, Kalvakolanu DV (2012) Chromatin immunoprecipitation assay as a tool for analyzing transcription factor activity. Methods Mol Biol 809:85–104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):916–921

    Article  CAS  PubMed  Google Scholar 

  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):621–632

    Article  CAS  PubMed  Google Scholar 

  43. Gao M, Skolnick J (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions. Nucleic Acids Res 36(12):3978–3992

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):e1000567

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  PubMed  Google Scholar 

  46. Gilmour DS. Lis JT (1985) In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster. Mol Cell Biol 5:2009–2018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 118:13073–13074

    Article  CAS  Google Scholar 

  48. Gross DS, Garrard WT (1998) Nuclease hypersensitive sites in chromatin. Annu Rev Biochem 57:159–197

    Article  Google Scholar 

  49. Hall James KB, Kranz K (1999) Nitrocellulose filter binding for determination of dissociation constants. RNA-Protein Interaction Protocols 118:105–114

    Article  Google Scholar 

  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):128–140

    Article  CAS  PubMed  Google Scholar 

  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):14053–14059

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Harteis S, Schneider S (2014) Making the bend: DNA tertiary structure and protein-DNA interactions. Int J Mol Sci 15(7):12335–12363

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Hellman LM, Fried MG (2007) Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc 2(8):1849–1861

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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–D181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):1031–1042

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):749–760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):634–636

    Article  CAS  PubMed  Google Scholar 

  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):499–508

    Article  CAS  PubMed  Google Scholar 

  59. Ji ZL, Chen X, Zhen CJ et al (2003) KDBI: kinetic data of bio-molecular Interactions database. Nucleic Acids Res 31(1):255–257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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–W361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):16030–16037

    Article  CAS  PubMed  Google Scholar 

  62. Joerger DR (2007) Antimicrobial films for food applications: a quantitative analysis of their effectiveness. Packag Technol Sci 20:231–273

    Article  CAS  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  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):7189–7198

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Jones S, Thornton JM (2003) Protein–DNA Interactions: The story so far and a new method for prediction. Comp Funct Genom 4(4):428–431

    Article  CAS  Google Scholar 

  66. Jones S, van Heyningen P, Berman HM, Thornton JM (1999) Protein-DNA interactions: a structural analysis. J Mol Biol 287(5):877–896

    Article  CAS  PubMed  Google Scholar 

  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):7382–7387

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Joyce AP, Zhang C, Bradley P, Havranek JJ (2015) Structure-based modeling of protein: DNA specificity. Brief Funct Genom 14(1):39–49

    Article  CAS  Google Scholar 

  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 York

    Google Scholar 

  70. Khabiri M, Freddolino PL (2017) Deficiencies in molecular dynamics simulation-based prediction of protein–DNA binding free energy landscapes. J Phys Chem 121:5151–5161

    Article  CAS  Google Scholar 

  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–D266

    Article  CAS  PubMed  Google Scholar 

  72. Kirsanov DD, Zanegina ON, Aksianov EA et al (2012) NPIDB: nucleic acid/protein interaction database. Nucleic Acids Res 41:D517–D523

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):244–257

    Article  CAS  PubMed  Google Scholar 

  74. Krężel A, Maret W (2014) The biological inorganic chemistry of zinc ions. Arch Biochem Biophys 611:3–19

    Article  CAS  Google Scholar 

  75. Krishna SS, Majumdar I, Grishin NV (2003) Survey and summary: structural classification of zinc fingers. Nucleic Acids Res 31(2):532–550

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 66–86

    Chapter  Google Scholar 

  77. Lebrun A, Shakked Z, Lavery R (1997) Local DNA stretching mimics the distortion caused by the TATA box-binding protein. PNAS 94(7):2993–2998

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Lee S, Blundell TL (2009) BIPA: a database for protein–nucleic acid interaction in 3D structures. Bioinformatics 25(12):1559–1560

    Article  CAS  PubMed  Google Scholar 

  79. Leon O, Roth M (2000) Zinc fingers: DNA binding and protein-protein interactions. Biol Res 33(1):21–30

    Article  CAS  PubMed  Google Scholar 

  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 24:1137–1144

    Article  CAS  PubMed  Google Scholar 

  81. Lewis BA, Walia RR, Terribilini M et al (2011) PRIDB: a protein–RNA interface database. Nucleic Acids Res 39(suppl 1):D277–D282

    Article  CAS  PubMed  Google Scholar 

  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 28:327–334

    Article  CAS  PubMed  Google Scholar 

  83. Lin CK, Chen CY (2013) PiDNA: predicting protein–DNA interactions with structural models. Nucleic Acids Res 41(W1):W523–W530

    Article  PubMed  PubMed Central  Google Scholar 

  84. Lin JS, Lai EM (2017) Protein–protein interactions: yeast two-hybrid system. Methods Mol Biol 1615:177–187

    Article  CAS  PubMed  Google Scholar 

  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):e24756

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):e106691

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):e86703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Luscombe NM, Austin SE, Berman HM, Thornton JM (2000) An overview of the structures of protein–DNA complexes. Genome Biol 1:1–37

    Article  Google Scholar 

  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):2860–2874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Lyskov S, Gray JJ (2008) The RosettaDock server for local protein–protein docking. Nucleic Acids Res 36:W233–W238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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–W449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. MacPherson S, Larochelle M, Turcotte B (2006) A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol Mol Biol Rev 70(3):583–604

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Mahony S, Benos PV (2007) STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 35(suppl 2):W253–W258

    Article  PubMed  PubMed Central  Google Scholar 

  94. Mangelsdorf DJ, Evans RM (1995) The RXR heterodimers and orphan receptors. Cell 83(6):841–850

    Article  CAS  PubMed  Google Scholar 

  95. Maple J, Møller SG (2007) Yeast two-hybrid screening. Methods Mol Biol 362:207–223

    Article  CAS  PubMed  Google Scholar 

  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–D115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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–D147

    Article  CAS  PubMed  Google Scholar 

  98. Matys V, Fricke E, Geffers R et al (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31(1):374–378

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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–D110

    Article  CAS  PubMed  Google Scholar 

  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):6137–6147

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):988–994

    Article  CAS  Google Scholar 

  102. Meng X, Wolfe SA (2006) Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nat Protoc 1(1):30–45

    Article  CAS  PubMed  Google Scholar 

  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):146–157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):16554–16558

    Article  Google Scholar 

  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 280:3669–3684

    Article  CAS  Google Scholar 

  106. Miller J, Stagljar I (2004) Using the yeast two-hybrid system to identify interacting proteins. Methods Mol Biol 261:247–262

    CAS  PubMed  Google Scholar 

  107. Milne TA, Zhao K, Hess JL (2009) Chromatin immunoprecipitation (ChIP) for analysis of histone modifications and chromatin-associated proteins. Methods Mol Biol 538:409–423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Molloy PL (2000) Electrophoretic mobility shift assays. Methods Mol Biol 130:235–246

    CAS  PubMed  Google Scholar 

  109. Morozov AV, Havranek JJ, Baker D, Siggia ED (2005) Protein–DNA binding specificity predictions with structural models. Nucleic Acids Res 33(18):5781–5798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):353–359

    Article  CAS  Google Scholar 

  111. Nelson JD, Denisenko O, Bomsztyk K (2006) Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nature Protocols-Electronic Edition 1(1):179

    Article  CAS  Google Scholar 

  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–D82

    Article  CAS  PubMed  Google Scholar 

  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):15128–15134

    Article  CAS  PubMed  Google Scholar 

  114. Nilkanta C, Angshuman B (2015) An overview of DNA–protein interactions. Curr Chem Biol 9(2):73–83

    Google Scholar 

  115. Nimrod G, Schushan M, Szilágyi A et al (2010) iDBPs: a web server for the identification of DNA binding proteins. Bioinformatics 26(5):692–693

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 387:1040–1053

    Article  CAS  Google Scholar 

  117. Norambuena T, Melo F (2010) The protein–DNA interface database. BMC Bioinformatics 11(1):262

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Noy A, Sutthibutpong T, Harris SA (2016) Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophysical Reviews 8(3):233–243

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Ofran Y, Rost B (2007) ISIS: interaction sites identified from sequence. Bioinformatics 23(2):e13–e16

    Article  CAS  PubMed  Google Scholar 

  120. Orlando V (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 25(3):99–104

    Article  CAS  PubMed  Google Scholar 

  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–W423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Pace NJ, Weerapana E (2014) Zinc-binding cysteines: diverse functions and structural motifs. Biomolecules 4(2):419–434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Park B, Kim H, Han K (2014) DBBP: database of binding pairs in protein-nucleic acid interactions. BMC Bioinformatics 15(Suppl 15):S5

    Article  PubMed  PubMed Central  Google Scholar 

  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):3217–3230

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):381–392

    Article  CAS  PubMed  Google Scholar 

  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):2129–2140

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 30:1771–1773

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):2647–2658

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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–D110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Prabakaran P, An J, Gromiha MM et al (2001) Thermodynamic database for protein–nucleic acid interactions (ProNIT). Bioinformatics 17(11):1027–1034

    Article  CAS  PubMed  Google Scholar 

  133. Pradhan L, Nam HJ (2015) NuProPlot: nucleic acid and protein interaction analysis and plotting program. Acta Crystallogr D Biol Crystallogr 71(Pt 3):667–674

    Article  CAS  PubMed  Google Scholar 

  134. Propper K, Meindl K, Sammito M et al (2014) Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries. Acta Cryst D70:1743–1757

    Google Scholar 

  135. Pugh B (2012) Methods, systems and kits for detecting protein-nucleic acid interactions. United States Application Publication, United States Patents

  136. Rio DC (2014) Electrophoretic mobility shift assays for RNA–protein complexes. Cold Spring Harb Protoc (4):435–440

  137. Rohs R, Dantas Machado AC, Yang L (2015) Exposing the secrets of sex determination. Nat Struct Mol Biol 22:437–438

    Article  CAS  PubMed  Google Scholar 

  138. Rohs R, Jin X, West SM et al (2010) Origins of specificity in protein–DNA recognition. Annu Rev Biochem 79:233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Rohs R, West S, Sosinsky A et al (2009) The role of DNA shape in protein–DNA recognition. Nature 461(7268):1248–1253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Rosinski JA, Atchley WR (1999) Molecular evolution of helix-turn-helix proteins. J Mol Evol 49(3):301–309

    Article  CAS  PubMed  Google Scholar 

  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–D94

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 15:12335–12363

    Google Scholar 

  143. Schindler C, Shuai K, Prezioso VR, Darnell JE Jr (1992) Interferon-dependent tyrosine phosphorylation of a latent cytoplasmic transcription factor. Science 257(5071):809–813

    Article  CAS  PubMed  Google Scholar 

  144. Schleif R (1988) DNA binding by proteins. Science 241(4870):1182–1187

    Article  CAS  PubMed  Google Scholar 

  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):2413–2419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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–W367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):S7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Si J, Zhao R, Wu R (2015) An overview of the prediction of protein DNA-binding sites. Int J Mol Sci 16(3):5194–5215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Siggers T, Gordân R (2014) Protein–DNA binding: complexities and multi-protein codes. Nucleic Acids Res 42(4):2099–2111

    Article  CAS  PubMed  Google Scholar 

  151. Spirin S, Titov M, Karyagina A, Alexeevski A (2007) NPIDB: a database of nucleic acids–protein interactions. Bioinformatics 23(23):3247–3248

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Stormo GD, Zhao Y (2010) Determining the specificity of protein–DNA interactions. Nat Rev Genet 11:751–760

    Article  CAS  PubMed  Google Scholar 

  154. Tainer J, Cunningham RP (1993) Molecular recognition in DNA-binding proteins and enzymes. Curr Opin Biotechnol 4(4):474–483

    Article  CAS  PubMed  Google Scholar 

  155. Teichmann SA, Wigge PA, Charoensawan V (2012) Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes. Cell Cycle 11(24):4487–4488

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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–W584

    Article  PubMed  PubMed Central  Google Scholar 

  157. Torchala M, Moal IH, Chaleil RA, Fernandez-Recio J, Bates PA (2013) SwarmDock: a server for flexible protein–protein docking. Bioinformatics 29:807–809

    Article  CAS  PubMed  Google Scholar 

  158. Tovchigrechko A, Vakser IA (2006) GRAMM-X public web server for protein–protein docking. Nucleic Acids Res 34:W310–W314

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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–W430

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):1255–1266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 93:10315–10320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Vinckevicius A, Chakravarti D (2012) Chromatin immunoprecipitation: advancing analysis of nuclear hormone signaling. J Mol Endocrinol 49(2):R113–R123

    Article  CAS  PubMed  Google Scholar 

  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–D97

    Article  CAS  PubMed  Google Scholar 

  165. Von-Hippel PH (2007) From “Simple” DNA–protein interactions to the macromolecular machines of gene expression. Annu Rev Biophys Biomol Struct 36:79–105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Wang HC, Ho CH, Hsu KC et al (2014) DNA mimic proteins: functions, structures, and bioinformatic analysis. Biochemistry 53(18):2865–2874

    Article  CAS  PubMed  Google Scholar 

  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–W248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):S3

    Article  CAS  Google Scholar 

  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):S1

    Article  CAS  Google Scholar 

  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):696–708

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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)

  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):238–241

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Wong E, Wei CL (2009) ChIP’ing the mammalian genome: technical advances and insights into functional elements. Genome Med 1(9):89

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):1182–1189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):30–35

    Article  CAS  PubMed  Google Scholar 

  176. Xie Z, Hu S, Blackshaw S, Zhu H, Qian J (2010) hPDI: a database of experimental human protein–DNA interactions. Bioinformatics 26(2):287–289

    Article  CAS  PubMed  Google Scholar 

  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–W373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):192

    Article  CAS  PubMed Central  Google Scholar 

  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–W549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 44:144–153

    Article  CAS  Google Scholar 

  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 52:51–59

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

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

Author information

Author notes

  1. Abbasali Emamjomeh and Behzad Hajieghrari contributed equally.

Authors and Affiliations

  1. Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, 98615-538, Iran

    Abbasali Emamjomeh & Nafiseh MahdiNezhad

  2. Agricultural Biotechnology, Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran

    Darush Choobineh

  3. Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, 74135-111, Iran

    Behzad Hajieghrari

  4. Division of Human Genetics, Department of Anatomy, St. John’s hospital, Bangalore, India

    Amir Khodavirdipour

Authors
  1. Abbasali Emamjomeh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Darush Choobineh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Behzad Hajieghrari
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nafiseh MahdiNezhad
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Amir Khodavirdipour
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Abbasali Emamjomeh or Behzad Hajieghrari.

Ethics declarations

Conflict of interest

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

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Emamjomeh, A., Choobineh, D., Hajieghrari, B. et al. DNA–protein interaction: identification, prediction and data analysis. Mol Biol Rep 46, 3571–3596 (2019). https://doi.org/10.1007/s11033-019-04763-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-019-04763-1

Keywords

Search

Navigation