Protein–DNA Complexes: Nonspecific

Abstract

Nonspecific protein–DNA complexes form largely independently of deoxyribonucleic acid (DNA) sequence or structure. Typically, the thermodynamic driving force for forming these complexes is electrostatic due to the polyelectrolyte (polyanionic) nature of the DNA.

Keywords: nonspecific binding; cooperativity; protein–nucleic interactions; polyelectrolyte effect

Figure 1.

Comparison of the Lac repressor DNA binding domain (DBD) dimer – nonoperator and operator DNA complexes. (a) When binding to a nonoperator (‘nonspecific’) DNA sequence (black), the helix‐turn‐helix motif of each DBD (purple) forms a network of electrostatic and hydrogen bond interactions primarily with the DNA phosphate backbone. Residues 50–58 (cyan) are disordered and the structure of the DNA site is unaltered. (b) In the complex formed between the repressor DBD and its highest affinity DNA operator sequence (Osym), the helix‐turn‐helix motif docks in the major grooves, making extensive contacts to base functional groups and the DNA backbone. On binding, both the protein and DNA undergo significant conformational changes. Residues 50–58, which are disordered in the free protein, fold into an α helix called the hinge helix. To accommodate two hinge helices, the minor groove widens, causing a ∼40° bend in the DNA (PDB file 1CJG; see Kalodimos et al., ). Figure a drawn from Protein Databank file 1OSL; see Kalodimos CG, Boelens R and Kaptein R () Toward an integrated model of protein–DNA recognition as inferred from NMR studies on the Lac repressor system. Chemical Reviews140: 3567–3586. Figure b drawn from Protein Databank File 1CJG; see Spronk CA, Bonvin AM, Radha PK et al. (1999) The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator. Structure7: 1483–1492.

Figure 2.

Structure of the single‐stranded DNA binding protein (SSB) from E. coli bound to two DNA (dC35) oligomers. SSB forms a tetramer of identical subunits (coloured orange, green, yellow and blue). The structure reveals that on binding, the DNA backbone (shown as a black ribbon) wraps in the surface grooves of SSB monomers with many of the bases (shown as sticks) unstacked. Some the bases of the oligomer are not resolved in the structure; this disorder is consistent with the nature of a semi‐loosely associated nonspecific complex. Figure drawn from Protein Databank file 1EYG; see Raghunathan S, Kozlov, AG, Lohman, TM and Waksman G () Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nature Structural Biology7: 648–652.

Figure 3.

Histone–DNA Interactions. Arginine (red) – minor groove interactions are highlighted. While arginine side chains are observed to uniformly penetrate the minor groove, no hydrogen bonds are formed with base functional groups. Instead, favourable electrostatic interactions allow the minor groove to narrow, causing the DNA to bend and wrap on the surface of the histone octamer. Figure drawn from Protein Databank file 1KX5; see Davey CA, Sargent DF, Luger K, Maeder AW and Richmond TJ () Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. Journal of Molecular Biology319:1097–1113.

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References

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Further Reading

Grayling RA, Sandman K and Reeve JN (1996) DNA stability and DNA binding proteins. Advances in Protein Chemistry 48: 437–467.

Kowalczykowski SC and Eggleston AK (1994) Homologous pairing and DNA‐strand exchange proteins. Annual Review of Biochemistry 63: 991–1043.

Lohman TM and Ferrari ME (1994) E. coli single‐stranded DNA‐binding protein: multiple DNA‐binding modes and cooperativities. Annual Review of Biochemistry 63: 527–570.

Lohman TM and Mascotti DP (1992) Thermodynamics of ligand–nucleic acid interactions. Methods in Enzymology 212: 400–424.

Lohman TM and Mascotti DP (1992) Nonspecific ligand–nucleic acid binding parameters by fluorescence methods. Methods in Enzymology 212: 424–458.

Record MT Jr, Zhang W and Anderson CF (1998) Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Advances in Protein Chemistry 51: 281–353.

Revzin A (ed.) (1990) The Biology of Nonspecific DNA–Protein Interactions. Boca Raton: FL: CRC Press.

Von Hippel P (2007) From ‘simple’ DNA‐protein interactions to the macromolecular machines of gene expression. Annual Review of Biophysics and Biomolecular Structure 36: 79–105.

Wold MS (1997) Replication protein A: a heterotrimeric, single‐stranded DNA‐binding protein required for eukaryotic DNA metabolism. Annual Review of Biochemistry 66: 61–92.

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Saecker, Ruth M(Sep 2007) Protein–DNA Complexes: Nonspecific. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001358.pub2]