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Model of a DNA-protein complex of the architectural monomeric protein MC1 from Euryarchaea.

Paquet F, Delalande O, Goffinont S, Culard F, Loth K, Asseline U, Castaing B, Landon C - PLoS ONE (2014)

Bottom Line: The polarity of protein binding was determined using paramagnetic probes attached to the DNA.The first structural model of the DNA-MC1 complex we propose here was obtained by two complementary docking approaches and is in good agreement with the experimental data previously provided by electron microscopy and biochemistry.It was found that the Arg25 side-chain was essential to neutralize the negative charge of two phosphates that come very close in response to a dramatic curvature of the DNA.

View Article: PubMed Central - PubMed

Affiliation: Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France.

ABSTRACT
In Archaea the two major modes of DNA packaging are wrapping by histone proteins or bending by architectural non-histone proteins. To supplement our knowledge about the binding mode of the different DNA-bending proteins observed across the three domains of life, we present here the first model of a complex in which the monomeric Methanogen Chromosomal protein 1 (MC1) from Euryarchaea binds to the concave side of a strongly bent DNA. In laboratory growth conditions MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55. Like most proteins that strongly bend DNA, MC1 is known to bind in the minor groove. Interaction areas for MC1 and DNA were mapped by Nuclear Magnetic Resonance (NMR) data. The polarity of protein binding was determined using paramagnetic probes attached to the DNA. The first structural model of the DNA-MC1 complex we propose here was obtained by two complementary docking approaches and is in good agreement with the experimental data previously provided by electron microscopy and biochemistry. Residues essential to DNA-binding and -bending were highlighted and confirmed by site-directed mutagenesis. It was found that the Arg25 side-chain was essential to neutralize the negative charge of two phosphates that come very close in response to a dramatic curvature of the DNA.

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Representative 3D-structures of complexes with DNA-bending proteins among the three domains of life.The dimeric bacterial protein IHF (PDB 1IHF) and the monomeric Euryarchaeal protein MC1 contact the concave side of the DNA curvature. In Eukaryota and Crenarchaea subdomain the proteins SRY (HMG-box protein) (PDB 1J46), Sul7d (PDB 1AZP) and Cren7 (PDB 3KXT) contact the convex side of the DNA curvature.
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pone-0088809-g006: Representative 3D-structures of complexes with DNA-bending proteins among the three domains of life.The dimeric bacterial protein IHF (PDB 1IHF) and the monomeric Euryarchaeal protein MC1 contact the concave side of the DNA curvature. In Eukaryota and Crenarchaea subdomain the proteins SRY (HMG-box protein) (PDB 1J46), Sul7d (PDB 1AZP) and Cren7 (PDB 3KXT) contact the convex side of the DNA curvature.

Mentions: Our experimental results converge to a protein/DNA model, in which the monomeric protein MC1 interacts on the concave side of a strongly bent DNA: 1) MC1 bears structural similarities to the small basic architectural proteins Sul7d and Cren7, belonging to the Sulfolobus strains of the Crenarchaea subdomain [37], [38], and interacts with the DNA minor groove. However, the later proteins bind on the convex side of the DNA curvature (Figure 6); and 2) Protein interactions with the concave side of DNA curvature have only been observed so far for dimeric proteins, such as histone-like HU or IHF, bound to U-shape DNA [39] (Figure 6). DNA-MC1 recognition is probably based on the shape readout such as minor groove narrowing, kink and bending [40]. Slight differences in minor groove shape, leading to slight differences in electrostatic potential may allow a fine grained recognition [41].


Model of a DNA-protein complex of the architectural monomeric protein MC1 from Euryarchaea.

Paquet F, Delalande O, Goffinont S, Culard F, Loth K, Asseline U, Castaing B, Landon C - PLoS ONE (2014)

Representative 3D-structures of complexes with DNA-bending proteins among the three domains of life.The dimeric bacterial protein IHF (PDB 1IHF) and the monomeric Euryarchaeal protein MC1 contact the concave side of the DNA curvature. In Eukaryota and Crenarchaea subdomain the proteins SRY (HMG-box protein) (PDB 1J46), Sul7d (PDB 1AZP) and Cren7 (PDB 3KXT) contact the convex side of the DNA curvature.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3928310&req=5

pone-0088809-g006: Representative 3D-structures of complexes with DNA-bending proteins among the three domains of life.The dimeric bacterial protein IHF (PDB 1IHF) and the monomeric Euryarchaeal protein MC1 contact the concave side of the DNA curvature. In Eukaryota and Crenarchaea subdomain the proteins SRY (HMG-box protein) (PDB 1J46), Sul7d (PDB 1AZP) and Cren7 (PDB 3KXT) contact the convex side of the DNA curvature.
Mentions: Our experimental results converge to a protein/DNA model, in which the monomeric protein MC1 interacts on the concave side of a strongly bent DNA: 1) MC1 bears structural similarities to the small basic architectural proteins Sul7d and Cren7, belonging to the Sulfolobus strains of the Crenarchaea subdomain [37], [38], and interacts with the DNA minor groove. However, the later proteins bind on the convex side of the DNA curvature (Figure 6); and 2) Protein interactions with the concave side of DNA curvature have only been observed so far for dimeric proteins, such as histone-like HU or IHF, bound to U-shape DNA [39] (Figure 6). DNA-MC1 recognition is probably based on the shape readout such as minor groove narrowing, kink and bending [40]. Slight differences in minor groove shape, leading to slight differences in electrostatic potential may allow a fine grained recognition [41].

Bottom Line: The polarity of protein binding was determined using paramagnetic probes attached to the DNA.The first structural model of the DNA-MC1 complex we propose here was obtained by two complementary docking approaches and is in good agreement with the experimental data previously provided by electron microscopy and biochemistry.It was found that the Arg25 side-chain was essential to neutralize the negative charge of two phosphates that come very close in response to a dramatic curvature of the DNA.

View Article: PubMed Central - PubMed

Affiliation: Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France.

ABSTRACT
In Archaea the two major modes of DNA packaging are wrapping by histone proteins or bending by architectural non-histone proteins. To supplement our knowledge about the binding mode of the different DNA-bending proteins observed across the three domains of life, we present here the first model of a complex in which the monomeric Methanogen Chromosomal protein 1 (MC1) from Euryarchaea binds to the concave side of a strongly bent DNA. In laboratory growth conditions MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55. Like most proteins that strongly bend DNA, MC1 is known to bind in the minor groove. Interaction areas for MC1 and DNA were mapped by Nuclear Magnetic Resonance (NMR) data. The polarity of protein binding was determined using paramagnetic probes attached to the DNA. The first structural model of the DNA-MC1 complex we propose here was obtained by two complementary docking approaches and is in good agreement with the experimental data previously provided by electron microscopy and biochemistry. Residues essential to DNA-binding and -bending were highlighted and confirmed by site-directed mutagenesis. It was found that the Arg25 side-chain was essential to neutralize the negative charge of two phosphates that come very close in response to a dramatic curvature of the DNA.

Show MeSH
Related in: MedlinePlus