title: A model of H-NS mediated compaction of bacterial DNA.
abstract: The histone-like nucleoid structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. H-NS can bind to DNA in two different ways: in trans, by binding to two separate DNA duplexes, or in cis, by binding to different sites on the same duplex. Based on scanning force microscopy imaging and optical trap-driven unzipping assays, it has recently been suggested that DNA compaction may result from the antagonistic effects of H-NS binding to DNA in trans and cis configurations. To get more insight into the compaction mechanism, we constructed a coarse-grained model description of the compaction of bacterial DNA by H-NS. These simulations highlight the fact that DNA compaction indeed results from the subtle equilibrium between several competing factors, which include the deformation dynamics of the plasmid and the several binding modes of protein dimers to DNA, i.e., dangling configurations, cis- and trans-binding. In particular, the degree of compaction is extremely sensitive to the difference in binding energies of the cis and trans configurations. Our simulations also point out that the conformations of the DNA-protein complexes are significantly different in bulk and in planar conditions, suggesting that conformations observed on mica surfaces may differ significantly from those that prevail in living cells.
authors.affiliation: Laboratoire Interdisciplinaire de Physique, Centre National de la Recherche Scientifique UMR5588, Université Joseph Fourier Grenoble 1, St. Martin d'Hères, France. marc.joyeux@ujf-grenoble.fr
authors.forename: Marc
authors.initials: M
authors.lastname: Joyeux
authors.forename: Jocelyne
authors.initials: J
authors.lastname: Vreede
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; C031908:H-NS protein, bacteria
references.citation: J Mol Biol. 2006 Dec 8;364(4):777-98
references.pmid: 17045294
references.citation: Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15728-32
references.pmid: 20798056
references.citation: Science. 2006 Jul 14;313(5784):236-8
references.pmid: 16763111
references.citation: Biopolymers. 1995 Mar;35(3):289-96
references.pmid: 7703374
references.citation: Genes Dev. 2010 Feb 15;24(4):339-44
references.pmid: 20159954
references.citation: Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10690-5
references.pmid: 21673140
references.citation: J Mol Biol. 1996 Oct 25;263(2):149-62
references.pmid: 8913298
references.citation: Science. 2011 Sep 9;333(6048):1445-9
references.pmid: 21903814
references.citation: J Biol Chem. 2000 Jan 14;275(2):729-34
references.pmid: 10625601
references.citation: Biophys J. 2009 Oct 7;97(7):1997-2003
references.pmid: 19804731
references.citation: J Phys Chem A. 2010 Sep 16;114(36):9662-72
references.pmid: 20394450
references.citation: Nat Struct Mol Biol. 2007 May;14(5):441-8
references.pmid: 17435766
references.citation: Trends Microbiol. 1999 Mar;7(3):124-8
references.pmid: 10203842
references.citation: Nat Struct Biol. 2003 Mar;10(3):212-8
references.pmid: 12592399
references.citation: Biochem J. 2005 Oct 15;391(Pt 2):203-13
references.pmid: 15966862
references.citation: J Mol Biol. 1996 Dec 20;264(5):919-32
references.pmid: 9000621
references.citation: J Chem Phys. 2011 Sep 28;135(12):125104
references.pmid: 21974563
references.citation: EMBO J. 1998 Dec 1;17(23):7033-43
references.pmid: 9843508
references.citation: Curr Opin Microbiol. 2010 Dec;13(6):773-80
references.pmid: 20951079
references.citation: J Chem Phys. 2009 Jan 7;130(1):015103
references.pmid: 19140636
references.citation: Crit Rev Biochem Mol Biol. 2008 Mar-Apr;43(2):89-134
references.pmid: 18365861
references.citation: Nucleic Acids Res. 2000 Sep 15;28(18):3504-10
references.pmid: 10982869
references.citation: Nucleic Acids Res. 2012 Apr;40(8):3316-28
references.pmid: 22187157
references.citation: J Bacteriol. 2009 Feb;191(3):1106-10
references.pmid: 19011022
references.citation: J Mol Biol. 2002 Dec 6;324(4):841-50
references.pmid: 12460581
references.citation: J Mol Biol. 2008 Oct 3;382(2):353-70
references.pmid: 18586040
references.citation: PLoS Pathog. 2006 Aug;2(8):e81
references.pmid: 16933988
references.citation: Nature. 2006 Nov 16;444(7117):387-90
references.pmid: 17108966
references.citation: J Biomol Struct Dyn. 1985 Feb;2(5):1005-12
references.pmid: 3916932
references.citation: Mol Microbiol. 2000 May;36(4):962-72
references.pmid: 10844682
references.citation: Mol Microbiol. 2005 May;56(4):858-70
references.pmid: 15853876
references.citation: Biopolymers. 1977 Jul;16(7):1435-48
references.pmid: 880366
references.citation: Mol Microbiol. 2001 Apr;40(1):20-36
references.pmid: 11298273
references.citation: Mol Microbiol. 2010 Jun 1;76(5):1250-65
references.pmid: 20444106
references.citation: Crit Rev Biochem Mol Biol. 2008 Nov-Dec;43(6):393-418
references.pmid: 19037758
references.citation: Biophys J. 2009 Dec 2;97(11):2993-9
references.pmid: 19948129