Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn

Rice, Phoebe A.; Yang, Shu-Wei; Mizuuchi, Kiyoshi; Nash, Howard A.

doi:10.1016/s0092-8674(00)81824-3

Cited by 781 publications

(941 citation statements)

References 56 publications

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“…Structures of HMGB/DNA complexes suggest that induced flexibility would likely be anisotropic [14;16]. HMGB proteins share some features with bacterial IHF [43] and X-ray structures of complexes of the similar HU protein with DNA suggest that a range of induced DNA bend angles are possible [44]. Results from atomic force microscopy for DNA/ HU complexes also suggest a range of protein-induced bend angles rather than a fixed geometry [42].…”

Section: Hmgb Mechanismsmentioning

confidence: 99%

Transient HMGB protein interactions with B-DNA duplexes and complexes

Zimmerman

Maher

2008

Biochemical and Biophysical Research Communications

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HMGB proteins are abundant, non-histone proteins in eukaryotic chromatin. HMGB proteins contain one or two conserved "HMG boxes" and can be sequence specific or nonspecific in their DNA binding. HMGB proteins cause strong DNA bending and bind preferentially to deformed DNAs. We wish to understand how HMGB proteins increase the apparent flexibility of non-distorted B-form DNA. We test the hypothesis that HMGB proteins bind transiently, creating an ensemble of distorted DNAs with rapidly-interconverting conformations. We show that binding of B-form DNA by HMGB proteins is both weak and transient under conditions where DNA cyclization is strongly enhanced. We also detect novel complexes in which HMGB proteins simultaneously bind more than one DNA duplex.Double-stranded DNA is among the least flexible biopolymers. The local stiffness of DNA is reflected in its persistence length, P, (~150 bp) [1]. The global flexibility of naked DNA in solution is insufficient to allow the degree of compaction required for packaging within cells, or for deformed structures involved in DNA replication, recombination, and transcriptional control. While some controversy exists concerning the accuracy of predictive models for DNA flexibility over short lengths [2;3;4], it is clear that short lengths of DNA require proteins to induce strongly bent and looped conformations.The apparent physical properties of DNA may differ in vitro and in vivo [5;6]. Activation over short distances in assays of eukaryotic transcription activation in vitro raised the possibility of apparent DNA flexibility enhancement by nuclear factors [7]. Indeed, heat-resistant HMGB proteins in nuclear extracts were found to dramatically enhance the cyclization of short DNA restriction fragments by DNA ligase [8].Eukaryotic HMGB proteins are abundant small non-histone chromosomal proteins [9;10;11; 12] that share one or two copies of an ~80-amino acid HMG box domain. Fig. 1A shows the amino acid alignment of HMG box domains, illustrating the partial conservation of intercalating residues [13]. As shown in Fig. 1B, this domain specifies three α-helices (red) whose L-shaped fold engages one face of DNA while delivering one or two intercalating residues into the minor groove [14;15;16]. Biophysical studies have provided some insights into the thermodynamic basis of DNA binding [17;18;19;20]. HMGB proteins to induce DNA kinking or bending of 22;23;24;25], and bind preferentially to distorted DNA structures [16;21;26]. HMGB proteins may stabilize DNA bending either by *To whom correspondence should be addressed at maher@mayo.edu. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all l...

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Section: Hmgb Mechanismsmentioning

confidence: 99%

Transient HMGB protein interactions with B-DNA duplexes and complexes

Zimmerman

Maher

2008

Biochemical and Biophysical Research Communications

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“…IHF bends DNA by 1608 [Rice et al, 1996;Lorenz et al, 1999], and this ability to induce topological changes might be relevant for nucleoid organization. In fact, a single-molecule study demonstrated that binding of IHF to multiple sites could condense linear DNA into a more compact, but randomly coiled structure [Ali et al, 2001].…”

Section: Mechansims Of Nucleoid Organizationmentioning

confidence: 99%

The bacterial nucleoid: A highly organized and dynamic structure

Thanbichler

Wang

Shapiro

2005

J of Cellular Biochemistry

122

101

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Recent advances in bacterial cell biology have revealed unanticipated structural and functional complexity, reminiscent of eukaryotic cells. Particular progress has been made in understanding the structure, replication, and segregation of the bacterial chromosome. It emerged that multiple mechanisms cooperate to establish a dynamic assembly of supercoiled domains, which are stacked in consecutive order to adopt a defined higher-level organization. The position of genetic loci on the chromosome is thereby linearly correlated with their position in the cell. SMC complexes and histone-like proteins continuously remodel the nucleoid to reconcile chromatin compaction with DNA replication and gene regulation. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress.

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“…A dramatic distortion of the canonical double-helix structure is observed in several DNAprotein complexes that bend DNA, sometimes by nearly 160°o ver a few helical turns (3)(4)(5)(6)(7)(8). The energetic costs of DNA bending on such short lengths is compensated by very specific interactions between protein and DNA that lower the free energy of the complex.…”

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confidence: 99%

Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF

Kuznetsov¹,

Sugimura

Vivas³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Regulation of gene expression involves formation of specific protein-DNA complexes in which the DNA is often bent or sharply kinked. Kinetics measurements of DNA bending when in complex with the protein are essential for understanding the molecular mechanism that leads to precise recognition of specific DNAbinding sites. Previous kinetics measurements on several DNAbending proteins used stopped-flow techniques that have limited time resolution of few milliseconds. Here we use a nanosecond laser temperature-jump apparatus to probe, with submillisecond time resolution, the kinetics of bending͞unbending of a DNA substrate bound to integration host factor (IHF), an architectural protein from Escherichia coli. The kinetics are monitored with time-resolved FRET, with the DNA substrates end-labeled with a FRET pair. The temperature-jump measurements, in combination with stopped-flow measurements, demonstrate that the binding of IHF to its cognate DNA site involves an intermediate state with straight or, possibly, partially bent DNA. The DNA bending rates range from Ϸ2 ms ؊1 at Ϸ37°C to Ϸ40 ms ؊1 at Ϸ10°C and correspond to an activation energy of Ϸ14 ؎ 3 kcal͞mol. These rates and activation energy are similar to those of a single A:T base pair opening inside duplex DNA. Thus, our results suggest that spontaneous thermal disruption in base-paring, nucleated at an A:T site, may be sufficient to overcome the free energy barrier needed to partially bend͞kink DNA before forming a tight complex with IHF.DNA bending kinetics ͉ laser temperature jump ͉ protein-DNA interactions ͉ time-resolved FRET measurements

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Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn

Cited by 781 publications

References 56 publications

Transient HMGB protein interactions with B-DNA duplexes and complexes

Transient HMGB protein interactions with B-DNA duplexes and complexes

The bacterial nucleoid: A highly organized and dynamic structure

Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF

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