Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations

Olson, Wilma K.; Grosner, Michael A.; Czapla, Luke; Swigon, David

doi:10.1042/bst20120341

Cited by 9 publications

(19 citation statements)

References 33 publications

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“…Our recent studies of the structures of DNA loops mediated by the Lac repressor, the tetrameric protein assembly that controls the expression of lac genes in E. coli, show how the deformations of the double helix found in known high-resolution complexes of HU with DNA compensate for the intrinsic stiffness of short DNA (10,11). The random binding of the protein, at levels approximating those found in vivo, brings the predicted looping propensities in line with values deduced from geneexpression studies.…”

supporting

confidence: 53%

“…S5 and S6). The different proportions of HU give rise to a slight phase shift in the computed chain-length dependence of ring closure compared with that of bare DNA (11,12). The spacing of proteins at integral helical repeats allows the DNA to remain in the vicinity of its minimum-energy rest state.…”

Section: Resultsmentioning

confidence: 99%

“…Chains of these lengths tend to cyclize somewhat less easily (11,12) and to take up additional proteins upon ring closure (Fig. 1A).…”

Section: Resultsmentioning

confidence: 99%

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DNA topology confers sequence specificity to nonspecific architectural proteins

Juan

Czapla

Grosner

et al. 2014

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

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Topological constraints placed on short fragments of DNA change the disorder found in chain molecules randomly decorated by nonspecific, architectural proteins into tightly organized 3D structures. The bacterial heat-unstable (HU) protein builds up, counter to expectations, in greater quantities and at particular sites along simulated DNA minicircles and loops. Moreover, the placement of HU along loops with the "wild-type" spacing found in the Escherichia coli lactose (lac) and galactose (gal ) operons precludes access to key recognition elements on DNA. The HU protein introduces a unique spatial pathway in the DNA upon closure. The many ways in which the protein induces nearly the same closed circular configuration point to the statistical advantage of its nonspecificity. The rotational settings imposed on DNA by the repressor proteins, by contrast, introduce sequential specificity in HU placement, with the nonspecific protein accumulating at particular loci on the constrained duplex. Thus, an architectural protein with no discernible DNA sequencerecognizing features becomes site-specific and potentially assumes a functional role upon loop formation. The locations of HU on the closed DNA reflect long-range mechanical correlations. The protein responds to DNA shape and deformability-the stiff, naturally straight double-helical structure-rather than to the unique features of the constituent base pairs. The structures of the simulated loops suggest that HU architecture, like nucleosomal architecture, which modulates the ability of regulatory proteins to recognize their binding sites in the context of chromatin, may influence repressoroperator interactions in the context of the bacterial nucleoid.NA behaves differently in a cellular milieu than in aqueous salt solution. Proteins attach to widely spaced sites along genomic sequences in vivo and force the intervening DNA into loops much shorter in length than those expected from the natural deformational properties of the double helix. For example, the control of gene expression in Escherichia coli entails the formation of short DNA loops, some ∼100 bp steps in length, that preclude access of RNA polymerase to the signals needed to transcribe the enzymes encoded within various operons (1, 2). DNA of the same length tends to be highly extended in vitro, with very low chances of closing spontaneously into a loop (3, 4).Aside from the proteins that hold specific sequences at the ends of short DNA loops in place, the cellular environment includes a number of other components that influence the properties of DNA loops. For example, the naturally abundant, nonspecific E. coli heat-unstable (HU) protein plays important roles both in cellular processing and in shaping the architecture of the bacterial nucleoid. The dimeric protein introduces large deformations in DNA-sharp bends, helical untwisting, and helical axis dislocation (5)-that are central to its activity. The binding of HU to an AT-rich sequence element stabilizes loops important for repression of the galactose (ga...

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confidence: 53%

Section: Resultsmentioning

confidence: 99%

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DNA topology confers sequence specificity to nonspecific architectural proteins

Juan

Czapla

Grosner

et al. 2014

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

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“…In vivo factors that increase flexibility or compaction of DNA such as DNA supercoiling and nonspecific DNA-binding proteins that bend or bridge DNA, such as the nucleoid protein HU, are thought to enhance short-range DNA looping (8,(33)(34)(35)(36). It is not clear whether these factors also act at distances over which DNA bending and twisting are not limiting.…”

Section: Effect Of Separation On Long-range Looping By λ Repressor Inmentioning

confidence: 99%

Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors

Priest

Cui

Kumar

et al. 2013

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

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Efficient and specific interactions between proteins bound to the same DNA molecule can be dependent on the length of the DNA tether that connects them. Measurement of the strength of this DNA tethering effect has been largely confined to short separations between sites, and it is not clear how it contributes to longrange DNA looping interactions, such as occur over separations of tens to hundreds of kilobase pairs in vivo. Here, gene regulation experiments using the LacI and λ CI repressors, combined with mathematical modeling, were used to quantitate DNA tethering inside Escherichia coli cells over the 250-to 10,000-bp range. Although LacI and CI loop DNA in distinct ways, measurements of the tethering effect were very similar for both proteins. Tethering strength decreased with increasing separation, but even at 5-to 10-kb distances, was able to increase contact probability 10-to 20-fold and drive efficient looping. Tethering in vitro with the Lac repressor was measured for the same 600-to 3,200-bp DNAs using tethered particle motion, a single molecule technique, and was 5-to 45-fold weaker than in vivo over this range. Thus, the enhancement of looping seen previously in vivo at separations below 500 bp extends to large separations, underlining the need to understand how in vivo factors aid DNA looping. Our analysis also suggests how efficient and specific looping could be achieved over very long DNA separations, such as what occurs between enhancers and promoters in eukaryotic cells. j factor | TPM | promoter-enhancer I nteractions between proteins bound to separate sites on the same DNA molecule are critical in gene regulation and other DNA processes (1-4). The DNA separation between functionally interacting sites ranges from a few base pairs to hundreds of kilobase pairs, as in the case of some eukaryotic enhancers and their promoters. At short separations, it is clear that the DNA acts as a tether that keeps one site in the vicinity of the other so that the proteins at one site can find the other site in 3D space more efficiently than if they were free in solution (Fig. 1). Tethering is also a way to provide specificity because it aids interaction with linked sites but not unlinked sites. However, as the separation between the sites increases, this tethering effect becomes weaker, and it is not understood how the DNA linkage between widely separated sites, for example, between enhancers and promoters, provides the efficiency and specificity required for proper regulation.The effect of DNA tethering can be quantified by the factor j LOOP (M), the effective molar concentration of one site on the DNA relative to the other, or as the free energy of the DNA looping reaction ΔG LOOP (Fig. 1) (5-9). These parameters are interconvertible: ΔG LOOP = -RTlnj LOOP (kcal/mol; the reference j is 1 M). The formation of a naked DNA loop is in itself an energetically unfavorable reaction (ΔG LOOP is positive) under physiological conditions due to the enthalpic cost of DNA bending and twisting (particularly important for s...

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“…[19][20][21][22][23][24][25][26][27] The fact that their coarse-grained model was based on elastic forces made the realization of a great number of atoms possible. 28 Their numerical simulations revealed a number of interesting physical mechanisms, including HU-assisted loop formation 24,26 and DNA-directed sequence speci¯city of nonspeci¯c bending proteins. 25 However, all the above mentioned models did not reveal the mechanism underlying the HU cooperative clustering and the related topological patterns.…”

Section: Introductionmentioning

confidence: 99%

A stochastic reaction-diffusion model for protein aggregation on DNA

Voulgarakis

2017

Int. J. Mod. Phys. C

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Vital functions of DNA, such as transcription and packaging, depend on the proper clustering of proteins on the double strand. The present study investigates how the interplay between DNA allostery and electrostatic interactions a®ects protein clustering. The statistical analysis of a simple but transparent computational model reveals two major consequences of this interplay. First, depending on the protein and salt concentration, protein¯laments exhibit a bimodal DNA sti®ening and softening behavior. Second, within a certain domain of the control parameters, electrostatic interactions can cause energetic frustration that forces proteins to assemble in rigid spiral con¯gurations. Such spiral¯laments might trigger both positive and negative supercoiling, which can ultimately promote gene compaction and regulate the promoter. It has been experimentally shown that bacterial histone-like proteins assemble in similar spiral patterns and/or exhibit the same bimodal behavior. The proposed model can, thus, provide computational insights into the physical mechanisms used by proteins to control the mechanical properties of the DNA.

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Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations

Cited by 9 publications

References 33 publications

DNA topology confers sequence specificity to nonspecific architectural proteins

DNA topology confers sequence specificity to nonspecific architectural proteins

Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors

A stochastic reaction-diffusion model for protein aggregation on DNA

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