Exploring the energetics of histone H1.1 and H1.4 duplex DNA interactions

Machha, Venkata R.; Jones, S.; Waddle, J R; Le, Vu; Wellman, Susan E.; Lewis, Edwin A.

doi:10.1016/j.bpc.2013.11.007

Cited by 4 publications

(9 citation statements)

References 37 publications

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“…The entropy-driven binding observed here is comparable to the binding thermodynamics of histone/DNA complexes 27 and could be due to GOx(n) displacing DNA-bound water molecules from the grooves. In that case, the data suggest that a minimum charge value (n = +30) is required for this kind of binding and overcoming local charge repulsion contexts.…”

Section: ■ Discussionsupporting

confidence: 58%

“…Previous work that studied the effect of increased protein concentration on DNA in histone/DNA complexes reported comparable decreased DNA CD intensity 26 or red-shifting of the DNA far-UV peak in addition to decreased DNA CD intensity. 27 Here, DNA signal intensity was comparable to DNA alone when 0.3 μM GOx(+50) was complexed to DNA but DNA signal intensity decreased by approximately 40% when compared to DNA alone if 0.6 μM GOx(+50) was added and there was an additional 25% reduction in DNA intensity when 0.9 μM GOx(+50) was added, resulting in a total reduction in DNA CD intensity of about 65% (Figure 4B). The effect of charge was studied by variation of n in the GOx(n) derivatives.…”

Section: ■ Discussionmentioning

confidence: 85%

“…The effect of increased GOx( n ) concentration on DNA helicity indicated decreased DNA intensity. Previous work that studied the effect of increased protein concentration on DNA in histone/DNA complexes reported comparable decreased DNA CD intensity or red-shifting of the DNA far-UV peak in addition to decreased DNA CD intensity …”

Section: Discussionmentioning

confidence: 85%

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Designer Histone Complexes: Controlling Protein–DNA Interactions with Protein Charge as an “All-or-None” Digital Switch

2016

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An artificial histone is synthesized that functions as a DNA-protein digital switch, where DNA binding is all or none, controlled by a sharp threshold of protein charge. A non-DNA-binding protein, glucose oxidase (GOx), was chemically modified by attaching an increasing number of triethylenetetramine (TETA) side chains to its glutamate/aspartate groups to obtain a small library of covalently modified GOx(n) derivatives. The parameter n denotes the net charge on the protein at pH 7, which was increased from -62 (pristine GOx) to +75 by attaching an increasing number of TETA residues to the protein. All GOx(n) derivatives retained their secondary structure to a good extent, as monitored by UV circular dichroism (CD) spectroscopy, and they also retained oxidase activities to a significant extent. The interaction of the GOx(n) with calf thymus DNA was examined by isothermal titration calorimetry (ITC). Pristine GOx of -62 charge at pH 7 in 10 mM Tris-HCl and 50 mM NaCl buffer had no affinity for the negatively charged DNA helix, and GOx(n) with n < +30 had no affinity for DNA either. However, binding has been turned on abruptly when n ≥ +30 with binding constants (K) ranging from (1.5 ± 0.7) × 10 to (7.3 ± 2.8) × 10 M for n values of +30 and +75, respectively, and this type of "all-or-none" binding based on protein charge is intriguing. Furthermore, thermodynamic analysis of the titration data revealed that binding is entirely entropy-driven with ΔS ranging from 0.09 ± 0.007 to 0.19 ± 0.008 kcal/mol K with enthalpic penalties of 17.0 ± 2.3 and 46.1 ± 2.1 kcal/mol, respectively. The binding had intrinsic propensities (ΔG) ranging from -9.8 ± 0.14 to -10.7 ± 0.25 kcal/mol, independent of n. DNA binding distorted protein-DNA secondary structure, as evidenced by CD spectroscopy, but oxidase activity of GOx(n)/DNA complexes has been unaffected. This is the very first example of an artificial histone (GOx(n)) where the protein charge functioned as a DNA-binding switch; protein charge is in turn under complete chemical control while preserving the biological activity of the protein. The new insight gained here could be useful in the design of novel "on-off" protein switches.

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Section: ■ Discussionsupporting

confidence: 58%

Section: ■ Discussionmentioning

confidence: 85%

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Designer Histone Complexes: Controlling Protein–DNA Interactions with Protein Charge as an “All-or-None” Digital Switch

2016

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“…Previous studies of the binding of the related mouse subtypes H1.1, H1 0 , and H1.4 to short dsDNA using isothermal titration calorimetry (ITC) reported a K d of ca. 100 nM, and a DNA site size of 32 bp to 36 bp for the full-length proteins and 28 bp for the Cterminal tail of H1 0 (29,30). [A similar value of 24 bp was reported for the average spacing of H1 molecules in complexes of two duplexes bridged by a cooperatively bound array of H1 molecules (31).]…”

Section: Resultsmentioning

confidence: 56%

“…Recombinant chicken histone H1 subtype H1.11L and CH1 (residues 115 to 225) were purified (4) and phosphorylated (47). Oligonucleotides were based on 36-mer dsDNAs (30). ITC data were fit to a one-site model in Origin, or to a two-step sequential process based on the Multiple Non-Interacting Sites model developed to fit two-site processes where K d,2 < K d,1 (48).…”

Section: Methodsmentioning

confidence: 99%

Highly disordered histone H1−DNA model complexes and their condensates

Turner

Watson

Wilkins

et al. 2018

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

165

162

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Disordered proteins play an essential role in a wide variety of biological processes, and are often posttranslationally modified. One such protein is histone H1; its highly disordered C-terminal tail (CH1) condenses internucleosomal linker DNA in chromatin in a way that is still poorly understood. Moreover, CH1 is phosphorylated in a cell cycle-dependent manner that correlates with changes in the chromatin condensation level. Here we present a model system that recapitulates key aspects of the in vivo process, and also allows a detailed structural and biophysical analysis of the stages before and after condensation. CH1 remains disordered in the DNA-bound state, despite its nanomolar affinity. Phase-separated droplets (coacervates) form, containing higher-order assemblies of CH1/DNA complexes. Phosphorylation at three serine residues, spaced along the length of the tail, has little effect on the local properties of the condensate. However, it dramatically alters higher-order structure in the coacervate and reduces partitioning to the coacervate phase. These observations show that disordered proteins can bind tightly to DNA without a disorder-to-order transition. Importantly, they also provide mechanistic insights into how higher-order structures can be exquisitely sensitive to perturbation by posttranslational modifications, thus broadening the repertoire of mechanisms that might regulate chromatin and other macromolecular assemblies.

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