Left-handed Superhelix Research Articles

Thermodynamics of nucleosome breathing and positioning.

Nucleosomes are fundamental units of chromatin in which a length of genomic DNA is wrapped around a histone octamer spool in a left-handed superhelix. Large-scale nucleosome maps show a wide distribution of DNA wrapping lengths, which in some cases are tens of base pairs (bp) shorter than the 147bp canonical wrapping length observed in nucleosome crystal structures. Here, we develop a thermodynamic model that assumes a constant free energy cost of unwrapping a nucleosomal bp. Our model also incorporates linker DNA-short DNA segments between neighboring nucleosomes imposed by the folding of nucleosome arrays into chromatin fibers and other higher-order chromatin structures. We use this model to study nucleosome positioning and occupancy in the presence of nucleosome "breathing"-partial unwrapping and rewrapping of nucleosomal DNA due to interactions with the neighboring particles. We find that, as the unwrapping cost per bp and the chemical potential are varied, the nucleosome arrays are characterized by three distinct states, with low, intermediate, and high densities. The transition between the latter two states proceeds through an equiprobable state in which all nucleosome wrapping lengths are equally likely. We study the equiprobable state theoretically using a mean-field approach, obtaining an excellent agreement with numerical simulations. Finally, we use our model to reproduce S. cerevisiae nucleosome occupancy profiles observed in the vicinity of transcription start sites, as well as genome-wide distributions of nucleosome wrapping lengths. Overall, our results highlight the key role of partial nucleosome unwrapping in shaping the genome-wide patterns of nucleosome positioning and occupancy.

Macroscopic Helical Assembly of One-Dimensional Coordination Polymers: Helicity Inversion Triggered by Solvent Isomerism.

Assembling macroscopic helices with controllable chirality and understanding their formation mechanism are highly desirable but challenging tasks for artificial systems, especially coordination polymers. Here, we utilize solvents as an effective tool to induce the formation of macroscopic helices of chiral coordination polymers (CPs) and manipulate their helical sense. We chose the Ni/R-,S-BrpempH2 system with a one-dimensional tubular structure, where R-,S-BrpempH2 stands for R-,S-(1-(4-bromophenyl)ethylaminomethylphosphonic acid). The morphology of the self-assemblies can be controlled by varying the cosolvent in water, resulting in the formation of twisted ribbons of R-,S-Ni(Brpemp)(H2O)·H2O (R-,S-2T) in pure H2O; needle-like crystals of R-,S-Ni(Brpemp)(H2O)2·1/3CH3CN (R-,S-1C) in 20 vol % CH3CN/H2O; nanofibers of R-,S-Ni(Brpemp)(H2O)·H2O (R-,S-3F) in 20-40 vol % methanol/H2O or ethanol/H2O; and superhelices of R-,S-Ni(Brpemp)(H2O)·H2O (R-,S-4H or 5H) in 40 vol % propanol/H2O. Interestingly, the helicity of the superhelix can be controlled by using a propanol isomer in water. For the Ni/R-BrpempH2 system, a left-handed superhelix of R-4H(M) was obtained in 40 vol % NPA/H2O, while a right-handed superhelix of R-5H(P) was isolated in 40 vol % IPA/H2O. These results were rationalized by theoretical calculations. Adsorption studies revealed the chiral recognition behavior of these compounds. This work may contribute to the development of chiral CPs with a macroscopic helical morphology and interesting functionalities.

PH and Salt-Assisted Macroscopic Chirality Inversion of Gadolinium Coordination Polymer.

The precise adjustment of handedness of helical architectures is important to regulate their functions. Macroscopic chirality inversion has been achieved in organic supramolecular systems by pH, metal ions, solvents, chiral and non-chiral additives, temperature, and light, but rarely in coordination polymers (CPs). In particular, salt-assisted macroscopic chirality inversion has not been reported. In this work, we carried out a systematic investigation on the role of pH and salt in regulating the morphology of CPs based on Gd(NO3)3 and R-(1-phenylethylamino)methylphosphonic acid (R-pempH2). Without extra NO3-, the chirality inversion from the left-handed superhelix R-M to the right-handed superhelix R-P can be achieved by pH modulation from 3.2 to 3.8. The addition of NaNO3 (2.0 eq) at pH 3.8 results in an inversion of chiral sense from R-P to R-M as a pure phase. To our knowledge, this is the first example of salt-assisted macroscopic helical inversion in artificial systems.

The giant mimivirus 1.2 Mb genome is elegantly organized into a 30-nm diameter helical protein shield.

Mimivirus is the prototype of the Mimiviridae family of giant dsDNA viruses. Little is known about the organization of the 1.2 Mb genome inside the membrane-limited nucleoid filling the ~0.5 µm icosahedral capsids. Cryo-electron microscopy, cryo-electron tomography, and proteomics revealed that it is encased into a ~30-nm diameter helical protein shell surprisingly composed of two GMC-type oxidoreductases, which also form the glycosylated fibrils decorating the capsid. The genome is arranged in 5- or 6-start left-handed super-helices, with each DNA-strand lining the central channel. This luminal channel of the nucleoprotein fiber is wide enough to accommodate oxidative stress proteins and RNA polymerase subunits identified by proteomics. Such elegant supramolecular organization would represent a remarkable evolutionary strategy for packaging and protecting the genome, in a state ready for immediate transcription upon unwinding in the host cytoplasm. The parsimonious use of the same protein in two unrelated substructures of the virion is unexpected for a giant virus with thousand genes at its disposal.

Helically Grooved Gold Nanoarrows: Controlled Fabrication, Superhelix, and Transcribed Chiroptical Switching

Plasmonic chiroptical materials, coupled by chirality and surface plasmons, have been attracting great interest due to their potential applications, such as photonics, chiral recognition, asymmetri...

Chromatin fibers stabilize nucleosomes under torsional stress

Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of 167 and 197. We find that both types of fibers fold into a left-handed superhelix that can be stabilized by positive torsion. We observe that the structural changes induced by twist were reversible, indicating that chromatin has a large degree of elasticity. Our direct measurements of torque confirmed the hypothesis of chromatin fibers as a twist buffer. Using a statistical mechanics-based torsional spring model, we extracted values of the chromatin twist modulus and the linking number per stacked nucleosome that were in good agreement with values measured here experimentally. Overall, our findings indicate that the supercoiling generated by DNA-processing enzymes, predicted by the twin-supercoiled domain model, can be largely accommodated by the higher-order structure of chromatin.

TMB Library of Nucleosome Simulations.

Nucleosomes are the fundamental building blocks of chromatin, the biomaterial that houses the genome in all higher organisms. A nucleosome consists of 145-147 base pairs of DNA wrapped 1.7 times around eight histones. Given a four-letter code (A, C, G, T), there are approximately 4147 or 1088 oligonucleotides that can form a nucleosome. Comparative, rather than comprehensive, studies are required. Here we introduce the TMB Library of nucleosome simulations and present a meta-analysis of over 20 μs of all atom molecular dynamics simulations representing 518 different realizations of the nucleosome. The TMB Library serves as a reference for future comparative, on-demand simulations of nucleosomes and a demonstration of iBIOMES Lite as a tool for managing a laboratory's simulation library. For every simulation, dewatered trajectories, RMSD, and DNA helical parameter data are provided through iBIOMES Lite in a Web browser and a file browser format. A novel view of nucleosomal DNA emerges from our meta-analysis of the TMB Library. DNA conformation is restricted to a specific left-handed superhelix, but the range of conformations observed for individual bases and base pairs is not more restricted nor more highly deformed than DNA free in solution. With the exception of Roll, mean DNA helical parameter values obtained from simulations of nucleosomes are largely within the range of thermal motion of DNA free in solution. The library provides evidence of DNA kinking in the nucleosome and clearly demonstrates the effects of DNA sequence on the gross structure and dynamics of nucleosomes. These effects and mispositioning of the 601 super strong nucleosome positioning sequence can be detected in short simulations (10 ns). Collectively, the results provide a basis for comparative simulation studies of nucleosomes and extend our understanding of the binding of proteins and drugs to nucleosomal DNA. The TMB Library can be found at http://dna.engr.latech.edu/~tmbshare/ .

ICTV Virus Taxonomy Profile: Clavaviridae.

The family Clavaviridae includes viruses that replicate in hyperthermophilic archaea from the genus Aeropyrum. The non-enveloped rigid virions are rod-shaped, with dimensions of about 143×16 nm, and have terminal cap structures, one of which is pointed and carries short fibres, while the other is rounded. The virion displays helical symmetry and is constructed from a single major α-helical protein, which is heavily glycosylated, and several minor capsid proteins. The 5278 bp, circular, double-stranded DNA genome of Aeropyrum pernix bacilliform virus 1 is packed inside the virion as a left-handed superhelix. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Clavaviridae, which is available at www.ictv.global/report/clavaviridae.

Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging

Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. However, there is a paucity of information on archaeal virion structures, genome packaging, and determinants of temperature resistance. The rod-shaped virus APBV1 (Aeropyrum pernix bacilliform virus 1) is among the most thermostable viruses known; it infects a hyperthermophile Aeropyrum pernix, which grows optimally at 90 °C. Here we report the structure of APBV1, determined by cryo-electron microscopy at near-atomic resolution. Tight packing of the major virion glycoprotein (VP1) is ensured by extended hydrophobic interfaces, and likely contributes to the extreme thermostability of the helical capsid. The double-stranded DNA is tightly packed in the capsid as a left-handed superhelix and held in place by the interactions with positively charged residues of VP1. The assembly is closed by specific capping structures at either end, which we propose to play a role in DNA packing and delivery.

Chiral symmetry breaking of a double-stranded helical chain through bend-writhe coupling.

This paper explores asymmetric elasticity of a double-stranded helical chain, which serves as a minimal model of biopolymers. The model consists of two elastic chains that mutually intertwine in a right-handed manner, forming a double-stranded helix. A simple numerical experiment for structural relaxation, which reduces the total elastic energy of the model monotonically without thermal fluctuations, reveals possible asymmetric elasticity inherent in the helical chain. It is first shown that a short segment of the double-stranded helical chain has a tendency to unwind when it is bent. It is also shown that a short segment of the helical chain has a tendency to writhe in the left direction upon bending. This tendency gives rise to a propensity for a longer segment of the chain to form a left-handed superhelix spontaneously upon bending. Finally, this propensity of the helical chain to form a left-handed superhelix is proposed to be a possible origin of the uniform left-handed wrapping of DNA around nucleosome core particles in nature. The results presented here could provide deeper insights into the roles and significance of helical chirality of biopolymers.

Unraveling the Higher Order Structure of Chromatin using Single Molecule Force Spectroscopy

The compaction of eukaryotic DNA into chromatin has been implicated in the regulation of all processes involving DNA. However, the structure of chromatin remains poorly understood. This lack of structural information impedes a functional understanding of chromatin at the molecular level. Here I will discuss recent developments in single molecule force and torque spectroscopy techniques to study this higher order structure.Using magnetic tweezers and reconstituted designer chromatin fibers, we show that such fibers stretch elastically up to three times their rest length. The stiffness is independent of the presence or absence of linker histones. At 3 pN an overstretching transition occurs that can be attributed to simultaneous rupture of nucleosome-nucleosome interactions and DNA unwrapping.For quantitative analysis of the compliance of the fibers we use a two-state model in which nucleosomes are stacked, as found in a folded fiber, or unfolded in a beads-on-a-string fiber. All force induced transitions up to 10 pN can be captured in this simple two-state model. Kinetic analysis of the rupture events suggests that stretching of the histone tails precedes the rupture of nucleosome-nucleosome interactions. Changes in extension upon exertion of torsional stress clearly show that the chromatin fibers fold into a left-handed super-helix. Overall, by new single-molecule force spectroscopy techniques and quantitative analysis of the force-extension behavior of single chromatin fibers we resolved a structural and dynamic picture of chromatin folding.

Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes

Much controversy exists regarding the structural organization of the yeast centromeric nucleosome and the role of the nonhistone protein, Scm3, in its assembly and architecture. Here we show that the substitution of H3 with its centromeric variant Cse4 results in octameric nucleosomes that organize DNA in a left-handed superhelix. We demonstrate by single-molecule approaches, micrococcal nuclease digestion and small-angle X-ray scattering that Cse4-nucleosomes exhibit an open conformation with weakly bound terminal DNA segments. The Cse4-octamer does not preferentially form nucleosomes on its cognate centromeric DNA. We show that Scm3 functions as a Cse4-specific nucleosome assembly factor, and that the resulting octameric nucleosomes do not contain Scm3 as a stably bound component. Taken together, our data provide insights into the assembly and structural features of the budding yeast centromeric nucleosome.

Sequence determinants of histone–DNA binding preferences: Comment on “Cracking the chromatin code: Precise rule of nucleosome positioning” by Edward N. Trifonov

DNA in eukaryotic cells is packaged into compact chromatin state. The fundamental unit of chromatin is a nucleosome, a highly conserved protein-DNA complex in which ~ 147 basepairs (bp) of DNA are wrapped around a histone octamer in a left-handed superhelix [1]. Histone-DNA binding affinity depends on the nucleotide sequence of the nucleosomal site: indeed, the ability of the DNA molecule to bend into the superhelix is mostly governed by dinucleotide base-stacking energies. The review by Trifonov [2] emphasizes the role of deformational properties of DNA in nucleosome positioning and energetics, proposing a novel sequence motif CGRAAATTTYCG that favors nucleosome formation. The motif is inferred from a large-scale map of C.elegans nucleosomes [3]. In building up the case for the 10–11 bp-periodic nucleosome positioning motif shown above, the author has chosen to focus mostly on his own work and the work of his colleagues. However, I find myself intrigued by how well the proposed pattern stacks up against some of the other models and datasets (nucleosome positioning determinants and the idea of the “nucleo-some code” have recently garnered a lot of interest in the chromatin field). The author argues that due to steric exclusion between neighboring particles only single-nucleosome conformations can be used to compare experiment with theory [4]. However, techniques similar to dynamic programming in computer science and transfer matrices in physics can be used to convert histone-DNA binding energies into probabilities of nucleosome formation at every bp, without any approximations related to the finite particle size (see e.g. [5]). Furthermore, because the DNA bendability matrix proposed by the author is capable of placing nucleosomes with 1 bp resolution, only seven nucleosomes whose positions are known precisely from experiment have been chosen to test the model, with impressive success [4]. This seems to be too restrictive – certainly a high-resolution algorithm can predict lower-resolution data. Besides, the vast majority of the algorithms proposed in the literature also have 1 bp resolution and have nonetheless been used to predict genome-wide occupancy profiles for nucleosomes mapped with ~ 10–20 bp precision by micrococcal nuclease (MNase). Moreover, C.elegans data from which the model was inferred in the first place employed MNase digestion followed by 454 pyrosequencing [3], and therefore has the usual ~ 10 – 20 bp accuracy. It would be especially interesting to see whether the DNA bendability model proposed by Trifonov and colleagues has greater predictive power against large-scale nucleosome maps than simple models that assign the same scores to mono- and dinucleotides of the same type, regardless of their position with respect to the DNA helical repeat [6, 7]. Finally, nucleosomes on which the analysis by Trifonov and colleagues is based come from in vivo chromatin in a mixture of C.elegans cells. The nucleosome positions in this sample are averaged over cell types and may have been affected, among other things, by chromatin remodeling enzymes and competition with other DNA-binding proteins. It would be reassuring to see the proposed motif also appear in two recent large-scale maps of nucleosomes positioned in vitro on genomic sequences from S.cerevisiae and E.coli [8, 9].

Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat

The regulation of mitochondrial DNA (mtDNA) processes is slowly being characterized at a structural level. We present here crystal structures of human mitochondrial regulator mTERF, a transcription termination factor also implicated in replication pausing, in complex with double-stranded DNA oligonucleotides containing the tRNA(Leu)(UUR) gene sequence. mTERF comprises nine left-handed helical tandem repeats that form a left-handed superhelix, the Zurdo domain.

Structure of β-β-hairpins closed into cycles by S-S-bridges

In the present study, a stereochemical analysis of proteins containing β-β-hairpins closed into cycles by S-S-bridges has been performed. A database of these proteins has been compiled from the Protein Data Bank (total 428 PDB entries). 390 β-β-hairpins closed into cycles by S-S-bridges have been found in non-homologous proteins included into the database. An alysis showed that 118 hairpins contain S-S-bridges formed by cysteins located opposite to each other in the neighboring β-strands. Among them, 110 hairpins are left-turned and 8 β-hairpins are right-turned when viewed from the same side where S-S-bridges are located. In the other group of 272 β-hairpins, the S-S-bridge is formed by two cysteins one of which is located in the β-strand and the other in the loop juxtaposed to the β-hairpin at the N- (84% cases) or C-terminus ( 16% cases). As shown, in most cases the loop-hairpin region closed into a cycle by the S-S-bridge formed a turn of a left-handed superhelix.

Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM

TraM is essential for F plasmid-mediated bacterial conjugation, where it binds to the plasmid DNA near the origin of transfer, and recognizes a component of the transmembrane DNA transfer complex, TraD. Here we report the 1.40 A crystal structure of the TraM core tetramer (TraM58-127). TraM58-127 is a compact eight-helical bundle, in which the N-terminal helices from each protomer interact to form a central, parallel four-stranded coiled-coil, whereas each C-terminal helix packs in an antiparallel arrangement around the outside of the structure. Four protonated glutamic acid residues (Glu88) are packed in a hydrogen-bonded arrangement within the central four-helix bundle. Mutational and biophysical analyses indicate that this protonated state is in equilibrium with a deprotonated tetrameric form characterized by a lower helical content at physiological pH and temperature. Comparison of TraM to its Glu88 mutants predicted to stabilize the helical structure suggests that the protonated state is the active form for binding TraD in conjugation.

The synaptic acetylcholinesterase tetramer assembles around a polyproline II helix

Functional localization of acetylcholinesterase (AChE) in vertebrate muscle and brain depends on interaction of the tryptophan amphiphilic tetramerization (WAT) sequence, at the C-terminus of its major splice variant (T), with a proline-rich attachment domain (PRAD), of the anchoring proteins, collagenous (ColQ) and proline-rich membrane anchor. The crystal structure of the WAT/PRAD complex reveals a novel supercoil structure in which four parallel WAT chains form a left-handed superhelix around an antiparallel left-handed PRAD helix resembling polyproline II. The WAT coiled coils possess a WWW motif making repetitive hydrophobic stacking and hydrogen-bond interactions with the PRAD. The WAT chains are related by an approximately 4-fold screw axis around the PRAD. Each WAT makes similar but unique interactions, consistent with an asymmetric pattern of disulfide linkages between the AChE tetramer subunits and ColQ. The P59Q mutation in ColQ, which causes congenital endplate AChE deficiency, and is located within the PRAD, disrupts crucial WAT-WAT and WAT-PRAD interactions. A model is proposed for the synaptic AChE(T) tetramer.

DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum.

DNA A-tracts have been defined as four or more consecutive A.T base pairs without a TpA step. When inserted in phase with the DNA helical repeat, bending is manifested macroscopically as anomalous migration on polyacrylamide gels, first observed >20 years ago. An unsolved conundrum is why DNA containing in-phase A-tract repeats of A(4)T(4) are bent, whereas T(4)A(4) is straight. We have determined the solution structures of the DNA duplexes formed by d(GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with NH(4)(+) counterions by using NMR spectroscopy, including refinement with residual dipolar couplings. Analysis of the structures shows that the ApT step has a large negative roll, resulting in a local bend toward the minor groove, whereas the TpA step has a positive roll and locally bends toward the major groove. For A4T4, this bend is nearly in phase with bends at the two A-tract junctions, resulting in an overall bend toward the minor groove of the A-tract, whereas for T4A4, the bends oppose each other, resulting in a relatively straight helix. NMR-based structural modeling of d(CAAAATTTTG)(15) and d(GTTTTAAAAC)(15) reveals that the former forms a left-handed superhelix with a diameter of approximately 110 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 A and diameter of approximately 50 A. Results of gel electrophoretic mobility studies are consistent with the higher-order structure of the DNA and furthermore depend on the nature of the monovalent cation present in the running buffer.

Structure of the catalytic fragment of translation initiation factor 2B and identification of a critically important catalytic residue.

Eukaryotic initiation factor (eIF) 2B catalyzes the nucleotide activation of eIF2 to its active GTP-bound state. The exchange activity has been mapped to the C terminus of the eIF2Bepsilon subunit. We have determined the crystal structure of residues 544-704 from yeast eIF2Bepsilon at 2.3-A resolution, and this fragment is an all-helical protein built around the conserved aromatic acidic (AA) boxes also found in eIF4G and eIF5. The eight helices are organized in a manner similar to HEAT repeats. The molecule is highly asymmetric with respect to surface charge and conservation. One area in the N terminus is proposed to be directly involved in catalysis. In agreement with this hypothesis, mutation of glutamate 569 is shown to be lethal. An acidic belt and a second area in the C terminus containing residues from the AA boxes are important for binding to eIF2. Two mutations causing the fatal human genetic disease leukoencephalopathy with vanishing white matter are buried and appear to disrupt the structural integrity of the catalytic domain rather than interfering directly with catalysis or binding of eIF2.

Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases

Escherichia coli topoisomerase (Topo) IV is an essential type II Topo that removes DNA entanglements created during DNA replication. Topo IV relaxes (+) supercoils much faster than (-) supercoils, promoting replication while sparing the essential (-) supercoils. Here, we investigate the mechanism underlying this chiral preference. Using DNA binding assays and a single-molecule DNA braiding system, we show that Topo IV recognizes the chiral crossings imposed by the left-handed superhelix of a (+) supercoiled DNA, rather than global topology, twist deformation, or local writhe. Monte Carlo simulations of braid, supercoil, and catenane configurations demonstrate how a preference for a single-crossing geometry during strand passage can allow Topo IV to perform its physiological functions. Single-enzyme braid relaxation experiments also provide a direct measure of the processivity of the enzyme and offer insight into its mechanochemical cycle.