Journal articles: 'Helical staircase'

1

Schmuck, Carsten. "Molecules with Helical Structure: How To Build a Molecular Spiral Staircase." Angewandte Chemie International Edition 42, no. 22 (June 6, 2003): 2448–52. http://dx.doi.org/10.1002/anie.200201625.

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Gibcus, Johan H., Kumiko Samejima, Anton Goloborodko, Itaru Samejima, Natalia Naumova, Johannes Nuebler, Masato T. Kanemaki, et al. "A pathway for mitotic chromosome formation." Science 359, no. 6376 (January 18, 2018): eaao6135. http://dx.doi.org/10.1126/science.aao6135.

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Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C analysis of synchronous DT40 cell cultures with polymer simulations. Here we show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner, and arrays of consecutive 60-kilobase (kb) loops are formed. During prometaphase, ~80-kb inner loops are nested within ~400-kb outer loops. The loop array acquires a helical arrangement with consecutive loops emanating from a central “spiral staircase” condensin scaffold. The size of helical turns progressively increases to ~12 megabases during prometaphase. Acute depletion of condensin I or II shows that nested loops form by differential action of the two condensins, whereas condensin II is required for helical winding.

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Benítez Hernández, Patricia, and Mercedes Valiente López. "The Tangent Solution to the Late Gothic Helical Staircase: A Justified Oblivion." Nexus Network Journal 17, no. 2 (March 5, 2015): 379–98. http://dx.doi.org/10.1007/s00004-015-0244-x.

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Dai, Weixiang, Jeffrey L. Petersen, and Kung K. Wang. "Synthesis and Structure of a Helical Diindenophenanthrene with Four Congested Phenyl Substituents as a Molecular Spiral Staircase†." Organic Letters 6, no. 23 (November 2004): 4355–57. http://dx.doi.org/10.1021/ol0481434.

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Ghosh, Sujit K., and Parimal K. Bharadwaj. "Octameric Water Clusters of Staircase Structure Present in a Metal-Organic Framework Built from Helical Lanthanide Coordination Polymers." European Journal of Inorganic Chemistry 2005, no. 24 (December 2005): 4886–89. http://dx.doi.org/10.1002/ejic.200500735.

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Roßenbeck, B., and W. S. Sheldrick. "Chiral Copper(I) Iodide Based Porous Coordination Frameworks with Asymmetrically Substituted Bridging N-Donor Ligands." Zeitschrift für Naturforschung B 55, no. 6 (June 1, 2000): 467–72. http://dx.doi.org/10.1515/znb-2000-0604.

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The 2-dimensional coordination polymers 2∞[{(CuI)2(Mepyz)2} · Mepyz] (1a), 2∞[CuX(Mepyz)] (2a, X = Br; 2b, X = Cl) and 2∞[(CuX)2(Mepyz)] (3a, X = I;3b, X = Br) may be prepared by reaction of the appropriate copper(I) halide with 2-methylpyrazine (Mepyz) either in acetonitrile solution at 130 °C (2a/2b, 3a/3b) or without solvent at 20 °C (la). Mepyz ligands bridge (CuI)2 rhomboid dimers in the chiral network of la, whose resulting 24-membered rings are large enough to accomodate an Mepyz guest molecule, la rapidly loses these guests to afford a crystalline powder (lb), that can reversibly imbibe benzonitrile molecules into its open channels. In contrast to la, the sheets of 2a/2b contain zigzag infinite CuX chains, those of 3a/3b staircase 1∞[CuX] double chains as their characteristic substructures. Helical 3∞[CuI] single chains in the 3-dimensional network of 3∞[CuI Mepip)4 are bridged by R-2-methylpiperazine (Mepip) ligands in a second example of a chiral coordination polymer.

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Yamaguchi, Maki, Masako Kimura, Zhao-bo Li, Tetsuo Ohno, Shigeru Takemori, Joseph F. Y. Hoh, and Naoto Yagi. "X-ray diffraction analysis of the effects of myosin regulatory light chain phosphorylation and butanedione monoxime on skinned skeletal muscle fibers." American Journal of Physiology-Cell Physiology 310, no. 8 (April 15, 2016): C692—C700. http://dx.doi.org/10.1152/ajpcell.00318.2015.

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The phosphorylation of the myosin regulatory light chain (RLC) is an important modulator of skeletal muscle performance and plays a key role in posttetanic potentiation and staircase potentiation of twitch contractions. The structural basis for these phenomena within the filament lattice has not been thoroughly investigated. Using a synchrotron radiation source at SPring8, we obtained X-ray diffraction patterns from skinned rabbit psoas muscle fibers before and after phosphorylation of myosin RLC in the presence of myosin light chain kinase, calmodulin, and calcium at a concentration below the threshold for tension development ([Ca2+] = 10−6.8 M). After phosphorylation, the first myosin layer line slightly decreased in intensity at ∼0.05 nm−1 along the equatorial axis, indicating a partial loss of the helical order of myosin heads along the thick filament. Concomitantly, the (1,1/1,0) intensity ratio of the equatorial reflections increased. These results provide a firm structural basis for the hypothesis that phosphorylation of myosin RLC caused the myosin heads to move away from the thick filaments towards the thin filaments, thereby enhancing the probability of interaction with actin. In contrast, 2,3-butanedione monoxime (BDM), known to inhibit contraction by impeding phosphate release from myosin, had exactly the opposite effects on meridional and equatorial reflections to those of phosphorylation. We hypothesize that these antagonistic effects are due to the acceleration of phosphate release from myosin by phosphorylation and its inhibition by BDM, the consequent shifts in crossbridge equilibria leading to opposite changes in abundance of the myosin-ADP-inorganic phosphate complex state associated with helical order of thick filaments.

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Qin, Jianhua, Yanyuan Jia, Huijun Li, Bei Zhao, Dongqing Wu, Shuangquan Zang, Hongwei Hou, and Yaoting Fan. "Conversion from a Heterochiral [2 + 2] Coaxially Nested Double-Helical Column to a Cationic Spiral Staircase Stimulated by an Ionic Liquid Anion." Inorganic Chemistry 53, no. 2 (January 7, 2014): 685–87. http://dx.doi.org/10.1021/ic402598p.

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9

Han, Han, Heidi L. Schubert, John McCullough, Nicole Monroe, Michael D. Purdy, Mark Yeager, Wesley I. Sundquist, and Christopher P. Hill. "Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation." Journal of Biological Chemistry 295, no. 2 (November 25, 2019): 435–43. http://dx.doi.org/10.1074/jbc.ac119.009890.

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Many members of the AAA+ ATPase family function as hexamers that unfold their protein substrates. These AAA unfoldases include spastin, which plays a critical role in the architecture of eukaryotic cells by driving the remodeling and severing of microtubules, which are cytoskeletal polymers of tubulin subunits. Here, we demonstrate that a human spastin binds weakly to unmodified peptides from the C-terminal segment of human tubulin α1A/B. A peptide comprising alternating glutamate and tyrosine residues binds more tightly, which is consistent with the known importance of glutamylation for spastin microtubule severing activity. A cryo-EM structure of the spastin-peptide complex at 4.2 Å resolution revealed an asymmetric hexamer in which five spastin subunits adopt a helical, spiral staircase configuration that binds the peptide within the central pore, whereas the sixth subunit of the hexamer is displaced from the peptide/substrate, as if transitioning from one end of the helix to the other. This configuration differs from a recently published structure of spastin from Drosophila melanogaster, which forms a six-subunit spiral without a transitioning subunit. Our structure resembles other recently reported AAA unfoldases, including the meiotic clade relative Vps4, and supports a model in which spastin utilizes a hand-over-hand mechanism of tubulin translocation and microtubule remodeling.

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10

Raney, Kevin D. "A helicase staircase." Nature Structural & Molecular Biology 13, no. 8 (August 2006): 671–72. http://dx.doi.org/10.1038/nsmb0806-671.

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11

Marmo, Francesco, Daniele Masi, and Luciano Rosati. "Thrust network analysis of masonry helical staircases." International Journal of Architectural Heritage 12, no. 5 (January 8, 2018): 828–48. http://dx.doi.org/10.1080/15583058.2017.1419313.

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12

Meagher, Martin, Alexander Myasnikov, and Eric J. Enemark. "Two Distinct Modes of DNA Binding by an MCM Helicase Enable DNA Translocation." International Journal of Molecular Sciences 23, no. 23 (November 24, 2022): 14678. http://dx.doi.org/10.3390/ijms232314678.

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A six-subunit ATPase ring forms the central hub of the replication forks in all domains of life. This ring performs a helicase function to separate the two complementary DNA strands to be replicated and drives the replication machinery along the DNA. Disruption of this helicase/ATPase ring is associated with genetic instability and diseases such as cancer. The helicase/ATPase rings of eukaryotes and archaea consist of six minichromosome maintenance (MCM) proteins. Prior structural studies have shown that MCM rings bind one encircled strand of DNA in a spiral staircase, suggesting that the ring pulls this strand of DNA through its central pore in a hand-over-hand mechanism where the subunit at the bottom of the staircase dissociates from DNA and re-binds DNA one step above the staircase. With high-resolution cryo-EM, we show that the MCM ring of the archaeal organism Saccharolobus solfataricus binds an encircled DNA strand in two different modes with different numbers of subunits engaged to DNA, illustrating a plausible mechanism for the alternating steps of DNA dissociation and re-association that occur during DNA translocation.

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13

Belobrov, P. I., V. V. Beloshapkin, G. M. Zaslavsky, and A. G. Tret'yakov. "Devil's staircase in double helices self-organization." Physics Letters A 122, no. 6-7 (June 1987): 323–26. http://dx.doi.org/10.1016/0375-9601(87)90834-6.

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14

Develioglu, Aysegul, Levent Trabzon, and Yunus Alphan. "Design, Fabrication and Characterization of n-Si Columnar Structures for Solar Cell Applications." Nanoscience & Nanotechnology-Asia 10, no. 1 (January 23, 2020): 74–79. http://dx.doi.org/10.2174/2210681208666181019123035.

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Background: Glancing Angle Deposition (GLAD) provides oblique deposition and substrate motion to engineer thin film microstructures in three dimensions on nano scale. Using this technique zigzag, chevrons, staircase, post, helical and various type of nanostructures including 3-D multilayers can be obtained from various metals with controllable morphologies. The aim of the study is to increase surface porosity and junction using GLAD method area for thin film solar cells and therefore to increase p-n junction area. This provides efficient charge separation and strong light absorption. Methods: Glancing angle deposition using e-beam evaporation technique has been employed to create 3- D silicon nano-structures on the surface. Al and Ag contact layers were deposited by thermal evaporation technique. Hole-conductor polymer PEDOT: PSS was spin coated onto n type silicon thin film. Reflectance spectra were measured using UV-VIS spectroscopy. Scanning electron microscopy was used to image surface and cross-section with and without PEDOT: PSS. Also, transmission spectra of PEDOT: PSS was measured using UV-VIS spectroscopy. Surface wettability properties and contact angles of silicon samples were measured by contact angle measurement with water. Results: Columnar structures possess less reflection compared to the flat surface depending on surface porosity. This phenomenon shows that these structures can be used as anti-reflection coatings for solar cells and optical devices to decrease reflectivity and increase light harvesting with higher efficiency. Contact angle decreases when surface roughness increases therefore we can see that columnar structures are more hydrophilic compared to dense films. Flat silicon has 98° contact angle while columnar structures have 71° and 61°. PEDOT: PSS exhibits high transparency in the range from 200 to 1100 nm of wavelength of light, which resembles to solar radiation inside the atmosphere. Also, SEM images of the samples show that silicon columnar structures form better contact with PEDOT: PSS than flat surface. Conclusion: GLAD technique has been used to achieve homogenous rough surface by e-beam evaporation. Both cross-sectional and top-view SEM images show that columnar structures have higher porosity than flat surfaces. The response of UV-VIS spectroscopy shows that columnar structures have less reflection due to highly porous surface. With increasing incident flux angle, antireflection property of the surfaces was enhanced by surpassing the surface reflection. Due to the reduced hydrophobicity of porous structures, organic polymer can be distributed homogenously in between the columnar structures with increased p-n junction interface area. PEDOT: PSS is highly conductive, and it is highly transparent material in the range of the wavelength typically seen in the solar radiation. This makes it easier for light to reach to Si interface to generate electrons and holes. These results provide better understanding of Si- based heterojunction solar cells efficiency improvement with surface modification. This study also shows dependency of optical and electrical activity to surface geometry and surface porosity.

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15

Perperi, A. A., N. M. Yavorskaya, and P. V. Yavorskyy. "RESEARCH OF GEOMETRY IN THE ARCHITECTURE OF ANTONIO GAUDI." Problems of theory and history of architecture of Ukraine, no. 20 (May 12, 2020): 312–21. http://dx.doi.org/10.31650/2519-4208-2020-20-312-321.

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Exploring the work of Antonio Gaudi and his knowledge in descriptive geometry, which develops a spatial imagination, we notice the use of lines, shapes, volumetric geometric images in architectural creativity. In his early work, Antonio Gaudi designs buildings under the influence of the Moorish style, using geometric shapes and lines that emphasize Arabic motifs in the patterns. So in the house of Vissenty, made in the style of modernism, he applied the idea of a self-repeating element of a simple form toa more complex one. In a fragment of the gallery of the city park Guell, which is an example of the urban style, Gaudi used the transformation of one surface to another, while showing the smoothness of lines and the accuracy of surface construction and without violating their regularity.Combining various forms in one building or structure, Gaudi perfectly mastered the geometry of the curved lines of the second and third order in space. To achieve a similar effect of shaping, scientists tried in the 60s of the XX century by constructing curved lines and Bezier surfaces. Gaudi achieved a similar effect of shaping in a practical way.n his work, he used cylindrical, conical and spherical surfaces that smoothly passed one into another, as well as the surfaces of Catalan: a hyperbolic paraboloid, conoid, cylindroid. In creating volumetric interior plastic, the curved lines with a kinematic movement created bizarre shapes of the ceiling, smoothly turning into other geometric shapes of the walls.The staircasein one of the towers of the Sagrada Familia is a geometric image of a helicoid, where a complex geometric shape is taken as the generatrix, and the guides are two helises -cylindrical helical lines of different radii.In the geometric construction of a direct or inclined helicoid, it is necessary to have two guides and a movement step, which can be set mathematically. In any case, such a surface remains one of the most unique in nature because the helicoid is a minimal surface.Park Guell is located in Barcelona on the Carmel hill, an area of 17.2 hectares. It was built in the first half of the last century. The customer, who was Eusebi Güell.He huge park complex includes a territory with residential buildings and comfortable relaxation areas, amazing picturesque gardens, quaint shady alleys, multi-tiered terraces, colorful flower arrangements, winding grottoes and gazebos.Working on a park project, Gaudi was inspired by the beauties of the surrounding nature of the Carmel Upland and its picturesque landscapes. In the project, walking paths stretched across the entire park, the mountains were not specially cut from the terrain to emphasize the natural landscape of nature.Necessary for the construction of the elements of the park: poles and beams, were decorated under palm trees. Despite the fact that the height difference was 60 meters, the master skillfully beat the landscape with bizarre forms, emphasizing the desire of a person from simple to sublime.If you delve into history, you can see that the construction work is divided into three stages: the strengthening of hills and slopes with the arrangement of terraces for curved paths and the erection of walls; the construction of a colonnade, a market and mansions; building a bench in the shape of a snake. To date, all the facilities of the complex have been preserved in their original form. At the entrance to the park there are two houses resembling fabulous gingerbread houses, the walls of which arelined with ceramic fragments. The facade of eachhouse is decorated with a medallion with the inscription “Park Guell”. In Gaudi’s work, the “hundred columns” hall, which is inscribed in the landscape of the hill, is a terrace with 86 columns of 6 meters each. These columns support a ceiling with a bizarre shape of complex geometric surfaces of revolution. The plastic of the ceiling vault is made of modern concrete of the time, the decoration of which is made of ceramic in the form of a mosaic. In practical work, Antonio Gaudi took a self-repeating algorithm that developed in space in the form necessary for his design. Gaudi perfectly mastered the skills and knowledge of the discipline called Descriptive Geometry. Developing the spatial imagination, this discipline offers us all kinds of lines, geometric shapes and three-dimensional bodies, for the embodiment of the ideas of masters of architecture, one of which is Antonio Gaudi.

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Schmuck, Carsten. "Molecules with Helical Structure: How To Build a Molecular Spiral Staircase." ChemInform 34, no. 32 (August 12, 2003). http://dx.doi.org/10.1002/chin.200332283.

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17

Dai, Weixiang, Jeffrey L. Petersen, and Kung K. Wang. "Synthesis and Structure of a Helical Diindenophenanthrene with Four Congested Phenyl Substituents as a Molecular Spiral Staircase." ChemInform 36, no. 10 (March 8, 2005). http://dx.doi.org/10.1002/chin.200510099.

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18

Ma, Chengying, Damu Wu, Qian Chen, and Ning Gao. "Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition." Nature Communications 13, no. 1 (November 9, 2022). http://dx.doi.org/10.1038/s41467-022-34511-2.

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AbstractThe type II AAA + ATPase Drg1 is a ribosome assembly factor, functioning to release Rlp24 from the pre-60S particle just exported from nucleus, and its activity in can be inhibited by a drug molecule diazaborine. However, molecular mechanisms of Drg1-mediated Rlp24 removal and diazaborine-mediated inhibition are not fully understood. Here, we report Drg1 structures in different nucleotide-binding and benzo-diazaborine treated states. Drg1 hexamers transits between two extreme conformations (planar or helical arrangement of protomers). By forming covalent adducts with ATP molecules in both ATPase domain, benzo-diazaborine locks Drg1 hexamers in a symmetric and non-productive conformation to inhibits both inter-protomer and inter-ring communication of Drg1 hexamers. We also obtained a substrate-engaged mutant Drg1 structure, in which conserved pore-loops form a spiral staircase to interact with the polypeptide through a sequence-independent manner. Structure-based mutagenesis data highlight the functional importance of the pore-loop, the D1-D2 linker and the inter-subunit signaling motif of Drg1, which share similar regulatory mechanisms with p97. Our results suggest that Drg1 may function as an unfoldase that threads a substrate protein within the pre-60S particle.

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19

Li, Ya-xin, Hong-fei Gao, Rui-bin Zhang, Kutlwano Gabana, Qing Chang, Gillian A. Gehring, Xiao-hong Cheng, Xiang-bing Zeng, and Goran Ungar. "A case of antiferrochirality in a liquid crystal phase of counter-rotating staircases." Nature Communications 13, no. 1 (January 19, 2022). http://dx.doi.org/10.1038/s41467-022-28024-1.

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AbstractHelical structures continue to inspire, prompted by examples such as DNA double-helix and alpha-helix in proteins. Most synthetic polymers also crystallize as helices, which relieves steric clashes by twisting, while keeping the molecules straight for their ordered packing. In columnar liquid crystals, which often display useful optoelectronic properties, overall helical chirality can be induced by inclusion of chiral chemical groups or dopants; these bias molecular twist to either left or right, analogous to a magnetic field aligning the spins in a paramagnet. In this work, however, we show that liquid-crystalline columns with long-range helical order can form by spontaneous self-assembly of straight- or bent-rod molecules without inclusion of any chiral moiety. A complex lattice with Fddd symmetry and 8 columns per unit cell (4 right-, 4 left-handed) characterizes this “antiferrochiral” structure. In selected compounds it allows close packing of their fluorescent groups reducing their bandgap and giving them promising light-emitting properties.

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20

Qiao, Cuncun, Gianluca Debiasi-Anders, and Ignacio Mir-Sanchis. "Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility." Nucleic Acids Research, July 25, 2022. http://dx.doi.org/10.1093/nar/gkac625.

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Abstract Replication is a crucial cellular process. Replicative helicases unwind DNA providing the template strand to the polymerase and promoting replication fork progression. Helicases are multi-domain proteins which use an ATPase domain to couple ATP hydrolysis with translocation, however the role that the other domains might have during translocation remains elusive. Here, we studied the unexplored self-loading helicases called Reps, present in Staphylococcus aureus pathogenicity islands (SaPIs). Our cryoEM structures of the PriRep5 from SaPI5 (3.3 Å), the Rep1 from SaPI1 (3.9 Å) and Rep1–DNA complex (3.1Å) showed that in both Reps, the C-terminal domain (CTD) undergoes two distinct movements respect the ATPase domain. We experimentally demonstrate both in vitro and in vivo that SaPI-encoded Reps need key amino acids involved in the staircase mechanism of translocation. Additionally, we demonstrate that the CTD′s presence is necessary for the maintenance of full ATPase and helicase activities. We speculate that this high interdomain flexibility couples Rep′s activities as initiators and as helicases.

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21

Yao, Nina Y., Dan Zhang, Olga Yurieva, and Michael E. O’Donnell. "CMG helicase can use ATPγS to unwind DNA: Implications for the rate-limiting step in the reaction mechanism." Proceedings of the National Academy of Sciences 119, no. 4 (January 18, 2022). http://dx.doi.org/10.1073/pnas.2119580119.

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Significance The rate-limiting step of hexameric replicative helicases is ill-understood and this study on the eukaryotic replicative helicase CMG identifies that the catalytic ATP hydrolysis step is not the rate-limiting step, implying that a conformational change may be rate-limiting for DNA-unwinding activity. The results support a “staircase” model of CMG movement along DNA, requiring a large conformational change after ATP hydrolysis. Many studies use ATPγS to “preload” CMG onto DNA. However, this study demonstrates that ATPγS hydrolysis fuels CMG to unwind DNA. To achieve preloading without unwinding, the current study provides an alternative nucleotide analog, AMP-PNP, that is not hydrolyzable and efficiently preloads CMG onto DNA.

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Journal articles on the topic 'Helical staircase'

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