keyword
https://read.qxmd.com/read/35598047/finite-element-modeling-of-%C3%AE-helices-and-tropocollagen-molecules-referring-to-spike-of-sars-cov-2
#21
JOURNAL ARTICLE
Tomasz Wierzbicki, Yuanli Bai
The newly developed finite element (FE) modeling at the atomic scale was used to predict the static and dynamic response of the α-helix (AH) and tropocollagen (TC) protein fragments, the main building blocks of the spike of the SARS-CoV-2. The geometry and morphology of the spike's stalk and its connection to the viral envelope were determined from the combination of most recent molecular dynamics (MD) simulation and images of cryoelectron microscopy. The stiffness parameters of the covalent bonds in the main chain of the helix were taken from the literature...
June 21, 2022: Biophysical Journal
https://read.qxmd.com/read/35487061/morphological-and-electrophysiological-evidences-of-synaptic-switching-in-vestibular-nerve-of-land-snail-helix-lucorum-l
#22
JOURNAL ARTICLE
Nikolay Aseyev
It is well known that the initiation of the reflex arcs of the vertebrate vestibular system occurs in the receptors of the labyrinthine organs which transmit the sensory signals via the ribbon synapses to the vestibular nerve afferents (an interneuron). In invertebrate species, and in particular, the statocyst of pulmonate mollusks, it is thought that the receptors send their axons out of the statocyst in the vestibular connective and establish the first synapse onto cerebral ganglia neurons, thereby bypassing the interneuron in the reflex arc...
April 12, 2022: Biochemical and Biophysical Research Communications
https://read.qxmd.com/read/34850144/chromosome-segregation-in-archaea-sega-and-segb-dna-complex-structures-provide-insights-into-segrosome-assembly
#23
JOURNAL ARTICLE
Cheng-Yi Yen, Min-Guan Lin, Bo-Wei Chen, Irene W Ng, Nicholas Read, Azhar F Kabli, Che-Ting Wu, Yo-You Shen, Chen-Hao Chen, Daniela Barillà, Yuh-Ju Sun, Chwan-Deng Hsiao
Genome segregation is a vital process in all organisms. Chromosome partitioning remains obscure in Archaea, the third domain of life. Here, we investigated the SegAB system from Sulfolobus solfataricus. SegA is a ParA Walker-type ATPase and SegB is a site-specific DNA-binding protein. We determined the structures of both proteins and those of SegA-DNA and SegB-DNA complexes. The SegA structure revealed an atypical, novel non-sandwich dimer that binds DNA either in the presence or in the absence of ATP. The SegB structure disclosed a ribbon-helix-helix motif through which the protein binds DNA site specifically...
December 16, 2021: Nucleic Acids Research
https://read.qxmd.com/read/34617734/chirality-induction-to-cdse-nanocrystals-self-organized-on-silica-nanohelices-tuning-chiroptical-properties
#24
JOURNAL ARTICLE
Peizhao Liu, Yann Battie, Marion Decossas, Sisareuth Tan, Emilie Pouget, Yutaka Okazaki, Takashi Sagawa, Reiko Oda
CdSe nanocrystals (NCs) were grafted on chiral silica nanoribbons, and the mechanism of resulting chirality induction was investigated. Because of their chiral organization, these NCs show optically active properties that depend strongly on their grafting densities and sizes of the NCs. The effect of the morphology of the chiral silica templates between helical (cylindrical curvature) vs twisted (saddle like curvature) ribbons was investigated. The g -factor of NCs-silica helical ribbons is larger than that of the NCs-silica twisted ribbons...
October 26, 2021: ACS Nano
https://read.qxmd.com/read/34512583/prospects-for-the-mechanism-of-spiroplasma-swimming
#25
REVIEW
Yuya Sasajima, Makoto Miyata
Spiroplasma are helical bacteria that lack a peptidoglycan layer. They are widespread globally as parasites of arthropods and plants. Their infectious processes and survival are most likely supported by their unique swimming system, which is unrelated to well-known bacterial motility systems such as flagella and pili. Spiroplasma swims by switching the left- and right-handed helical cell body alternately from the cell front. The kinks generated by the helicity shift travel down along the cell axis and rotate the cell body posterior to the kink position like a screw, pushing the water backward and propelling the cell body forward...
2021: Frontiers in Microbiology
https://read.qxmd.com/read/34029078/linear-and-helical-carbonic-acid-clusters
#26
JOURNAL ARTICLE
Austin M Wallace, Ryan C Fortenberry
Crystallization of carbonic acid likely begins with a linear or ribbon-esque oligomerization, but a helical spiral is shown here to be a new, competing motif for this process. The present combined density functional theory and coupled-cluster theory work examines both the ribbon and the new helical spiral motifs in terms of relative energies, sequential binding energies, and electronic spectra which could potentially aid in distinguishing between the two forms. The helix diverges in energy from the ribbon by roughly 0...
May 24, 2021: Journal of Physical Chemistry. A
https://read.qxmd.com/read/33812270/a-novel-%C3%AE-hairpin-peptide-derived-from-the-arc-repressor-selectively-interacts-with-the-major-groove-of-b-dna
#27
JOURNAL ARTICLE
Azzurra Stefanucci, Jussara Amato, Diego Brancaccio, Bruno Pagano, Antonio Randazzo, Federica Santoro, Laura Mayol, Soraya Learte-Aymamí, Jessica Rodriguez, José Luis Mascareñas, Ettore Novellino, Alfonso Carotenuto, Adriano Mollica
Transcription factors (TFs) have a remarkable role in the homeostasis of the organisms and there is a growing interest in how they recognize and interact with specific DNA sequences. TFs recognize DNA using a variety of structural motifs. Among those, the ribbon-helix-helix (RHH) proteins, exemplified by the MetJ and ARC repressors, form dimers that insert antiparallel β-sheets into the major groove of DNA. A great chemical challenge consists of using the principles of DNA recognition by TFs to design minimized peptides that maintain the DNA affinity and specificity characteristics of the natural counterparts...
July 2021: Bioorganic Chemistry
https://read.qxmd.com/read/33782130/the-myosin-ii-coiled-coil-domain-atomic-structure-in-its-native-environment
#28
JOURNAL ARTICLE
Hamidreza Rahmani, Wen Ma, Zhongjun Hu, Nadia Daneshparvar, Dianne W Taylor, J Andrew McCammon, Thomas C Irving, Robert J Edwards, Kenneth A Taylor
The atomic structure of the complete myosin tail within thick filaments isolated from Lethocerus indicus flight muscle is described and compared to crystal structures of recombinant, human cardiac myosin tail segments. Overall, the agreement is good with three exceptions: the proximal S2, in which the filament has heads attached but the crystal structure doesn't, and skip regions 2 and 4. At the head-tail junction, the tail α-helices are asymmetrically structured encompassing well-defined unfolding of 12 residues for one myosin tail, ∼4 residues of the other, and different degrees of α-helix unwinding for both tail α-helices, thereby providing an atomic resolution description of coiled-coil "uncoiling" at the head-tail junction...
April 6, 2021: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/33674783/structure-of-human-rna-polymerase-iii-elongation-complex
#29
JOURNAL ARTICLE
Liang Li, Zishuo Yu, Dan Zhao, Yulei Ren, Haifeng Hou, Yanhui Xu
RNA polymerase III (Pol III) transcribes essential structured small RNAs, such as tRNAs, 5S rRNA and U6 snRNA. The transcriptional activity of Pol III is tightly controlled and its dysregulation is associated with human diseases, such as cancer. Human Pol III has two isoforms with difference only in one of its subunits RPC7 (α and β). Despite structural studies of yeast Pol III, structure of human Pol III remains unsolved. Here, we determined the structures of 17-subunit human Pol IIIα complex in the backtracked and post-translocation states, respectively...
July 2021: Cell Research
https://read.qxmd.com/read/33078824/chiral-filament-self-assembly-on-curved-manifolds
#30
JOURNAL ARTICLE
Sebastian Rode, Jens Elgeti, Gerhard Gompper
Rod-like and banana-shaped proteins, like BAR-domain proteins and MreB proteins, adsorb on membranes and regulate the membrane curvature. The formation of large filamentous complexes of these proteins plays an important role in cellular processes like membrane trafficking, cytokinesis and cell motion. We propose a simplified model to investigate such curvature-dependent self-assembly processes. Anisotropic building blocks, modeled as trimer molecules, which have a preferred binding site, interact via pair-wise Lennard-Jones potentials...
December 14, 2020: Soft Matter
https://read.qxmd.com/read/32851833/zinc-fingers
#31
JOURNAL ARTICLE
Carla Isernia, Gaetano Malgieri, Luigi Russo, Gianluca D'Abrosca, Ilaria Baglivo, Paolo V Pedone, Roberto Fattorusso
Zinc finger (ZF) domains, that represent the majority of the DNA-binding motifs in eukaryotes, are involved in several processes ranging from RNA packaging to transcriptional activation, regulation of apoptosis, protein folding and assembly, and lipid binding. While their amino acid composition varies from one domain to the other, a shared feature is the coordination of a zinc ion, with a structural role, by a different combination of cysteines and histidines. The classical zinc finger domain (also called Cys2His2) that represents the most common class, uses two cysteines and two histidines to coordinate the metal ion, and forms a compact ββα architecture consisting in a β-sheet and an α-helix...
March 23, 2020: Metal Ions in Life Sciences
https://read.qxmd.com/read/32788376/the-ribbon-helix-helix-domain-protein-cdrs-regulates-the-tubulin-homolog-ftsz2-to-control-cell-division-in-archaea
#32
JOURNAL ARTICLE
Cynthia L Darnell, Jenny Zheng, Sean Wilson, Ryan M Bertoli, Alexandre W Bisson-Filho, Ethan C Garner, Amy K Schmid
Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life. Here, we use genetics, functional genomics, and quantitative imaging to identify and characterize the novel CdrSL gene regulatory network in a model species of archaea. We demonstrate the central role of these ribbon-helix-helix family transcription factors in the regulation of cell division through specific transcriptional control of the gene encoding FtsZ2, a putative tubulin homolog...
August 11, 2020: MBio
https://read.qxmd.com/read/32286293/cdba-is-a-dna-binding-protein-and-c-di-gmp-receptor-important-for-nucleoid-organization-and-segregation-in-myxococcus-xanthus
#33
JOURNAL ARTICLE
Dorota Skotnicka, Wieland Steinchen, Dobromir Szadkowski, Ian T Cadby, Andrew L Lovering, Gert Bange, Lotte Søgaard-Andersen
Cyclic di-GMP (c-di-GMP) is a second messenger that modulates multiple responses to environmental and cellular signals in bacteria. Here we identify CdbA, a DNA-binding protein of the ribbon-helix-helix family that binds c-di-GMP in Myxococcus xanthus. CdbA is essential for viability, and its depletion causes defects in chromosome organization and segregation leading to a block in cell division. The protein binds to the M. xanthus genome at multiple sites, with moderate sequence specificity; however, its depletion causes only modest changes in transcription...
April 14, 2020: Nature Communications
https://read.qxmd.com/read/32239779/the-trak-accessory-factor-activates-substrate-transfer-through-the-pkm101-type-iv-secretion-system-independently-of-its-role-in-relaxosome-assembly
#34
JOURNAL ARTICLE
Yang Grace Li, Peter J Christie
A large subfamily of the type IV secretion systems (T4SSs), termed the conjugation systems, transmit mobile genetic elements (MGEs) among many bacterial species. In the initiating steps of conjugative transfer, DNA transfer and replication (Dtr) proteins assemble at the origin-of-transfer (oriT) sequence as the relaxosome, which nicks the DNA strand destined for transfer and couples the nicked substrate with the VirD4-like substrate receptor. Here, we defined contributions of the Dtr protein TraK, a predicted member of the Ribbon-Helix-Helix (RHH) family of DNA-binding proteins, to transfer of DNA and protein substrates through the pKM101-encoded T4SS...
August 2020: Molecular Microbiology
https://read.qxmd.com/read/32200630/twisting-of-charged-nanoribbons-to-helicoids-driven-by-electrostatics
#35
JOURNAL ARTICLE
Gervasio Zaldivar, Martin Conda-Sheridan, Mario Tagliazucchi
Charged amphiphiles in solution usually self-assemble into flat nanoribbons that spontaneously twist into different shapes. The role of electrostatics in this process is still under strong debate. This work studies the electrostatic free energy of twisting a nanoribbon at the level of the non-linear Poisson-Boltzmann approximation. It is shown that helicoid-shaped ribbons are more stable than flat ribbons, while other shapes under consideration (cylindrical helixes and bent ribbons) are always less stable than the flat ribbon...
March 22, 2020: Journal of Physical Chemistry. B
https://read.qxmd.com/read/32004770/synthetic-nrg-1-functionalized-dna-nanospindels-towards-her2-neu-targets-for-in-vitro-anti-cancer-activity-assessment-against-breast-cancer-mcf-7-cells
#36
JOURNAL ARTICLE
Mirza Muhammad Faran Ashraf Baig, Wing-Fu Lai, Reyaj Mikrani, Mehreen Jabeen, Muhammad Naveed, Muhammad Abbas, Muhammad Asim Farooq, Anam Ahsan, Said Abasse Kassim, Ghulam Jilany Khan, Muhammad Tayyab Ansari
DNA based nano-carriers synthesized from short circular scaffolds (circular DNA nanotechnology) attains stiffer topology for ligand functionalization (neuregulin-1/NRG-1 ligand) and biological applications (targeted drug delivery). Daunorubicin (DR) is a hydrophobic chemical that requires robust vectors to efficiently encapsulate and avoid its free dispersion in water, biological media and cell culture. Here we design DNA nanospindels (DNA-NS) to efficiently load DR and target the (highly expressed) HER2/neu receptors on the plasma membrane of drug-resistant MCF-7 (breast cancer) cells...
January 25, 2020: Journal of Pharmaceutical and Biomedical Analysis
https://read.qxmd.com/read/31898812/the-crystal-structure-of-the-tcp-domain-of-pcf6-in-oryza-sativa-l-reveals-an-rhh-like-fold
#37
JOURNAL ARTICLE
Lifang Sun, Xiaoming Zou, Meiqin Jiang, Xiuling Wu, Yayu Chen, Qianchao Wang, Qin Wang, Lifei Chen, Yunkun Wu
The TCP domain is an evolutionarily conserved DNA binding domain unique to the plant kingdom. To date, the functions of TCPs have been well studied, but the three-dimensional structure of the TCP domain is lacking. Here, we have determined the crystal structure of the TCP domain from OsPCF6. The structure reveals that the TCP domain adopts three short β strands followed by a helix-loop-helix structure, distinct from the canonical basic helix-loop-helix (bHLH) structure. This folded domain shows high structural similarity to the ribbon-helix-helix (RHH) transcriptional repressors, a family of DNA-binding proteins with a conserved 3D structural motif (RHH fold), indicating that TCPs could be reclassified as RHH proteins...
January 3, 2020: FEBS Letters
https://read.qxmd.com/read/31636993/crystal-structures-of-3-chloro-2-nitro-benzoic-acid-with-quinoline-derivatives-3-chloro-2-nitro-benzoic-acid-5-nitro-quinoline-1-1-3-chloro-2-nitro-benzoic-acid-6-nitro-quinoline-1-1-and-8-hy-droxy-quinolinium-3-chloro-2-nitro-benzoate
#38
JOURNAL ARTICLE
Kazuma Gotoh, Hiroyuki Ishida
The structures of three compounds of 3-chloro-2-nitro-benzoic acid with 5-nitro-quinoline, (I), 6-nitro-quinoline, (II), and 8-hy-droxy-quinoline, (III), have been determined at 190 K. In each of the two isomeric compounds, (I) and (II), C7 H4 ClNO4 ·C9 H6 N2 O2 , the acid and base mol-ecules are held together by O-H⋯N and C-H⋯O hydrogen bonds. In compound (III), C9 H8 NO+ ·C7 H3 ClNO4 - , an acid-base inter-action involving H-atom transfer occurs and the H atom is located at the N site of the base mol-ecule...
October 1, 2019: Acta Crystallographica. Section E, Crystallographic Communications
https://read.qxmd.com/read/31495532/the-e-coli-hicb-antitoxin-contains-a-structurally-stable-helix-turn-helix-dna-binding-domain
#39
JOURNAL ARTICLE
Melek Cemre Manav, Kathryn Jane Turnbull, Dukas Jurėnas, Abel Garcia-Pino, Kenn Gerdes, Ditlev Egeskov Brodersen
The E. coli hicAB type II toxin-antitoxin locus is unusual by being controlled by two promoters and by having the toxin encoded upstream of the antitoxin. HicA toxins contain a double-stranded RNA-binding fold and cleaves both mRNA and tmRNA in vivo, while HicB antitoxins contain a partial RNase H fold and either a helix-turn-helix (HTH) or ribbon-helix-helix domain. It is not known how an HTH DNA-binding domain affects higher-order structure for the HicAB modules. Here, we present crystal structures of the isolated E...
September 4, 2019: Structure
https://read.qxmd.com/read/31260525/toxin-antitoxin-operon-kacat-of-klebsiella-pneumoniae-is-regulated-by-conditional-cooperativity-via-a-w-shaped-kaca-kact-complex
#40
JOURNAL ARTICLE
Hongliang Qian, Hao Yu, Peifei Li, E Zhu, Qingqing Yao, Cui Tai, Zixin Deng, Kenn Gerdes, Xinyi He, Jianhua Gan, Hong-Yu Ou
Bacterial toxin-antitoxin pairs play important roles in bacterial multidrug tolerance. Gcn5-related N-acetyltransferase (GNAT) toxins inhibit translation by acetylation of aminoacyl-tRNAs and are counteracted by direct contacts with cognate ribbon-helix-helix (RHH) antitoxins. Our previous analysis showed that the GNAT toxin KacT and RHH antitoxin KacA of Klebsiella pneumoniae form a heterohexamer in solution and that the complex interacts with the cognate promoter DNA, resulting in negative autoregulation of kacAT transcription...
July 1, 2019: Nucleic Acids Research
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