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ribbon helix helix

Chew Chieng Yeo
GCN5-related N-acetyltransferase (GNAT) is a huge superfamily of proteins spanning the prokaryotic and eukaryotic domains of life. GNAT proteins usually transfer an acetyl group from acetyl-CoA to a wide variety of substrates ranging from aminoglycoside antibiotics to large macromolecules. Type II toxin-antitoxin (TA) modules are typically bicistronic and widespread in bacterial and archael genomes with diverse cellular functions. Recently, a novel family of type II TA toxins was described which presents a GNAT-fold and functions by acetylating charged tRNA thereby precluding translation...
April 6, 2018: Molecular Microbiology
Adarsh Kumar, Subramanian Karthikeyan
The MSMEG_4306 gene from Mycobacterium smegmatis encodes a protein of unknown function with 242 amino-acid residues that contains a conserved zinc-ribbon domain at its C-terminus. Here, the crystal structure of MSMEG_4306 determined by the single-wavelength anomalous dispersion method using just one zinc ion co-purified with the protein is reported. The crystal structure of MSMEG_4306 shows a coiled-coil helix domain in the N-terminal region and a zinc-ribbon domain in the C-terminal region. A structural similarity search against the Protein Data Bank using MSMEG_4306 as a query revealed two similar structures, namely CT398 from Chlamydia trachomatis and HP0958 from Helicobacter pylori, although they share only ∼15% sequence identity with MSMEG_4306...
March 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
Hongliang Qian, Qingqing Yao, Cui Tai, Zixin Deng, Jianhua Gan, Hong-Yu Ou
A type II toxin-antitoxin (TA) system, in which the toxin contains a Gcn5-related N-acetyltransferase (GNAT) domain, has been characterized recently. GNAT toxin acetylates aminoacyl-tRNA and blocks protein translation. It is abolished by the cognate antitoxin that contains the ribbon-helix-helix (RHH) domain. Here, we present an experimental demonstration of the interaction of the GNAT-RHH complex with TA promoter DNA. First, the GNAT-RHH TA locus kacAT was found in Klebsiella pneumoniae HS11286, a strain resistant to multiple antibiotics...
May 2018: Molecular Microbiology
Andrés Miguel-Arribas, Jian-An Hao, Juan R Luque-Ortega, Gayetri Ramachandran, Jorge Val-Calvo, César Gago-Córdoba, Daniel González-Álvarez, David Abia, Carlos Alfonso, Ling J Wu, Wilfried J J Meijer
Bacterial conjugation is the process by which a conjugative element (CE) is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer ( oriT ), where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host...
2017: Frontiers in Microbiology
Clément Bonnel, Baptiste Legrand, Matthieu Simon, Jean Martinez, Jean-Louis Bantignies, Young Kee Kang, Emmanuel Wenger, Francois Hoh, Nicolas Masurier, Ludovic T Maillard
According to their restricted conformational freedom, heterocyclic γ-amino acids are usually considered to be related to Z-vinylogous γ-amino acids. In this context, oligomers alternating α-amino acids and thiazole-based γ-amino acids (ATCs) were expected to fold into a canonical 12-helical shape as described for α/γ-hybrid peptides composed of cis-α/β-unsaturated γ-amino acids. However, through a combination of X-ray crystallography, NMR spectroscopy, FTIR experiments, and DFT calculations, it was determined that the folding behavior of ATC-containing hybrid peptides is much more complex...
December 11, 2017: Chemistry: a European Journal
Carol Sheppard, Finn Werner
Virus-encoded transcription factors have been pivotal in exploring the molecular mechanisms and regulation of gene expression in bacteria and eukaryotes since the birth of molecular biology, while our understanding of viral transcription in archaea is still in its infancy. Archaeal viruses do not encode their own RNA polymerases (RNAPs) and are consequently entirely dependent on their hosts for gene expression; this is fundamentally different from many bacteriophages and requires alternative regulatory strategies...
September 2017: Extremophiles: Life Under Extreme Conditions
Sung-Min Kang, Do-Hee Kim, Ki-Young Lee, Sung Jean Park, Hye-Jin Yoon, Sang Jae Lee, Hookang Im, Bong-Jin Lee
Toxin-antitoxin (TA) systems are essential for bacterial persistence under stressful conditions. In particular, Mycobacterium tuberculosis express VapBC TA genes that encode the stable VapC toxin and the labile VapB antitoxin. Under normal conditions, these proteins interact to form a non-toxic TA complex, but the toxin is activated by release from the antitoxin in response to unfavorable conditions. Here, we present the crystal structure of the M. tuberculosis VapBC26 complex and show that the VapC26 toxin contains a pilus retraction protein (PilT) N-terminal (PIN) domain that is essential for ribonuclease activity and that, the VapB26 antitoxin folds into a ribbon-helix-helix DNA-binding motif at the N-terminus...
August 21, 2017: Nucleic Acids Research
Cheng-Tsung Lai, Nathaniel L Rosi, George C Schatz
Self-assembly of peptide amphiphiles (PAs) has been an active research area as the assemblies can be programmed into variously shaped nanostructures. Although cylindrical micelles are common structures, gold-binding peptide conjugates can self-assemble into chiral nanofibers with single or double helices. When gold nanoparticles bind to the helices, the resulting chiral nanoparticle assemblies have a collective plasmonic circular dichroism signal that can serve as nanoscale circular polarizers or chiroptical sensors...
May 18, 2017: Journal of Physical Chemistry Letters
Jorge González, Imanol Usabiaga, Pedro F Arnaiz, Iker León, Rodrigo Martínez, Judith Millán, José A Fernández
The four bases of DNA constitute what is known as the "alphabet of life". Their combination of proton-donor and acceptor groups and aromatic rings allows them to form stacking structures and at the same time establish hydrogen bonds with their counterparts, resulting in the formation of the well-known double-helix structure of DNA. Here we explore the aggregation preferences of cytosine in supersonic expansions, using a combination of laser spectroscopic techniques and computations. The data obtained from the experiments carried out in the cold and isolated environment of the expansion allowed us to establish which are the leading interactions behind aggregation of cytosine molecules...
March 29, 2017: Physical Chemistry Chemical Physics: PCCP
Hang Zhang, Ahmed Mourran, Martin Möller
We report on a microscopic poly(N-isopropylacrylamide) hydrogel ribbon, coated by a thin gold layer, that shows helical coiling. Confined swelling and shrinkage of the hydrogel below and above its characteristic volume phase transition leads to a temperature actuated reversal of the sense of the helix. The extent and the shape of the winding are controlled by the dimensions and mechanical properties of the bilayer ribbon. We focus on a cylindrical helix geometry and monitor the morphing under equilibrium and nonequilibrium conditions, that is, when the temperature changes faster than the volume (millisecond range)...
March 8, 2017: Nano Letters
Thomas D Montenegro-Johnson, Lyndon Koens, Eric Lauga
Numerical study of the hydrodynamics of thin sheets and ribbons presents difficulties associated with resolving multiple length scales. To circumvent these difficulties, asymptotic methods have been developed to describe the dynamics of slender fibres and ribbons. However, such theories entail restrictions on the shapes that can be studied, and often break down in regions where standard boundary element methods are still impractical. In this paper we develop a regularised stokeslet method for ribbons and sheets in order to bridge the gap between asymptotic and boundary element methods...
January 18, 2017: Soft Matter
Benjamin W Arentson, Erin L Hayes, Weidong Zhu, Harkewal Singh, John J Tanner, Donald F Becker
Proline utilization A (PutA) is a bifunctional flavoenzyme with proline dehydrogenase (PRODH) and Δ1 -pyrroline-5-carboxylate (P5C) dehydrogenase (P5CDH) domains that catalyses the two-step oxidation of proline to glutamate. Trifunctional PutAs also have an N-terminal ribbon-helix-helix (RHH) DNA-binding domain and moonlight as autogenous transcriptional repressors of the put regulon. A unique property of trifunctional PutA is the ability to switch functions from DNA-bound repressor to membrane-associated enzyme in response to cellular nutritional needs and proline availability...
December 2016: Bioscience Reports
Alexander Schoedel, Mian Li, Dan Li, Michael O'Keeffe, Omar M Yaghi
Rod MOFs are metal-organic frameworks in which the metal-containing secondary building units consist of infinite rods of linked metal-centered polyhedra. For such materials, we identify the points of extension, often atoms, which define the interface between the organic and inorganic components of the structure. The pattern of points of extension defines a shape such as a helix, ladder, helical ribbon, or cylinder tiling. The linkage of these shapes into a three-dimensional framework in turn defines a net characteristic of the original structure...
October 12, 2016: Chemical Reviews
Hirofumi Wada
Helices are ubiquitous in nature, and helical shape transition is often observed in residually stressed bodies, such as composites, wherein materials with different mechanical properties are glued firmly together to form a whole body. Inspired by a variety of biological examples, the basic physical mechanism responsible for the emergence of twisting and bending in such thin composite structures has been extensively studied. Here, we propose a simplified analytical model wherein a slender membrane tube undergoes a helical transition driven by the contraction of an elastic ribbon bound to the membrane surface...
September 21, 2016: Soft Matter
Elias Nakouzi, Pamela Knoll, Kenzie B Hendrix, Oliver Steinbock
Biomorphs are complex, life-like structures that emerge from the precipitation of barium carbonate and amorphous silica in alkaline media. Despite their inorganic nature, these microstructures have non-crystallographic morphologies such as helices and cardioid sheets. At the nanoscale, biomorphs arrange thousands of crystalline nanorods as hierarchical assemblies that resemble natural biominerals suggesting novel approaches towards the production of biomimetic materials. We report the synthesis of silica-carbonate biomorphs in single-phase, gradient-free solutions that differ markedly from the typical solution-gas or gel-solution setups...
August 17, 2016: Physical Chemistry Chemical Physics: PCCP
Saima Bashar, Si Un Hwang, Junwye Lee, Rashid Amin, Sreekantha Reddy Dugasani, Tai Hwan Ha, Sung Ha Park
We report on the concentration-dependent surface-assisted growth and time-temperature-dependent detachment of one-dimensional 5 helix DNA ribbons (5HR) on a mica substrate. The growth coverage ratio was determined by varying the concentration of the 5HR strands in a test tube, and the detachment rate of 5HR on mica was determined by varying the incubation time at a fixed temperature on a heat block. The topological changes in the concentration-dependent attachment and the time-temperature-dependent detachment for 5HR on mica were observed via atomic force microscopy...
April 2016: Journal of Nanoscience and Nanotechnology
C Plaschka, M Hantsche, C Dienemann, C Burzinski, J Plitzko, P Cramer
Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH...
May 19, 2016: Nature
Yusuke Kobayashi, Takuto Otani, Kota Ishibashi, Toshiharu Shikanai, Yoshiki Nishimura
Chloroplast (cp) DNA is compacted into cpDNA-protein complexes, called cp nucleoids. An abundant and extensively studied component of cp nucleoids is the bifunctional protein sulfite reductase (SiR). The preconceived role of SiR as the core cp nucleoid protein, however, is becoming less likely because of the recent findings that SiRs do not associate with cp nucleoids in some plant species, such as Zea mays and Arabidopsis thaliana To address this discrepancy, we have performed a detailed phylogenetic analysis of SiRs, which shows that cp nucleoid-type SiRs share conserved C-terminally encoded peptides (CEPs)...
May 22, 2016: Genome Biology and Evolution
Fabian Blombach, Katherine L Smollett, Dina Grohmann, Finn Werner
Transcription initiation requires that the promoter DNA is melted and the template strand is loaded into the active site of the RNA polymerase (RNAP), forming the open complex (OC). The archaeal initiation factor TFE and its eukaryotic counterpart TFIIE facilitate this process. Recent structural and biophysical studies have revealed the position of TFE/TFIIE within the pre-initiation complex (PIC) and illuminated its role in OC formation. TFE operates via allosteric and direct mechanisms. Firstly, it interacts with the RNAP and induces the opening of the flexible RNAP clamp domain, concomitant with DNA melting and template loading...
June 19, 2016: Journal of Molecular Biology
Young-Joo Kim, Do-Nyun Kim
In this article, we investigate the principal structural features of the DNA double helix and their effects on its elastic mechanical properties. We develop, in the pursuit of this purpose, a helical continuum model consisting of a soft helical core and two stiff ribbons wrapping around it. The proposed model can reproduce the negative twist-stretch coupling of the helix successfully as well as its global stretching, bending, and torsional rigidities measured experimentally. Our parametric study of the model using the finite element method further reveals that the stiffness of phosphate backbones is a crucial factor for the counterintuitive overwinding behavior of the duplex and its extraordinarily high torsional rigidity, the major-minor grooves augment the twist-stretch coupling, and the change of the helicity might be responsible for the transition from a negative to a positive twist-stretching coupling when a tensile force is applied to the duplex...
2016: PloS One
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