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ribbon helix helix

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 Δ(1)-pyrroline-5-carboxylate dehydrogenase domains that catalyzes 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...
October 14, 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)...
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
Binjie Xu, Yue Ju, Randal J Soukup, Deborah M Ramsey, Richard Fishel, Vicki H Wysocki, Daniel J Wozniak
Pseudomonas aeruginosa is an important bacterial opportunistic pathogen, presenting a significant threat towards individuals with underlying diseases such as cystic fibrosis. The transcription factor AmrZ regulates expression of multiple P. aeruginosa virulence factors. AmrZ belongs to the ribbon-helix-helix protein superfamily, in which many members function as dimers, yet others form higher order oligomers. In this study, four independent approaches were undertaken and demonstrated that the primary AmrZ form in solution is tetrameric...
February 2016: Environmental Microbiology Reports
Manos Gkikas, Johannes S Haataja, Janne Ruokolainen, Hermis Iatrou, Nikolay Houbenov
Novel poly(L-lysine)-block-poly(L-proline) (PLL-b-PLP)-based materials with all PLP helical conformers, i.e., PLP II and the rare PLP I are here reported. Electrostatic supramolecular complexation of the adjacent cationic PLL with anionic molecules bearing DNA analogue H-bonding functionalities, such as deoxyguanosine monophosphate (dGMP), preserves the extended PLP II helix, and the complexed molecule is locked and held in position by orthogonal shape-persistent hydrogen-bonded dGMP ribbons and their extended π-stacking...
November 9, 2015: Biomacromolecules
Andrey B Lysenko, Ganna A Senchyk, Konstantin V Domasevitch, Jürg Hauser, Daniel Fuhrmann, Merten Kobalz, Harald Krautscheid, Patrícia Neves, Anabela A Valente, Isabel S Gonçalves
A large family of bifunctional 1,2,4-triazole molecular tectons (tr) has been explored for engineering molybdenum(VI) oxide hybrid solids. Specifically, tr ligands bearing auxiliary basic or acidic groups were of the type amine, pyrazole, 1H-tetrazole, and 1,2,4-triazole. The organically templated molybdenum(VI) oxide solids with the general compositions [MoO3(tr)], [Mo2O6(tr)], and [Mo2O6(tr)(H2O)2] were prepared under mild hydrothermal conditions or by refluxing in water. Their crystal structures consist of zigzag chains, ribbons, or helixes of alternating cis-{MoO4N2} or {MoO5N} polyhedra stapled by short [N-N]-tr bridges that for bitriazole ligands convert the motifs into 2D or 3D frameworks...
September 8, 2015: Inorganic Chemistry
Jonathan T Pham, Alexander Morozov, Alfred J Crosby, Anke Lindner, Olivia du Roure
We examine experimentally the deformation of flexible, microscale helical ribbons with nanoscale thickness subject to viscous flow in a microfluidic channel. Two aspects of flexible microhelices are quantified: the overall shape of the helix and the viscous frictional properties. The frictional coefficients determined by our experiments are consistent with calculated values in the context of resistive-force theory. The deformation of helices by viscous flow is well described by nonlinear finite extensibility...
July 2015: Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Frances G O'Brien, Karina Yui Eto, Riley J T Murphy, Heather M Fairhurst, Geoffrey W Coombs, Warren B Grubb, Joshua P Ramsay
Staphylococcus aureus is a common cause of hospital, community and livestock-associated infections and is increasingly resistant to multiple antimicrobials. A significant proportion of antimicrobial-resistance genes are plasmid-borne, but only a minority of S. aureus plasmids encode proteins required for conjugative transfer or Mob relaxase proteins required for mobilisation. The pWBG749 family of S. aureus conjugative plasmids can facilitate the horizontal transfer of diverse antimicrobial-resistance plasmids that lack Mob genes...
September 18, 2015: Nucleic Acids Research
María A Luján, Jesús I Martínez, Pablo J Alonso, Alejandro Torrado, Mercedes Roncel, José M Ortega, Javier Sancho, Rafael Picorel
The cytochrome b559 is a heme-bridged heterodimeric protein with two subunits, α and β. Both subunits from Synechocystis sp. PCC 6803 have previously been cloned and overexpressed in Escherichia coli and in vivo reconstitution experiments have been carried out. The formation of homodimers in the bacterial membrane with endogenous heme was only observed in the case of the β-subunit (β/β) but not with the full length α-subunit. In the present work, reconstitution of a homodimer (α/α) cytochrome b559 like structure was possible using a chimeric N-terminus α-subunit truncated before the amino acid isoleucine 17, eliminating completely a short amphipathic α-helix that lays on the surface of the membrane...
November 2015: Journal of Photochemistry and Photobiology. B, Biology
Sulan Luo, Dongting Zhangsun, Peta J Harvey, Quentin Kaas, Yong Wu, Xiaopeng Zhu, Yuanyan Hu, Xiaodan Li, Victor I Tsetlin, Sean Christensen, Haylie K Romero, Melissa McIntyre, Cheryl Dowell, James C Baxter, Keith S Elmslie, David J Craik, J Michael McIntosh
We identified a previously unidentified conotoxin gene from Conus generalis whose precursor signal sequence has high similarity to the O1-gene conotoxin superfamily. The predicted mature peptide, αO-conotoxin GeXIVA (GeXIVA), has four Cys residues, and its three disulfide isomers were synthesized. Previously pharmacologically characterized O1-superfamily peptides, exemplified by the US Food and Drug Administration-approved pain medication, ziconotide, contain six Cys residues and are calcium, sodium, or potassium channel antagonists...
July 28, 2015: Proceedings of the National Academy of Sciences of the United States of America
Lincong Wang, Hui Qiao, Chen Cao, Shutan Xu, Shuxue Zou
Helices are the most abundant secondary structural elements in proteins and the structural forms assumed by double stranded DNAs (dsDNA). Though the mathematical expression for a helical curve is simple, none of the previous models for the biomolecular helices in either proteins or DNAs use a genuine helical curve, likely because of the complexity of fitting backbone atoms to helical curves. In this paper we model a helix as a series of different but all bona fide helical curves; each one best fits the coordinates of four consecutive backbone Cα atoms for a protein or P atoms for a DNA molecule...
2015: PloS One
Sadia Saeed, Thomas A Jowitt, Jim Warwicker, Finbarr Hayes
The ribbon-helix-helix (RHH) superfamily of DNA-binding proteins is dispersed widely in procaryotes. The dimeric RHH fold is generated by interlocking of two monomers into a 2-fold symmetrical structure that comprises four α-helices enwrapping a pair of antiparallel β-strands (ribbon). Residues in the ribbon region are the principal determinants of DNA binding, whereas the RHH hydrophobic core is assembled from amino acids in both the α-helices and ribbon element. The ParG protein encoded by multiresistance plasmid TP228 is a RHH protein that functions dually as a centromere binding factor during segrosome assembly and as a transcriptional repressor...
April 3, 2015: Journal of Biological Chemistry
Jingjing Li, Kaiqi Fan, Xidong Guan, Yingzhe Yu, Jian Song
Dibenzylidene-D-sorbitol (DBS) and its derivatives are known to form gels in organic solvents; however, the mechanism of the gel formation has been a subject of much debate. The present work is undertaken to elucidate the organization mechanism of a DBS derivative, 1,3:2,4-di(3,4-dichlorobenzylidene)-D-sorbitol (DCDBS), by taking into account the solvent effects and comparing the experiment data with theoretical calculation. These molecules form smooth nonhelical fibers with a rest circular dichroism (CD) signal in polar solvents, in contrast to rope-liked left-helical fibers with a strong negative CD signal observed in nonpolar solvents...
November 11, 2014: Langmuir: the ACS Journal of Surfaces and Colloids
Yun Peng, Jun Lu, Joyce J W Wong, Ross A Edwards, Laura S Frost, J N Mark Glover
The conjugative transfer of bacterial F plasmids relies on TraM, a plasmid-encoded protein that recognizes multiple DNA sites to recruit the plasmid to the conjugative pore. In spite of the high degree of amino acid sequence conservation between TraM proteins, many of these proteins have markedly different DNA binding specificities that ensure the selective recruitment of a plasmid to its cognate pore. Here we present the structure of F TraM RHH (ribbon-helix-helix) domain bound to its sbmA site. The structure indicates that a pair of TraM tetramers cooperatively binds an underwound sbmA site containing 12 base pairs per turn...
November 11, 2014: Journal of Molecular Biology
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