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Helix stabilization

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https://www.readbyqxmd.com/read/28102930/modulation-of-the-thermodynamic-signatures-of-an-rna-thermometer-by-osmolytes-and-salts
#1
Mimi Gao, Loana Arns, Roland Winter
Folding of ribonucleic acids (RNAs) is driven by several factors, such as base pairing and stacking, chain entropy, and ion-mediated electrostatics, which have been studied in great detail. However, the power of background molecules in the cellular milieu is often neglected. Herein, we study the effect of common osmolytes on the folding equilibrium of a hairpin-structured RNA and, using pressure perturbation, provide novel thermodynamic and volumetric insights into the modulation mechanism. The presence of TMAO causes an increased thermal stability and a more positive volume change for the helix-to-coil transition, whereas urea destabilizes the hairpin and leads to an increased expansibility of the unfolded state...
January 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28101874/bioengineered-collagens
#2
Barbara Brodsky, John A M Ramshaw
There is a great deal of interest in obtaining recombinant collagen as an alternative source of material for biomedical applications and as an approach for obtaining basic structural and biological information. However, application of recombinant technology to collagen presents challenges, most notably the need for post-translational hydroxylation of prolines for triple-helix stability. Full length recombinant human collagens have been successfully expressed in cell lines, yeast, and several plant systems, while collagen fragments have been expressed in E...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101868/dystrophin-and-spectrin-two-highly-dissimilar-sisters-of-the-same-family
#3
Olivier Delalande, Aleksander Czogalla, Jean-François Hubert, Aleksander Sikorski, Elisabeth Le Rumeur
Dystrophin and Spectrin are two proteins essential for the organization of the cytoskeleton and for the stabilization of membrane cells. The comparison of these two sister proteins, and with the dystrophin homologue utrophin, enables us to emphasise that, despite a similar topology with common subdomains and a common structural basis of a three-helix coiled-coil, they show a large range of dissimilarities in terms of genetics, cell expression and higher level structural organisation. Interactions with cellular partners, including proteins and membrane phospholipids, also show both strikingly similar and very different behaviours...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101860/the-structure-and-topology-of-%C3%AE-helical-coiled-coils
#4
Andrei N Lupas, Jens Bassler, Stanislaw Dunin-Horkawicz
α-Helical coiled coils constitute one of the most diverse folds yet described. They range in length over two orders of magnitude; they form rods, segmented ropes, barrels, funnels, sheets, spirals, and rings, which encompass anywhere from two to more than 20 helices in parallel or antiparallel orientation; they assume different helix crossing angles, degrees of supercoiling, and packing geometries. This structural diversity supports a wide range of biological functions, allowing them to form mechanically rigid structures, provide levers for molecular motors, project domains across large distances, mediate oligomerization, transduce conformational changes and facilitate the transport of other molecules...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101207/structure-function-analysis-of-dna-helicase-helq-a-new-diagnostic-marker-in-ovarian-cancer
#5
Ya-Ping Li, Jun-Juan Yang, Hui Xu, En-Yu Guo, Yan Yu
It has been previously reported that a deficiency of the helicase, POLQ-like (HELQ) gene increases the risk of ovarian cancer. The present study aimed to explore the structure-function association of HELQ and discuss the effect of molecular structure on the occurrence of tumors. ExPASy tools were employed to analyze the physicochemical properties and secondary structure of the genes. PHYRE2 Protein Fold Recognition Server was used to construct the three-dimensional model and find the ligand-binding sites of HELQ...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28100778/structure-of-the-z-ring-associated-protein-zapd-bound-to-the-c-terminal-domain-of-the-tubulin-like-protein-ftsz-suggests-mechanism-of-z-ring-stabilization-through-ftsz-crosslinking
#6
Maria Schumacher, Kuo-Hsiang Huang, Wenjie Zeng, Anuradha Janakiraman
Cell division in most bacteria is mediated by the tubulin-like FtsZ protein, which polymerizes in a GTP-dependent manner to form the cytokinetic Z ring. A diverse repertoire of FtsZ binding proteins affect FtsZ localization and polymerization to ensure correct Z ring formation. Many of these proteins bind the C-terminal domain (CTD) of FtsZ, which serves as a hub for FtsZ regulation. FtsZ ring-associated proteins, ZapA-D (Zaps), are important FtsZ regulatory proteins that stabilize FtsZ assembly and enhance Z ring formation by increasing lateral assembly of FtsZ protofilaments, which then form the Z ring...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28099806/melting-behavior-of-zipper-structured-lipopeptides-in-lipid-bilayer
#7
Sijia Wang, Xia Han, Danyang Liu, Mengya Li, Shouhong Xu, Honglai Liu
A zipper-structured lipopeptide is expected to play a role of "intelligent valve" in the lipid bilayer. In this paper, a series of zipper-structured lipopeptides have been designed for preparing thermo-controllable hybrid liposomes. Their conformational transition as a function of temperature in lipid bilayer has been investigated for understanding the influences of molecular structure and bilayer property on bio-function. The melting temperatures Tm of the lipopeptides have been found to depend on their molecular structures...
January 18, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28096388/competition-of-calcified-calmodulin-n-lobe-and-pip2-to-an-lqt-mutation-site-in-kv7-1-channel
#8
William Sam Tobelaim, Meidan Dvir, Guy Lebel, Meng Cui, Tal Buki, Asher Peretz, Milit Marom, Yoni Haitin, Diomedes E Logothetis, Joel Alan Hirsch, Bernard Attali
Voltage-gated potassium 7.1 (Kv7.1) channel and KCNE1 protein coassembly forms the slow potassium current IKS that repolarizes the cardiac action potential. The physiological importance of the IKS channel is underscored by the existence of mutations in human Kv7.1 and KCNE1 genes, which cause cardiac arrhythmias, such as the long-QT syndrome (LQT) and atrial fibrillation. The proximal Kv7.1 C terminus (CT) binds calmodulin (CaM) and phosphatidylinositol-4,5-bisphosphate (PIP2), but the role of CaM in channel function is still unclear, and its possible interaction with PIP2 is unknown...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096375/do-guanidinium-and-tetrapropylammonium-ions-specifically-interact-with-aromatic-amino-acid-side-chains
#9
Bei Ding, Debopreeti Mukherjee, Jianxin Chen, Feng Gai
Many ions are known to affect the activity, stability, and structural integrity of proteins. Although this effect can be generally attributed to ion-induced changes in forces that govern protein folding, delineating the underlying mechanism of action still remains challenging because it requires assessment of all relevant interactions, such as ion-protein, ion-water, and ion-ion interactions. Herein, we use two unnatural aromatic amino acids and several spectroscopic techniques to examine whether guanidinium chloride, one of the most commonly used protein denaturants, and tetrapropylammonium chloride can specifically interact with aromatic side chains...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096372/helical-structure-stability-and-dynamics-in-human-apolipoprotein-e3-and-e4-by-hydrogen-exchange-and-mass-spectrometry
#10
Palaniappan S Chetty, Leland Mayne, Sissel Lund-Katz, S Walter Englander, Michael C Phillips
Apolipoprotein E (apoE) plays a critical role in cholesterol transport in both peripheral circulation and brain. Human apoE is a polymorphic 299-residue protein in which the less common E4 isoform differs from the major E3 isoform only by a C112R substitution. ApoE4 interacts with lipoprotein particles and with the amyloid-β peptide, and it is associated with increased incidence of cardiovascular and Alzheimer's disease. To understand the structural basis for the differences between apoE3 and E4 functionality, we used hydrogen-deuterium exchange coupled with a fragment separation method and mass spectrometric analysis to compare their secondary structures at near amino acid resolution...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28094514/structural-model-of-the-tubular-assembly-of-the-rous-sarcoma-virus-capsid-protein
#11
Jaekyun Jeon, Xin Qiao, Ivan Hung, Alok K Mitra, Ambroise Desfosses, Daniel Huang, Peter L Gor'kov, Rebecca C Craven, Richard L Kingston, Zhehong Gan, Fangqiang Zhu, Bo Chen
The orthoretroviral capsid protein (CA) assembles into polymorphic capsids, whose architecture, assembly and stability are still being investigated. The N-terminal and C-terminal domains of CA (NTD and CTD, respectively) engage in both homotypic and heterotypic interactions to create the capsid. Hexameric turrets formed by the NTD decorate the majority of the capsid surface. We report nearly-complete solid-state NMR (ssNMR) resonance assignments of Rous sarcoma virus (RSV) CA, assembled into hexamer tubes that mimic the authentic capsid...
January 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28090689/%C3%AE-aminoxy-peptoids-a-unique-peptoid-backbone-with-a-preference-for-cis-amide-bonds
#12
Viktoria Krieger, Emanuele Ciglia, Roland Thoma, Vera Vasylyeva, Benedikt Frieg, Nader de Sousa Amadeu, Thomas Kurz, Christoph Janiak, Holger Gohlke, Finn Kristian Hansen
α-Peptoids, or N-substituted glycine oligomers, are an important class of peptidomimetic foldamers with proteolytic stability. Nevertheless, the presence of cis-/trans-amide bond conformers, which contribute to the high flexibility of α-peptoids, is considered as a major drawback. A modified peptoid backbone with an improved control of the amide bond geometry could therefore help to overcome this limitation. Here we have performed the first thorough analysis of the folding propensities of α-aminoxy peptoids (or N-substituted 2-aminoxyacetic acid oligomers)...
January 16, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28088792/impact-of-nudt15-polymorphisms-on-thiopurines-induced-myelotoxicity-and-thiopurines-tolerance-dose
#13
Dandan Yin, Xuyang Xia, Junlong Zhang, Shouyue Zhang, Fei Liao, Ge Zhang, Yan Zhang, Qianqian Hou, Xue Yang, Hong Wang, Zhigui Ma, Heyao Wang, Yiping Zhu, Wei Zhang, Yuelan Wang, Bo Liu, Lanlan Wang, Heng Xu, Yang Shu
Thiopurines are widely used as anticancer and immunosuppressive agents. However, life-threatening myelotoxicity has been noticed and largely explained by genetic variations, including NUDT15 polymorphisms (e.g., rs116855232). In this study, we conduct a meta-analysis to investigate the impact of rs116855232 on thiopurines-induced myelotoxicity susceptibility (1752 patients from 7 independent cohorts), as well as on thiopurines intolerance dose (2745 patients from 13 cohorts). Variant allele of rs116855232 contributes 7...
January 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28076345/structure-of-a-spliceosome-remodelled-for-exon-ligation
#14
Sebastian M Fica, Chris Oubridge, Wojciech P Galej, Max E Wilkinson, Xiao-Chen Bai, Andrew J Newman, Kiyoshi Nagai
The spliceosome excises introns from pre-mRNAs in two sequential trans-esterifications - branching and exon ligation(1) - catalysed at a single catalytic metal site in U6 snRNA(2,3). The recent structures of the spliceosomal C complex(4,5) with the cleaved 5'-exon and lariat-3'-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5'-splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site(4)...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28074848/crystal-structure-of-stna-for-the-biosynthesis-of-antitumor-drug-streptonigrin-reveals-a-unique-substrate-binding-mode
#15
Tianle Qian, Jing Wo, Yan Zhang, Quanwei Song, Guoqiang Feng, Ray Luo, Shuangjin Lin, Geng Wu, Hai-Feng Chen
Streptonigrin methylesterase A (StnA) is one of the tailoring enzymes that modify the aminoquinone skeleton in the biosynthesis pathway of Streptomyces species. Although StnA has no significant sequence homology with the reported α/β-fold hydrolases, it shows typical hydrolytic activity in vivo and in vitro. In order to reveal its functional characteristics, the crystal structures of the selenomethionine substituted StnA (SeMet-StnA) and the complex (S185A mutant) with its substrate were resolved to the resolution of 2...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28069812/cooperative-substrate-cofactor-interactions-and-membrane-localization-of-the-bacterial-pla2-enzyme-exou
#16
Maxx H Tessmer, David M Anderson, Adam Buchaklian, Dara W Frank, Jimmy B Feix
The ExoU type III secretion enzyme is a potent phospholipase A2 secreted by the Gram-negative opportunistic pathogen, Pseudomonas aeruginosa. Activation of phospholipase activity is induced by protein-protein interactions with ubiquitin in the cytosol of a targeted eukaryotic cell, leading to destruction of host cell membranes. Previous work in our laboratory suggested that conformational changes within a C-terminal domain of the toxin might be involved in the activation mechanism. In this study, we use site-directed spin labeling electron paramagnetic resonance spectroscopy to investigate conformational changes in a C-terminal four-helical bundle region of ExoU as it interacts with lipid substrates and ubiquitin, and to examine the localization of this domain with respect to the lipid bilayer...
January 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28067787/effects-of-replication-and-transcription-on-dna-structure-related-genetic-instability
#17
REVIEW
Guliang Wang, Karen M Vasquez
Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e...
January 5, 2017: Genes
https://www.readbyqxmd.com/read/28065835/nmr-investigation-of-the-isolated-second-voltage-sensing-domain-of-human-nav1-4-channel
#18
A S Paramonov, E N Lyukmanova, M Yu Myshkin, M A Shulepko, D S Kulbatskii, N S Petrosian, A O Chugunov, D A Dolgikh, M P Kirpichnikov, A S Arseniev, Z O Shenkarev
Voltage-gated Na(+) channels are essential for the functioning of cardiovascular, muscular, and nervous systems. The α-subunit of eukaryotic Na(+) channel consists of ~2000 amino acid residues and encloses 24 transmembrane (TM) helices, which form five membrane domains: four voltage-sensing (VSD) and one pore domain. The structural complexity significantly impedes recombinant production and structural studies of full-sized Na(+) channels. Modular organization of voltage-gated channels gives an idea for studying of the isolated second VSD of human skeletal muscle Nav1...
January 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28064306/-dna-tandem-lesion-5-8-cyclo-2-deoxyadenosine-the-influence-on-human-health
#19
A Merecz, B T Karwowski
Nucleic acids are the targets for various endogenous and exogenous genotoxic agents, including reactive oxygen species. The appearance of a hydroxyl racial (^(<b>.</b>)OH), the most harmful molecule, next to an oligonucleotide can lead to two types of DNA damage: strand breaks or nucleobase modifications. Since clustered DNA damage is defined as the presence of two or more lesions in one helix turn, purine 5',8-cyclo-2'-deoxynucleosides are recognized as tandem lesions: both sugar moieties and base have been modified within one nucleoside/nucleotide...
November 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28064131/a-bio-chemical-application-of-n-gqds-and-g-c3n4-qds-sensitized-tio2-nanopillars-for-the-quantitative-detection-of-pcdna3-hbv
#20
Xuehui Pang, Hongjun Bian, Weijie Wang, Cheng Liu, Malik Saddam Khan, Qiao Wang, Jianni Qi, Qin Wei, Bin Du
Herein, TiO2 nanopillars (NPs)/N-doped graphene quantum dots (N-GQDs)/g-C3N4 QDs heterojunction efficiently suppressed the photogenerated charges recombination and improved photo-to-current conversion efficiency. The introduced N-GQDs and g-C3N4 QDs could result in more effective separation of the photogenerated charges, and thus produce a further increase of the photocurrent. TiO2 NPs/N-GQDs/g-C3N4 QDs were firstly applied as the photoactive materials for the fabrication of the biosensors, and the primers of pcDNA3-HBV were then adsorbed on the TiO2 NPs/N-GQDs/g-C3N4 QDs modified electrode under the activation of EDC/NHS...
December 30, 2016: Biosensors & Bioelectronics
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