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Helix stabilisation

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https://www.readbyqxmd.com/read/29740657/nematic-colloidal-knots-in-topological-environments
#1
S Masoomeh Hashemi, Miha Ravnik
The role of environment in shaping material properties is of great significance, but less is known about how non-trivial topology of the environment couples to material states, which can be of non-trivial topology themselves. In this paper, we demonstrate the role of the topology of the environment on the formation of complex nematic fields and defect structures, specifically in the system of nematic colloidal knots. The topological environments around knotted colloidal particles are suggested to exist as spherical surface-patterned nematic cavities imposing radial, uniform or hyperbolic nematic profiles...
May 9, 2018: Soft Matter
https://www.readbyqxmd.com/read/29410984/the-role-of-water-molecules-in-phototransduction-of-retinal-proteins-and-g-protein-coupled-receptors
#2
Elena Lesca, Valérie Panneels, Gebhard F X Schertler
G protein coupled receptors (GPCRs) are a key family of membrane proteins in all eukaryotes and also very important drug targets for medical intervention. The extensively studied visual pigment rhodopsin is a prime example of a family A GPCR. Its chromophore ligand retinal is covalently linked to a lysine in helix seven forming a protonated Schiff base. Interestingly, this is the same situation in other-non-GPCR-retinal proteins, like the prototype light-driven microbial proton pump bacteriorhodopsin, albeit there is no (or only a very remote) phylogenetical link...
April 17, 2018: Faraday Discussions
https://www.readbyqxmd.com/read/29369425/roles-of-amphipathicity-and-hydrophobicity-in-the-micelle-driven-structural-switch-of-a-14-mer-peptide-core-from-a-choline-binding-repeat
#3
Hector Zamora-Carreras, Beatriz Maestro, Erik Strandberg, Anne S Ulrich, Jesús M Sanz, M Angeles Jimenez
Choline-binding repeats (CBRs) are ubiquitous sequences with a β-hairpin core that are found in the surface proteins of several microorganisms such as S. pneumoniae (pneumococcus). Previous studies on a 14-mer CBR sequence derived from the pneumoccal LytA autolysin (LytA₂₃₉-₂₅₂ peptide) have demonstrated a switch behaviour for this peptide, so that it acquires a stable, native-like β-hairpin conformation in aqueous solution but is reversibly transformed into an amphipathic α-helix in the presence of detergent micelles...
January 25, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29233227/dna-partitions-into-triplets-under-tension-in-the-presence-of-organic-cations-with-sequence-evolutionary-age-predicting-the-stability-of-the-triplet-phase
#4
Amirhossein Taghavi, Paul van der Schoot, Joshua T Berryman
Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure-function relationship in Σ DNA...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29044185/structural-analysis-of-variant-of-helicobacter-pylori-motb-in-its-activated-form-engineered-as-chimera-of-motb-and-leucine-zipper
#5
Daniel A Andrews, Yuri E Nesmelov, Matthew C Wilce, Anna Roujeinikova
Rotation of the bacterial flagellum is powered by a proton influx through the peptidoglycan (PG)-tethered stator ring MotA/B. MotA and MotB form an inner-membrane complex that does not conduct protons and does not bind to PG until it is inserted into the flagellar motor. The opening of the proton channel involves association of the plug helices in the periplasmic region of the MotB dimer into a parallel coiled coil. Here, we have characterised the structure of a soluble variant of full-length Helicobacter pylori MotB in which the plug helix was engineered to be locked in a parallel coiled coil state, mimicking the open state of the stator...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28755644/impact-of-potent-bioremediation-enhancing-plant-extracts-on-raoultella-ornithinolytica-properties
#6
A Zdarta, B Dudzińska-Bajorek, A Nowak, U Guzik, E Kaczorek
Long-term contact of microorganisms with different compounds in the environment can cause significant changes in cell metabolism. Surfactants adsorption on cell surface or incorporation in the cell membrane, lead to their modification, which helps microorganisms adopt to the conditions of metabolic stress. The main objective of this study was to investigate the effects of three saponin-reach plant extracts from Hedera helix, Saponaria officinalis and Sapindus mucorossi on growth and adaptation of Raoultella ornithinolytica to high concentrations of these substances...
November 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28646497/geometrical-principles-of-homomeric-%C3%AE-barrels-and-%C3%AE-helices-application-to-modeling-amyloid-protofilaments
#7
Steven Hayward, E James Milner-White
Examples of homomeric β-helices and β-barrels have recently emerged. Here we generalize the theory for the shear number in β-barrels to encompass β-helices and homomeric structures. We introduce the concept of the "β-strip," the set of parallel or antiparallel neighboring strands, from which the whole helix can be generated giving it n-fold rotational symmetry. In this context, the shear number is interpreted as the sum around the helix of the fixed register shift between neighboring identical β-strips...
October 2017: Proteins
https://www.readbyqxmd.com/read/28554535/a-phosphorylation-motif-for-tuneable-helix-stabilisation-in-intrinsically-disordered-proteins-lessons-from-the-sodium-proton-exchanger-1-nhe1
#8
Ruth Hendus-Altenburger, Matteo Lambrughi, Thilde Terkelsen, Stine F Pedersen, Elena Papaleo, Kresten Lindorff-Larsen, Birthe B Kragelund
Intrinsically disordered proteins (IDPs) are involved in many pivotal cellular processes including phosphorylation and signalling. The structural and functional effects of phosphorylation of IDPs remain poorly understood and difficult to predict. Thus, a need exists to identify motifs that confer phosphorylation-dependent perturbation of the local preferences for forming e.g. helical structures as well as motifs that do not. The disordered distal tail of the Na(+)/H(+) exchanger 1 (NHE1) is six-times phosphorylated (S693, S723, S726, S771, T779, S785) by the mitogen activated protein kinase 2 (MAPK1, ERK2)...
May 26, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/28530653/structure-of-a-pre-catalytic-spliceosome
#9
Clemens Plaschka, Pei-Chun Lin, Kiyoshi Nagai
Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae pre-catalytic B complex spliceosome at near-atomic resolution. The mobile U2 small nuclear ribonucleoprotein particle (snRNP) associates with U4/U6.U5 tri-snRNP through the U2/U6 helix II and an interface between U4/U6 di-snRNP and the U2 snRNP SF3b-containing domain, which also transiently contacts the helicase Brr2...
June 29, 2017: Nature
https://www.readbyqxmd.com/read/28504839/the-pathological-trento-variant-of-alpha-1-antitrypsin-e75v-shows-nonclassical-behaviour-during-polymerization
#10
Elena Miranda, Ilaria Ferrarotti, Romina Berardelli, Mattia Laffranchi, Marta Cerea, Fabrizio Gangemi, Imran Haq, Stefania Ottaviani, David A Lomas, James A Irving, Annamaria Fra
Severe alpha-1-antitrypsin deficiency (AATD) is most frequently associated with the alpha-1-antitrypsin (AAT) Z variant (E342K). ZZ homozygotes exhibit accumulation of AAT as polymers in the endoplasmic reticulum of hepatocytes. This protein deposition can lead to liver disease, with the resulting low circulating levels of AAT predisposing to early-onset emphysema due to dysregulation of elastinolytic activity in the lungs. An increasing number of rare AAT alleles have been identified in patients with severe AATD, typically in combination with the Z allele...
July 2017: FEBS Journal
https://www.readbyqxmd.com/read/28132097/membrane-traversing-mechanism-of-thyroid-hormone-transport-by-monocarboxylate-transporter-8
#11
Jonas Protze, Doreen Braun, Katrin Manuela Hinz, Dorothea Bayer-Kusch, Ulrich Schweizer, Gerd Krause
Monocarboxylate transporter 8 (MCT8) mediates thyroid hormone (TH) transport across the plasma membrane in many cell types. In order to better understand its mechanism, we have generated three new MCT8 homology models based on sugar transporters XylE in the intracellular opened (PDB ID: 4aj4) and the extracellular partly occluded (PDB ID: 4gby) conformations as well as FucP (PDB ID: 3o7q) and GLUT3 (PDB ID: 4zwc) in the fully extracellular opened conformation. T3 -docking studies from both sides revealed interactions with His192, His415, Arg445 and Asp498 as previously identified...
June 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/27876844/the-n-terminal-loop-of-irak-4-death-domain-regulates-ordered-assembly-of-the-myddosome-signalling-scaffold
#12
Anthony C G Dossang, Precious G Motshwene, Yang Yang, Martyn F Symmons, Clare E Bryant, Satty Borman, Julie George, Alexander N R Weber, Nicholas J Gay
Activation of Toll-like receptors induces dimerization and the recruitment of the death domain (DD) adaptor protein MyD88 into an oligomeric post receptor complex termed the Myddosome. The Myddosome is a hub for inflammatory and oncogenic signaling and has a hierarchical arrangement with 6-8 MyD88 molecules assembling with exactly 4 of IRAK-4 and 4 of IRAK-2. Here we show that a conserved motif in IRAK-4 (Ser8-X-X-X-Arg12) is autophosphorylated and that the phosphorylated DD is unable to form Myddosomes. Furthermore a mutant DD with the phospho-mimetic residue Asp at this position is impaired in both signalling and Myddosome assembly...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27677223/a-novel-homozygous-variant-in-serpinh1-associated-with-a-severe-lethal-presentation-of-osteogenesis-imperfecta-with-hydranencephaly
#13
Charlotte Marshall, Jaime Lopez, Laura Crookes, Rebecca C Pollitt, Meena Balasubramanian
Osteogenesis imperfecta (OI) is a genetic disorder characterised by low bone mineral density resulting in fractures. 85-90% of patients with OI carry a variant in the type 1 collagen genes, COL1A1 and COL1A2, which follows an autosomal dominant pattern of inheritance. However, within the last two decades, there have been growing number of variants identified in genes that follow an autosomal recessive pattern of inheritance. Our proband is a child born in Mexico with multiple fractures of ribs, minimal calvarial mineralisation, platyspondyly, marked compression and deformed long bones...
December 20, 2016: Gene
https://www.readbyqxmd.com/read/27459055/cryo-em-structure-of-the-spliceosome-immediately-after-branching
#14
Wojciech P Galej, Max E Wilkinson, Sebastian M Fica, Chris Oubridge, Andrew J Newman, Kiyoshi Nagai
Precursor mRNA (pre-mRNA) splicing proceeds by two consecutive transesterification reactions via a lariat-intron intermediate. Here we present the 3.8 Å cryo-electron microscopy structure of the spliceosome immediately after lariat formation. The 5'-splice site is cleaved but remains close to the catalytic Mg(2+) site in the U2/U6 small nuclear RNA (snRNA) triplex, and the 5'-phosphate of the intron nucleotide G(+1) is linked to the branch adenosine 2'OH. The 5'-exon is held between the Prp8 amino-terminal and linker domains, and base-pairs with U5 snRNA loop 1...
September 8, 2016: Nature
https://www.readbyqxmd.com/read/27422871/molecular-basis-of-rna-guanine-7-methyltransferase-rnmt-activation-by-ram
#15
Dhaval Varshney, Alain-Pierre Petit, Juan A Bueren-Calabuig, Chimed Jansen, Dan A Fletcher, Mark Peggie, Simone Weidlich, Paul Scullion, Andrei V Pisliakov, Victoria H Cowling
Maturation and translation of mRNA in eukaryotes requires the addition of the 7-methylguanosine cap. In vertebrates, the cap methyltransferase, RNA guanine-7 methyltransferase (RNMT), has an activating subunit, RNMT-Activating Miniprotein (RAM). Here we report the first crystal structure of the human RNMT in complex with the activation domain of RAM. A relatively unstructured and negatively charged RAM binds to a positively charged surface groove on RNMT, distal to the active site. This results in stabilisation of a RNMT lobe structure which co-evolved with RAM and is required for RAM binding...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27160967/insights-into-the-structural-dynamics-of-liver-kinase-b1-lkb1-by-the-binding-of-ste20-related-adapter%C3%AE-strad%C3%AE-and-mouse-protein-25%C3%AE-mo25%C3%AE-co-activators
#16
Ikrormi Rungsung, Amutha Ramaswamy
LKB1, the tumour suppressor, is found mutated in Peutz-Jeghers syndrome (PJS). The LKB1 is a serine-threonine kinase protein that is allosterically activated by the binding of STRADα and MO25α without phosphorylating the Thr212 present at activation loop. The present study aims to highlight the structural dynamics and complexation mechanism during the allosteric activation of LKB1 by these co-activators using molecular dynamics simulations. The all atom simulations performed on the complexes of LKB1 with ATP, STRADα, and MO25α for a period of 30 ns reveal that binding of STRADα and MO25α significantly stabilizes the highly flexible regions of LKB1 such as ATP binding region (β1-β2 loop), catalytic & activation loop segments and αG helix...
April 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27038511/the-functional-role-of-el19-and-eb12-intersubunit-bridge-in-the-eukaryotic-ribosome
#17
Ivan Kisly, Suna P Gulay, Uno Mäeorg, Jonathan D Dinman, Jaanus Remme, Tiina Tamm
During translation, the two eukaryotic ribosomal subunits remain associated through 17 intersubunit bridges, five of which are eukaryote specific. These are mainly localized to the peripheral regions and are believed to stabilize the structure of the ribosome. The functional importance of these bridges remains largely unknown. Here, the essentiality of the eukaryote-specific bridge eB12 has been investigated. The main component of this bridge is ribosomal protein eL19 that is composed of an N-terminal globular domain, a middle region, and a long C-terminal α-helix...
May 22, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/26965894/the-binding-landscape-of-plasmepsin-v-and-the-implications-for-flap-dynamics
#18
McGillewie L, Mahmoud E Soliman
Plasmepsin V belongs to the plasmepsin family of aspartic proteases. PlmV is unique compared to other plasmepsins, as this membrane bound aspartic protease resides in the endoplasmic reticulum and is responsible for the cleavage of PEXEL tagged proteins destined for export outside of the host red blood cell. Plasmepsin V is highly conserved throughout the Plasmodium species, and is essential to the survival of the parasite. Recently, two potent inhibitors of Plmv have been identified, WEHI-916 and WEHI-842...
April 26, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/26659814/sh3-domains-differentially-stimulate-distinct-dynamin-i-assembly-modes-and-g-domain-activity
#19
Sai Krishnan, Michael Collett, Phillip J Robinson
Dynamin I is a highly regulated GTPase enzyme enriched in nerve terminals which mediates vesicle fission during synaptic vesicle endocytosis. One regulatory mechanism involves its interactions with proteins containing Src homology 3 (SH3) domains. At least 30 SH3 domain-containing proteins bind dynamin at its proline-rich domain (PRD). Those that stimulate dynamin activity act by promoting its oligomerisation. We undertook a systematic parallel screening of 13 glutathione-S-transferase (GST)-tagged endocytosis-related SH3 domains on dynamin binding, GTPase activity and oligomerisation...
2015: PloS One
https://www.readbyqxmd.com/read/26312850/pharmacokinetics-and-pharmacodynamics-of-subcutaneously-administered-pyy3-36-and-its-analogues-in-vivo
#20
Jaimini Cegla, Joyceline Cuenco, James Minnion, Samar Ghourab, Klara Hostomska, Tricia Tan, Stephen Bloom
BACKGROUND: Obesity is an emergent epidemic associated with morbidity, mortality, and psychosocial effects. One of the key gut hormones that controls appetite is peptide tyrosine-tyrosine 3-36 (PYY3-36) whose circulating half-life is only 8 min. A long-acting analogue of PYY3-36 would therefore have great potential as an antiobesity agent. The aims of this study were to investigate the effect of various aminoacid modifications of PYY3-36 on pharmacokinetics and their ability to suppress food intake...
February 26, 2015: Lancet
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