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Unstructured Proteins

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https://www.readbyqxmd.com/read/28109185/folding-of-intrinsically-disordered-plant-lea-proteins-is-driven-by-glycerol-induced-crowding-and-the-presence-of-membranes
#1
Anne Bremer, Martin Wolff, Anja Thalhammer, Dirk K Hincha
Late embryogenesis abundant (LEA) proteins are related to cellular dehydration tolerance. Most LEA proteins are predicted to have no stable secondary structure in solution, i.e. to be intrinsically disordered proteins (IDPs), but they may acquire α-helical structure upon drying. In the model plant Arabidopsis thaliana the LEA proteins COR15A and COR15B are highly induced upon cold treatment and are necessary for the plants to attain full freezing tolerance. Freezing leads to increased intracellular crowding due to dehydration by extracellular ice crystals...
January 21, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28106390/tubulin-binding-and-polymerization-promoting-properties-of-tppp-proteins-are-evolutionarily-conserved
#2
Judit Oláh, Tibor Szénási, Adél Szabó, Kinga Kovács, Péter Lőw, Mauro Stifanic, Ferenc Orosz
Tubulin Polymerization Promoting Proteins (TPPPs) constitute a new eukaryotic protein family. There are three TPPP paralogs in the human genome; denoted as TPPP1, TPPP2 and TPPP3. TPPP1 and TPPP3 are intrinsically unstructured proteins (IUPs) that bind and polymerize tubulin and stabilize microtubules but TPPP2 does not. Vertebrate TPPPs originated from the ancient invertebrate TPPP by two-round whole-genome-duplication thus it was an open question whether the tubulin/microtubule binding function of TPPP1 and TPPP3 is a newly acquired property or it was present in the invertebrate orthologs (generally one TPPP/species)...
January 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28104810/the-foxp2-forkhead-domain-binds-to-a-variety-of-dna-sequences-with-different-rates-and-affinities
#3
Helen Webb, Olga Steeb, Ashleigh Blane, Lia Rotherham, Shaun Aron, Phillip Machanick, Heini Dirr, Sylvia Fanucchi
FOXP2 is a member of the P subfamily of FOX transcription factors, the DNA binding domain of which is the winged helix forkhead domain. In this work we show that the FOXP2 forkhead domain is able to bind to various DNA sequences, including a novel sequence identified in this work, with different affinities and rates as detected using surface plasmon resonance. Combining the experimental work with molecular docking, we show that high affinity sequences remain bound to the protein for longer, form a greater number of interactions with the protein and induce a greater structural change in the protein than low affinity sequences...
January 18, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28102071/temperature-induced-misfolding-in-prion-protein-evidences-of-multiple-partially-disordered-states-stabilized-by-non-native-hydrogen-bonds
#4
Neharika G Chamachi, Suman Chakrabarty
The structural basis of misfolding pathways of a cellular Prion (PrP(C)) into the toxic scrapie form (PrP(SC)) and identification of possible intermediates (e.g. PrP(*)) still eludes us. In this work, we have used a cumulative ~65µs of Replica Exchange Molecular Dynamics simulation data to construct the conformational free energy landscapes and capture the structural and thermodynamic characteristics associated with various stages of the thermal denaturation process in human Prion protein. The temperature dependent free energy surfaces consist of multiple metastable states stabilized by non-native contacts and hydrogen bonds, thus rendering the protein prone towards misfolding...
January 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28096372/helical-structure-stability-and-dynamics-in-human-apolipoprotein-e3-and-e4-by-hydrogen-exchange-and-mass-spectrometry
#5
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/28092832/sampling-conformational-space-of-intrinsically-disordered-proteins-in-explicit-solvent-comparison-between-well-tempered-ensemble-approach-and-solute-tempering-method
#6
Mengzhi Han, Ji Xu, Ying Ren
Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent...
December 28, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28092367/molecular-architecture-and-dynamics-of-ash1-mrna-recognition-by-its-mrna-transport-complex
#7
Franziska Theresia Edelmann, Andreas Schlundt, Roland Gerhard Heym, Andreas Jenner, Annika Niedner-Boblenz, Muhammad Ibrahim Syed, Jean-Christophe Paillart, Ralf Stehle, Robert Janowski, Michael Sattler, Ralf-Peter Jansen, Dierk Niessing
mRNA localization is an essential mechanism of gene regulation and is required for processes such as stem-cell division, embryogenesis and neuronal plasticity. It is not known which features in the cis-acting mRNA localization elements (LEs) are specifically recognized by motor-containing transport complexes. To the best of our knowledge, no high-resolution structure is available for any LE in complex with its cognate protein complex. Using X-ray crystallography and complementary techniques, we carried out a detailed assessment of an LE of the ASH1 mRNA from yeast, its complex with its shuttling RNA-binding protein She2p, and its highly specific, cytoplasmic complex with She3p...
January 16, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28079879/the-cluspro-web-server-for-protein-protein-docking
#8
Dima Kozakov, David R Hall, Bing Xia, Kathryn A Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda
The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28079140/methionine-residues-around-phosphorylation-sites-are-preferentially-oxidized-in-vivo-under-stress-conditions
#9
Francisco J Veredas, Francisco R Cantón, J Carlos Aledo
Protein phosphorylation is one of the most prevalent and well-understood protein modifications. Oxidation of protein-bound methionine, which has been traditionally perceived as an inevitable damage derived from oxidative stress, is now emerging as another modification capable of regulating protein activity during stress conditions. However, the mechanism coupling oxidative signals to changes in protein function remains unknown. An appealing hypothesis is that methionine oxidation might serve as a rheostat to control phosphorylation...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28060425/strong-tough-stretchable-and-self-adhesive-hydrogels-from-intrinsically-unstructured-proteins
#10
Mark A Gonzalez, Joseph R Simon, Ali Ghoorchian, Zachary Scholl, Shaoting Lin, Michael Rubinstein, Piotr Marszalek, Ashutosh Chilkoti, Gabriel P López, Xuanhe Zhao
Strong, tough, stretchable, and self-adhesive hydrogels have been designed with intrinsically unstructured proteins. The extraordinary mechanical properties exhibited by these materials are enabled by an integration of toughening mechanisms that maintain high elasticity and dissipate mechanical energy within the protein networks.
January 6, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28001375/novel-kinetic-intermediates-populated-along-the-folding-pathway-of-the-transmembrane-%C3%AE-barrel-ompa
#11
Emily J Danoff, Karen G Fleming
We examined the folding of the β-barrel membrane protein OmpA from Escherichia coli. Although previous studies identified several intermediate states followed by a concerted translocation mechanism across the bilayer, some aspects of the pathway were still unclear, including the extent of secondary structure formation in the intermediate states and how the mechanism gave rise to multiple exponential phases in the folding kinetics. We addressed these questions by investigating the folding kinetics of the OmpA transmembrane β-barrel domain over a range of bilayer thicknesses, allowing us to observe different regions of the folding pathway...
December 21, 2016: Biochemistry
https://www.readbyqxmd.com/read/27998984/the-assembly-factor-pet117-couples-heme-a-synthase-activity-to-cytochrome-oxidase-assembly
#12
Nicholas G Taylor, Samantha Swenson, Nicholas J Harris, Edward M Germany, Jennifer L Fox, Oleh Khalimonchuk
Heme a is an essential metalloporphyrin cofactor of the mitochondrial respiratory enzyme cytochrome c oxidase (CcO). Its synthesis from heme b requires several enzymes including the evolutionarily conserved heme a synthase (Cox15). Oligomerization of Cox15 appears to be important for the process of heme a biosynthesis and transfer to maturing CcO. However, the details of this process remain elusive, and the roles of any additional CcO assembly factors that may be involved remain unclear. Here we report the systematic analysis of one such uncharacterized assembly factor, Pet117, and demonstrate in Saccharomyces cerevisiae that this evolutionarily conserved protein is necessary for Cox15 oligomerization and function...
December 20, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27997568/longipin-an-amyloid-antimicrobial-peptide-from-the-harvestman-acutisoma-longipes-arachnida-opiliones-with-preferential-affinity-for-anionic-vesicles
#13
Raphael Santa Rosa Sayegh, Isabel de Fátima Correia Batista, Robson Lopes de Melo, Karin A Riske, Sirlei Daffre, Guillermo Montich, Pedro Ismael da Silva Junior
In contrast to vertebrate immune systems, invertebrates lack an adaptive response and rely solely on innate immunity in which antimicrobial peptides (AMPs) play an essential role. Most of them are membrane active molecules that are typically unstructured in solution and adopt secondary/tertiary structures upon binding to phospholipid bilayers. This work presents the first characterization of a constitutive AMP from the hemolymph of an Opiliones order animal: the harvestman Acutisoma longipes. This peptide was named longipin...
2016: PloS One
https://www.readbyqxmd.com/read/27993012/rational-design-of-small-molecules-targeting-oncogenic-noncoding-rnas-from-sequence
#14
Matthew D Disney, Alicia J Angelbello
The discovery of RNA catalysis in the 1980s and the dissemination of the human genome sequence at the start of this century inspired investigations of the regulatory roles of noncoding RNAs in biology. In fact, the Encyclopedia of DNA Elements (ENCODE) project has shown that only 1-2% of the human genome encodes protein, yet 75% is transcribed into RNA. Functional studies both preceding and following the ENCODE project have shown that these noncoding RNAs have important roles in regulating gene expression, developmental timing, and other critical functions...
December 20, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/27984194/the-human-trna-modifying-protein-trit1-forms-amyloid-fibers-in-vitro
#15
T J Waller, D F Read, D R Engelke, P J Smaldino
TRIT1 is a highly conserved tRNA isopentenyl transferase that modifies a subset of tRNAs in human cells and is a candidate tumor suppressor in lung cancer in certain ethnic populations. The yeast homologue, Mod5, has similar tRNA-modifying functions in the cytoplasm and is required for the transcriptional silencing activity of RNA polymerase II promoters near tRNA genes in the nucleus, a phenomenon termed tRNA gene mediated (tgm) silencing. Furthermore, Mod5 can fold into amyloid fibers in vitro and in vivo, which confers resistance to certain fungicides in yeast...
October 28, 2016: Gene
https://www.readbyqxmd.com/read/27973707/moonlighting-chaperone-like-activity-of-the-universal-regulatory-14-3-3-proteins
#16
REVIEW
Nikolai N Sluchanko, Nikolai B Gusev
The ubiquitous eukaryotic 14-3-3 proteins coordinate multiple cellular processes due to their well-known regulatory function that is based on specific recognition of phosphorylated motifs in their partners. In this context, 14-3-3 proteins have, in reports, been called 'chaperones'. Although in the classical meaning this is not fully correct, recent studies have revealed that 14-3-3 can indeed be an integral part of the protein quality control system, as they: (i) display ATP-independent anti-aggregation ('holdase') activity, similar to that of the unrelated small heat shock proteins; (ii) assist in clearing misfolded proteins by directing them to proteasomes or aggresomes; (iii) cooperate with classical chaperones for substrate refolding; and also (iv) are associated with neurodegenerative disorders by affecting aggregation of tau, prion protein, α-synuclein, and huntingtin, etc...
December 14, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27960036/emerin-self-assembly-mechanism-role-of-the-lem-domain
#17
Camille Samson, Florian Celli, Kitty Hendriks, Maximilian Zinke, Nada Essawy, Isaline Herrada, Ana-Andreea Arteni, François-Xavier Theillet, Béatrice Alpha-Bazin, Jean Armengaud, Catherine Coirault, Adam Lange, Sophie Zinn-Justin
At the nuclear envelope, the inner nuclear membrane protein emerin contributes to the interface between the nucleoskeleton and the chromatin. Emerin is an essential actor of the nuclear response to a mechanical signal. Genetic defects in emerin cause Emery-Dreifuss muscular dystrophy. It was proposed that emerin oligomerization regulates nucleoskeleton binding and impaired oligomerization contributes to the loss of function of emerin disease-causing mutants. We here report the first structural characterization of emerin oligomers...
December 13, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27959512/distinct-dynamic-modes-enable-the-engagement-of-dissimilar-ligands-in-a-promiscuous-atypical-rna-recognition-motif
#18
Kerene A Brown, Samel Sharifi, Rawaa Hussain, Logan Donaldson, Mark A Bayfield, Derek J Wilson
Conformational dynamics play a critical role in ligand binding, often conferring divergent activities and specificities even in species with highly similar ground-state structures. Here, we employ time-resolved electrospray ionization hydrogen-deuterium exchange (TRESI-HDX) to characterize the changes in dynamics that accompany oligonucleotide binding in the atypical RNA recognition motif (RRM2) in the C-terminal domain (CTD) of human La protein. Using this approach, which is uniquely capable of probing changes in the structure and dynamics of weakly ordered regions of proteins, we reveal that binding of RRM2 to a model 23-mer single-stranded RNA and binding of RRM2 to structured IRES domain IV of the hepatitis C viral (HCV) RNA are driven by fundamentally different dynamic processes...
December 27, 2016: Biochemistry
https://www.readbyqxmd.com/read/27936623/automated-strong-cation-exchange-cleanup-to-remove-macromolecular-crowding-agents-for-protein-hydrogen-exchange-mass-spectrometry
#19
Farai I Rusinga, David D Weis
Measuring amide hydrogen exchange (HX) of intrinsically disordered proteins (IDPs) in solutions containing high concentrations of macromolecular crowding agents would give new insights into the structure and dynamics of these proteins under crowded conditions. High concentrations of artificial crowders, required to simulate cellular crowding, introduce overwhelming interferences to mass spectrometry (MS) analysis. We have developed a fully automated, dual-stage online cleanup that uses strong cation-exchange (SCX) followed by reversed-phase desalting to remove Ficoll, a synthetic polymer, for HX-MS analysis of proteins under crowded conditions...
December 23, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27917837/purification-crystallization-and-characterization-of-the-pseudomonas-outer-membrane-protein-fapf-a-functional-amyloid-transporter
#20
Sarah L Rouse, Wlliam J Hawthorne, Sebastian Lambert, Marc L Morgan, Stephen A Hare, Stephen Matthews
Bacteria often produce extracellular amyloid fibres via a multi-component secretion system. Aggregation-prone, unstructured subunits cross the periplasm and are secreted through the outer membrane, after which they self-assemble. Here, significant progress is presented towards solving the high-resolution crystal structure of the novel amyloid transporter FapF from Pseudomonas, which facilitates the secretion of the amyloid-forming polypeptide FapC across the bacterial outer membrane. This represents the first step towards obtaining structural insight into the products of the Pseudomonas fap operon...
December 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
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