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Intrinsically disordered protein

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https://www.readbyqxmd.com/read/28104628/mobidb-lite-fast-and-highly-specific-consensus-prediction-of-intrinsic-disorder-in-proteins
#1
Marco Necci, Damiano Piovesan, Zsuzsanna Dosztányi, Silvio C E Tosatto
MOTIVATION: Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder...
January 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28098335/not-an-exception-to-the-rule-the-functional-significance-of-intrinsically-disordered-protein-regions-in-enzymes
#2
Shelly DeForte, Vladimir N Uversky
Intrinsically disordered protein regions (IDPRs) are remarkably common and have unique and important biological functions. Enzymes have long been considered an exception to the rule of protein intrinsic disorder due to the structural requirements for catalysis. Although functionally significant IDPRs have been described in several enzymes, there has been no study quantifying the extent of this phenomenon. We have conducted a multilevel computational analysis of missing regions in X-ray crystal structures in the PDB and predicted disorder in 66 representative proteomes...
January 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28097742/differential-dehydration-effects-on-globular-proteins-and-intrinsically-disordered-proteins-during-film-formation
#3
Juliana Sakamoto Yoneda, Andew J Miles, Ana Paula Ulian de Araujo, B A Wallace
Globular proteins composed of different secondary structures and fold types were examined by synchrotron radiation circular dichroism spectroscopy to determine the effects of dehydration on their secondary structures. They exhibited only minor changes upon removal of bulk water during film formation, contrary to previously reported studies of proteins dehydrated by lyophilisation (where substantial loss of helical structure and gain in sheet structure was detected). This near lack of conformational change observed for globular proteins contrasts with intrinsically disordered proteins (IDPs) dried in the same manner: the IDPs, which have almost completely unordered structures in solution, exhibited increased amounts of regular (mostly helical) secondary structures when dehydrated, suggesting formation of new intra-protein hydrogen bonds replacing solvent-protein hydrogen bonds, in a process which may mimic interactions that occur when IDPs bind to partner molecules...
January 18, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28095698/evaluation-of-the-coupled-two-dimensional-main-chain-torsional-potential-in-modeling-intrinsically-disordered-proteins
#4
Ya Gao, Chaomin Zhang, John Z H Zhang, Ye Mei
Intrinsically Disordered Proteins (IDPs) carry out crucial biological functions in essential biological processes of life. Due to the highly dynamic and conformationally heterogeneous nature of the disordered states of IDPs, molecular dynamics simulations are becoming an indispensable tool for the investigation of the conformational ensembles and dynamic properties of IDPs. Nevertheless, there is still no consensus on the most reliable force field in molecular dynamics simulations for IDPs hitherto. In this work, a recently proposed AMBER99SB2D force field is evaluated in modeling some disordered polypeptides and proteins by checking its ability in reproducing NMR experimental data...
January 18, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28094514/structural-model-of-the-tubular-assembly-of-the-rous-sarcoma-virus-capsid-protein
#5
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/28094373/conformational-dynamics-and-self-association-of-intrinsically-disordered-huntingtin-exon-1-in-cells
#6
Steffen Büning, Abhishek Sharma, Shivang Vachharajani, Estella Newcombe, Angelique Ormsby, Mimi Gao, David Gnutt, Tobias Vöpel, Danny M Hatters, Simon Ebbinghaus
Huntington's disease is caused by a CAG trinucleotide expansion mutation in the Huntingtin gene that leads to an artificially long polyglutamine sequence in the Huntingtin protein. A key feature of the disease is the intracellular aggregation of the Huntingtin exon 1 protein (Httex1) into micrometer sized inclusion bodies. The aggregation process of Httex1 has been extensively studied in vitro, however, the crucial early events of nucleation and aggregation in the cell remain elusive. Here, we studied the conformational dynamics and self-association of Httex1 by in-cell experiments using laser-induced temperature jumps and analytical ultracentrifugation...
January 17, 2017: Physical Chemistry Chemical Physics: PCCP
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
#7
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/28089448/structural-basis-for-the-interaction-of-a-human-small-heat-shock-protein-with-the-14-3-3-universal-signaling-regulator
#8
Nikolai N Sluchanko, Steven Beelen, Alexandra A Kulikova, Stephen D Weeks, Alfred A Antson, Nikolai B Gusev, Sergei V Strelkov
By interacting with hundreds of protein partners, 14-3-3 proteins coordinate vital cellular processes. Phosphorylation of the small heat shock protein, HSPB6, within its intrinsically disordered N-terminal domain activates its interaction with 14-3-3, ultimately triggering smooth muscle relaxation. After analyzing the binding of an HSPB6-derived phosphopeptide to 14-3-3 using isothermal calorimetry and X-ray crystallography, we have determined the crystal structure of the complete assembly consisting of the 14-3-3 dimer and full-length HSPB6 dimer and further characterized this complex in solution using fluorescence spectroscopy, small-angle X-ray scattering, and limited proteolysis...
December 30, 2016: Structure
https://www.readbyqxmd.com/read/28078740/simlabel-a-graphical-user-interface-to-simulate-continuous-wave-epr-spectra-from-site-directed-spin-labeling-experiments
#9
E Etienne, N Le Breton, M Martinho, E Mileo, V Belle
Site Directed Spin Labeling (SDSL) combined with continuous wave Electron Paramagnetic Resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the residue level, structural transitions in proteins. SDSL-EPR is based on the selective grafting of a paramagnetic label on the protein under study, followed by cw EPR analysis. To extract valuable quantitative information from SDSL-EPR spectra and thus give reliable interpretation on biological system dynamics, numerical simulations of the spectra are required...
January 12, 2017: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/28078722/ssb-and-the-recg-dna-helicase-an-intimate-association-to-rescue-a-stalled-replication-fork
#10
REVIEW
Piero R Bianco, Yuri L Lyubchenko
In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy...
January 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28078720/the-intrinsically-disordered-linker-of-e-coli-ssb-is-critical-for-the-release-from-single-stranded-dna
#11
Hui Yin Tan, Luke A Wilczek, Sasheen Pottinger, Maria Manosas, Cong Yu, Trong Nguyenduc, Piero R Bianco
The Escherichia coli single stranded DNA binding protein (SSB) is crucial for DNA replication, recombination and repair. Within each process, it has two seemingly disparate roles: it stabilizes single-stranded DNA (ssDNA) intermediates generated during DNA processing and, forms complexes with a group of proteins known as the SSB-interactome. Key to both roles is the C-terminal, one-third of the protein, in particular the intrinsically disordered linker (IDL). Previously, we have shown using a series of linker deletion mutants that the IDL links both ssDNA and target protein binding by mediating interactions with the oligosaccharide/oligonucleotide binding fold in the target...
January 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28076807/cider-resources-to-analyze-sequence-ensemble-relationships-of-intrinsically-disordered-proteins
#12
Alex S Holehouse, Rahul K Das, James N Ahad, Mary O G Richardson, Rohit V Pappu
Intrinsically disordered proteins and regions (IDPs) represent a large class of proteins that are defined by conformational heterogeneity and lack of persistent tertiary/secondary structure. IDPs play important roles in a range of biological functions, and their dysregulation is central to numerous diseases, including neurodegeneration and cancer. The conformational ensembles of IDPs are encoded by their amino acid sequences. Here, we present two computational tools that are designed to enable rapid and high-throughput analyses of a wide range of physicochemical properties encoded by IDP sequences...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28074868/nucleoplasmin-like-domain-of-fkbp39-from-drosophila-melanogaster-forms-a-tetramer-with-partly-disordered-tentacle-like-c-terminal-segments
#13
Małgorzata Kozłowska, Aneta Tarczewska, Michał Jakób, Dominika Bystranowska, Michał Taube, Maciej Kozak, Mariusz Czarnocki-Cieciura, Andrzej Dziembowski, Marek Orłowski, Katarzyna Tkocz, Andrzej Ożyhar
Nucleoplasmins are a nuclear chaperone family defined by the presence of a highly conserved N-terminal core domain. X-ray crystallographic studies of isolated nucleoplasmin core domains revealed a β-propeller structure consisting of a set of five monomers that together form a stable pentamer. Recent studies on isolated N-terminal domains from Drosophila 39-kDa FK506-binding protein (FKBP39) and from other chromatin-associated proteins showed analogous, nucleoplasmin-like (NPL) pentameric structures. Here, we report that the NPL domain of the full-length FKBP39 does not form pentameric complexes...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28069923/map7-regulates-axon-collateral-branch-development-in-dorsal-root-ganglia-neurons
#14
Stephen R Tymanskyj, Benjamin Yang, Aditi Falnikar, Angelo C Lepore, Le Ma
: Collateral branches from axons are key components of functional neural circuits that allow neurons to connect with multiple synaptic targets. Like axon growth and guidance, formation of collateral branches depends on the regulation of microtubules, but how such regulation is coordinated to ensure proper circuit development is not known. Based on microarray analysis, we have identified a role for microtubule-associated protein 7 (MAP7) during collateral branch development of dorsal root ganglia (DRG) sensory neurons...
January 9, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28068774/mechanism-of-phosphorylation-induced-folding-of-4e-bp2-revealed-by-molecular-dynamics-simulations
#15
Juan Zeng, Fan Jiang, Yun-Dong Wu
Site-specific phosphorylation of an intrinsically disordered protein, eIF4E-binding protein isoform 2 (4E-BP2), can suppress its native function by folding it into a four-stranded β-sheet, but the mechanism of this phosphorylation-induced folding is unclear. In this work, we use all-atom molecular dynamics simulations to investigate both the folded and unfolded states of 4E-BP2 under different phosphorylation states of T37 and T46. The results show that the phosphorylated forms of both T37 and T46 play important roles in stabilizing the folded structure, especially for the β-turns and the sequestered binding motif...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28066974/hydrogen-mobility-and-protein-water-interaction-in-proteins-of-solid-state
#16
Kalman Tompa, Monika Bokor, Dorina Ágner, Dávid Iván, Denes Kovacs, Tamas Verebélyi, Peter Tompa
In this work we lay the groundwork of characterizing the mobility of hydrogen-hydrogen pairs (proton-proton radial vectors) in proteins in the solid state that contains only residual water. In this novel approach we introduce new ways of analyzing and interpreting data, by: i) representing hydrogen mobility (HM) and melting diagram (MD) data recorded by wide-line 1H-NMR as a function of fundamental temperature (thermal excitation energy); ii) suggesting novel mode of interpretation of these parameters that sheds light on details of protein-water interaction such as the exact amount of water molecules and the distribution of barrier potentials pertaining to their rotational and surface translational mobility; iii) relying on directly determined physical observables...
January 8, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28063007/oxygen-exchange-and-energy-metabolism-in-erythrocytes-of-rett-syndrome-and-their-relationships-with-respiratory-alterations
#17
Chiara Ciaccio, Donato Di Pierro, Diego Sbardella, Grazia Raffaella Tundo, Paolo Curatolo, Cinzia Galasso, Marta Elena Santarone, Maurizio Casasco, Paola Cozza, Alessio Cortelazzo, Marcello Rossi, Claudio De Felice, Joussef Hayek, Massimo Coletta, Stefano Marini
Rett syndrome (RTT) is a neurodevelopmental disorder, mainly affecting females, which is associated to a mutation on the methyl-CpG-binding protein 2 gene. In the pathogenesis and progression of classic RTT, red blood cell (RBC) morphology has been shown to be an important biosensor for redox imbalance and chronic hypoxemia. Here we have evaluated the impact of oxidation and redox imbalance on several functional properties of RTT erythrocytes. In particular, we report for the first time a stopped-flow measurement of the kinetics of oxygen release by RBCs and the analysis of the intrinsic affinity of the hemoglobin (Hb)...
January 7, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28060278/nuclear-magnetic-resonance-spectroscopy-for-the-identification-of-multiple-phosphorylations-of-intrinsically-disordered-proteins
#18
Clément Danis, Clément Despres, Luiza M Bessa, Idir Malki, Hamida Merzougui, Isabelle Huvent, Haoling Qi, Guy Lippens, François-Xavier Cantrelle, Robert Schneider, Xavier Hanoulle, Caroline Smet-Nocca, Isabelle Landrieu
Aggregates of the neuronal Tau protein are found inside neurons of Alzheimer's disease patients. Development of the disease is accompanied by increased, abnormal phosphorylation of Tau. In the course of the molecular investigation of Tau functions and dysfunctions in the disease, nuclear magnetic resonance (NMR) spectroscopy is used to identify the multiple phosphorylations of Tau. We present here detailed protocols of recombinant production of Tau in bacteria, with isotopic enrichment for NMR studies. Purification steps that take advantage of Tau's heat stability and high isoelectric point are described...
December 27, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28057753/a-novel-kleefstra-syndrome-associated-variant-that-affects-the-conserved-tplx-motif-within-the-ankyrin-repeat-of-ehmt1-leads-to-abnormal-protein-folding
#19
Patrick R Blackburn, Alexander Tischer, Michael T Zimmermann, Jennifer L Kemppainen, Sujatha Sastry, Amy E Knight Johnson, Margot A Cousin, Nicole J Boczek, Gavin Oliver, Vinod K Misra, Ralitza H Gavrilova, Gwen A Lomberk, Matthew Auton, Raul A Urrutia, Eric W Klee
Kleefstra syndrome (KS) (MIM# 610253), also known as 9q34 deletion syndrome, is an autosomal dominant disorder caused by haploinsufficiency of euchromatic histone methyltransferase-1 (EHMT1). The clinical phenotype of KS includes moderate to severe intellectual disability with absent speech, hypotonia, brachycephaly, congenital heart defects, and dysmorphic facial features with hypertelorism, synophrys, macroglossia, protruding tongue, and prognathism. Only a few cases of de novo missense mutations in EHMT1 giving rise to KS have been described...
January 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28054562/identification-of-a-drug-targeting-an-intrinsically-disordered-protein-involved-in-pancreatic-adenocarcinoma
#20
José L Neira, Jennifer Bintz, María Arruebo, Bruno Rizzuti, Thomas Bonacci, Sonia Vega, Angel Lanas, Adrián Velázquez-Campoy, Juan L Iovanna, Olga Abián
Intrinsically disordered proteins (IDPs) are prevalent in eukaryotes, performing signaling and regulatory functions. Often associated with human diseases, they constitute drug-development targets. NUPR1 is a multifunctional IDP, over-expressed and involved in pancreatic ductal adenocarcinoma (PDAC) development. By screening 1120 FDA-approved compounds, fifteen candidates were selected, and their interactions with NUPR1 were characterized by experimental and simulation techniques. The protein remained disordered upon binding to all fifteen candidates...
January 5, 2017: Scientific Reports
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