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Intrinsically disordered protein

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https://www.readbyqxmd.com/read/28805390/sampling-long-versus-short-range-interactions-defines-the-ability-of-force-fields-to-reproduce-the-dynamics-of-intrinsically-disordered-proteins
#1
Davide Mercadante, Johannes Andreas Wagner, Iker Valle Aramburu, Edward A Lemke, Frauke Gräter
Molecular dynamics simulations have valuably complemented experiments describing the dynamics of intrinsically disordered proteins (IDPs), particularly since the proposal of models to solve the artificial collapse of IDPs in silico. Such models suggest redefining non-bonded interactions, by either increasing water dispersion forces or adopting the Kirkwood-Buff force field. These approaches yield extended conformers that better comply with experiments, but it is unclear if they all sample the same intra-chain dynamics of IDPs...
August 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28805312/the-dock-and-coalesce-mechanism-for-the-association-of-a-wasp-disordered-region-with-the-cdc42-gtpase
#2
Li Ou, Megan Matthews, Xiaodong Pang, Huan-Xiang Zhou
Intrinsically disordered proteins (IDPs) play key roles in signaling and regulation. Many IDPs undergo folding upon binding to their targets. We have proposed that coupled folding and binding of IDPs generally follow a dock-and-coalesce mechanism, whereby a segment of the IDP, through diffusion, docks to its cognate subsite and, subsequently, the remaining segments coalesce around their subsites. Here, by a combination of experiment and computation, we determined the precise form of dock-and-coalesce operating in the association between the intrinsically disordered GTPase binding domain (GBD) of the Wiskott-Aldrich Syndrome protein (WASP) and the Cdc42 GTPase...
August 14, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28804999/diversity-of-astroglial-responses-across-human-neurodegenerative-disorders-and-brain-aging
#3
Isidro Ferrer
Astrogliopathy refers to alterations of astrocytes occurring in diseases of the nervous system, and it implies the involvement of astrocytes as key elements in the pathogenesis and pathology of diseases and injuries of the central nervous system. Reactive astrocytosis refers to the response of astrocytes to different insults to the nervous system, whereas astrocytopathy indicates hypertrophy, atrophy/degeneration and loss of function and pathological remodeling occurring as a primary cause of a disease or as a factor contributing to the development and progression of a particular disease...
September 2017: Brain Pathology
https://www.readbyqxmd.com/read/28801357/the-autoimmune-risk-variant-ptpn22-c1858t-alters-b-cell-tolerance-at-discrete-checkpoints-and-differentially-shapes-the-naive-repertoire
#4
Genita Metzler, Xuezhi Dai, Christopher D Thouvenel, Socheath Khim, Tania Habib, Jane H Buckner, David J Rawlings
A common genetic variant in the gene encoding the protein tyrosine phosphatase nonreceptor type 22 (PTPN22 C1858T) has been linked to a wide range of autoimmune disorders. Although a B cell-intrinsic role in promoting disease has been reported, the mechanism(s) through which this variant functions to alter the preimmune B cell repertoire remains unknown. Using a series of polyclonal and transgenic self-reactive models harboring the analogous mutation in murine Ptpn22, we show evidence for enhanced BCR, B cell-activating factor receptor, and CD40 coreceptor programs, leading to broadly enhanced positive selection of B cells at two discrete checkpoints in the bone marrow and spleen...
August 11, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28799215/secondary-structure-and-dynamics-study-of-the-intrinsically-disordered-silica-mineralizing-peptide-p5-s3-during-silicic-acid-condensation-and-silica-decondensation
#5
Christian Zerfaß, Garry W Buchko, Wendy J Shaw, Stephan Hobe, Harald Paulsen
The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5 S3 , a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains five protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5 S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2 ) at globally undersaturated concentrations. The secondary structure of P5 S3 during these two processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in the absence of silicate...
August 11, 2017: Proteins
https://www.readbyqxmd.com/read/28797243/polymorphism-and-structure-of-style-specific-arabinogalactan-proteins-as-determinants-of-pollen-tube-growth-in-nicotiana
#6
Andrzej K Noyszewski, Yi-Cheng Liu, Koichiro Tamura, Alan G Smith
BACKGROUND: Pollen tube growth and fertilization are key processes in angiosperm sexual reproduction. The transmitting tract (TT) of Nicotiana tabacum controls pollen tube growth in part by secreting pistil extensin-like protein III (PELPIII), transmitting-tract-specific (TTS) protein and 120 kDa glycoprotein (120 K) into the stylar extracellular matrix. The three arabinogalactan proteins (AGP) are referred to as stylar AGPs and are the focus of this research. The transmitting tract regulates pollen tube growth, promoting fertilization or rejecting pollen tubes...
August 10, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28793212/intrinsically-disordered-stress-protein-cor15a-resides-at-the-membrane-surface-during-dehydration
#7
Anne Bremer, Ben Kent, Thomas Hauß, Anja Thalhammer, Nageshwar R Yepuri, Tamim A Darwish, Christopher J Garvey, Gary Bryant, Dirk K Hincha
Plants from temperate climate zones are able to increase their freezing tolerance during exposure to low, above-zero temperatures in a process termed cold acclimation. During this process, several cold-regulated (COR) proteins are accumulated in the cells. One of them is COR15A, a small, intrinsically disordered protein that contributes to leaf freezing tolerance by stabilizing cellular membranes. The isolated protein folds into amphipathic α-helices in response to increased crowding conditions, such as high concentrations of glycerol...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28793210/an-efficient-method-for-estimating-the-hydrodynamic-radius-of-disordered-protein-conformations
#8
Mads Nygaard, Birthe B Kragelund, Elena Papaleo, Kresten Lindorff-Larsen
Intrinsically disordered proteins play important roles throughout biology, yet our understanding of the relationship between their sequences, structural properties, and functions remains incomplete. The dynamic nature of these proteins, however, makes them difficult to characterize structurally. Many disordered proteins can attain both compact and expanded conformations, and the level of expansion may be regulated and important for function. Experimentally, the level of compaction and shape is often determined either by small-angle x-ray scattering experiments or pulsed-field-gradient NMR diffusion measurements, which provide ensemble-averaged estimates of the radius of gyration and hydrodynamic radius, respectively...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28792212/the-lc8-recognition-motif-preferentially-samples-polyproline-ii-structure-in-its-free-state
#9
Jessica Morgan, Malene Ringkjøbing Jensen, Valéry Ozenne, Martin Blackledge, Elisar J Barbar
LC8 is a ubiquitous hub protein that binds intrinsically disordered proteins and promotes their assembly into higher order complexes. A common feature among the over 100 essential LC8-binding proteins is that in the 10-12 amino acid recognition sequence there is a conserved QT motif but variable amino acids N- and C-terminal to the QT pair. The sequence diversity among LC8-binding partners implies that structural factors also contribute to specificity. To investigate whether one such factor is the transient secondary structure favored by an LC8-binding sequence, we report here a molecular ensemble description of ICTL, a domain of dynein intermediate chain that includes binding sites for light chains LC8 and Tctex1...
August 9, 2017: Biochemistry
https://www.readbyqxmd.com/read/28790177/phosphorylation-of-the-fus-low-complexity-domain-disrupts-phase-separation-aggregation-and-toxicity
#10
Zachary Monahan, Veronica H Ryan, Abigail M Janke, Kathleen A Burke, Shannon N Rhoads, Gül H Zerze, Robert O'Meally, Gregory L Dignon, Alexander E Conicella, Wenwei Zheng, Robert B Best, Robert N Cole, Jeetain Mittal, Frank Shewmaker, Nicolas L Fawzi
Neuronal inclusions of aggregated RNA-binding protein fused in sarcoma (FUS) are hallmarks of ALS and frontotemporal dementia subtypes. Intriguingly, FUS's nearly uncharged, aggregation-prone, yeast prion-like, low sequence-complexity domain (LC) is known to be targeted for phosphorylation. Here we map in vitro and in-cell phosphorylation sites across FUS LC We show that both phosphorylation and phosphomimetic variants reduce its aggregation-prone/prion-like character, disrupting FUS phase separation in the presence of RNA or salt and reducing FUS propensity to aggregate...
August 8, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28783193/protein-intrinsic-disorder-negatively-associates-with-gene-age-in-different-eukaryotic-lineages
#11
Sanghita Banerjee, Sandip Chakraborty
The emergence of new protein-coding genes in a specific lineage or species provides raw materials for evolutionary adaptations. Until recently, the biology of new genes emerging particularly from non-genic sequences remained unexplored. Although the new genes are subjected to variable selection pressure and face rapid deletion, some of them become functional and are retained in the gene pool. To acquire functional novelties, new genes often get integrated into the pre-existing ancestral networks. However, the mechanism by which young proteins acquire novel interactions remains unanswered till date...
August 7, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28782560/glutamate-promotes-ssb-protein-protein-interactions-via-intrinsically-disordered-regions
#12
Alexander G Kozlov, Min Kyung Shinn, Elizabeth A Weiland, Timothy M Lohman
E. coli single strand (ss) DNA binding protein (SSB) is an essential protein that binds to ssDNA intermediates formed during genome maintenance. SSB homotetramers bind ssDNA in several modes that differ in occluded site size and cooperativity. High "unlimited" cooperativity is associated with the 35 site size ((SSB)35) mode at low [NaCl], whereas the 65 site size ((SSB)65) mode formed at higher [NaCl] (> 200mM), where ssDNA wraps completely around the tetramer, displays "limited" cooperativity forming dimers of tetramers...
August 3, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28780862/structure-and-dynamics-of-an-intrinsically-disordered-protein-region-that-partially-folds-upon-binding-by-chemical-exchange-nmr
#13
Cyril Charlier, Guillaume Bouvignies, Philippe Pelupessy, Astrid Walrant, Rodrigue Marquant, Mikhail Kozlov, Pablo De Ioannes, Nicolas Bolik-Coulon, Sandrine Sagan, Patricia Cortes, Aneel K Aggarwal, Ludovic Carlier, Fabien Ferrage
Many intrinsically disordered proteins (IDPs) and protein regions (IDRs) engage in transient, yet specific, interactions with a variety of protein partners. Often, if not always, interactions with a protein partner lead to partial folding of the IDR. Characterizing the conformational space of such complexes is challenging: in solution-state NMR, signals of the IDR in the interacting region become broad, weak and often invisible; while X-ray crystallography only provides information on fully ordered regions...
August 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28780133/altered-glua1-gria1-function-and-accumbal-synaptic-plasticity-in-the-clock%C3%AE-19-model-of-bipolar-mania
#14
Puja K Parekh, Darius Becker-Krail, Poornima Sundaravelu, Shinsuke Ishigaki, Haruo Okado, Gen Sobue, Yanhua Huang, Colleen A McClung
BACKGROUND: Disruptions in circadian rhythms are associated with an increased risk for bipolar disorder. Moreover, studies show that the circadian protein CLOCK (circadian locomotor output cycles kaput) is involved in regulating monoaminergic systems and mood-related behavior. However, the molecular and synaptic mechanisms underlying this relationship remain poorly understood. METHODS: Using ex vivo whole-cell patch-clamp electrophysiology in ClockΔ19 mutant and wild-type mice we characterized alterations in excitatory synaptic transmission, strength, and intrinsic excitability of nucleus accumbens (NAc) neurons...
June 27, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/28780023/shared-acvr1-mutations-in-fop-and-dipg-opportunities-and-challenges-in-extending-biological-and-clinical-implications-across-rare-diseases
#15
Harry J Han, Payal Jain, Adam C Resnick
Gain-of-function mutations in the Type I Bone Morphogenic Protein (BMP) receptor ACVR1 have been identified in two diseases: Fibrodysplasia Ossificans Progressiva (FOP), a rare autosomal dominant disorder characterized by genetically driven heterotopic ossification, and in 20-25% of Diffuse Intrinsic Pontine Gliomas (DIPGs), a pediatric brain tumor with no effective therapies and dismal median survival. While the ACVR1 mutation is causal for FOP, its role in DIPG tumor biology remains under active investigation...
August 2, 2017: Bone
https://www.readbyqxmd.com/read/28774197/thrombotic-and-hemorrhagic-conditions-due-to-a-gain-of-function-of-coagulation-proteins-a-special-type-of-clotting-disorders
#16
Antonio Girolami, Elisabetta Cosi, Silvia Ferrari, Annamaria Lombardi, Fabrizio Fabris
Coagulation disorders can be classified into 2 types, namely, type I and type II. In the former, there is a concomitant decrease in factor activity and antigen (activity-antigen ratio is 1), whereas in the latter, there is a discrepancy between factor activity which is always low and antigen which is normal or near normal (activity-antigen ratio is <1, eg, 0.5). Recently, several gain-of-function disorders have been described. These are characterized by an increased activity with respect to the antigen level...
January 1, 2017: Clinical and Applied Thrombosis/hemostasis
https://www.readbyqxmd.com/read/28765603/predictions-of-backbone-dynamics-in-intrinsically-disordered-proteins-using-de-novo-fragment-based-protein-structure-predictions
#17
Tomasz Kosciolek, Daniel W A Buchan, David T Jones
Intrinsically disordaered proteins (IDPs) are a prevalent phenomenon with over 30% of human proteins estimated to have long disordered regions. Computational methods are widely used to study IDPs, however, nearly all treat disorder in a binary fashion, not accounting for the structural heterogeneity present in disordered regions. Here, we present a new de novo method, FRAGFOLD-IDP, which addresses this problem. Using 200 protein structural ensembles derived from NMR, we show that FRAGFOLD-IDP achieves superior results compared to methods which can predict related data (NMR order parameter, or crystallographic B-factor)...
August 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28763201/tracking-reactive-water-and-hydrogen-bonding-networks-in-photosynthetic-oxygen-evolution
#18
Bridgette A Barry, Udita Brahmachari, Zhanjun Guo
In oxygenic photosynthesis, photosystem II (PSII) converts water to molecular oxygen through four photodriven oxidation events at a Mn4CaO5 cluster. A tyrosine, YZ (Y161 in the D1 polypeptide), transfers oxidizing equivalents from an oxidized, primary chlorophyll donor to the metal center. Calcium or its analogue, strontium, is required for activity. The Mn4CaO5 cluster and YZ are predicted to be hydrogen bonded in a water-containing network, which involves amide carbonyl groups, amino acid side chains, and water...
August 1, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28762198/directly-watching-biomolecules-in-action-by-high-speed-atomic-force-microscopy
#19
REVIEW
Toshio Ando
Proteins are dynamic in nature and work at the single molecule level. Therefore, directly watching protein molecules in dynamic action at high spatiotemporal resolution must be the most straightforward approach to understanding how they function. To make this observation possible, high-speed atomic force microscopy (HS-AFM) has been developed. Its current performance allows us to film biological molecules at 10-16 frames/s, without disturbing their function. In fact, dynamic structures and processes of various proteins have been successfully visualized, including bacteriorhodopsin responding to light, myosin V walking on actin filaments, and even intrinsically disordered proteins undergoing order/disorder transitions...
July 31, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28760960/oligomerization-of-the-tetramerization-domain-of-p53-probed-by-two-and-three-color-single-molecule-fret
#20
Hoi Sung Chung, Fanjie Meng, Jae-Yeol Kim, Kevin McHale, Irina V Gopich, John M Louis
We describe a method that combines two- and three-color single-molecule FRET spectroscopy with 2D FRET efficiency-lifetime analysis to probe the oligomerization process of intrinsically disordered proteins. This method is applied to the oligomerization of the tetramerization domain (TD) of the tumor suppressor protein p53. TD exists as a monomer at subnanomolar concentrations and forms a dimer and a tetramer at higher concentrations. Because the dissociation constants of the dimer and tetramer are very close, as we determine in this paper, it is not possible to characterize different oligomeric species by ensemble methods, especially the dimer that cannot be readily separated...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
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