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Unstructured Proteins

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https://www.readbyqxmd.com/read/28644863/a-rule-based-named-entity-recognition-method-for-knowledge-extraction-of-evidence-based-dietary-recommendations
#1
Tome Eftimov, Barbara Koroušić Seljak, Peter Korošec
Evidence-based dietary information represented as unstructured text is a crucial information that needs to be accessed in order to help dietitians follow the new knowledge arrives daily with newly published scientific reports. Different named-entity recognition (NER) methods have been introduced previously to extract useful information from the biomedical literature. They are focused on, for example extracting gene mentions, proteins mentions, relationships between genes and proteins, chemical concepts and relationships between drugs and diseases...
2017: PloS One
https://www.readbyqxmd.com/read/28644829/swapping-the-n-and-c-terminal-domains-of-human-apolipoprotein-e3-and-ai-reveals-insights-into-their-structure-activity-relationship
#2
Mark T Lek, Siobanth Cruz, Nnejiuwa U Ibe, Wendy H J Beck, John K Bielicki, Paul M M Weers, Vasanthy Narayanaswami
Apolipoprotein (apo) E3 and apoAI are exchangeable apolipoproteins that play a dominant role in regulating plasma lipoprotein metabolism. ApoE3 (299 residues) is composed of an N-terminal (NT) domain bearing a 4-helix bundle and a C-terminal (CT) domain bearing a series of amphipathic α-helices. ApoAI (243 residues) also comprises a highly helical NT domain and a less structured CT tail. The objective of this study was to understand their structural and functional role by generating domain swapped chimeras: apoE3-NT/apoAI-CT and apoAI-NT/apoE-CT...
2017: PloS One
https://www.readbyqxmd.com/read/28644713/an-unstructured-loop-that-is-critical-for-interactions-of-the-stalk-domain-of-drp1-with-saturated-phosphatidic-acid
#3
Yoshihiro Adachi, Miho Iijima, Hiromi Sesaki
Dynamin-related protein 1 (Drp1) is a dynamin superfamily GTPase, which drives membrane constriction during mitochondrial division. To mediate mitochondrial division, Drp1 is recruited to the mitochondrial outer membrane and is assembled into the division machinery. We previously showed that Drp1 interacts with phosphatidic acid (PA) and saturated phospholipids in the mitochondrial membrane, and this interaction restrains Drp1 in initiating the constriction of mitochondria. Here, we show that the role of saturated acyl chains of phospholipids is independent of their contribution to the membrane curvature or lipid packing suggesting their direct interaction with Drp1...
June 23, 2017: Small GTPases
https://www.readbyqxmd.com/read/28629619/slow-interconversion-in-a-heterogeneous-unfolded-state-ensemble-of-outer-membrane-phospholipase-a
#4
Georg Krainer, Pablo Gracia, Erik Frotscher, Andreas Hartmann, Philip Gröger, Sandro Keller, Michael Schlierf
Structural and dynamic investigations of unfolded proteins are important for understanding protein-folding mechanisms as well as the interactions of unfolded polypeptide chains with other cell components. In the case of outer-membrane proteins (OMPs), unfolded-state properties are of particular physiological relevance, because these proteins remain unfolded for extended periods of time during their biogenesis and rely on interactions with binding partners to support proper folding. Using a combination of ensemble and single-molecule spectroscopy, we have scrutinized the unfolded state of outer-membrane phospholipase A (OmpLA) to provide a detailed view of its structural dynamics on timescales from nanoseconds to milliseconds...
June 16, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28629029/chitosan-coated-amyloid-fibrils-increase-adipogenesis-of-mesenchymal-stem-cells
#5
Jay Gilbert, Nicholas P Reynolds, Sarah M Russell, David Haylock, Sally McArthur, Mirren Charnley, Owen G Jones
Mesenchymal stem cells (MSCs) have the potential to revolutionize medicine due to their ability to differentiate into specific lineages for targeted tissue repair. Development of materials and cell culture platforms that improve differentiation of either autologous or allogenic stem cell sources into specific lineages would enhance clinical utilization of MCSs. In this study, nanoscale amyloid fibrils were evaluated as substrate materials to encourage viability, proliferation, multipotency, and differentiation of MSCs...
October 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28623092/ctip-ctp1-sae2-molecular-form-fit-for-function
#6
REVIEW
Sara N Andres, R Scott Williams
Vertebrate CtIP, and its fission yeast (Ctp1), budding yeast (Sae2) and plant (Com1) orthologs have emerged as key regulatory molecules in cellular responses to DNA double strand breaks (DSBs). By modulating the nucleolytic 5'-3' resection activity of the Mre11/Rad50/Nbs1 (MRN) DSB repair processing and signaling complex, CtIP/Ctp1/Sae2/Com1 is integral to the channeling of DNA double strand breaks through DSB repair by homologous recombination (HR). Nearly two decades since its discovery, emerging new data are defining the molecular underpinnings for CtIP DSB repair regulatory activities...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28622544/conformational-transition-of-%C3%AE%C2%BA-casein-in-micellar-environment-insight-from-the-tryptophan-fluorescence
#7
Smruti Mishra, Geetanjali Meher, Hirak Chakraborty
Intrinsically disordered proteins (IDPs) are under intense analysis due to their structural flexibility and importance in biological functions. Minuscule modulation in the microenvironment induces significant conformational changes in IDPs, and these non-native conformations of the IDPs often induce aggregation and cause cell death. Changes in the membrane composition often change the microenvironment, which promote conformational change and aggregation of IDPs. κ-Casein, an important milk protein, belongs to the class of IDPs containing net negative charges...
June 8, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28621526/orthogonal-mass-spectrometry-based-footprinting-for-epitope-mapping-and-structural-characterization-the-il-6-receptor-upon-binding-of-protein-therapeutics
#8
Ke Sherry Li, Guodong Chen, Jingjie Mo, Richard Y-C Huang, Ekaterina G Deyanova, Brett R Beno, Steve O'Neil, Adrienne A Tymiak, Michael L Gross
Higher order structure (HOS) is a crucial determinant for the biological functions and quality attributes of protein therapeutics. Mass spectrometry (MS)-based protein footprinting approaches play an important role in elucidating the relationship between protein biophysical properties and structure. Here, we describe the use of a combined method including hydrogen-deuterium exchange (HDX), fast photochemical oxidation of proteins (FPOP) and site-specific carboxyl group footprinting to investigate the HOS of protein and protein complexes...
June 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28620036/substrate-selectivity-in-the-zdhhc-family-of-s-acyltransferases
#9
REVIEW
Kimon Lemonidis, Christine Salaun, Marianna Kouskou, Cinta Diez-Ardanuy, Luke H Chamberlain, Jennifer Greaves
S-acylation is a reversible lipid modification occurring on cysteine residues mediated by a family of membrane-bound 'zDHHC' enzymes. S-acylation predominantly results in anchoring of soluble proteins to membrane compartments or in the trafficking of membrane proteins to different compartments. Recent work has shown that although S-acylation of some proteins may involve very weak interactions with zDHHC enzymes, a pool of zDHHC enzymes exhibit strong and specific interactions with substrates, thereby recruiting them for S-acylation...
June 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28616972/dss1-regulates-association-of-brh2-with-rad51
#10
Qingwen Zhou, William K Holloman
Brh2, the BRCA2 ortholog in the fungus Ustilago maydis, mediates delivery of Rad51 to DNA during the course of homology-directed DNA repair. Rad51 interacts with Brh2 through the highly conserved BRC element and through a second region termed CRE located at the extreme carboxy-terminus. Dss1, a small intrinsically unstructured protein that interacts with Brh2 is crucial for its activity in DNA repair, but the mechanism of this regulation is uncertain. In previous studies we found that Brh2 interaction with DNA was strongly modulated by association with Dss1...
June 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28609090/emerging-%C3%AE-sheet-rich-conformations-in-super-compact-huntingtin-exon-1-mutant-structures
#11
Hongsuk Kang, Francisco X Vázquez, Leili Zhang, Payel Das, Leticia Marisel Toledo-Sherman, Binquan Luan, Michael Levitt, Ruhong Zhou
There exits strong correlation between the extended poly-glutamines (polyQ) within exon-1 of Huntingtin protein (Htt) and age onset of Huntington's disease (HD), however, the underlying molecular mechanism is still poorly understood. Here we apply extensive molecular dynamics simulations to study the folding of Htt-exon-1 across five different polyQ-lengths. We find an increase in secondary structure motifs at longer Q-lengths, including β-sheet content that seems to contribute to the formation of increasingly compact structures...
June 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28608348/identification-and-analysis-of-wg-gw-argonaute-binding-domains
#12
Andrzej Zielezinski, Wojciech M Karlowski
WG/GW domains recruit ARGONAUTE (AGO) proteins to distinct silencing effector complexes using combinations of just two amino acids: tryptophan (W) and glycine (G), forming a wide arsenal of highly simplified interaction surfaces. These unstructured domains exhibit very low sequence identity and excessive length polymorphism, which makes identification of new AGO-binding proteins a challenging task as they escape detection with standard sequence comparison-based methods (e.g., BLAST, HMMER).In this chapter, we explain the use of tools for prediction of AGO-binding WG/GW domains in protein sequences...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28593560/-1-h-13-c-and-15-n-nmr-chemical-shift-assignments-of-a-thaliana-rcd1-rst
#13
Helena Tossavainen, Maarit Hellman, Julia P Vainonen, Jaakko Kangasjärvi, Perttu Permi
The A. thaliana RCD1 (radical-induced cell death1) protein is a cellular signaling hub protein which interacts with numerous plant transcription factors from different families. It consists of three conserved domains and intervening unstructured regions, the C-terminal RST domain being responsible for the interactions with the transcription factors. It has been shown that many partner proteins interact with RCD1 RST via their intrinsically disordered regions, and that the domain is able to house partners with divergent folds...
June 7, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28591514/elastin-like-polypeptide-linkers-for-single-molecule-force-spectroscopy
#14
Wolfgang Ott, Markus A Jobst, Magnus S Bauer, Ellis Durner, Lukas F Milles, Michael A Nash, Hermann E Gaub
Single-molecule force spectroscopy (SMFS) is by now well established as a standard technique in biophysics and mechanobiology. In recent years, the technique has benefitted greatly from new approaches to bioconjugation of proteins to surfaces. Indeed, optimized immobilization strategies for biomolecules and refined purification schemes are being steadily adapted and improved, which in turn has enhanced data quality. In many previously reported SMFS studies, poly(ethylene glycol) (PEG) was used to anchor molecules of interest to surfaces and/or cantilever tips...
June 12, 2017: ACS Nano
https://www.readbyqxmd.com/read/28559482/a-screen-for-rfah-suppressors-reveals-a-key-role-for-a-connector-region-of-termination-factor-rho
#15
Kuang Hu, Irina Artsimovitch
RfaH activates horizontally acquired operons that encode lipopolysaccharide core components, pili, toxins, and capsules. Unlike its paralog NusG, which potentiates Rho-mediated silencing, RfaH strongly inhibits Rho. RfaH is recruited to its target operons via a network of contacts with an elongating RNA polymerase (RNAP) and a specific DNA element called ops to modify RNAP into a pause- and NusG-resistant state. rfaH null mutations confer hypersensitivity to antibiotics and detergents, altered susceptibility to bacteriophages, and defects in virulence...
May 30, 2017: MBio
https://www.readbyqxmd.com/read/28546148/translation-initiation-factor-eif4g1-preferentially-binds-yeast-transcript-leaders-containing-conserved-oligo-uridine-motifs
#16
Boris Zinshteyn, Maria F Rojas Duran, Wendy V Gilbert
Translational control of gene expression plays essential roles in cellular stress responses and organismal development by enabling rapid, selective, and localized control of protein production. Translational regulation depends on context-dependent differences in the protein output of mRNAs, but the key mRNA features that distinguish efficiently translated mRNAs are largely unknown. Here we comprehensively determined the RNA-binding preferences of the initiation factor eIF4G to assess whether this core translation initiation factor has intrinsic sequence preferences that may contribute to preferential translation of specific mRNAs...
May 25, 2017: RNA
https://www.readbyqxmd.com/read/28542210/drosophila-dna-polymerase-theta-utilizes-both-helicase-like-and-polymerase-domains-during-microhomology-mediated-end-joining-and-interstrand-crosslink-repair
#17
Kelly Beagan, Robin L Armstrong, Alice Witsell, Upasana Roy, Nikolai Renedo, Amy E Baker, Orlando D Schärer, Mitch McVey
Double strand breaks (DSBs) and interstrand crosslinks (ICLs) are toxic DNA lesions that can be repaired through multiple pathways, some of which involve shared proteins. One of these proteins, DNA Polymerase θ (Pol θ), coordinates a mutagenic DSB repair pathway named microhomology-mediated end joining (MMEJ) and is also a critical component for bypass or repair of ICLs in several organisms. Pol θ contains both polymerase and helicase-like domains that are tethered by an unstructured central region. While the role of the polymerase domain in promoting MMEJ has been studied extensively both in vitro and in vivo, a function for the helicase-like domain, which possesses DNA-dependent ATPase activity, remains unclear...
May 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28530826/high-speed-atomic-force-microscopy-reveals-loss-of-nuclear-pore-resilience-as-a-dying-code-in-colorectal-cancer-cells
#18
Mahmoud Shaaban Mohamed, Akiko Kobayashi, Azuma Taoka, Takahiro Watanabe-Nakayama, Yosuke Kikuchi, Masaharu Hazawa, Toshinari Minamoto, Yoshihiro Fukumori, Noriyuki Kodera, Takayuki Uchihashi, Toshio Ando, Richard W Wong
Nuclear pore complexes (NPCs) are the sole turnstile implanted in the nuclear envelope (NE), acting as a central nano-regulator of transport between the cytosol and the nucleus. NPCs consist of ~30 proteins, termed nucleoporins. About one-third of nucleoporins harbour natively unstructured, intrinsically disordered phenylalanine-glycine strings (FG-Nups), which engage in transport selectivity. Because the barriers insert deeply in the NPC, they are nearly inaccessible. Several in vitro barrier models have been proposed; however, the dynamic FG-Nups protein molecules themselves are imperceptible in vivo...
May 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28515062/changes-in-total-energy-intake-and-macronutrient-composition-after-bariatric-surgery-predict-long-term-weight-outcome-findings-from-the-swedish-obese-subjects-sos-study
#19
Noora Kanerva, Ingrid Larsson, Markku Peltonen, Anna-Karin Lindroos, Lena M Carlsson
Background: Approximately 20-30% of obese patients do not achieve successful weight outcomes after bariatric surgery.Objective: We examined whether short-term changes (≤0.5 y postsurgery) in energy intake and macronutrient composition after bariatric surgery could predict 10-y weight change.Design: Participants were recruited from the Swedish Obese Subjects (SOS) study, which was a matched (nonrandomized) prospective trial that compared bariatric surgery with usual care for obese patients. A total of 2010 patients who underwent bariatric surgery were included in the study...
May 17, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28507157/translation-and-folding-of-single-proteins-in-real-time
#20
Florian Wruck, Alexandros Katranidis, Knud H Nierhaus, Georg Büldt, Martin Hegner
Protein biosynthesis is inherently coupled to cotranslational protein folding. Folding of the nascent chain already occurs during synthesis and is mediated by spatial constraints imposed by the ribosomal exit tunnel as well as self-interactions. The polypeptide's vectorial emergence from the ribosomal tunnel establishes the possible folding pathways leading to its native tertiary structure. How cotranslational protein folding and the rate of synthesis are linked to a protein's amino acid sequence is still not well defined...
May 30, 2017: Proceedings of the National Academy of Sciences of the United States of America
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