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Unstructured Proteins

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https://www.readbyqxmd.com/read/28725901/zinc-binding-sites-in-pra1-a-zincophore-from-candida-albicans
#1
Dorota Łoboda, Magdalena Rowińska-Żyrek
The aim of this work is to understand the interactions of Zn(ii) with Pra1, a zincophore from Candida albicans, one of the most common causes of serious fungal infections in humans. Pra1 is a 299 amino acid protein, secreted from the fungus to specifically bind Zn(ii) and deliver it to a transmembrane zinc transporter, Zrt1. We take the first step towards understanding the bioinorganic chemistry of this process, by pointing out the Zn(ii) binding sites in Pra1 and understanding the thermodynamics of such interactions...
July 20, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28723106/proteins-breaking-bad-a-free-energy-perspective
#2
Jessica Valle-Orero, Rafael Tapia-Rojo, Edward C Eckels, Jaime Andres Rivas-Pardo, Ionel Popa, Julio M Fernandez
Protein ageing may manifest as a mechanical disease that compromises tissue elasticity. As proved recently, while proteins respond to changes in force with an instantaneous elastic recoil followed by a folding contraction, aged proteins break bad, becoming unstructured polymers. Here, we explain this phenomenon in the context of a free energy model, predicting the changes in the folding landscape of proteins upon oxidative ageing. Our findings validate that protein folding under force is constituted by two separable components, polymer properties and hydrophobic collapse, and demonstrate that the latter becomes irreversibly blocked by oxidative damage...
July 19, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28722139/structure-based-release-analysis-of-the-jc-virus-agnoprotein-regions-a-role-for-the-hydrophilic-surface-of-the-major-alpha-helix-domain-in-release
#3
A Sami Saribas, Martyn K White, Mahmut Safak
Agnoprotein (Agno) is an important regulatory protein of JC virus (JCV), BK virus (BKV) and simian virus 40 (SV40) and these viruses are unable to replicate efficiently in the absence of this protein. Recent 3D-NMR structural data revealed that Agno contains two alpha-helices (a minor and a major) while the rest of the protein adopts an unstructured conformation (Coric et al., 2017, J Cell Biochem). Previously, release of the JCV Agno from the Agno-positive cells was reported. Here, we have further mapped the regions of Agno responsible for its release by a structure-based systematic mutagenesis approach...
July 19, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28714684/the-surface-of-protein-%C3%AE-6-85-can-act-as-a-template-for-recurring-peg-structure
#4
Shu-Han Chao, Jan Schaefer, Martin Gruebele
PEGylated proteins play an increasingly important role in pharmaceutical drug delivery. We recently showed that short PEG chains can affect protein structure, even when they are not making extensive contact with the protein surface. In contrast, PEG is generally assumed to form a relatively unstructured coil, whose compactness depends on solvent conditions. Here we test whether a host protein could allow PEG to form recurrent structural motifs while the PEG chain is in contact with the protein surface. We link a PEG oligomer (n=45) to one of two nearly opposite locations on the small alpha-helical protein 6-85 to investigate this question...
July 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28712389/rescuing-p53-from-mdm2-by-intrinsically-unfolded-sumo-protease-4
#5
Do-Hyoung Kim, Chewook Lee, Bom Kim, Si-Hyung Lee, Kyou-Hoon Han
Many intrinsically unstructured/unfolded proteins (IUPs) contain transient local secondary structures even though they are "unstructured" in a tertiary sense. These local secondary structures are named "pre-structured motifs (PreSMos)" and in fact are the specificity determinants for IUP-target binding, i.e., the active sites in IUPs. Using high-resolution NMR we have delineated a PreSMo active site in the intrinsically unfolded mid-domain (residues 201-300) of SUMO-specific protease 4 (SUSP4). This 29-residue motif which we termed a p53 rescue motif can protect p53 from mdm2 quenching by binding to the p53-helix binding pocket in mdm2(3-109)...
July 17, 2017: BMB Reports
https://www.readbyqxmd.com/read/28711731/insulin-chains-as-efficient-fusion-tags-for-prokaryotic-expression-of-short-peptides
#6
Ligang Deng, Xiaoying Xue, Cangjie Shen, Xiaohan Song, Chunyang Wang, Nan Wang
Insulin chains are usually expressed in Escherichia coli as fusion proteins with different tags, including various low molecular weight peptide tags. The objective of this study was to determine if insulin chains could facilitate the recombinant expression of other target proteins, with an emphasis on low molecular weight peptides. A series of short peptides were fused to mini-proinsulin, chain B or chain A, and induced for expression in Escherichia coli. All the tested peptides including glucagon-like peptide 1 (GLP-1), a C-terminal extended GLP-1, oxyntomodulin, enfuvirtide, linaclotide, and an unstructured artificial peptide were expressed with reasonable yields, identified by Tricine-SDS-PAGE and immunoblotting...
July 13, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28702545/direct-examination-of-the-relevance-for-folding-binding-and-electron-transfer-of-a-conserved-protein-folding-intermediate
#7
Emilio Lamazares, Sonia Vega, Patricia Ferreira, Milagros Medina, Juan J Galano-Frutos, Marta Martínez-Júlvez, Adrián Velázquez-Campoy, Javier Sancho
Near the minimum free energy basin of proteins where the native ensemble resides, partly unfolded conformations of slightly higher energy can be significantly populated under native conditions. It has been speculated that they play roles in molecular recognition and catalysis, but they might represent contemporary features of the evolutionary process without functional relevance. Obtaining conclusive evidence on these alternatives is difficult because it requires comparing the performance of a given protein when populating and when not populating one such intermediate, in otherwise identical conditions...
July 12, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28701724/dynamic-microtubule-association-of-doublecortin-x-dcx-is-regulated-by-its-c-terminus
#8
Maryam Moslehi, Dominic C H Ng, Marie A Bogoyevitch
Doublecortin X (DCX), known to be essential for neuronal migration and cortical layering in the developing brain, is a 40 kDa microtubule (MT)-associated protein. DCX directly interacts with MTs via its two structured doublecortin (DC) domains, but the dynamics of this association and the possible regulatory roles played by the flanking unstructured regions remain poorly defined. Here, we employ quantitative fluorescence recovery after photobleaching (FRAP) protocols in living cells to reveal that DCX shows remarkably rapid and complete exchange within the MT network but that the removal of the C-terminal region significantly slows this exchange...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28700219/versatile-site-selective-protein-reaction-guided-by-ww-domain-peptide-motif-interaction
#9
Miao Liu, Zeyang Ji, Mingjie Zhang, Jiang Xia
A short, flexible and unstructured peptide tag that has versatile and facile use in protein labeling applications is highly desirable. Here, we report an 11-residue peptide tag with an internal cysteine (a W-tag, derived from a Comm PY peptide motif that is known to bind with Nedd4 WW3* domain) that can be installed at different regions of the target protein without compromising its covalent reactivity with the reactive label (a 35-residue synthetic Nedd4 WW3* domain derivative). This versatility is explained by the unique structural features of the reaction...
July 12, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28698826/expression-refolding-and-spectroscopic-characterization-of-fibronectin-type-iii-fniii-homology-domains-derived-from-human-fibronectin-leucine-rich-transmembrane-protein-flrt-1-2-and-3
#10
Lila Yang, Maria Hansen Falkesgaard, Peter Waaben Thulstrup, Peter Schledermann Walmod, Leila Lo Leggio, Kim Krighaar Rasmussen
The fibronectin leucine rich transmembrane (FLRT) protein family consists in humans of 3 proteins, FLRT1, -2, and -3. The FLRT proteins contain two extracellular domains separated by an unstructured linker. The most membrane distal part is a leucine rich repeat (LRR) domain responsible for both cis- and trans-interactions, whereas the membrane proximal part is a fibronectin type III (FnIII) domain responsible for a cis-interaction with members of the fibroblast growth factor receptor 1 (FGFR1) family, which results in FGFR tyrosine kinase activation...
2017: PeerJ
https://www.readbyqxmd.com/read/28695742/the-human-regulatory-protein-ki-1-57-is-a-target-of-sumoylation-and-affects-pml-nuclear-body-formation
#11
Ângela Saito, Edmarcia E de Souza, Fernanda C Costa, Gabriela V Meirelles, Kaliandra de Almeida Gonçalves, Marcos T Santos, Gustavo C Bressan, Mark E McComb, Catherine E Costello, Stephen A Whelan, Jörg Kobarg
Ki-1/57 is a nuclear and cytoplasmic regulatory protein first identified in malignant cells from Hodgkin's lymphoma. It is involved in gene expression regulation on both transcriptional and mRNA metabolism levels. Ki-1/57 belongs to the family of intrinsically unstructured proteins, undergoes phosphorylation by PKC and methylation by PRMT1. Previous characterization of its protein interaction profile by yeast two-hybrid screening showed that Ki- 1/57 interacts with proteins of the SUMOylation machinery: the SUMO E2 conjugating enzyme UBC9 and the SUMO E3 ligase PIAS3, which suggested that Ki-1/57 could be involved with this process...
July 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28691351/structures-of-designed-armadillo-repeat-proteins-binding-to-peptides-fused-to-globular-domains
#12
Simon Hansen, Jonathan D Kiefer, Chaithanya Madhurantakam, Peer R E Mittl, Andreas Plückthun
Designed armadillo repeat proteins (dArmRP) are α-helical solenoid repeat proteins with an extended peptide binding groove that were engineered to develop a generic modular technology for peptide recognition. In this context, the term "peptide" not only denotes a short unstructured chain of amino acids, but also an unstructured region of a protein, as they occur in termini, loops or linkers between folded domains. Here we report two crystal structures of dArmRPs, in complex with peptides fused either to the N-terminus of Green Fluorescent Protein and to the C-terminus of a phage lambda protein D...
July 10, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28689380/-conformations-of-multi-domain-and-partially-disordered-proteins-simulations-and-experiments
#13
Bartosz Różycki
Structural biology unravels three-dimensional structures of macromolecules such as proteins, DNA, RNA, and their complexes in the attempt to explain the basic mechanisms of their functions. Among the proteins that are most difficult to characterize structurally are those which have several large domains connected by long, unstructured polypeptide segments. Such proteins perform diverse functions in living organisms and, at the same time, they are very difficult to characterize using conventional methods of structural biology...
2017: Postepy Biochemii
https://www.readbyqxmd.com/read/28687353/p27-kip1-and-human-cancers-a-reappraisal-of-a-still-enigmatic-protein
#14
Debora Bencivenga, Ilaria Caldarelli, Emanuela Stampone, Francesco Paolo Mancini, Maria Luisa Balestrieri, Fulvio Della Ragione, Adriana Borriello
p27(Kip1) is a cell cycle regulator firstly identified as a cyclin-dependent kinase inhibitor. For a long time, its function has been associated to cell cycle progression inhibition at G1/S boundary in response to antiproliferative stimuli. The picture resulted complicated by the discovery that p27(Kip1) is an intrinsically unstructured protein, with numerous CDK-dependent and -independent functions and involvement in many cellular processes, such as cytoskeleton dynamics and cell motility control, apoptosis and autophagy activation...
July 5, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28676851/aaa-atpases-in-protein-degradation
#15
REVIEW
Ravikiran S Yedidi, Petra Wendler, Cordula Enenkel
Proteolytic machineries containing multisubunit protease complexes and AAA-ATPases play a key role in protein quality control and the regulation of protein homeostasis. In these protein degradation machineries, the proteolytically active sites are formed by either threonines or serines which are buried inside interior cavities of cylinder-shaped complexes. In eukaryotic cells, the proteasome is the most prominent protease complex harboring AAA-ATPases. To degrade protein substrates, the gates of the axial entry ports of the protease need to be open...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28675294/quantifying-protection-in-disordered-proteins-using-millisecond-hydrogen-exchange-mass-spectrometry-and-peptic-reference-peptides
#16
Mohammed A Al-Naqshabandi, David D Weis
The extent and location of transient structure in intrinsically disordered proteins (IDPs) provide valuable insights into their conformational ensembles and can lead to a better understanding of coupled binding and folding. Millisecond amide hydrogen exchange (HX) can provide such information, but it is difficult to quantify the degree of transient structuring. One reason is that transiently disordered proteins undergo HX at rates only slightly slower than the rate of amide HX by an unstructured random coil, the chemical HX rate...
July 4, 2017: Biochemistry
https://www.readbyqxmd.com/read/28669632/regulation-of-the-equilibrium-between-closed-and-open-conformations-of-annexin-a2-by-n-terminal-phosphorylation-and-s100a4-binding
#17
Péter Ecsédi, Bence Kiss, Gergő Gógl, László Radnai, László Buday, Kitti Koprivanacz, Károly Liliom, Ibolya Leveles, Beáta Vértessy, Norbert Jeszenői, Csaba Hetényi, Gitta Schlosser, Gergely Katona, László Nyitray
Annexin A2 (ANXA2) has a versatile role in membrane-associated functions including membrane aggregation, endo- and exocytosis, and it is regulated by post-translational modifications and protein-protein interactions through the unstructured N-terminal domain (NTD). Our sequence analysis revealed a short motif responsible for clamping the NTD to the C-terminal core domain (CTD). Structural studies indicated that the flexibility of the NTD and CTD are interrelated and oppositely regulated by Tyr24 phosphorylation and Ser26Glu phosphomimicking mutation...
June 21, 2017: Structure
https://www.readbyqxmd.com/read/28653853/post-translational-modifications-ptms-identified-on-endogenous-huntingtin-cluster-within-proteolytic-domains-between-heat-repeats
#18
Tamara Ratovitski, Robert N O'Meally, Mali Jiang, Raghothama Chaerkady, Ekaterine Chighladze, Jacqueline C Stewart, Xiaofang Wang, Nicolas Arbez, Elaine Roby, Athanasios Alexandris, Wenzhen Duan, Ravi Vijayvargia, Ihn Sik Seong, Daniel J Lavery, Robert N Cole, Christopher A Ross
Post-translational modifications (PTMs) of proteins regulate various cellular processes. PTMs of polyglutamine-expanded huntingtin (Htt) protein, which causes Huntington's disease (HD), are likely modulators of HD pathogenesis. Previous studies have identified and characterized several PTMs on exogenously expressed Htt fragments, but none of them were designed to systematically characterize PTMs on the endogenous full-length Htt protein. We found that full-length endogenous Htt, which was immunoprecipitated from HD knock-in mouse and human post-mortem brain, is suitable for detection of PTMs by mass spectrometry...
July 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28650145/the-dead-box-protein-cyt-19-uses-arginine-residues-in-its-c-tail-to-tether-rna-substrates
#19
Veronica F Busa, Maxwell J Rector, Rick Russell
DEAD-box proteins are nonprocessive RNA helicases that play diverse roles in cellular processes. The Neurospora crassa DEAD-box protein CYT-19 promotes mitochondrial group I intron splicing and functions as a general RNA chaperone. CYT-19 includes a disordered, arginine-rich "C-tail" that binds RNA, positioning the helicase core to capture and unwind nearby RNA helices. Here we probed the C-tail further by varying the number and positions of arginines within it. We found that removing sets of as few as four of the 11 arginines reduced RNA unwinding activity (kcat/KM) to a degree equivalent to that seen upon removal of the C-tail, suggesting that a minimum or "threshold" number of arginines is required...
July 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28644863/a-rule-based-named-entity-recognition-method-for-knowledge-extraction-of-evidence-based-dietary-recommendations
#20
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
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