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Unstructured Proteins

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https://www.readbyqxmd.com/read/28432632/tryptophan-fluorescence-yields-and-lifetimes-as-a-probe-of-conformational-changes-in-human-glucokinase
#1
Bogumil Zelent, Chris Bialas, Ignacy Gryczynski, Pan Chen, Rahul Chib, Karina Lewerissa, Maria G Corradini, Richard D Ludescher, Jane M Vanderkooi, Franz M Matschinsky
Five variants of glucokinase (ATP-D-hexose-6-phosphotransferase, EC 2.7.1.1) including wild type and single Trp mutants with the Trp residue at positions 65, 99, 167 and 257 were prepared. The fluorescence of Trp in all locations studied showed intensity changes when glucose bound, indicating that conformational change occurs globally over the entire protein. While the fluorescence quantum yield changes upon glucose binding, the enzyme's absorption spectra, emission spectra and fluorescence lifetimes change very little...
April 22, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28427262/melting-proteins-evidence-for-multiple-stable-structures-upon-thermal-denaturation-of-native-ubiquitin-from-ims-ms-measurements
#2
Tarick J El-Baba, Daniel W Woodall, Shannon A Raab, Daniel R Fuller, Arthur Laganowsky, David H Russell, David E Clemmer
Ion mobility and mass spectrometry techniques have been coupled with a new temperature-controlled electrospray ionization source in order to follow the structural transitions of ubiquitin in aqueous solution (pH = 3) at elevated solution temperatures (T = 26 to 96 °C). Changes in the charge state distribution are consistent with a two-state, cooperative unfolding transition having a melting temperature of Tm = 71 ± 2 °C, in agreement with prior calorimetric measurements [Wintrode, P. L.; Makhatadze, G. I...
April 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28404644/preprotein-mature-domains-contain-translocase-targeting-signals-that-are-essential-for-secretion
#3
Katerina E Chatzi, Marios Frantzeskos Sardis, Alexandra Tsirigotaki, Marina Koukaki, Nikolina Šoštarić, Albert Konijnenberg, Frank Sobott, Charalampos G Kalodimos, Spyridoula Karamanou, Anastassios Economou
Secretory proteins are only temporary cytoplasmic residents. They are typically synthesized as preproteins, carrying signal peptides N-terminally fused to their mature domains. In bacteria secretion largely occurs posttranslationally through the membrane-embedded SecA-SecYEG translocase. Upon crossing the plasma membrane, signal peptides are cleaved off and mature domains reach their destinations and fold. Targeting to the translocase is mediated by signal peptides. The role of mature domains in targeting and secretion is unclear...
April 12, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28393136/development-of-%C3%AE-hairpin-peptides-for-the-measurement-of-scf-family-e3-ligase-activity-in-vitro-via-ornithine-ubiquitination
#4
Kaiulani M Houston, Adam T Melvin, Gregery S Woss, Effrat L Fayer, Marcey L Waters, Nancy L Allbritton
Regulation of the ubiquitin-proteasome system (UPS) to treat select types of cancer has become a popular area of drug discovery research. The FDA approval of proteasome inhibitors Bortezomib and Carfilzomib in the treatment of multiple myeloma has led to an increased need for chemical reporters capable of detecting and quantifying protein ubiquitination and the activity of members of the UPS including E3 ubiquitin ligases and the proteasome in the tumor cells of the patients. One limitation of peptide-based reporters is their rapid degradation in the cellular environment by cytosolic peptidases...
March 31, 2017: ACS Omega
https://www.readbyqxmd.com/read/28391594/the-functional-roles-of-the-unstructured-n-and-c-terminal-regions-in-%C3%AE-b-crystallin-and-other-mammalian-small-heat-shock-proteins
#5
John A Carver, Aidan B Grosas, Heath Ecroyd, Roy A Quinlan
Small heat-shock proteins (sHsps), such as αB-crystallin, are one of the major classes of molecular chaperone proteins. In vivo, under conditions of cellular stress, sHsps are the principal defence proteins that prevent large-scale protein aggregation. Progress in determining the structure of sHsps has been significant recently, particularly in relation to the conserved, central and β-sheet structured α-crystallin domain (ACD). However, an understanding of the structure and functional roles of the N- and C-terminal flanking regions has proved elusive mainly because of their unstructured and dynamic nature...
April 8, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/28387381/on-the-role-of-residue-phosphorylation-in-14-3-3-partners-aanat-as-a-case-study
#6
Diego Masone, Marina Uhart, Diego M Bustos
Twenty years ago, a novel concept in protein structural biology was discovered: the intrinsically disordered regions (IDRs). These regions remain largely unstructured under native conditions and the more are studied, more properties are attributed to them. Possibly, one of the most important is their ability to conform a new type of protein-protein interaction. Besides the classical domain-to-domain interactions, IDRs follow a 'fly-casting' model including 'induced folding'. Unfortunately, it is only possible to experimentally explore initial and final states...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28381244/disbind-a-database-of-classified-functional-binding-sites-in-disordered-and-structured-regions-of-intrinsically-disordered-proteins
#7
Jia-Feng Yu, Xiang-Hua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou, Ji-Hua Wang
BACKGROUND: Intrinsically unstructured or disordered proteins function via interacting with other molecules. Annotation of these binding sites is the first step for mapping functional impact of genetic variants in coding regions of human and other genomes, considering that a significant portion of eukaryotic genomes code for intrinsically disordered regions in proteins. RESULTS: DisBind (available at http://biophy.dzu.edu.cn/DisBind ) is a collection of experimentally supported binding sites in intrinsically disordered proteins and proteins with both structured and disordered regions...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28370412/pthrp-12-48-modulates-the-bone-marrow-microenvironment-and-suppresses-human-osteoclast-differentiation-and-lifespan
#8
Archana Kamalakar, Charity L Washam, Nisreen S Akel, Bethany J Allen, Diarra K Williams, Frances L Swain, Kim Leitzel, Alan Lipton, Dana Gaddy, Larry J Suva
Bone is a common site for metastasis in breast cancer patients and is associated with a series of complications which significantly compromise patient survival, partially due to the advanced stage of disease at the time of detection. Currently, no clinically-approved biomarkers can identify or predict the development of bone metastasis. We recently identified a unique peptide fragment of parathyroid hormone-related protein (PTHrP), PTHrP(12-48), as a validated serum biomarker in breast cancer patients that correlates with and predicts the presence of bone metastases...
March 29, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28368279/crystal-structure-of-the-human-heterogeneous-ribonucleoprotein-a18-rna-recognition-motif
#9
Katherine Coburn, Zephan Melville, Ehson Aligholizadeh, Braden M Roth, Kristen M Varney, France Carrier, Edwin Pozharski, David J Weber
The heterogeneous ribonucleoprotein A18 (hnRNP A18) is upregulated in hypoxic regions of various solid tumors and promotes tumor growth via the coordination of mRNA transcripts associated with pro-survival genes. Thus, hnRNP A18 represents an important therapeutic target in tumor cells. Presented here is the first X-ray crystal structure to be reported for the RNA-recognition motif of hnRNP A18. By comparing this structure with those of homologous RNA-binding proteins (i.e. hnRNP A1), three residues on one face of an antiparallel β-sheet (Arg48, Phe50 and Phe52) and one residue in an unstructured loop (Arg41) were identified as likely to be involved in protein-nucleic acid interactions...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28363677/large-rotation-of-the-n-terminal-domain-of-hsp90-is-important-for-interaction-with-some-but-not-all-client-proteins
#10
Soumya Daturpalli, Robert A Knieß, Chung-Tien Lee, Matthias P Mayer
Hsp90 chaperones the late folding steps of many protein kinases, transcription factors and a diverse set of other protein clients not related in sequence and structure. Hsp90's interaction with clients appears to be coupled to a series of conformational changes. How these conformational changes contribute to its chaperone activity is currently unclear. Using crosslinking, hydrogen exchange mass spectrometry, and fluorescence experiments we demonstrate here that the N-terminal domain of Hsp90 rotates by approximately 180° as compared to the crystal structure of yeast Hsp90 in complex with Sba1 and AMPPNP...
March 28, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28357416/a-system-for-enzymatic-lysine-methylation-in-a-desired-sequence-context
#11
Vinay Kumar Aileni, Erna Davydova, Anders Moen, Pål Ø Falnes
A number of lysine-specific methyltransferases (KMTs) are responsible for the post-translational modification of cellular proteins on lysine residues. Most KMTs typically recognize specific motifs in unstructured, short peptide sequences. However, we have recently discovered a novel KMT that appeared to have a more relaxed sequence specificity, namely, valosin-containing protein (VCP)-KMT, which trimethylates Lys-315 in the molecular chaperone VCP. On the basis of this, here, we explored the possibility of using the VCP-KMT/VCP system to obtain specific lysine methylation of desired sequences grafted onto a VCP-derived scaffold...
February 28, 2017: ACS Omega
https://www.readbyqxmd.com/read/28349680/expression-and-purification-of-zasp-subdomains-and-clinically-important-isoforms-high-affinity-binding-to-g-actin
#12
Norman R Watts, Xiaolei Zhuang, Joshua D Kaufman, Ira W Palmer, Altaira D Dearborn, Stephen Coscia, Yotam Blech-Hermoni, Caterina Alfano, Annalisa Pastore, Ami Mankodi, Paul T Wingfield
Z-disc-associated, alternatively spliced, PDZ motif-containing protein (ZASP) is a principal component of the sarcomere. The three prevalent isoforms of ZASP in skeletal muscle are generated by alternative splicing of exons 9 and 10. The long isoforms, either having (ZASP-L) or lacking exon 10 (ZASP-LΔex10), include an N-terminal PDZ domain, an actin-binding region (ABR) with a conserved motif (ZM), and three C-terminal LIM domains. The short isoform (ZASP-S) lacks the LIM domains. Mutations, A147T and A165V, within the ZM of ZASP-LΔex10 cause myofibrillar myopathy, but the mechanism is unknown...
April 3, 2017: Biochemistry
https://www.readbyqxmd.com/read/28315679/charged-groups-at-binding-interfaces-of-the-psbo-subunit-of-photosystem-ii-a-combined-bioinformatics-and-simulation-study
#13
Coral Del Val, Ana-Nicoleta Bondar
PsbO is an extrinsic subunit of photosystem II engaged in complex binding interactions within photosystem II. At the interface between PsbO, D1 and D2 subunits of photosystem II, a cluster of charged and polar groups of PsbO is part of an extended hydrogen-bond network thought to participate in proton transfer. The precise role of specific amino acid residues at this complex binding interface remains a key open question. Here, we address this question by carrying out extensive bioinformatics analyses and molecular dynamics simulations of PsbO proteins with mutations at the binding interface...
March 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28297649/influence-of-flexible-%C3%AF-on-the-activity-of-e-%C3%A2-coli-rna-polymerase-a-thermodynamic-analysis
#14
Debipreeta Bhowmik, Neerupma Bhardwaj, Dipankar Chatterji
The Escherichia coli RNA polymerase (RNAP) is a multisubunit protein complex containing the smallest subunit, ω. Despite the evolutionary conservation of ω and its role in assembly of RNAP, E. coli mutants lacking rpoZ (codes for ω) are viable due to the association of RNAP with the global chaperone protein GroEL. With an aim to get better insight into the structure and functional role of ω, we isolated a dominant negative mutant of ω (ω6), which is predominantly α-helical, in contrast to largely unstructured native ω, and then studied its assembly with reconstituted core1 (α2ββ') by a biophysical approach...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28295503/nuclear-magnetic-resonance-structure-of-the-human-polyoma-jc-virus-agnoprotein
#15
Pascale Coric, A Sami Saribas, Magid Abou-Gharbia, Wayne Childers, Jon Condra, Martyn K White, Mahmut Safak, Serge Bouaziz
Agnoprotein is an important regulatory protein of the human polyoma JC virus (JCV) and plays critical roles during the viral replication cycle. It forms highly stable dimers and oligomers through its Leu/Ile/Phe-rich domain, which is important for the stability and function of the protein. We recently resolved the partial 3D structure of this protein by NMR using a synthetic peptide encompassing amino acids Thr17 to Gln52, where the Leu/Ile/Phe- rich domain was found to adopt a major alpha-helix conformation spanning amino acids 23 to 39...
March 10, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28289188/ligand-induced-allostery-in-the-interaction-of-the-pseudomonas-aeruginosa-heme-binding-protein-with-heme-oxygenase
#16
Daniel J Deredge, Weiliang Huang, Colleen Hui, Hirotoshi Matsumura, Zhi Yue, Pierre Moënne-Loccoz, Jana Shen, Patrick L Wintrode, Angela Wilks
A heme-dependent conformational rearrangement of the C-terminal domain of heme binding protein (PhuS) is required for interaction with the iron-regulated heme oxygenase (HemO). Herein, we further investigate the underlying mechanism of this conformational rearrangement and its implications for heme transfer via site-directed mutagenesis, resonance Raman (RR), hydrogen-deuterium exchange MS (HDX-MS) methods, and molecular dynamics (MD). HDX-MS revealed that the apo-PhuS C-terminal α6/α7/α8-helices are largely unstructured, whereas the apo-PhuS H212R variant showed an increase in structure within these regions...
March 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28284018/chemical-shift-assignments-of-the-first-and-second-rrms-of-nrd1-a-fission-yeast-mapk-target-rna-binding-protein
#17
Ayaho Kobayashi, Teppei Kanaba, Ryosuke Satoh, Yutaka Ito, Reiko Sugiura, Masaki Mishima
Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1...
March 11, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28272524/atomistic-structural-ensemble-refinement-reveals-non-native-structure-stabilizes-a-sub-millisecond-folding-intermediate-of-chey
#18
Jade Shi, R Paul Nobrega, Christian Schwantes, Sagar V Kathuria, Osman Bilsel, C Robert Matthews, T J Lane, Vijay S Pande
The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28259129/structural-properties-of-potexvirus-coat-proteins-detected-by-optical-methods
#19
P I Semenyuk, O V Karpova, A L Ksenofontov, N O Kalinina, E N Dobrov, V V Makarov
It has been shown by X-ray analysis that cores of coat proteins (CPs) from three potexviruses, flexible helical RNA-containing plant viruses, have similar α-helical structure. However, this similarity cannot explain structural lability of potexvirus virions, which is believed to determine their biological activity. Here, we used circular dichroism (CD) spectroscopy in the far UV region to compare optical properties of CPs from three potexviruses with the same morphology and similar structure. CPs from Alternanthera mosaic virus (AltMV), potato aucuba mosaic virus (PAMV), and potato virus X (PVX) have been studied in a free state and in virions...
December 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28249940/a-structural-organization-for-disrupted-in-schizophrenia-1-identified-by-high-throughput-screening-reveals-distinctly-folded-regions-which-are-bisected-by-mental-illness-related-mutations
#20
Antony S K Yerabham, Philippe J Mas, Christina Decker, Dinesh C Soares, Oliver H Weiergräber, Luitgard Nagel-Steger, Dieter Willbold, Darren J Hart, Nicholas J Bradshaw, Carsten Korth
Disrupted in Schizophrenia 1 (DISC1) is a scaffolding protein of significant importance for neurodevelopment and a prominent candidate protein in the pathology of major mental illness. DISC1 modulates a number of critical neuronal signaling pathways through protein-protein interactions; however, the mechanism by which this occurs and how DISC1 causes mental illness is unclear, partly because knowledge of the structure of DISC1 is lacking. A lack of homology with known proteins has hindered attempts to define its domain composition...
March 1, 2017: Journal of Biological Chemistry
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