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Intrinsically disordered protein

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https://www.readbyqxmd.com/read/28630323/role-of-the-cbp-catalytic-core-in-intramolecular-sumoylation-and-control-of-histone-h3-acetylation
#1
Sangho Park, Robyn L Stanfield, Maria A Martinez-Yamout, H Jane Dyson, Ian A Wilson, Peter E Wright
The histone acetyl transferases CREB-binding protein (CBP) and its paralog p300 play a critical role in numerous cellular processes. Dysregulation of their catalytic activity is associated with several human diseases. Previous work has elucidated the regulatory mechanisms of p300 acetyltransferase activity, but it is not known whether CBP activity is controlled similarly. Here, we present the crystal structure of the CBP catalytic core encompassing the bromodomain (BRD), CH2 (comprising PHD and RING), HAT, and ZZ domains at 2...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28627461/8-methoxypsoralen-reduces-akt-phosphorylation-induces-intrinsic-and-extrinsic-apoptotic-pathways-and-suppresses-cell-growth-of-sk-n-as-neuroblastoma-and-sw620-metastatic-colon-cancer-cells
#2
Magdalena Bartnik, Adrianna Sławińska-Brych, Aleksandra Żurek, Martyna Kandefer-Szerszeń, Barbara Zdzisińska
ETHNOPHARMACOLOGICAL RELEVANCE: 8-methoxypsoralen (8-MOP) is a furanocoumarin and an active compound of a traditional Egyptian medicinal plant Ammi majus L, whose juice/fruit has been used for many years in folk phototherapy for the treatment of vitiligo or a hyperproliferative skin disorder, psoriasis. 8-MOP together with UVA light is also used as an anticancer drug for the treatment of cutaneous T-cell lymphoma. However, furanocoumarins exert anticancer activity even without UV irradiation...
June 13, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28627366/pqbp1-an-intrinsically-disordered-denatured-protein-at-the-crossroad-of-intellectual-disability-and-neurodegenerative-diseases
#3
REVIEW
Hitoshi Okazawa
PQBP1 (polyglutamine binding protein-1) is the earliest identified molecule among the group of disease-related intrinsically disordered/denatured proteins. PQBP1 interacts with splicing-related factors via the disordered/denatured domain and regulates post-transcriptional gene expression. The mutations cause intellectual disability due to decreased dendritic spines and abnormal expression of synapse molecules in neurons, and microcephaly due to elongated cell cycle time and abnormal expression of cell cycle proteins in neural stem progenitor cells...
June 13, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28625737/insights-into-the-conformations-and-dynamics-of-intrinsically-disordered-proteins-using-single-molecule-fluorescence
#4
REVIEW
Gregory-Neal Gomes, Claudiu C Gradinaru
Most proteins are not static structures, but many of them are found in a dynamic state, exchanging conformations on various time scales as a key aspect of their biological function. An entire spectrum of structural disorder exists in proteins and obtaining a satisfactory quantitative description of these states remains a challenge. Single-molecule fluorescence spectroscopy techniques are uniquely suited for this task, by measuring conformations without ensemble averaging and kinetics without interference from asynchronous processes...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28623264/structural-characterization-of-the-smrt-corepressor-interacting-with-histone-deacetylase-7
#5
Danielle C Desravines, Itziar Serna Martin, Robert Schneider, Philippe J Mas, Nataliia Aleksandrova, Malene Ringkjøbing Jensen, Martin Blackledge, Darren J Hart
The 2525 amino acid SMRT corepressor is an intrinsically disordered hub protein responsible for binding and coordinating the activities of multiple transcription factors and chromatin modifying enzymes. Here we have studied its interaction with HDAC7, a class IIa deacetylase that interacts with the corepressor complex together with the highly active class I deacetylase HDAC3. The binding site of class IIa deacetylases was previously mapped to an approximate 500 amino acid region of SMRT, with recent implication of short glycine-serine-isoleucine (GSI) containing motifs...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28622544/conformational-transition-of-%C3%AE%C2%BA-casein-in-micellar-environment-insight-from-the-tryptophan-fluorescence
#6
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/28620032/a-moving-target-structure-and-disorder-in-pursuit-of-myc-inhibitors
#7
REVIEW
Richard Bayliss, Selena G Burgess, Eoin Leen, Mark W Richards
The Myc proteins comprise a family of ubiquitous regulators of gene expression implicated in over half of all human cancers. They interact with a large number of other proteins, such as transcription factors, chromatin-modifying enzymes and kinases. Remarkably, few of these interactions have been characterized structurally. This is at least in part due to the intrinsically disordered nature of Myc proteins, which adopt a defined conformation only in the presence of binding partners. Owing to this behaviour, crystallographic studies on Myc proteins have been limited to short fragments in complex with other proteins...
June 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28614115/trafficking-and-regulation-of-the-nkcc2-cotransporter-in-the-thick-ascending-limb
#8
Kerim Mutig
PURPOSE OF REVIEW: The kidney Na-K-2Cl cotransporter (NKCC2) is essential for urinary concentration and renal electrolyte handling. Loss of function mutations in the NKCC2 gene cause urinary salt and potassium wasting, whereas excessive NKCC2 function has been linked to high blood pressure. Loop diuretics, targeting the transporter, are instrumental for relieving edema or hypertension. This review focuses on intrinsic mechanisms regulating NKCC2 activity at the posttranslational level, namely its trafficking and phosphorylation...
June 12, 2017: Current Opinion in Nephrology and Hypertension
https://www.readbyqxmd.com/read/28612216/to-be-disordered-or-not-to-be-disordered-is-that-still-a-question-for-proteins-in-the-cell
#9
REVIEW
Kris Pauwels, Pierre Lebrun, Peter Tompa
There is ample evidence that many proteins or regions of proteins lack a well-defined folded structure under native-like conditions. These are called intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). Whether this intrinsic disorder is also their main structural characteristic in living cells has been a matter of intense debate. The structural analysis of IDPs became an important challenge also because of their involvement in a plethora of human diseases, which made IDPs attractive targets for therapeutic development...
June 13, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28611588/time-dependent-hiv-tat-induced-perturbation-of-human-neurons-in-vitro-towards-a-model-for-the-molecular-pathology-of-hiv-associated-neurocognitive-disorders
#10
Kim T Gurwitz, Richard J Burman, Brandon D Murugan, Shaun Garnett, Tariq Ganief, Nelson C Soares, Joseph V Raimondo, Jonathan M Blackburn
A significant proportion of human immunodeficiency virus type 1 (HIV)-positive individuals are affected by the cognitive, motor and behavioral dysfunction that characterizes HIV-associated neurocognitive disorders (HAND). While the molecular etiology of HAND remains largely uncharacterized, HIV transactivator of transcription (HIV-Tat) is thought to be an important etiological cause. Here we have used mass spectrometry (MS)-based discovery proteomics to identify the quantitative, cell-wide changes that occur when non-transformed, differentiated human neurons are treated with HIV-Tat over time...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28610839/fly-fishing-for-histones-catch-and-release-by-histone-chaperone-intrinsically-disordered-regions-and-acidic-stretches
#11
REVIEW
Christopher Warren, David Shechter
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly two-meter long human genome into a roughly ten-micron diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly, and thus the fluidity of the ever-changing chromatin landscape...
June 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28608840/sequence-identification-recombinant-production-and-analysis-of-the-self-assembly-of-egg-stalk-silk-proteins-from-lacewing-chrysoperla-carnea
#12
Martin Neuenfeldt, Thomas Scheibel
Egg stalk silks of the common green lacewing Chrysoperla carnea likely comprise at least three different silk proteins. Based on the natural spinning process, it was hypothesized that these proteins self-assemble without shear stress, as adult lacewings do not use a spinneret. To examine this, the first sequence identification and determination of the gene expression profile of several silk proteins and various transcript variants thereof was conducted, and then the three major proteins were recombinantly produced in Escherichia coli encoded by their native complementary DNA (cDNA) sequences...
June 13, 2017: Biomolecules
https://www.readbyqxmd.com/read/28608407/disulfide-bonds-and-disorder-in-granulin-3-an-unusual-handshake-between-structural-stability-and-plasticity
#13
Gaurav Ghag, Christopher J Holler, Georgia Taylor, Thomas L Kukar, Vladimir N Uversky, Vijayaraghavan Rangachari
Granulins (GRNs) are a family of small (∼6 kDa) proteins generated by the proteolytic processing of their precursor, progranulin (PGRN), in many cell types. Both PGRN and GRNs are implicated in a plethora of biological functions, often in opposing roles to each other. Lately, GRNs have generated significant attention due to their implicated roles in neurodegenerative disorders. Despite their physiological and pathological significance, the structure-function relationships of GRNs are poorly defined. GRNs contain 12 conserved cysteines forming six intramolecular disulfide bonds, making them rather exceptional, even among a few proteins with high disulfide bond density...
June 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28608349/identification-and-evolutionary-characterization-of-argonaute-binding-platforms
#14
Joshua T Trujillo, Rebecca A Mosher
ARGONAUTE (AGO) proteins are eukaryotic RNA silencing effectors that interact with their binding partners via short peptide motifs known as AGO hooks. AGO hooks tend to cluster in one region of the protein to create an AGO-binding platform. In addition to the presence of AGO hooks, AGO-binding platforms are intrinsically disordered, contain tandem repeat arrays, and have weak sequence conservation even between close relatives. These characteristics make it difficult to identify and perform evolutionary analysis of these regions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28604862/dissecting-mechanism-of-coupled-folding-and-binding-of-an-intrinsically-disordered-protein-by-chemical-synthesis-of-conformationally-constrained-analogues
#15
Boris Schmidtgall, Olivier Chaloin, Valentin Bauer, Manuela Sumyk, Catherine Birck, Vladimir Torbeev
Non-canonical α-methyl amino acids were incorporated at various sites in the sequence of intrinsically disordered activation domain from the p160 transcriptional co-activator (ACTR) to facilitate the formation of α-helical structures. Kinetic and thermodynamic data confirm the induced fit mechanism of complex formation between the synthesized ACTR variants and the nuclear co-activator binding domain (NCBD).
June 12, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28603985/hydrogen-bond-networks-and-hydrophobic-effects-in-the-amyloid-%C3%AE-30-35-chain-in-water-a-molecular-dynamics-study
#16
KwangHyok Jong, Luca Grisanti, Ali A Hassanali
We study the conformational landscape of the C-terminal fragment of the Amyloid protein Aβ30-35 in water using well-tempered metadynamics simulations and find that it resembles an intrinsically disordered protein. The conformational fluctuations of the protein are facilitated by a collective reorganization of both protein and water hydrogen bond networks, combined with electrostatic interactions between termini as well as hydrophobic interactions of the side chains. The stabilization of hydrophobic interactions in one of the conformers involves a collective collapse of the sidechains along with a squeeze out of water sandwiched in between...
June 12, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28601983/functions-of-intrinsic-disorder-in-transmembrane-proteins
#17
REVIEW
Magnus Kjaergaard, Birthe B Kragelund
Intrinsic disorder is common in integral membrane proteins, particularly in the intracellular domains. Despite this observation, these domains are not always recognized as being disordered. In this review, we will discuss the biological functions of intrinsically disordered regions of membrane proteins, and address why the flexibility afforded by disorder is mechanistically important. Intrinsically disordered regions are present in many common classes of membrane proteins including ion channels and transporters; G-protein coupled receptors (GPCRs), receptor tyrosine kinases and cytokine receptors...
June 10, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28600653/how-order-and-disorder-within-paramyxoviral-nucleoproteins-and-phosphoproteins-orchestrate-the-molecular-interplay-of-transcription-and-replication
#18
REVIEW
Sonia Longhi, Louis-Marie Bloyet, Stefano Gianni, Denis Gerlier
In this review, we summarize computational and experimental data gathered so far showing that structural disorder is abundant within paramyxoviral nucleoproteins (N) and phosphoproteins (P). In particular, we focus on measles, Nipah, and Hendra viruses and highlight both commonalities and differences with respect to the closely related Sendai virus. The molecular mechanisms that control the disorder-to-order transition undergone by the intrinsically disordered C-terminal domain (NTAIL) of their N proteins upon binding to the C-terminal X domain (XD) of the homologous P proteins are described in detail...
June 9, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28597297/intrinsic-protein-disorder-in-oncogenic-kras-signaling
#19
REVIEW
Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Tsung-Jen Liao, Shuai Li, David Fushman, Jian Zhang
How Ras, and in particular its most abundant oncogenic isoform K-Ras4B, is activated and signals in proliferating cells, poses some of the most challenging questions in cancer cell biology. In this paper, we ask how intrinsically disordered regions in K-Ras4B and its effectors help promote proliferative signaling. Conformational disorder allows spanning long distances, supports hinge motions, promotes anchoring in membranes, permits segments to fulfil multiple roles, and broadly is crucial for activation mechanisms and intensified oncogenic signaling...
June 8, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28597296/behaviour-of-intrinsically-disordered-proteins-in-protein-protein-complexes-with-an-emphasis-on-fuzziness
#20
REVIEW
Johan G Olsen, Kaare Teilum, Birthe B Kragelund
Intrinsically disordered proteins (IDPs) do not, by themselves, fold into a compact globular structure. They are extremely dynamic and flexible, and are typically involved in signalling and transduction of information through binding to other macromolecules. The reason for their existence may lie in their malleability, which enables them to bind several different partners with high specificity. In addition, their interactions with other macromolecules can be regulated by a variable amount of chemically diverse post-translational modifications...
June 8, 2017: Cellular and Molecular Life Sciences: CMLS
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