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Intrinsically disordered protein

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https://www.readbyqxmd.com/read/28547871/sequence-based-analysis-of-protein-degradation-rates-a-computational-study-of-protein-degradation
#1
Miguel Correa Marrero, Aalt D J van Dijk, Dick de Ridder
Protein turnover is a key aspect of cellular homeostasis and proteome dynamics. However, there is little consensus on which properties of a protein determine its lifetime in the cell. In this work, we exploit two reliable datasets of experimental protein degradation rates to learn models and uncover determinants of protein degradation, with particular focus on properties that can be derived from the sequence. Our work shows that simple sequence features suffice to obtain predictive models of which the output correlates reasonably well with the experimentally measured values...
May 25, 2017: Proteins
https://www.readbyqxmd.com/read/28542243/covalent-dye-attachment-influences-the-dynamics-and-conformational-properties-of-flexible-peptides
#2
Manuel P Luitz, Anders Barth, Alvaro H Crevenna, Rainer Bomblies, Don C Lamb, Martin Zacharias
Fluorescence spectroscopy techniques like Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) have become important tools for the in vitro and in vivo investigation of conformational dynamics in biomolecules. These methods rely on the distance-dependent quenching of the fluorescence signal of a donor fluorophore either by a fluorescent acceptor fluorophore (FRET) or a non-fluorescent quencher, as used in FCS with photoinduced electron transfer (PET). The attachment of fluorophores to the molecule of interest can potentially alter the molecular properties and may affect the relevant conformational states and dynamics especially of flexible biomolecules like intrinsically disordered proteins (IDP)...
2017: PloS One
https://www.readbyqxmd.com/read/28539360/a-dock-and-coalesce-mechanism-driven-by-hydrophobic-interactions-governs-cdc42-binding-with-its-effector-protein-ack
#3
George J N Tetley, Helen R Mott, R Neil Cooley, Darerca Owen
Cdc42 is a Rho-family small G protein that has been widely studied for its role in controlling the actin cytoskeleton and plays a part in several potentially oncogenic signalling networks. Similar to most other small G proteins, Cdc42 binds to many downstream effector proteins to elicit its cellular effects. These effector proteins all engage the same face of Cdc42, the conformation of which is governed by the activation state of the G protein. Previously, the importance of individual residues in conferring binding affinity has been explored for residues within Cdc42 for three of its CRIB effectors, activated Cdc42 kinase (ACK), p21-activated kinase (PAK), and Wiskott-Aldrich syndrome protein (WASP)...
May 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28537592/programming-molecular-self-assembly-of-intrinsically-disordered-proteins-containing-sequences-of-low-complexity
#4
Joseph R Simon, Nick J Carroll, Michael Rubinstein, Ashutosh Chilkoti, Gabriel P López
Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments...
June 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28535337/overall-structural-model-of-ns5a-protein-from-hepatitis-c-virus-and-modulation-by-mutations-confering-resistance-of-virus-replication-to-cyclosporin-a
#5
Aurelie Badillo, Veronique Brechot, Stephane Sarrazin, François-Xavier Cantrelle, Frederic Delolme, Marie-Laure Fogeron, Jennifer Molle, Roland Montserret, Anja Bockmann, Ralf Bartenschlager, Volker Lohmann, Guy Lippens, Sylvie Ricard-Blum, Xavier Hanoulle, Francois Penin
Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a RNA-binding phosphoprotein composed of a N-terminal membrane anchor (AH), a structured domain 1 (D1) and two intrinsically disordered domains (D2 and D3). The knowledge of the functional architecture of this multifunctional protein remains limited. We report here that NS5A-D1D2D3 produced in a wheat germ cell-free system is obtained under a highly phosphorylated state. Its NMR analysis revealed that these phosphorylations do not change the disordered nature of D2 and D3 domains but increase the number of conformers due to partial phosphorylations...
May 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28533975/an-exhaustive-survey-of-regular-peptide-conformations-using-a-new-metric-for-backbone-handedness-h
#6
Ranjan V Mannige
The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom-the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide's conformation simply from knowing the φ and ψ values of a peptide (e...
2017: PeerJ
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
#7
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/28525284/intrinsically-disordered-proteins-as-important-players-during-desiccation-stress-of-the-soybean-radicles
#8
Yun Liu, Jiahui Wu, Nan Sun, Chengjian Tu, Xiaoying Shi, Hua Cheng, Simu Liu, Shuiming Li, Yong Wang, Yizhi Zheng, Vladimir N Uversky
Intrinsically disordered proteins (IDPs) play a variety of important physiological roles in all living organisms. However, there is no comprehensive analysis of the abundance of IDPs associated with environmental stress in plants. Here, we show that a set of heat-stable proteins (i.e., proteins that do not denature after boiling at 100°C for 10 min) was present in R0mm and R15mm radicles (i.e., before the radicle emergence and the 15 mm long radicles) of soybean (Glycine max) seeds. This set of 795 iTRAQ-quantified heat-stable proteins contained a high proportion of wholly or highly disordered proteins (15%), which was significantly higher than that estimated for the whole soybean proteome containing 55,787 proteins (9%)...
May 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28523540/rubinstein-taybi-syndrome-and-epigenetic-alterations
#9
Edward Korzus
Rubinstein-Taybi syndrome (RSTS) is a rare genetic disorder in humans characterized by growth and psychomotor delay, abnormal gross anatomy, and mild to severe mental retardation (Rubinstein and Taybi, Am J Dis Child 105:588-608, 1963, Hennekam et al., Am J Med Genet Suppl 6:56-64, 1990). RSTS is caused by de novo mutations in epigenetics-associated genes, including the cAMP response element-binding protein (CREBBP), the gene-encoding protein referred to as CBP, and the EP300 gene, which encodes the p300 protein, a CBP homologue...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28523538/mecp2-a-modulator-of-neuronal-chromatin-organization-involved-in-rett-syndrome
#10
Alexia Martínez de Paz, Juan Ausió
From an epigenetic perspective, the genomic chromatin organization of neurons exhibits unique features when compared to somatic cells. Methyl CpG binding protein 2 (MeCP2), through its ability to bind to methylated DNA, seems to be a major player in regulating such unusual organization. An important contribution to this uniqueness stems from the intrinsically disordered nature of this highly abundant chromosomal protein in neurons. Upon its binding to methylated/hydroxymethylated DNA, MeCP2 is able to recruit a plethora of interacting protein and RNA partners...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28514664/lack-of-mttp-activity-in-pluripotent-stem-cell-derived-hepatocytes-and-cardiomyocytes-abolishes-apob-secretion-and-increases-cell-stress
#11
Ying Liu, Donna M Conlon, Xin Bi, Katherine J Slovik, Jianting Shi, Hailey I Edelstein, John S Millar, Ali Javaheri, Marina Cuchel, Evanthia E Pashos, Jahangir Iqbal, M Mahmood Hussain, Robert A Hegele, Wenli Yang, Stephen A Duncan, Daniel J Rader, Edward E Morrisey
Abetalipoproteinemia (ABL) is an inherited disorder of lipoprotein metabolism resulting from mutations in microsomal triglyceride transfer protein (MTTP). In addition to expression in the liver and intestine, MTTP is expressed in cardiomyocytes, and cardiomyopathy has been reported in several ABL cases. Using induced pluripotent stem cells (iPSCs) generated from an ABL patient homozygous for a missense mutation (MTTP(R46G)), we show that human hepatocytes and cardiomyocytes exhibit defects associated with ABL disease, including loss of apolipoprotein B (apoB) secretion and intracellular accumulation of lipids...
May 16, 2017: Cell Reports
https://www.readbyqxmd.com/read/28511899/signaling-pathways-to-and-from-the-hypophysial-pars-tuberalis-an-important-center-for-the-control-of-seasonal-rhythms
#12
REVIEW
Horst-Werner Korf
Seasonal (circannual) rhythms play an important role for the control of body functions (reproduction, metabolism, immune responses) in nearly all living organisms. Also humans are affected by the seasons with regard to immune responses and mental functions, the seasonal affective disorder being one of the most prominent examples. The hypophysial pars tuberalis (PT), an important interface between the hypophysial pars distalis and neuroendocrine centers in the brain, plays an essential role in the regulation of seasonal functions and may even be the seat of the circannual clock...
May 13, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28510458/interplay-between-hydrogen-bonding-and-vibrational-coupling-in-liquid-n-methylacetamide
#13
Ana Maria Cunha, Evgeniia Salamatova, Robbert Bloem, Steven Joop Roeters, Sander Woutersen, Maxim S Pshenichnikov, Thomas L C Jansen
Intrinsically disordered proteins play an important role in biology, and unraveling their labile structure presents a vital challenge. However, the dynamical structure of such proteins thwarts their study by standard techniques such as x-ray diffraction and NMR spectroscopy. Here, we use a neat liquid composed of N-methylacetamide molecules as a model system to elucidate dynamical and structural properties similar to the those one can expect to see in intrinsically disordered peptide systems. To examine the structural dynamics in the neat liquid, we combine molecular dynamics, response-function based spectral simulations, and two-dimensional polarization-resolved infrared spectroscopy in the amide I (CO stretch) region...
May 16, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28510050/a-review-of-multi-domain-and-flexible-molecular-chaperones-studies-by-small-angle-x-ray-scattering
#14
REVIEW
Júlio C Borges, Thiago V Seraphim, Paulo R Dores-Silva, Leandro R S Barbosa
Intrinsic flexibility is closely related to protein function, and a plethora of important regulatory proteins have been found to be flexible, multi-domain or even intrinsically disordered. On the one hand, understanding such systems depends on how these proteins behave in solution. On the other, small-angle X-ray scattering (SAXS) is a technique that fulfills the requirements to study protein structure and dynamics relatively quickly with few experimental limitations. Molecular chaperones from Hsp70 and Hsp90 families are multi-domain proteins containing flexible and/or disordered regions that play central roles in cellular proteostasis...
June 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28508552/real-time-analysis-of-folding-upon-binding-of-a-disordered-protein-by-using-dissolution-dnp%C3%A2-nmr-spectroscopy
#15
Mukundan Ragavan, Luigi I Iconaru, Cheon-Gil Park, Richard W Kriwacki, Christian Hilty
The kinase inhibitory domain of the cell cycle regulatory protein p27(Kip1) (p27) was nuclear spin hyperpolarized using dissolution dynamic nuclear polarization (D-DNP). While intrinsically disordered in isolation, p27 adopts secondary structural motifs, including an α-helical structure, upon binding to cyclin-dependent kinase 2 (Cdk2)/cyclin A. The sensitivity gains obtained with hyperpolarization enable the real-time observation of (13) C NMR signals during p27 folding upon binding to Cdk2/cyclin A on a time scale of several seconds...
May 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28505312/soda-prediction-of-protein-solubility-from-disorder-and-aggregation-propensity
#16
Lisanna Paladin, Damiano Piovesan, Silvio C E Tosatto
Solubility is an important, albeit not well understood, feature determining protein behavior. It is of paramount importance in protein engineering, where similar folded proteins may behave in very different ways in solution. Here we present SODA, a novel method to predict the changes of protein solubility based on several physico-chemical properties of the protein. SODA uses the propensity of the protein sequence to aggregate as well as intrinsic disorder, plus hydrophobicity and secondary structure preferences to estimate changes in solubility...
May 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28504081/dissecting-physical-structure-of-calreticulin-an-intrinsically-disordered-ca-2-buffering-chaperone-from-endoplasmic-reticulum
#17
Anna Rita Migliaccio, Vladimir N Uversky
Calreticulin (CALR) is a Ca(2+) binding multifunctional protein that mostly resides in the endoplasmic reticulum (ER) and plays a number of important roles in various physiological and pathological processes. Although the major functions ascribed to CALR are controlling the Ca(2+) homeostasis in ER and acting as a lectin-like ER chaperon for many glycoproteins, this moonlighting protein can be found in various cellular compartments where it has many non-ER functions. To shed more light on the mechanisms underlying polyfunctionality of this moonlighting protein that can be found in different cellular compartments and that possesses a wide spectrum of unrelated biological activities, being able to interact with Ca(2+) (and potentially other metal ions), RNA, oligosaccharides, and numerous proteins, we used a set of experimental and computational tools to evaluate the intrinsic disorder status of CALR and the role of calcium binding on structural properties and conformational stability of the full-length CALR and its isolated P- and C-domains...
May 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28502465/application-of-nmr-to-studies-of-intrinsically-disordered-proteins
#18
Eric B Gibbs, Erik C Cook, Scott A Showalter
The prevalence of intrinsically disordered protein regions, particularly in eukaryotic proteins, and their clear functional advantages for signaling and gene regulation have created an imperative for high-resolution structural and mechanistic studies. NMR spectroscopy has played a central role in enhancing not only our understanding of the intrinsically disordered native state, but also how that state contributes to biological function. While pathological functions associated with protein aggregation are well established, it has recently become clear that disordered regions also mediate functionally advantageous assembly into high-order structures that promote the formation of membrane-less sub-cellular compartments and even hydrogels...
May 11, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28497792/structural-heterogeneity-in-the-intrinsically-disordered-rna-polymerase-ii-c-terminal-domain
#19
Bede Portz, Feiyue Lu, Eric B Gibbs, Joshua E Mayfield, M Rachel Mehaffey, Yan Jessie Zhang, Jennifer S Brodbelt, Scott A Showalter, David S Gilmour
RNA polymerase II contains a repetitive, intrinsically disordered, C-terminal domain (CTD) composed of heptads of the consensus sequence YSPTSPS. The CTD is heavily phosphorylated and serves as a scaffold, interacting with factors involved in transcription initiation, elongation and termination, RNA processing and chromatin modification. Despite being a nexus of eukaryotic gene regulation, the structure of the CTD and the structural implications of phosphorylation are poorly understood. Here we present a biophysical and biochemical interrogation of the structure of the full length CTD of Drosophila melanogaster, which we conclude is a compact random coil...
May 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28497574/protein-destabilization-and-loss-of-protein-protein-interaction-are-fundamental-mechanisms-in-cbla-type-methylmalonic-aciduria
#20
Tanja Plessl, Céline Bürer, Seraina Lutz, Wyatt W Yue, Matthias R Baumgartner, D Sean Froese
Mutations in the human MMAA gene cause the metabolic disorder cblA-type methylmalonic aciduria (MMA), although knowledge of the mechanism of dysfunction remains lacking. MMAA regulates the incorporation of the cofactor adenosylcobalamin, generated from the MMAB adenosyltransferase, into the destination enzyme methylmalonyl-CoA mutase (MUT). This function of MMAA depends on its GTPase activity, which is stimulated by an interaction with MUT. Here, we present 67 new patients with cblA-type MMA, identifying 19 novel mutations...
May 12, 2017: Human Mutation
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