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https://www.readbyqxmd.com/read/29643398/deciphering-the-dark-proteome-of-chikungunya-virus
#1
Ankur Singh, Ankur Kumar, Rakhi Yadav, Vladimir N Uversky, Rajanish Giri
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus. The outbreak of CHIKV infection has been seen in many tropical and subtropical regions of the biosphere. Current reports evidenced that after outbreaks in 2005-06, the fitness of this virus propagating in Aedes albopictus enhanced due to the epistatic mutational changes in its envelope protein. In our study, we evaluated the prevalence of intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) in CHIKV proteome. IDPs/IDPRs are known as members of a 'Dark Proteome' that defined as a set of polypeptide segments or whole protein without unique three-dimensional structure within the cellular milieu but with significant biological functions, such as cell cycle regulation, control of signaling pathways, and maintenance of viral proteomes...
April 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29596915/a-structural-ensemble-modulation-mechanism-of-small-molecule-binding-to-disordered-proteins
#2
REVIEW
Gabriella T Heller, Massimiliano Bonomi, Michele Vendruscolo
Over the past decade, there has been a growing interest in investigating whether disordered proteins can be targeted for clinical purposes using small molecules (Metallo, 2010; Dunker and Uversky, 2010; Heller et al., 2015, 2017a; Michel and Cuchillo, 2012; Zhu et al., 2013; Ban et al., 2017; Csizmok et al., 2016 [1-8]). While small molecule binding to disordered proteins can be seen as unorthodox, examples of this phenomenon have been reported. In order to rationalize these observations, a variety of models are emerging, sometimes in apparent contradiction...
March 26, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29547954/mbd2-cp2c-loop-drives-adult-type-globin-gene-expression-and-definitive-erythropoiesis
#3
Min Young Kim, Ji Sook Kim, Seung Han Son, Chang Su Lim, Hea Young Eum, Dae Hyun Ha, Mi Ae Park, Eun Jung Baek, Buom-Yong Ryu, Ho Chul Kang, Vladimir N Uversky, Chul Geun Kim
During hematopoiesis, red blood cells originate from the hematopoietic stem cell reservoir. Although the regulation of erythropoiesis and globin expression has been intensively investigated, the underlining mechanisms are not fully understood, including the interplay between transcription factors and epigenetic factors. Here, we uncover that the Mbd2-free NuRD chromatin remodeling complex potentiates erythroid differentiation of proerythroblasts via managing functions of the CP2c complexes. We found that both Mbd2 and Mbd3 expression is downregulated during differentiation of MEL cells in vitro and in normal erythropoiesis in mouse bone marrow, and Mbd2 downregulation is crucial for erythropoiesis...
March 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29514077/conserved-functional-dynamics-i-like-to-move-it-move-it
#4
Vladimir N Uversky
The catalytic activities of enzymes are typically associated with their unique structures. However, structural dynamics may also play a functional role in enzyme catalysis. In support of this idea, Narayanan et al. (2018) show in this issue of Structure that enzymes are characterized by the presence of evolutionarily conserved dynamic traits.
March 6, 2018: Structure
https://www.readbyqxmd.com/read/29511990/on-the-regularities-of-the-polar-profiles-of-proteins-related-to-ebola-virus-infection-and-their-functional-domains
#5
Carlos Polanco, José Lino Samaniego Mendoza, Thomas Buhse, Vladimir N Uversky, Ingrid Paola Bañuelos Chao, Marcela Angola Bañuelos Cedano, Fernando Michel Tavera, Daniel Michel Tavera, Manuel Falconi, Abelardo Vela Ponce de León
The number of fatalities and economic losses caused by the Ebola virus infection across the planet culminated in the havoc that occurred between August and November 2014. However, little is known about the molecular protein profile of this devastating virus. This work represents a thorough bioinformatics analysis of the regularities of charge distribution (polar profiles) in two groups of proteins and their functional domains associated with Ebola virus disease: Ebola virus proteins and Human proteins interacting with Ebola virus...
March 6, 2018: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29453740/arrestins-structural-disorder-creates-rich-functionality
#6
REVIEW
Vsevolod V Gurevich, Eugenia V Gurevich, Vladimir N Uversky
Arrestins are soluble relatively small 44-46 kDa proteins that specifically bind hundreds of active phosphorylated GPCRs and dozens of non-receptor partners. There are binding partners that demonstrate preference for each of the known arrestin conformations: free, receptor-bound, and microtubule-bound. Recent evidence suggests that conformational flexibility in every functional state is the defining characteristic of arrestins. Flexibility, or plasticity, of proteins is often described as structural disorder, in contrast to the fixed conformational order observed in high-resolution crystal structures...
February 16, 2018: Protein & Cell
https://www.readbyqxmd.com/read/29452354/alpha-synuclein-inhibits-snx3-retromer-mediated-retrograde-recycling-of-iron-transporters-in-s-cerevisiae-and-c-elegans-models-of-parkinson-s-disease
#7
Dhaval Patel, Chuan Xu, Sureshbabu Nagarajan, Zhengchang Liu, Wayne O Hemphill, Runhua Shi, Vladimir N Uversky, Guy A Caldwell, Kim A Caldwell, Stephan N Witt
We probed the role of alpha-synuclein (α-syn) in modulating sorting nexin 3 (Snx3)-retromer-mediated recycling of iron transporters in Saccharomyces cerevisiae and Caenorhabditis elegans. In yeast, the membrane-bound heterodimer Fet3/Ftr1 is the high affinity iron importer. Fet3 is a membrane-bound multicopper ferroxidase, whose ferroxidase domain is orthologous to human ceruloplasmin (Cp), that oxidizes external Fe+2 to Fe+3; the Fe+3 ions then channel through the Ftr1 permease into the cell. When the concentration of external iron is low (< 1 µM), Fet3/Ftr1 is maintained on the plasma membrane by retrograde endocytic-recycling; whereas, when the concentration of external iron is high (> 10 µM), Fet3/Ftr1 is endocytosed and shunted to the vacuole for degradation...
February 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29414700/structural-impact-of-phosphorylation-and-dielectric-constant-variation-on-synaptotagmin-s-idr
#8
Michael E Fealey, Benjamin P Binder, Vladimir N Uversky, Anne Hinderliter, David D Thomas
We used time-resolved Förster resonance energy transfer, circular dichroism, and molecular dynamics simulation to investigate the structural dependence of synaptotagmin 1's intrinsically disordered region (IDR) on phosphorylation and dielectric constant. We found that a peptide corresponding to the full-length IDR sequence, a ∼60-residue strong polyampholyte, can sample structurally collapsed states in aqueous solution, consistent with its κ-predicted behavior, where κ is a sequence-dependent parameter that is used to predict IDR compaction...
February 6, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29413001/intrinsic-disorder-protein-protein-interactions-and-disease
#9
Vladimir N Uversky
It is recognized now that biologically active proteins without stable tertiary structure (known as intrinsically disordered proteins, IDPs) and hybrid proteins containing ordered domains and intrinsically disordered protein regions (IDPRs) are important players found in any given proteome. These IDPs/IDPRs possess functions that complement functional repertoire of their ordered counterparts, being commonly related to recognition, as well as control and regulation of various signaling pathways. They are interaction masters, being able to utilize a wide spectrum of interaction mechanisms, ranging from induced folding to formation of fuzzy complexes where significant levels of disorder are preserved, to polyvalent stochastic interactions playing crucial roles in the liquid-liquid phase transitions leading to the formation of proteinaceous membrane-less organelles...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29401697/prediction-of-disordered-regions-and-their-roles-in-the-anti-pathogenic-and-immunomodulatory-functions-of-butyrophilins
#10
Elrashdy M Redwan, Ahmed M Al-Hejin, Hussein A Almehdar, Abdelrahman M Elsaway, Vladimir N Uversky
Butyrophilins (BTNs) are a group of the moonlighting proteins, some members of which are secreted in milk. They constitute a large family of structurally similar type 1 transmembrane proteins from the immunoglobulin superfamily. Although the founding member of this family is related to lactation, participating in the secretion, formation and stabilization of milk fat globules, it may also have a cell surface receptor function. Generally, the BTN family members are known to modulate co-stimulatory responses, T cell selection, differentiation, and cell fate determination...
February 4, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29364151/insights-into-the-molecular-mechanisms-of-alzheimer-s-and-parkinson-s-diseases-with-molecular-simulations-understanding-the-roles-of-artificial-and-pathological-missense-mutations-in-intrinsically-disordered-proteins-related-to-pathology
#11
REVIEW
Orkid Coskuner-Weber, Vladimir N Uversky
Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects...
January 24, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29303563/in-aqua-veritas-the-indispensable-yet-mostly-ignored-role-of-water-in-phase-separation-and-membrane-less-organelles
#12
Boris Y Zaslavsky, Vladimir N Uversky
Despite the common practice of presenting structures of biological molecules on an empty background and the assumption that interactions between biological macromolecules take place within the inert solvent, water represents an active component of various biological processes. This Perspective addresses indispensable, yet mostly ignored, roles of water in biological liquid-liquid phase transitions and in the biogenesis of various proteinaceous membrane-less organelles. We point out that changes in the structure of water reflected in the changes in its abilities to donate and/or accept hydrogen bonds and participate in dipole-dipole and dipole-induced dipole interactions in the presence of various solutes (ranging from small molecules to synthetic polymers and biological macromolecules) might represent a driving force for the liquid-liquid phase separation, define partitioning of various solutes in formed phases, and define the exceptional ability of intrinsically disordered proteins to be engaged in the formation of proteinaceous membrane-less organelles...
January 19, 2018: Biochemistry
https://www.readbyqxmd.com/read/29237329/not-all-amlets-are-made-equal-complexes-of-cow-and-camel-%C3%AE-lactalbumin-with-oleic-acid-show-different-structure-and-stability
#13
Leonid Breydo, Hussein A Almehdar, Esmail M El-Fakharany, Elrashdy M Redwan, Vladimir N Uversky
No abstract text is available yet for this article.
January 2, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29218307/calreticulin-challenges-posed-by-the-intrinsically-disordered-nature-of-calreticulin-to-the-study-of-its-function
#14
Lilian Varricchio, Mario Falchi, Massimiliano Dall'Ora, Caterina De Benedittis, Alessandra Ruggeri, Vladimir N Uversky, Anna Rita Migliaccio
Calreticulin is a Ca2+ -binding chaperone protein, which resides mainly in the endoplasmic reticulum but also found in other cellular compartments including the plasma membrane. In addition to Ca2+ , calreticulin binds and regulates almost all proteins and most of the mRNAs deciding their intracellular fate. The potential functions of calreticulin are so numerous that identification of all of them is becoming a nightmare. Still the recent discovery that patients affected by the Philadelphia-negative myeloproliferative disorders essential thrombocytemia or primary myelofibrosis not harboring JAK2 mutations carry instead calreticulin mutations disrupting its C-terminal domain has highlighted the clinical need to gain a deeper understanding of the biological activity of this protein...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29183267/in-silico-evaluation-of-the-resistance-of-the-t790m-variant-of-epidermal-growth-factor-receptor-kinase-to-cancer-drug-erlotinib
#15
Inderpal Singh, Shashank Singh, Vijeshwar Verma, Vladimir N Uversky, Ratna Chandra
Epidermal growth factor receptor kinase is implicated in cancer development due to either overexpression or activation variants in its functional intracellular kinase domain. Threonine to methionine (Thr 790 Met) is one such variant observed commonly in patients showing resistance to kinase inhibitor drug Erlotinib. Two mechanisms for resistance have been proposed (1) steric hindrance and (2) enhanced binding to ATP. In this study, we employed molecular dynamics simulations and studied both the mechanisms. Extensive simulations and free energy of binding analyses has shown that steric hindrance does not explain appropriately the mechanism for resistance against Erlotinib therapy for this variant...
December 11, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29165363/identification-and-initial-characterization-of-the-effectors-of-an-anther-smut-fungus-and-potential-host-target-proteins
#16
Venkata S Kuppireddy, Vladimir N Uversky, Su San Toh, Ming-Chang Tsai, William C Beckerson, Catarina Cahill, Brittany Carman, Michael H Perlin
(1) Background: Plant pathogenic fungi often display high levels of host specificity and biotrophic fungi; in particular, they must manipulate their hosts to avoid detection and to complete their obligate pathogenic lifecycles. One important strategy of such fungi is the secretion of small proteins that serve as effectors in this process. Microbotryum violaceum is a species complex whose members infect members of the Caryophyllaceae; M. lychnidis-dioicae , a parasite on Silene latifolia , is one of the best studied interactions...
November 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29080786/molecular-recognition-features-in-zika-virus-proteome
#17
Pushpendra Mani Mishra, Vladimir N Uversky, Rajanish Giri
Viruses have compact genomes that encode limited number of proteins in comparison to other biological entities. Interestingly, viral proteins have shown natural abundance of either completely disordered proteins that are recognized as intrinsically disorder proteins (IDPs) or partially disordered segments known as intrinsically disordered protein regions (IDPRs). IDPRs are involved in interactions with multiple binding partners to accomplish signaling, regulation, and control functions in cells. Tuning of IDPs and IDPRs are mediated through post-translational modification and alternative splicing...
October 25, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29068531/intrinsically-disordered-proteome-of-human-membrane-less-organelles
#18
REVIEW
April L Darling, Yun Liu, Christopher J Oldfield, Vladimir N Uversky
It is recognized now that various proteinaceous membrane-less organelles (PMLOs) are commonly found in cytoplasm, nucleus, and mitochondria of various eukaryotic cells (as well as in the chloroplasts of plant cells). Being different from the "traditional" membrane-encapsulated organelles, such as chloroplasts, endoplasmic reticulum, Golgi apparatus, lysosomes, mitochondria, nucleus, and vacuoles, PMLOs solve the cellular need to facilitate and regulate molecular interactions via reversible and controllable isolation of target molecules in specialized compartments...
March 2018: Proteomics
https://www.readbyqxmd.com/read/29029791/in-search-for-globally-disordered-apo-parvalbumins-case-of-parvalbumin-%C3%AE-1-from-coho-salmon
#19
Alisa A Vologzhannikova, Polina A Khorn, Alexei S Kazakov, Ramis G Ismailov, Andrei S Sokolov, Vladimir N Uversky, Eugene A Permyakov, Sergei E Permyakov
Parvalbumin (PA) is a classical EF-hand calcium-binding protein of muscle, neuronal, and other tissues, and a major fish allergen. Although certain apo-PAs lack tertiary structure, functional implications of that feature and its structural prerequisites remain unclear. In a search for unstable PAs, we probed conformational stability of parvalbumin β-1 from coho salmon (csPA), a cold water fish species, using circular dichroism, scanning calorimetry, hydrophobic probe fluorescence, limited proteolysis, chemical crosslinking and dynamic light scattering techniques...
November 2017: Cell Calcium
https://www.readbyqxmd.com/read/29018861/role-of-solvent-properties-of-water-in-crowding-effects-induced-by-macromolecular-agents-and-osmolytes
#20
L A Ferreira, V N Uversky, B Y Zaslavsky
Solvent properties of water in aqueous solutions of polyethylene glycols of various molecular weights, l-proline, betaine, and a series of chlorides of varied concentrations are assayed using three solvatochromic dyes. The properties include solvent dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity. These properties are also evaluated in mixtures of two polymers, polymer and osmolyte, and two osmolytes. It is shown that linear combinations of solvent dipolarity/polarizability and hydrogen bond donor acidity assayed in individual solutions of crowders strongly correlate with the effects of the crowders on the stability of various proteins and nucleic acids reported in the literature...
November 21, 2017: Molecular BioSystems
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