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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
#1
Leonid Breydo, Hussein A Almehdar, Esmail M El-Fakharany, Elrashdy M Redwan, Vladimir N Uversky
No abstract text is available yet for this article.
December 13, 2017: 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
#2
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
#3
Inderpal Singh, Shashank Singh, Vijeshwar Verma, Vladimir N Uversky, Ratna Chandra
Epidermal growth factor receptor (EGFR) 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...
November 28, 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
#4
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
#5
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
#6
REVIEW
April 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...
October 25, 2017: Proteomics
https://www.readbyqxmd.com/read/29029791/in-search-for-globally-disordered-apo-parvalbumins-case-of-parvalbumin-%C3%AE-1-from-coho-salmon
#7
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
#8
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
https://www.readbyqxmd.com/read/28980860/the-roles-of-intrinsic-disorder-based-liquid-liquid-phase-transitions-in-the-dr-jekyll-mr-hyde-behavior-of-proteins-involved-in-amyotrophic-lateral-sclerosis-and-frontotemporal-lobar-degeneration
#9
Vladimir N Uversky
Pathological developments leading to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are associated with misbehavior of several key proteins, such as SOD1 (superoxide dismutase 1), TARDBP/TDP-43, FUS, C9orf72, and dipeptide repeat proteins generated as a result of the translation of the intronic hexanucleotide expansions in the C9orf72 gene, PFN1 (profilin 1), GLE1 (GLE1, RNA export mediator), PURA (purine rich element binding protein A), FLCN (folliculin), RBM45 (RNA binding motif protein 45), SS18L1/CREST, HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), ATXN2 (ataxin 2), MAPT (microtubule associated protein tau), and TIA1 (TIA1 cytotoxic granule associated RNA binding protein)...
October 5, 2017: Autophagy
https://www.readbyqxmd.com/read/28971739/potential-functions-of-lea-proteins-from-the-brine-shrimp-artemia-franciscana-anhydrobiosis-meets-bioinformatics
#10
Brett Janis, Vladimir N Uversky, Michael A Menze
Late embryogenesis abundant (LEA) proteins are a large group of anhydrobiosis-associated intrinsically disordered proteins (IDP), which are commonly found in plants and some animals. The brine shrimp Artemiafranciscana is the only known animal that expresses LEA proteins from three, and not only one, different groups in its anhydrobiotic life stage. The reason for the higher complexity in the A. franciscana LEA proteome (LEAome), compared with other anhydrobiotic animals, remains mostly unknown. To address this issue, we have employed a suite of bioinformatics tools to evaluate the disorder status of the ArtemiaLEAome and to analyze the roles of intrinsic disorder in functioning of brine shrimp LEA proteins...
October 3, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28949782/divergent-anticancer-activity-of-free-and-formulated-camel-milk-%C3%AE-lactalbumin
#11
COMPARATIVE STUDY
Vladimir N Uversky, Esmail M El-Fakharany, Marwa M Abu-Serie, Hussein A Almehdar, Elrashdy M Redwan
Alpha-lactalbumin (α-LA), a small milk calcium-binding globular protein, is known to possess noticeable anticancer activity, which is determined by the ability of this protein to form complexes with oleic acid (OA). To date, in addition to human and bovine α-LA, the ability to form such anti-tumor complexes with OA was described for goat and camel α-LA. Although the mechanisms of the anticancer activity of human and bovine α-LA are already well-studied, little is currently known about the anticancer action of this camel protein...
October 21, 2017: Cancer Investigation
https://www.readbyqxmd.com/read/28934129/a-comprehensive-survey-of-the-roles-of-highly-disordered-proteins-in-type-2-diabetes
#12
Zhihua Du, Vladimir N Uversky
Type 2 diabetes mellitus (T2DM) is a chronic and progressive disease that is strongly associated with hyperglycemia (high blood sugar) related to either insulin resistance or insufficient insulin production. Among the various molecular events and players implicated in the manifestation and development of diabetes mellitus, proteins play several important roles. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database has information on 34 human proteins experimentally shown to be related to the T2DM pathogenesis...
September 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28925982/osmolyte-like-stabilizing-effects-of-low-gdnhcl-concentrations-on-d-glucose-d-galactose-binding-protein
#13
Alexander V Fonin, Alexandra D Golikova, Irina A Zvereva, Sabato D'Auria, Maria Staiano, Vladimir N Uversky, Irina M Kuznetsova, Konstantin K Turoverov
The ability of d-glucose/d-galactose-binding protein (GGBP) to reversibly interact with its ligands, glucose and galactose, makes this protein an attractive candidate for sensing elements of glucose biosensors. This potential is largely responsible for attracting researchers to study the conformational properties of this protein. Previously, we showed that an increase in the fluorescence intensity of the fluorescent dye 6-bromoacetyl-2-dimetylaminonaphtalene (BADAN) is linked to the holo-form of the GGBP/H152C mutant in solutions containing sub-denaturing concentrations of guanidine hydrochloride (GdnHCl)...
September 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28869862/bmp-2-and-bmp-9-binding-specificities-with-alk-3-in-aqueous-solution-with-dynamics
#14
Orkid Coskuner, Vladimir N Uversky
Signal ligands of the transforming growth factor-β (TGF-β) superfamily include the bone morphogenetic proteins (BMPs). BMPs bind to type I and type II serine-threonine kinase receptors and trigger the transphosphorylation cascade, wherein the active type II receptor phosphorylates the inactive type I receptor. This process further activates the cytoplasmic effectors of the pathway, such as SMAD proteins, which are homologs of both the Drosophila protein MAD (mothers against decapentaplegic) and the Caenorhabditis elegans protein SMA (small body size)...
August 9, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28867216/the-effect-of-phosphorylation-on-the-salt-tolerance-related-functions-of-the-soybean-protein-pm18-a-member-of-the-group-3-lea-protein-family
#15
Yun Liu, Meiyan Yang, Hua Cheng, Nan Sun, Simu Liu, Shuiming Li, Yong Wang, Yizhi Zheng, Vladimir N Uversky
Enzymatically driven post-translated modifications (PTMs) usually happen within the intrinsically disordered regions of a target protein and can modulate variety of protein functions. Late embryogenesis abundant (LEA) proteins are a family of the plant intrinsically disordered proteins (IDPs). Despite their important roles in plant stress response, there is currently limited knowledge on the presence and functional and structural effects of phosphorylation on LEA proteins. In this study, we identified three phosphorylation sites (Ser(90), Tyr(136), and Thr(266)) in the soybean PM18 protein that belongs to the group-3 LEA proteins...
September 1, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28757614/high-level-intrinsic-disorder-explains-the-universality-of-clip-binding-to-diverse-mhc-class-ii-variants
#16
Vladimir N Uversky, Yaping N Tu, Onyekachi Nwogu, Shanitra N Butler, Michael Ramsamooj, George Blanck
No abstract text is available yet for this article.
July 31, 2017: Cellular & Molecular Immunology
https://www.readbyqxmd.com/read/28746777/functionality-of-intrinsic-disorder-in-tumor-necrosis-factor-%C3%AE-and-its-receptors
#17
Vladimir N Uversky, Nawal Abd El-Baky, Esmail M El-Fakharany, Amira Sabry, Ehab H Mattar, Alexey V Uversky, Elrashdy M Redwan
Tumor necrosis factor-α (TNF-α) is a pleiotropic inflammatory cytokine that exerts potent cytotoxic effects on solid tumor cells, while not affecting their normal counterparts. It is also known that TNF-α exerts many of its biological functions via interaction with specific receptors. To understand the potential roles of intrinsic disorder in the functioning of this important cytokine, we explored the peculiarities of intrinsic disorder distribution in human TNF-α and its homologs from various species, ranging from zebrafish to chimpanzee...
July 26, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28729736/the-relationship-between-folding-and-activity-in-ureg-an-intrinsically-disordered-enzyme
#18
Marta Palombo, Alessio Bonucci, Emilien Etienne, Stefano Ciurli, Vladimir N Uversky, Bruno Guigliarelli, Valérie Belle, Elisabetta Mileo, Barbara Zambelli
A growing body of literature on intrinsically disordered proteins (IDPs) led scientists to rethink the structure-function paradigm of protein folding. Enzymes are often considered an exception to the rule of intrinsic disorder (ID), believed to require a unique structure for catalysis. However, recent studies revealed the presence of disorder in several functional native enzymes. In the present work, we address the importance of dynamics for catalysis, by investigating the relationship between folding and activity in Sporosarcina pasteurii UreG (SpUreG), a P-loop GTPase and the first discovered native ID enzyme, involved in the maturation of the nickel-containing urease...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28726924/peculiarities-of-thermal-denaturation-of-ompf-porin-from-yersinia-ruckeri
#19
Olga D Novikova, Dmitry K Chistyulin, Valentina A Khomenko, Evgeny V Sidorin, Natalya Yu Kim, Nina M Sanina, Olga Yu Portnyagina, Tamara F Solov'eva, Vladimir N Uversky, Valery L Shnyrov
Irreversible denaturation of membrane proteins in detergent solutions is similar to unfolding of water-soluble multidomain proteins and represents a complex, multistage process. Pore-forming proteins of Gram-negative bacteria are heat-modifiable proteins, i.e., proteins altering their molecular forms (trimers or monomers), and accordingly, their electrophoretic mobilities depending upon denaturation conditions. There are still some contradictory data on the peculiarities of the conformational changes in the porin structure with temperature...
August 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28692085/functional-roles-of-intrinsic-disorder-in-crispr-associated-protein-cas9
#20
Zhihua Du, Vladimir N Uversky
Protein intrinsic disorder is an important characteristic commonly detected in multifunctional or RNA- and DNA-binding proteins. Due to their high conformational flexibility and solvent accessibility, intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) execute diverse functions including interaction with multiple partners, and are frequently subjected to various post-translational modifications. Recent studies on the components comprising the CRISPR (clustered regularly interspaced short palindromic repeats) system have elucidated the crystal structure of Cas9 proteins and the mechanism by which the Cas9-sgRNA complex recognizes and cleaves its target DNA...
August 22, 2017: Molecular BioSystems
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