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https://www.readbyqxmd.com/read/28525284/intrinsically-disordered-proteins-as-important-players-during-desiccation-stress-of-the-soybean-radicles
#1
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/28504081/dissecting-physical-structure-of-calreticulin-an-intrinsically-disordered-ca-2-buffering-chaperone-from-endoplasmic-reticulum
#2
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/28500420/purification-biochemical-and-structural-characterization-of-a-novel-fibrinolytic-enzyme-from-mucor-subtilissimus-ucp-1262
#3
Thiago Pajeú Nascimento, Amanda Emmanuelle Sales, Tatiana Souza Porto, Romero Marcos Pedrosa Brandão Costa, Leonid Breydo, Vladimir N Uversky, Ana Lúcia Figueiredo Porto, Attilio Converti
Fibrinolytic proteases are enzymes that degrade fibrin. They provide a promising alternative to existing drugs for thrombolytic therapy. A protease isolated from the filamentous fungus Mucor subtilissimus UCP 1262 was purified in three steps by ammonium sulfate fractionation, ion exchange, and molecular exclusion chromatographies, and characterized biochemically and structurally. The purified protease exhibited a molecular mass of 20 kDa, an apparent isoelectric point of 4.94 and a secondary structure composed mainly of α-helices...
May 12, 2017: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/28491292/looking-at-the-recent-advances-in-understanding-%C3%AE-synuclein-and-its-aggregation-through-the-proteoform-prism
#4
REVIEW
Vladimir N Uversky
Despite attracting the close attention of multiple researchers for the past 25 years, α-synuclein continues to be an enigma, hiding sacred truth related to its structure, function, and dysfunction, concealing mechanisms of its pathological spread within the affected brain during disease progression, and, above all, covering up the molecular mechanisms of its multipathogenicity, i.e. the ability to be associated with the pathogenesis of various diseases. The goal of this article is to present the most recent advances in understanding of this protein and its aggregation and to show that the remarkable structural, functional, and dysfunctional multifaceted nature of α-synuclein can be understood using the proteoform concept...
2017: F1000Research
https://www.readbyqxmd.com/read/28480793/effect-of-human-heat-shock-protein-hspb6-on-the-solvent-features-of-water-in-aqueous-solutions
#5
Luisa A Ferreira, Nikolai B Gusev, Vladimir N Uversky, Boris Y Zaslavsky
No abstract text is available yet for this article.
May 7, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28474890/tyrosine-regulates-%C3%AE-sheet-structure-formation-in-amyloid-%C3%AE-42-a-new-clustering-algorithm-for-disordered-proteins
#6
Orkid Coskuner, Vladimir N Uversky
Our recent studies show that the single Tyr residue in the sequence of amyloid-β42 (Aβ42) is reactive toward various ligands, including metals and adenosine trisphospate (see: Coskuner , O. J. Biol. Inorg. Chem. 2016 , 21 , 957 - 973 and Coskuner , O. ; Murray , I. V. J. J. Alzheimer's Dis. 2014 , 41 , 561 - 574 ). However, the exact role of Tyr in the structures of Aβ42 remains unknown. To fill this gap, here we analyzed the role of Tyr and the impact of the Tyr10Ala mutation on the structural ensemble of Aβ42...
May 12, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28412749/diagnostic-and-prognostic-relevance-of-cp2c-and-yy1-expression-in-hepatocellular-carcinoma
#7
Ji Sook Kim, Seung Han Son, Min Young Kim, DongHo Choi, Ik-Soon Jang, Seung Sam Paik, Ji Hyung Chae, Vladimir N Uversky, Chul Geun Kim
Recent studies have demonstrated an oncogenic role of the transcription factor (TF) CP2c in hepatocellular carcinoma (HCC) based on a strong correlation between CP2c expression, tumor grade, and aggressiveness. We recently found that CP2c directly interacts with another TF, YY1, which is also overexpressed in multiple cancers, including HCC. To evaluate if these proteins are co-regulated in carcinogenesis, we analyzed the expression of CP2c and YY1 in HCC (n = 136) tissues and examined the correlation between their expression and clinicopathological characteristics of HCC...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28369666/computational-prediction-of-intrinsic-disorder-in-proteins
#8
Fanchi Meng, Vladimir Uversky, Lukasz Kurgan
Computational prediction of intrinsically disordered proteins (IDPs) is a mature research field. These methods predict disordered residues and regions in an input protein chain. More than 60 predictors of IDPs have been developed. This unit defines computational prediction of intrinsic disorder, summarizes major types of predictors of disorder, and provides details about three accurate and recently released methods. We demonstrate the use of these methods to predict intrinsic disorder for several illustrative proteins, provide insights into how predictions should be interpreted, and quantify and discuss predictive performance...
April 3, 2017: Current Protocols in Protein Science
https://www.readbyqxmd.com/read/28362316/cancer-testis-antigens-smart-biomarkers-for-diagnosis-and-prognosis-of-prostate-and-other-cancers
#9
Prakash Kulkarni, Vladimir N Uversky
A clinical dilemma in the management of prostate cancer (PCa) is to distinguish men with aggressive disease who need definitive treatment from men who may not require immediate intervention. Accurate prediction of disease behavior is critical because radical treatment is associated with high morbidity. Here, we highlight the cancer/testis antigens (CTAs) as potential PCa biomarkers. The CTAs are a group of proteins that are typically restricted to the testis in the normal adult but are aberrantly expressed in several types of cancers...
March 31, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28331777/on-the-potential-of-using-peculiarities-of-the-protein-intrinsic-disorder-distribution-in-mitochondrial-cytochrome-b-to-identify-the-source-of-animal-meats
#10
Haitham A Yacoub, Mahmoud A Sadek, Vladimir N Uversky
This study was conducted to identify the source of animal meat based on the peculiarities of protein intrinsic disorder distribution in mitochondrial cytochrome b (mtCyt-b). The analysis revealed that animal and avian species can be discriminated based on the proportions of the two groups of residues, Leu+Ile, and Ser+Pro+Ala, in the amino acid sequences of their mtCyt-b. Although levels of the overall intrinsic disorder in mtCyt-b is not very high, the peculiarities of disorder distribution within the sequences of mtCyt-b from different species varies in a rather specific way...
2017: Intrinsically Disordered Proteins
https://www.readbyqxmd.com/read/28328918/simultaneous-quantification-of-protein-order-and-disorder
#11
Pietro Sormanni, Damiano Piovesan, Gabriella T Heller, Massimiliano Bonomi, Predrag Kukic, Carlo Camilloni, Monika Fuxreiter, Zsuzsanna Dosztanyi, Rohit V Pappu, M Madan Babu, Sonia Longhi, Peter Tompa, A Keith Dunker, Vladimir N Uversky, Silvio C E Tosatto, Michele Vendruscolo
No abstract text is available yet for this article.
March 22, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28321370/quarterly-intrinsic-disorder-digest-april-may-june-2014
#12
Shelly DeForte, Vladimir N Uversky
This is the 6(th) issue of the Digested Disorder series that continues to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the second quarter of 2014; i.e., during the period of April, May, and June of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings...
2017: Intrinsically Disordered Proteins
https://www.readbyqxmd.com/read/28316126/hemodialysis-clinic-social-networks-sex-differences-and-renal-transplantation
#13
A Gillespie, E L Fink, H M Traino, A Uversky, S B Bass, J Greener, J Hunt, T Browne, H Hammer, P P Reese, Z Obradovic
This study describes patient social networks within a new hemodialysis clinic and models the association between social network participation and kidney transplantation. Survey and observational data collected between 8/2012 and 2/2015 were used to observe the formation of a social network of 46 hemodialysis patients in a newly opened clinic. Thirty-two (70%) patients formed a social network, discussing health (59%) and transplantation (44%) with other patients. While transplant eligible women participated in the network less often than men (56% vs...
March 18, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28289760/pten-proteoforms-in-biology-and-disease
#14
REVIEW
Prerna Malaney, Vladimir N Uversky, Vrushank Davé
Proteoforms are specific molecular forms of protein products arising from a single gene that possess different structures and different functions. Therefore, a single gene can produce a large repertoire of proteoforms by means of allelic variations (mutations, indels, SNPs), alternative splicing and other pre-translational mechanisms, post-translational modifications (PTMs), conformational dynamics, and functioning. Resulting proteoforms that have different sizes, alternative splicing patterns, sets of post-translational modifications, protein-protein interactions, and protein-ligand interactions, might dramatically increase the functionality of the encoded protein...
March 13, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28281231/intrinsically-disordered-regions-in-serum-albumin-what-are-they-for
#15
REVIEW
Ekaterina A Litus, Sergei E Permyakov, Vladimir N Uversky, Eugene A Permyakov
Serum albumin is a major plasma protein in mammalian blood. The importance of this protein lies in its roles in both bioregulation and transport phenomena. Serum albumin binds various metal ions and participates in the transport and storage of fatty acids, bilirubin, steroids amino acids, and many other ligands, usually with regions of hydrophobic surface. Although the primary role of serum albumin is to transport various ligand, its versatile binding capacities and high concentration mean that it can assume a number of additional functions...
March 10, 2017: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28190397/when-good-goes-awry-the-aggregation-of-protein-therapeutics
#16
Jennifer M Redington, Leonid Breydo, Vladimir N Uversky
Protein therapeutics are playing an increasingly important role in treatment of a variety of human diseases. However, like the rest of proteins, they are susceptible to aggregation. Aggregation of proteinaceous pharmaceuticals can cause a loss of efficacy and, potentially, cytotoxicity and an immunogenic response. This review describes various ways protein therapeutics aggregate and a variety of approaches taken to prevent or minimize this process.
February 9, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28178192/structure-and-conformational-properties-of-d-glucose-d-galactose-binding-protein-in-crowded-milieu
#17
Alexander V Fonin, Sergey A Silonov, Asiya K Sitdikova, Irina M Kuznetsova, Vladimir N Uversky, Konstantin K Turoverov
Conformational changes of d-glucose/d-galactose-binding protein (GGBP) were studied under molecular crowding conditions modeled by concentrated solutions of polyethylene glycols (PEG-12000, PEG-4000, and PEG-600), Ficoll-70, and Dextran-70, addition of which induced noticeable structural changes in the GGBP molecule. All PEGs promoted compaction of GGBP and lead to the increase in ordering of its structure. Concentrated solutions of PEG-12000 and PEG-4000 caused GGBP aggregation. Although Ficoll-70 and Dextran-70 also promoted increase in the GGBP ordering, the structural outputs were different for different crowders...
February 6, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28150000/effects-of-the-hofmeister-series-of-sodium-salts-on-the-solvent-properties-of-water
#18
L A Ferreira, V N Uversky, B Y Zaslavsky
The solvent features of water (solvent dipolarity/polarizability, π*, hydrogen bond donor acidity, α, and hydrogen bond acceptor basicity, β) were examined in aqueous solutions of Na2SO4, NaF, CH3COONa, NaCl, NaBr, NaI, and NaClO4 at concentrations of each salt from 0 to 1.0 M (up to 2.0 M for NaClO4). The solvent features of water in solutions of different concentrations for each salt were found to be linearly related as π* = z + aα + bβ. The coefficients of this relationship were suggested to represent the signature of the salt effect on the solvent features of water...
February 2, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28109327/effects-of-intrinsic-and-extrinsic-factors-on-aggregation-of-physiologically-important-intrinsically-disordered-proteins
#19
L Breydo, J M Redington, V N Uversky
Misfolding and aggregation of proteins and peptides play an important role in a number of diseases as well as in many physiological processes. Many of the proteins that misfold and aggregate in vivo are intrinsically disordered. Protein aggregation is a complex multistep process, and aggregates can significantly differ in morphology, structure, stability, cytotoxicity, and self-propagation ability. The aggregation process is influenced by both intrinsic (e.g., mutations and expression levels) and extrinsic (e...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28098335/not-an-exception-to-the-rule-the-functional-significance-of-intrinsically-disordered-protein-regions-in-enzymes
#20
Shelly DeForte, Vladimir N Uversky
Intrinsically disordered protein regions (IDPRs) are remarkably common and have unique and important biological functions. Enzymes have long been considered an exception to the rule of protein intrinsic disorder due to the structural requirements for catalysis. Although functionally significant IDPRs have been described in several enzymes, there has been no study quantifying the extent of this phenomenon. We have conducted a multilevel computational analysis of missing regions in X-ray crystal structures in the PDB and predicted disorder in 66 representative proteomes...
January 18, 2017: Molecular BioSystems
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