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https://www.readbyqxmd.com/read/28608407/disulfide-bonds-and-disorder-in-granulin-3-an-unusual-handshake-between-structural-stability-and-plasticity
#1
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/28589442/comprehensive-review-of-methods-for-prediction-of-intrinsic-disorder-and-its-molecular-functions
#2
REVIEW
Fanchi Meng, Vladimir N Uversky, Lukasz Kurgan
Computational prediction of intrinsic disorder in protein sequences dates back to late 1970 and has flourished in the last two decades. We provide a brief historical overview, and we review over 30 recent predictors of disorder. We are the first to also cover predictors of molecular functions of disorder, including 13 methods that focus on disordered linkers and disordered protein-protein, protein-RNA, and protein-DNA binding regions. We overview their predictive models, usability, and predictive performance...
June 6, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28589440/intrinsic-disorder-here-there-and-everywhere-and-nowhere-to-escape-from-it
#3
REVIEW
Vladimir N Uversky
The concept of protein intrinsic disorder persistently penetrates into all areas of modern protein science. It cannot be ignored anymore, and cannot be shrugged off, as it represents a vital feature (or, more correctly, a broad spectrum of important features), which, when added to and mixed with features arising from the well established protein structure-function paradigm, complete the picture of a functioning protein. The field of protein intrinsic disorder is very dynamic and fast developing. This Multi-Author Review represents a snapshot of this field by introducing some recent advances...
June 6, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28542206/carbonyl-based-blue-autofluorescence-of-proteins-and-amino-acids
#4
Chamani Niyangoda, Tatiana Miti, Leonid Breydo, Vladimir Uversky, Martin Muschol
Intrinsic protein fluorescence is inextricably linked to the near-UV autofluorescence of aromatic amino acids. Here we show that a novel deep-blue autofluorescence (dbAF), previously thought to emerge as a result of protein aggregation, is present at the level of monomeric proteins and even poly- and single amino acids. Just as its aggregation-related counterpart, this autofluorescence does not depend on aromatic residues, can be excited at the long wavelength edge of the UV and emits in the deep blue. Differences in dbAF excitation and emission peaks and intensities from proteins and single amino acids upon changes in solution conditions suggest dbAF's sensitivity to both the chemical identity and solution environment of amino acids...
2017: PloS One
https://www.readbyqxmd.com/read/28532244/virucidal-activity-of-cell-penetrating-peptides-of-viral-origin
#5
Nawal Abd El-Baky, Vladimir N Uversky, Elrashdy M Redwan
No abstract text is available yet for this article.
May 31, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28525284/intrinsically-disordered-proteins-as-important-players-during-desiccation-stress-of-soybean-radicles
#6
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 radicle emergence and 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 30, 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
#7
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 26, 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
#8
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
#9
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
#10
Luisa A Ferreira, Nikolai B Gusev, Vladimir N Uversky, Boris Y Zaslavsky
No abstract text is available yet for this article.
May 22, 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
#11
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
#12
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
#13
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
#14
REVIEW
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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