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Keith dunker

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https://www.readbyqxmd.com/read/29719237/regulating-protein-function-by-delayed-folding
#1
Jianhong Zhou, A Keith Dunker
In this issue of Structure, Tsirigotaki et al. (2018) use bioinformatics and biophysical tools to demonstrate that many secreted proteins form long-lived, loosely packed folding intermediates. This delayed folding correlates with elevated disorder and reduced hydrophobicity compared to structured cytosolic proteins and is often stabilized by signal peptides by yet to be determined mechanisms.
May 1, 2018: Structure
https://www.readbyqxmd.com/read/29626537/intrinsically-disordered-proteins-link-alternative-splicing-and-post-translational-modifications-to-complex-cell-signaling-and-regulation
#2
Jianhong Zhou, Suwen Zhao, A Keith Dunker
Intrinsically disordered proteins and regions (IDPs and IDRs) lack well-defined tertiary structures, yet carry out various important cellular functions, especially those associated with cell signaling and regulation. In eukaryotes, IDPs and IDRs contain the preferred loci for both alternative splicing (AS) and many post-translational modifications (PTMs). Furthermore, AS and/or PTMs at these loci generally alter the signaling outcomes associated with these IDPs or IDRs, where the functional cooperation of these three features is named the IDP-AS-PTM toolkit...
April 4, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29394379/the-evolutionary-origins-of-cell-type-diversification-and-the-role-of-intrinsically-disordered-proteins
#3
Karl J Niklas, A Keith Dunker, Inmaculada Yruela
The evolution of complex multicellular life forms occurred multiple times and was attended by cell type specialization. We review seven lines of evidence indicating that intrinsically disordered/ductile proteins (IDPs) played a significant role in the evolution of multicellularity and cell type specification: (i) most eukaryotic transcription factors (TFs) and multifunctional enzymes contain disproportionately long IDP sequences (≥30 residues in length), whereas highly conserved enzymes are normally IDP region poor; (ii) ~80% of the proteome involved in development are IDPs; (iii) the majority of proteins undergoing alternative splicing (AS) of pre-mRNA contain significant IDP regions; (iv) proteins encoded by DNA regions flanking crossing-over 'hot spots' are significantly enriched in IDP regions; (v) IDP regions are disproportionately subject to combinatorial post-translational modifications (PTMs) as well as AS; (vi) proteins involved in transcription and RNA processing are enriched in IDP regions; and (vii) a strong positive correlation exists between the number of different cell types and the IDP proteome fraction across a broad spectrum of uni- and multicellular algae, plants, and animals...
March 24, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29228892/sequence-fingerprints-distinguish-erroneous-from-correct-predictions-of-intrinsically-disordered-protein-regions
#4
Konda Mani Saravanan, A Keith Dunker, Sankaran Krishnaswamy
More than 60 prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the World Wide Web. Nearly, all of these predictors give balanced accuracies in the ~65%-~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions...
December 27, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28714803/comparing-nmr-and-x-ray-protein-structure-lindemann-like-parameters-and-nmr-disorder
#5
Eshel Faraggi, A Keith Dunker, Joel L Sussman, Andrzej Kloczkowski
Disordered protein chains and segments are fast becoming a major pathway for our understanding of biological function, especially in more evolved species. However, the standard definition of disordered residues: the inability to constrain them in X-ray derived structures, is not easily applied to NMR derived structures. We carry out a statistical comparison between proteins whose structure was resolved using NMR and using X-ray protocols. We start by establishing a connection between these two protocols for obtaining protein structure...
August 8, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28430951/evidence-for-a-strong-correlation-between-transcription-factor-protein-disorder-and-organismic-complexity
#6
Inmaculada Yruela, Christopher J Oldfield, Karl J Niklas, A Keith Dunker
Studies of diverse phylogenetic lineages reveal that protein disorder increases in concert with organismic complexity but that differences nevertheless exist among lineages. To gain insight into this phenomenology, we analyzed all of the transcription factor (TF) families for which sequences are known for 17 species spanning bacteria, yeast, algae, land plants, and animals and for which the number of different cell types has been reported in the primary literature. Although the fraction of disordered residues in TF sequences is often moderately or poorly correlated with organismic complexity as gauged by cell-type number (r2 < 0...
May 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28328918/simultaneous-quantification-of-protein-order-and-disorder
#7
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/28145059/time-space-and-disorder-in-the-expanding-proteome-universe
#8
David-Paul Minde, A Keith Dunker, Kathryn S Lilley
Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins' dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (i) alternative sequences, (ii) alternative conformations, (iii) alternative interactions with a range of biomolecules, (iv) cellular localizations, (v) alternative behaviors in different cell types...
April 2017: Proteomics
https://www.readbyqxmd.com/read/27965415/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#9
Damiano Piovesan, Francesco Tabaro, Ivan Mičetić, Marco Necci, Federica Quaglia, Christopher J Oldfield, Maria Cristina Aspromonte, Norman E Davey, Radoslav Davidović, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V Kajava, Lajos Kalmar, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B Roche, Edoardo Salladini, Eva Schad, Antoine Schramm, Beata Szabo, Agnes Tantos, Fiorella Tonello, Konstantinos D Tsirigos, Nevena Veljković, Salvador Ventura, Wim Vranken, Per Warholm, Vladimir N Uversky, A Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C E Tosatto
No abstract text is available yet for this article.
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899601/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#10
Damiano Piovesan, Francesco Tabaro, Ivan Mičetić, Marco Necci, Federica Quaglia, Christopher J Oldfield, Maria Cristina Aspromonte, Norman E Davey, Radoslav Davidović, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V Kajava, Lajos Kalmar, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B Roche, Edoardo Salladini, Eva Schad, Antoine Schramm, Beata Szabo, Agnes Tantos, Fiorella Tonello, Konstantinos D Tsirigos, Nevena Veljković, Salvador Ventura, Wim Vranken, Per Warholm, Vladimir N Uversky, A Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C E Tosatto
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27557078/lipopolysaccharide-treatment-induces-genome-wide-pre-mrna-splicing-pattern-changes-in-mouse-bone-marrow-stromal-stem-cells
#11
Ao Zhou, Meng Li, Bo He, Weixing Feng, Fei Huang, Bing Xu, A Keith Dunker, Curt Balch, Baiyan Li, Yunlong Liu, Yue Wang
BACKGROUND: Lipopolysaccharide (LPS) is a gram-negative bacterial antigen that triggers a series of cellular responses. LPS pre-conditioning was previously shown to improve the therapeutic efficacy of bone marrow stromal cells/bone-marrow derived mesenchymal stem cells (BMSCs) for repairing ischemic, injured tissue. RESULTS: In this study, we systematically evaluated the effects of LPS treatment on genome-wide splicing pattern changes in mouse BMSCs by comparing transcriptome sequencing data from control vs...
August 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27270343/prostate-associated-gene-4-page4-an-intrinsically-disordered-cancer-testis-antigen-is-a-novel-therapeutic-target-for-prostate-cancer
#12
REVIEW
Prakash Kulkarni, A Keith Dunker, Keith Weninger, John Orban
Prostate-associated gene 4 (PAGE4) is a remarkably prostate-specific Cancer/Testis Antigen that is highly upregulated in the human fetal prostate and its diseased states but not in the adult normal gland. PAGE4 is an intrinsically disordered protein (IDP) that functions as a stress-response protein to suppress reactive oxygen species as well as prevent DNA damage. In addition, PAGE4 is also a transcriptional regulator that potentiates transactivation by the oncogene c-Jun. c-Jun forms the AP-1 complex by heterodimerizing with members of the Fos family and plays an important role in the development and pathology of the prostate gland, underscoring the importance of the PAGE4/c-Jun interaction...
September 2016: Asian Journal of Andrology
https://www.readbyqxmd.com/read/27102744/correlating-flavivirus-virulence-and-levels-of-intrinsic-disorder-in-shell-proteins-protective-roles-vs-immune-evasion
#13
Gerard Kian-Meng Goh, A Keith Dunker, Vladimir N Uversky
Computational analyses revealed correlations between the intrinsic disorder propensity of shell proteins and case fatality rates (CFRs) among Flaviviruses and within at least two Flavivirus species, such as tick-borne encephalitis virus (TBEV) and dengue virus (DENV). The shell proteins analyzed in this study are capsid (C) and membrane (PrM, Pr, and M) proteins. The highest correlations can be found when regression analyses were conducted using Pr (Flavivirus: r(2) = 0.78, p < 0.01) or M (Flavivirus: r(2) = 0...
May 24, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/26651072/molecular-recognition-features-morfs-in-three-domains-of-life
#14
Jing Yan, A Keith Dunker, Vladimir N Uversky, Lukasz Kurgan
Intrinsically disordered proteins and protein regions offer numerous advantages in the context of protein-protein interactions when compared to the structured proteins and domains. These advantages include ability to interact with multiple partners, to fold into different conformations when bound to different partners, and to undergo disorder-to-order transitions concomitant with their functional activity. Molecular recognition features (MoRFs) are widespread elements located in disordered regions that undergo disorder-to-order transition upon binding to their protein partners...
March 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/26387098/back-to-the-future-nuclear-magnetic-resonance-and-bioinformatics-studies-on-intrinsically-disordered-proteins
#15
REVIEW
A Keith Dunker, Christopher J Oldfield
From the 1970s to the present, regions of missing electron density in protein structures determined by X-ray diffraction and the characterization of the functions of these regions have suggested that not all protein regions depend on prior 3D structure to carry out function. Motivated by these observations, in early 1996 we began to use bioinformatics approaches to study these intrinsically disordered proteins (IDPs) and IDP regions. At just about the same time, several laboratory groups began to study a collection of IDPs and IDP regions using nuclear magnetic resonance...
2015: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/26227315/erratum-to-improving-protein-order-disorder-classification-using-charge-hydropathy-plots
#16
Fei Huang, Christopher J Oldfield, Bin Xue, Wei-Lun Hsu, Jingwei Meng, Xiaowen Liu, Li Shen, Pedro Romero, Vladimir N Uversky, A Keith Dunker
No abstract text is available yet for this article.
2015: BMC Bioinformatics
https://www.readbyqxmd.com/read/26086270/detection-of-links-between-ebola-nucleocapsid-and-virulence-using-disorder-analysis
#17
Gerard Kian-Meng Goh, A Keith Dunker, Vladimir N Uversky
The underlying reasons for the differences in the virulence of various types of Ebola virus (EBOV) remain unknown. Comparison of the percentage of disorder (PID) in nucleocapsid proteins VP30 and NP reveals high correlation between nucleocapsid PIDs and the case-fatality rates of EBOV. The higher disorder of these proteins is likely to be needed for more efficient multiplication of virus copies via more efficient viral RNA transcription and more promiscuous protein binding potential. This is important for the more efficient assistance of nucleocapsid in viral particle budding and of the assembly and mobility of viral proteins across the host membrane and within the cytoplasm...
August 2015: Molecular BioSystems
https://www.readbyqxmd.com/read/26080321/shell-disorder-immune-evasion-and-transmission-behaviors-among-human-and-animal-retroviruses
#18
Gerard Kian-Meng Goh, A Keith Dunker, Vladimir N Uversky
This study involves measurements of percentages of intrinsic disorder (PIDs) in the GAG protein shells of various retroviruses. Unique patterns of shell protein disorder can be seen especially when GAG proteins (matrix M, capsid C, and nucleocapsid N) of primate and non-primate retroviruses are compared. HIV-1 presents the most unique pattern of disorder distribution with generally high levels of disorder in all three proteins, while EIAV (PIDs:: 26, 29, 13) is diametrically different from HIV-1 (N C M PIDs: 39...
August 2015: Molecular BioSystems
https://www.readbyqxmd.com/read/25767796/rethinking-gene-regulatory-networks-in-light-of-alternative-splicing-intrinsically-disordered-protein-domains-and-post-translational-modifications
#19
Karl J Niklas, Sarah E Bondos, A Keith Dunker, Stuart A Newman
Models for genetic regulation and cell fate specification characteristically assume that gene regulatory networks (GRNs) are essentially deterministic and exhibit multiple stable states specifying alternative, but pre-figured cell fates. Mounting evidence shows, however, that most eukaryotic precursor RNAs undergo alternative splicing (AS) and that the majority of transcription factors contain intrinsically disordered protein (IDP) domains whose functionalities are context dependent as well as subject to post-translational modification (PTM)...
2015: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/25424537/intrinsic-disorder-mediates-hepatitis-c-virus-core-host-cell-protein-interactions
#20
Patrick T Dolan, Andrew P Roth, Bin Xue, Ren Sun, A Keith Dunker, Vladimir N Uversky, Douglas J LaCount
Viral proteins bind to numerous cellular and viral proteins throughout the infection cycle. However, the mechanisms by which viral proteins interact with such large numbers of factors remain unknown. Cellular proteins that interact with multiple, distinct partners often do so through short sequences known as molecular recognition features (MoRFs) embedded within intrinsically disordered regions (IDRs). In this study, we report the first evidence that MoRFs in viral proteins play a similar role in targeting the host cell...
February 2015: Protein Science: a Publication of the Protein Society
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