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  1. AU="Puterbaugh, Ryan"
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  1. Article: Dual DNA/RNA-binding factor regulates dynamics of hnRNP splicing condensates.

    Ray, Mukulika / Zaborowsky, Julia / Mahableshwarkar, Pranav / Vaidyanathan, Smriti / Shum, Jasmine / Viswanathan, Renjith / Huang, Annie / Wang, Szu-Huan / Johnson, Victoria / Wake, Noah / Conard, Ashley M / Conicella, Alexander E / Puterbaugh, Ryan / Fawzi, Nicolas L / Larschan, Erica

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Despite decades of research, mechanisms by which co-transcriptional alternative splicing events are targeted to the correct genomic locations to drive cell fate decisions remain unknown. By combining structural and molecular approaches, we define a new ... ...

    Abstract Despite decades of research, mechanisms by which co-transcriptional alternative splicing events are targeted to the correct genomic locations to drive cell fate decisions remain unknown. By combining structural and molecular approaches, we define a new mechanism by which an essential transcription factor (TF) targets co-transcriptional splicing through physical and functional interaction with RNA and RNA binding proteins (RBPs). We show that an essential TF co-transcriptionally regulates sex-specific alternative splicing by directly interacting with a subset of target RNAs on chromatin and modulating the dynamics of hnRNPA2 homolog nuclear splicing condensates.
    Language English
    Publishing date 2024-01-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.11.575216
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Intrinsically Disordered Bacterial Polar Organizing Protein Z, PopZ, Interacts with Protein Binding Partners Through an N-terminal Molecular Recognition Feature

    Nordyke, Christopher T / Ahmed, Yasin M / Puterbaugh, Ryan Z / Bowman, Grant R / Varga, Krisztina

    Journal of molecular biology. 2020 Nov. 20, v. 432, no. 23

    2020  

    Abstract: The polar organizing protein Z (PopZ) is necessary for the formation of three-dimensional microdomains at the cell poles in Caulobacter crescentus, where it functions as a hub protein that recruits multiple regulatory proteins from the cytoplasm. ... ...

    Abstract The polar organizing protein Z (PopZ) is necessary for the formation of three-dimensional microdomains at the cell poles in Caulobacter crescentus, where it functions as a hub protein that recruits multiple regulatory proteins from the cytoplasm. Although a large portion of the protein is predicted to be natively unstructured, in reconstituted systems PopZ can self-assemble into a macromolecular scaffold that directly binds to at least ten different proteins. Here we report the solution NMR structure of PopZΔ¹³⁴–¹⁷⁷, a truncated form of PopZ that does not self-assemble but retains the ability to interact with heterologous proteins. We show that the unbound form of PopZΔ¹³⁴–¹⁷⁷ is unstructured in solution, with the exception of a small amphipathic α-helix in residues M10-I17, which is included within a highly conserved region near the N-terminal. In applying NMR techniques to map the interactions between PopZΔ¹³⁴–¹⁷⁷ and one of its binding partners, RcdA, we find evidence that the α-helix and adjoining amino acids extending to position E23 serve as the core of the binding motif. Consistent with this, a point mutation at position I17 severely compromises binding. Our results show that a partially structured Molecular Recognition Feature (MoRF) within an intrinsically disordered domain of PopZ contributes to the assembly of polar microdomains, revealing a structural basis for complex network assembly in Alphaproteobacteria that is analogous to those formed by intrinsically disordered hub proteins in other kingdoms.
    Keywords Caulobacter crescentus ; amino acids ; cytoplasm ; nuclear magnetic resonance spectroscopy ; point mutation ; protein binding ; regulatory proteins ; surfactants
    Language English
    Dates of publication 2020-1120
    Size p. 6092-6107.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2020.09.020
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    In stock of ZB MED Bonn / Germany

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  3. Article ; Online: Intrinsically Disordered Bacterial Polar Organizing Protein Z, PopZ, Interacts with Protein Binding Partners Through an N-terminal Molecular Recognition Feature.

    Nordyke, Christopher T / Ahmed, Yasin M / Puterbaugh, Ryan Z / Bowman, Grant R / Varga, Krisztina

    Journal of molecular biology

    2020  Volume 432, Issue 23, Page(s) 6092–6107

    Abstract: The polar organizing protein Z (PopZ) is necessary for the formation of three-dimensional microdomains at the cell poles in Caulobacter crescentus, where it functions as a hub protein that recruits multiple regulatory proteins from the cytoplasm. ... ...

    Abstract The polar organizing protein Z (PopZ) is necessary for the formation of three-dimensional microdomains at the cell poles in Caulobacter crescentus, where it functions as a hub protein that recruits multiple regulatory proteins from the cytoplasm. Although a large portion of the protein is predicted to be natively unstructured, in reconstituted systems PopZ can self-assemble into a macromolecular scaffold that directly binds to at least ten different proteins. Here we report the solution NMR structure of PopZ
    MeSH term(s) Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Blood Proteins/chemistry ; Blood Proteins/genetics ; Caulobacter crescentus/genetics ; Chromosomes, Bacterial/genetics ; Intrinsically Disordered Proteins/genetics ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding/genetics ; Protein Conformation ; Protein Multimerization/genetics
    Chemical Substances Bacterial Proteins ; Blood Proteins ; Intrinsically Disordered Proteins ; plasma protein Z
    Language English
    Publishing date 2020-10-12
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2020.09.020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 867: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article: Structural Analysis of the Regulatory GAF Domains of cGMP Phosphodiesterase Elucidates the Allosteric Communication Pathway

    Gupta, Richa / Liu, Yong / Wang, Huanchen / Nordyke, Christopher T / Puterbaugh, Ryan Z / Cui, Wenjun / Varga, Krisztina / Chu, Feixia / Ke, Hengming / Vashisth, Harish / Cote, Rick H

    Elsevier Ltd Journal of molecular biology. 2020 Oct. 02, v. 432, no. 21

    2020  

    Abstract: Regulation of photoreceptor phosphodiesterase (PDE6) activity is responsible for the speed, sensitivity, and recovery of the photoresponse during visual signaling in vertebrate photoreceptor cells. It is hypothesized that physiological differences in the ...

    Abstract Regulation of photoreceptor phosphodiesterase (PDE6) activity is responsible for the speed, sensitivity, and recovery of the photoresponse during visual signaling in vertebrate photoreceptor cells. It is hypothesized that physiological differences in the light responsiveness of rods and cones may result in part from differences in the structure and regulation of the distinct isoforms of rod and cone PDE6. Although rod and cone PDE6 catalytic subunits share a similar domain organization consisting of tandem GAF domains (GAFa and GAFb) and a catalytic domain, cone PDE6 is a homodimer whereas rod PDE6 consists of two homologous catalytic subunits. Here we provide the x-ray crystal structure of cone GAFab regulatory domain solved at 3.3 Å resolution, in conjunction with chemical cross-linking and mass spectrometric analysis of conformational changes to GAFab induced upon binding of cGMP and the PDE6 inhibitory γ-subunit (Pγ). Ligand-induced changes in cross-linked residues implicate multiple conformational changes in the GAFa and GAFb domains in forming an allosteric communication network. Molecular dynamics simulations of cone GAFab revealed differences in conformational dynamics of the two subunits forming the homodimer and allosteric perturbations on cGMP binding. Cross-linking of Pγ to GAFab in conjunction with solution NMR spectroscopy of isotopically labeled Pγ identified the central polycationic region of Pγ interacting with the GAFb domain. These results provide a mechanistic basis for developing allosteric activators of PDE6 with therapeutic implications for halting the progression of several retinal degenerative diseases.
    Keywords active sites ; catalytic activity ; crosslinking ; crystal structure ; cyclic GMP ; mass spectrometry ; molecular dynamics ; nuclear magnetic resonance spectroscopy ; phosphoric diester hydrolases ; photoreceptors ; protein subunits ; simulation models ; therapeutics ; vertebrates
    Language English
    Dates of publication 2020-1002
    Size p. 5765-5783.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2020.08.026
    Database NAL-Catalogue (AGRICOLA)

    Full text online

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    In stock of ZB MED Bonn / Germany

    Z 4' 63/108: Show issues

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  5. Article ; Online: Structural Analysis of the Regulatory GAF Domains of cGMP Phosphodiesterase Elucidates the Allosteric Communication Pathway.

    Gupta, Richa / Liu, Yong / Wang, Huanchen / Nordyke, Christopher T / Puterbaugh, Ryan Z / Cui, Wenjun / Varga, Krisztina / Chu, Feixia / Ke, Hengming / Vashisth, Harish / Cote, Rick H

    Journal of molecular biology

    2020  Volume 432, Issue 21, Page(s) 5765–5783

    Abstract: Regulation of photoreceptor phosphodiesterase (PDE6) activity is responsible for the speed, sensitivity, and recovery of the photoresponse during visual signaling in vertebrate photoreceptor cells. It is hypothesized that physiological differences in the ...

    Abstract Regulation of photoreceptor phosphodiesterase (PDE6) activity is responsible for the speed, sensitivity, and recovery of the photoresponse during visual signaling in vertebrate photoreceptor cells. It is hypothesized that physiological differences in the light responsiveness of rods and cones may result in part from differences in the structure and regulation of the distinct isoforms of rod and cone PDE6. Although rod and cone PDE6 catalytic subunits share a similar domain organization consisting of tandem GAF domains (GAFa and GAFb) and a catalytic domain, cone PDE6 is a homodimer whereas rod PDE6 consists of two homologous catalytic subunits. Here we provide the x-ray crystal structure of cone GAFab regulatory domain solved at 3.3 Å resolution, in conjunction with chemical cross-linking and mass spectrometric analysis of conformational changes to GAFab induced upon binding of cGMP and the PDE6 inhibitory γ-subunit (Pγ). Ligand-induced changes in cross-linked residues implicate multiple conformational changes in the GAFa and GAFb domains in forming an allosteric communication network. Molecular dynamics simulations of cone GAFab revealed differences in conformational dynamics of the two subunits forming the homodimer and allosteric perturbations on cGMP binding. Cross-linking of Pγ to GAFab in conjunction with solution NMR spectroscopy of isotopically labeled Pγ identified the central polycationic region of Pγ interacting with the GAFb domain. These results provide a mechanistic basis for developing allosteric activators of PDE6 with therapeutic implications for halting the progression of several retinal degenerative diseases.
    MeSH term(s) Allosteric Regulation ; Animals ; Avian Proteins/chemistry ; Avian Proteins/metabolism ; Catalytic Domain ; Chickens/metabolism ; Crystallography, X-Ray ; Cyclic GMP/metabolism ; Cyclic Nucleotide Phosphodiesterases, Type 6/chemistry ; Cyclic Nucleotide Phosphodiesterases, Type 6/metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Protein Domains ; Protein Multimerization ; Protein Subunits/chemistry ; Protein Subunits/metabolism
    Chemical Substances Avian Proteins ; Protein Subunits ; Cyclic Nucleotide Phosphodiesterases, Type 6 (EC 3.1.4.35) ; Cyclic GMP (H2D2X058MU)
    Language English
    Publishing date 2020-09-06
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2020.08.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 867: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

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