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  1. AU="Perry, Zion R"
  2. AU="Wei, Kaiming"
  3. AU="Gunawan, Christa"
  4. AU="Bonneau, Peter N"
  5. AU="Heditsian, Diane"
  6. AU="Almane, Dace N"
  7. AU="Lerman, Dorothea C."
  8. AU="Góes, C"
  9. AU="Searle, Philip A"
  10. AU="Hudecek, Michael"
  11. AU="Joyce, Doireann P."
  12. AU="Müller, Werner Eg"
  13. AU="Takahashi, Tsutomo"
  14. AU="Jenny Zhaoying Xiang"
  15. AU=Ferraro Elisabetta
  16. AU="Jonathan Downar"
  17. AU=Rahmanzade Ramin AU=Rahmanzade Ramin
  18. AU="Edwards, Lisa-Jayne"
  19. AU="Tominaga, Shintaro"
  20. AU="Chan, Brian"
  21. AU="Julieta Carilla"

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  1. Artikel ; Online: Arena: Rapid and accurate reconstruction of full atomic RNA structures from coarse-grained models

    Perry, Zion R. / Marie Pyle, Anna / Zhang, Chengxin

    Journal of Molecular Biology. 2023, p.168210-

    2023  , Seite(n) 168210–

    Abstract: RNA tertiary structures from experiments or computational predictions often contain missing atoms, which prevents analyses requiring full atomic structures. Current programs for RNA reconstruction can be slow, inaccurate, and/or require specific atoms to ...

    Abstract RNA tertiary structures from experiments or computational predictions often contain missing atoms, which prevents analyses requiring full atomic structures. Current programs for RNA reconstruction can be slow, inaccurate, and/or require specific atoms to be present in the input. We present Arena (Atomic Reconstruction of RNA), which reconstructs a full atomic RNA structure from residues that can have as few as one atom. Arena first fills in missing atoms and then iteratively refines their placement to reduce nonideal geometries. We benchmarked Arena on a dataset of 361 RNA structures, where Arena achieves high accuracy and speed compared to other structure reconstruction programs. For example, Arena was used to reconstruct full atomic structures from a single phosphorus atom per nucleotide to, on average, within 3.63 Å RMSD of the experimental structure, while virtually removing all clashes and running in < 3 sec, which is 353× and 46× times faster than state-of-the-art programs PDBFixer and C2A. The Arena source code and webserver are freely available at https://github.com/pylelab/Arena and https://zhanggroup.org/Arena/, respectively.
    Schlagwörter RNA ; data collection ; molecular biology ; phosphorus ; RNA tertiary structure ; RNA structure prediction ; full atomic reconstruction ; structure refinement ; coarse-grained structure ; RMSD ; INF ; nt ; PDB
    Sprache Englisch
    Erscheinungsort Elsevier Ltd
    Dokumenttyp Artikel ; Online
    Anmerkung Pre-press version
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2023.168210
    Datenquelle NAL Katalog (AGRICOLA)

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    Verfügbar in ZB MED Bonn

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  2. Artikel ; Online: Arena: Rapid and Accurate Reconstruction of Full Atomic RNA Structures From Coarse-grained Models.

    Perry, Zion R / Pyle, Anna Marie / Zhang, Chengxin

    Journal of molecular biology

    2023  Band 435, Heft 18, Seite(n) 168210

    Abstract: RNA tertiary structures from experiments or computational predictions often contain missing atoms, which prevent analyses requiring full atomic structures. Current programs for RNA reconstruction can be slow, inaccurate, and/or require specific atoms to ... ...

    Abstract RNA tertiary structures from experiments or computational predictions often contain missing atoms, which prevent analyses requiring full atomic structures. Current programs for RNA reconstruction can be slow, inaccurate, and/or require specific atoms to be present in the input. We present Arena (Atomic Reconstruction of RNA), which reconstructs a full atomic RNA structure from residues that can have as few as one atom. Arena first fills in missing atoms and then iteratively refines their placement to reduce nonideal geometries. We benchmarked Arena on a dataset of 361 RNA structures, where Arena achieves high accuracy and speed compared to other structure reconstruction programs. For example, Arena was used to reconstruct full atomic structures from a single phosphorus atom per nucleotide to, on average, within 3.63 Å RMSD of the experimental structure, while virtually removing all clashes and running in <3 s, which is 353× and 46× faster than state-of-the-art programs PDBFixer and C2A, respectively. The Arena source code is available at https://github.com/pylelab/Arena and the webserver at https://zhanggroup.org/Arena/.
    Mesh-Begriff(e) RNA/chemistry ; Models, Molecular ; Software ; Nucleotides ; Nucleic Acid Conformation
    Chemische Substanzen RNA (63231-63-0) ; Nucleotides
    Sprache Englisch
    Erscheinungsdatum 2023-07-20
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2023.168210
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Volltext online

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    Zs.A 867: Hefte anzeigen Standort:
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  3. Artikel ; Online: Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor.

    Glasgow, Anum / Hobbs, Helen T / Perry, Zion R / Wells, Malcolm L / Marqusee, Susan / Kortemme, Tanja

    Nature communications

    2023  Band 14, Heft 1, Seite(n) 1179

    Abstract: Biological regulation ubiquitously depends on protein allostery, but the regulatory mechanisms are incompletely understood, especially in proteins that undergo ligand-induced allostery with few structural changes. Here we used hydrogen-deuterium exchange ...

    Abstract Biological regulation ubiquitously depends on protein allostery, but the regulatory mechanisms are incompletely understood, especially in proteins that undergo ligand-induced allostery with few structural changes. Here we used hydrogen-deuterium exchange with mass spectrometry (HDX/MS) to map allosteric effects in a paradigm ligand-responsive transcription factor, the lac repressor (LacI), in different functional states (apo, or bound to inducer, anti-inducer, and/or DNA). Although X-ray crystal structures of the LacI core domain in these states are nearly indistinguishable, HDX/MS experiments reveal widespread differences in flexibility. We integrate these results with modeling of protein-ligand-solvent interactions to propose a revised model for allostery in LacI, where ligand binding allosterically shifts the conformational ensemble as a result of distinct changes in the rigidity of secondary structures in the different states. Our model provides a mechanistic basis for the altered function of distal mutations. More generally, our approach provides a platform for characterizing and engineering protein allostery.
    Mesh-Begriff(e) Lac Repressors ; Ligands ; Hydrogen Deuterium Exchange-Mass Spectrometry ; Molecular Conformation ; Mutation
    Chemische Substanzen Lac Repressors ; Ligands
    Sprache Englisch
    Erscheinungsdatum 2023-03-02
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-36798-1
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Author Correction: Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor.

    Glasgow, Anum / Hobbs, Helen T / Perry, Zion R / Wells, Malcolm L / Marqusee, Susan / Kortemme, Tanja

    Nature communications

    2023  Band 14, Heft 1, Seite(n) 4208

    Sprache Englisch
    Erscheinungsdatum 2023-07-14
    Erscheinungsland England
    Dokumenttyp Published Erratum
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-39918-z
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: RSCanner: rapid assessment and visualization of RNA structure content.

    Mahadeshwar, Gandhar / Tavares, Rafael de Cesaris Araujo / Wan, Han / Perry, Zion R / Pyle, Anna Marie

    Bioinformatics (Oxford, England)

    2023  Band 39, Heft 3

    Abstract: Motivation: The increasing availability of RNA structural information that spans many kilobases of transcript sequence imposes a need for tools that can rapidly screen, identify, and prioritize structural modules of interest.: Results: We describe ... ...

    Abstract Motivation: The increasing availability of RNA structural information that spans many kilobases of transcript sequence imposes a need for tools that can rapidly screen, identify, and prioritize structural modules of interest.
    Results: We describe RNA Structural Content Scanner (RSCanner), an automated tool that scans RNA transcripts for regions that contain high levels of secondary structure and then classifies each region for its relative propensity to adopt stable or dynamic structures. RSCanner then generates an intuitive heatmap enabling users to rapidly pinpoint regions likely to contain a high or low density of discrete RNA structures, thereby informing downstream functional or structural investigation.
    Availability and implementation: RSCanner is freely available as both R script and R Markdown files, along with full documentation and test data (https://github.com/pylelab/RSCanner).
    Mesh-Begriff(e) RNA ; Software ; Protein Structure, Secondary ; Documentation ; Sequence Analysis, RNA
    Chemische Substanzen RNA (63231-63-0)
    Sprache Englisch
    Erscheinungsdatum 2023-03-21
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad111
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 2374: Hefte anzeigen Standort:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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