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MD simulations reveal the basis for dynamic assembly of Hfq-RNA complexes

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F21%3A00553643" target="_blank" >RIV/68081707:_____/21:00553643 - isvavai.cz</a>

  • Result on the web

    <a href="https://www.jbc.org/action/showPdf?pii=S0021-9258%2821%2900443-9" target="_blank" >https://www.jbc.org/action/showPdf?pii=S0021-9258%2821%2900443-9</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.1016/j.jbc.2021.100656" target="_blank" >10.1016/j.jbc.2021.100656</a>

Alternative languages

  • Result language

    angličtina

  • Original language name

    MD simulations reveal the basis for dynamic assembly of Hfq-RNA complexes

  • Original language description

    The conserved protein Hfq is a key factor in the RNA-mediated control of gene expression in most known bacteria. The transient intermediates Hfq forms with RNA support intricate and robust regulatory networks. In Pseudomonas, Hfq recognizes repeats of adenine-purine-any nucleotide (ARN) in target mRNAs via its distal binding side, and together with the catabolite repression control (Crc) protein, assembles into a translation-repression complex. Earlier experiments yielded static, ensemble-averaged structures of the complex, but details of its interface dynamics and assembly pathway remained elusive. Using explicit solvent atomistic molecular dynamics simulations, we modeled the extensive dynamics of the Hfq-RNA interface and found implications for the assembly of the complex. We predict that syn/anti flips of the adenine nucleotides in each ARN repeat contribute to a dynamic recognition mechanism between the Hfq distal side and mRNA targets. We identify a previously unknown binding pocket that can accept any nucleotide and propose that it may serve as a 'status quo' staging point, providing nonspecific binding affinity, until Crc engages the Hfq-RNA binary complex. The dynamical components of the Hfq-RNA recognition can speed up screening of the pool of the surrounding RNAs, participate in rapid accommodation of the RNA on the protein surface, and facilitate competition among different RNAs. The register of Crc in the ternary assembly could be defined by the recognition of a guanine-specific base-phosphate interaction between the first and last ARN repeats of the bound RNA. This dynamic substrate recognition provides structural rationale for the stepwise assembly of multicomponent ribonucleoprotein complexes nucleated by Hfq-RNA binding.

  • Czech name

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • OECD FORD branch

    10608 - Biochemistry and molecular biology

Result continuities

  • Project

    <a href="/en/project/GA20-16554S" target="_blank" >GA20-16554S: Molecular modeling of RNA molecules and their complexes: the role of structural dynamics</a><br>

  • Continuities

    I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Others

  • Publication year

    2021

  • Confidentiality

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Data specific for result type

  • Name of the periodical

    Journal of Biological Chemistry

  • ISSN

    0021-9258

  • e-ISSN

    1083-351X

  • Volume of the periodical

    296

  • Issue of the periodical within the volume

    JAN-JUN 2021

  • Country of publishing house

    US - UNITED STATES

  • Number of pages

    15

  • Pages from-to

    100656

  • UT code for WoS article

    000672866400627

  • EID of the result in the Scopus database