The Cold Shock Domain of YB-1 Segregates RNA from DNA by Non-Bonded Interactions

PLoS One. 2015 Jul 6;10(7):e0130318. doi: 10.1371/journal.pone.0130318. eCollection 2015.

Abstract

The human YB-1 protein plays multiple cellular roles, of which many are dictated by its binding to RNA and DNA through its Cold Shock Domain (CSD). Using molecular dynamics simulation approaches validated by experimental assays, the YB1 CSD was found to interact with nucleic acids in a sequence-dependent manner and with a higher affinity for RNA than DNA. The binding properties of the YB1 CSD were close to those observed for the related bacterial Cold Shock Proteins (CSP), albeit some differences in sequence specificity. The results provide insights in the molecular mechanisms whereby YB-1 interacts with nucleic acids.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / genetics
  • Binding Sites / genetics
  • Cold Shock Proteins and Peptides / genetics*
  • DNA / genetics*
  • DNA-Binding Proteins / genetics
  • Humans
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Nucleic Acids / genetics
  • Protein Structure, Tertiary
  • RNA / genetics*
  • RNA-Binding Proteins / genetics
  • Sequence Alignment
  • Y-Box-Binding Protein 1 / genetics*

Substances

  • Bacterial Proteins
  • Cold Shock Proteins and Peptides
  • DNA-Binding Proteins
  • Nucleic Acids
  • RNA-Binding Proteins
  • Y-Box-Binding Protein 1
  • YBX1 protein, human
  • RNA
  • DNA

Grants and funding

VK receive a PhD grant from the GDRI “Early Events in Human Diseases (EEHD)” and the Programs on "Molecular and Cellular Biology" and on "Basic Sciences to Medicine" from the Presidium of Russian Academy of Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.