Capturing the Mechanism Underlying TOP mRNA Binding to LARP1

Structure. 2019 Dec 3;27(12):1771-1781.e5. doi: 10.1016/j.str.2019.10.006. Epub 2019 Oct 31.

Abstract

The RNA-binding protein La-related protein 1 (LARP1) plays a central role in ribosome biosynthesis. Its C-terminal DM15 region binds the 7-methylguanosine (m7G) cap and 5' terminal oligopyrimidine (TOP) motif characteristic of transcripts encoding ribosomal proteins and translation factors. Under the control of mammalian target of rapamycin complex 1 (mTORC1), LARP1 regulates translation of these transcripts. Characterizing the dynamics of DM15-TOP recognition is essential to understanding this fundamental biological process. We use molecular dynamics simulations, biophysical assays, and X-ray crystallography to reveal the mechanism of DM15 binding to TOP transcripts. Residues C-terminal to the m7G-binding site play important roles in cap recognition. Furthermore, we show that the unusually static pocket that recognizes the +1 cytosine characteristic of TOP transcripts drives binding specificity. Finally, we demonstrate that the DM15 pockets involved in TOP-specific m7GpppC-motif recognition are likely druggable. Collectively, these studies suggest unique opportunities for further pharmacological development.

Keywords: DM15; LARP1; RNA-binding protein; TOP mRNA; X-ray crystallography; molecular dynamics; translation regulation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Autoantigens / chemistry*
  • Autoantigens / genetics
  • Autoantigens / metabolism
  • Base Sequence
  • Binding Sites
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Genetic Vectors / chemistry
  • Genetic Vectors / metabolism
  • Guanosine / analogs & derivatives*
  • Guanosine / chemistry
  • Guanosine / metabolism
  • Humans
  • Molecular Dynamics Simulation
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Interaction Domains and Motifs
  • RNA, Messenger / chemistry*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Ribonucleoproteins / chemistry*
  • Ribonucleoproteins / genetics
  • Ribonucleoproteins / metabolism
  • Ribosomal Protein S6 / chemistry*
  • Ribosomal Protein S6 / genetics
  • Ribosomal Protein S6 / metabolism
  • Substrate Specificity
  • Thermodynamics

Substances

  • Autoantigens
  • RNA, Messenger
  • Recombinant Proteins
  • Ribonucleoproteins
  • Ribosomal Protein S6
  • SS-B antigen
  • Guanosine
  • 7-methylguanosine