Visualizing induced fit in early assembly of the human signal recognition particle

Nat Struct Biol. 2001 Jun;8(6):515-20. doi: 10.1038/88577.

Abstract

Assembly of almost all ribonucleoprotein complexes involves induced fit in the RNA and, thus, formation of one or more intermediate states. In assembly of the human signal recognition particle (SRP), we show that SRP19 binding to SRP RNA involves obligatory intermediates. An apparent discrepancy exists between the ratio of dissociation and association rate constants, determined in a partitioning experiment, and the equilibrium binding constant; this kinetic signature reflects formation of a stable intermediate in assembly of the ribonucleoprotein complex. Assembly intermediates were observed directly by time-resolved footprinting. SRP19 binds rapidly to SRP RNA to form an initial labile, but structurally specific, encounter complex involving both helices III and IV. Two subsequent steps of structural consolidation yield the native RNA-protein interface. SRP19 binding stabilizes helix IV in the region recognized by SRP54, consistent with protein-protein cooperativity mediated in part by mutual recognition of similar RNA structures. This mechanism illustrates principles general to ribonucleoprotein assembly reactions that rely on recruitment of architectural RNA binding proteins.

Publication types

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

MeSH terms

  • Allosteric Regulation
  • Allosteric Site
  • Base Sequence
  • Humans
  • Iodine / metabolism
  • Kinetics
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Conformation
  • RNA / chemistry
  • RNA / genetics
  • RNA / metabolism*
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism
  • Saccharomyces cerevisiae Proteins*
  • Signal Recognition Particle / chemistry
  • Signal Recognition Particle / genetics*
  • Signal Recognition Particle / metabolism*
  • Sulfuric Acid Esters / metabolism
  • Thermodynamics

Substances

  • RNA-Binding Proteins
  • SRP19 protein, human
  • SRP54 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Signal Recognition Particle
  • Sulfuric Acid Esters
  • RNA
  • Iodine
  • dimethyl sulfate