Differences in dynamic structure of LC8 monomer, dimer, and dimer-peptide complexes

Biochemistry. 2008 Nov 18;47(46):11940-52. doi: 10.1021/bi801093k. Epub 2008 Oct 23.

Abstract

Dimerization of dynein light chain LC8 creates two symmetric grooves at the dimer interface with diverse binding capabilities. In addition to pH and protein concentration, dimerization is affected by phosphorylation, as illustrated by a phosphomimetic mutation that promotes dissociation of LC8 to a monomer and subsequent dissociation from the dynein complex in vitro. In this work we characterize the dynamic structure and unfolding profiles of an LC8 mutant, H55K, as a model for monomeric LC8 at neutral pH. Backbone (15)N relaxation experiments show that the monomer, while primarily ordered, has more heterogeneous dynamics relative to the LC8 dimer, predominantly in residues that ultimately form the binding groove, particularly those in beta 1 and beta 3 strands. This heterogeneity suggests that conformations that are primed for binding are sampled in the inactive monomer and favored in the active dimer. Further changes of LC8 backbone dynamics upon binding to short peptides from Swallow (Swa) and dynein intermediate chain (IC) were elucidated. The conformational heterogeneity apparent in the LC8 dimer is retained in LC8/IC but is lost in LC8/Swa, suggesting that the degree of ordering upon binding is ligand dependent. The reduced complexity of motion in LC8/Swa correlates with the less favorable entropy of binding of LC8 to Swa relative to IC. We propose that the conformational motility of beta 3 has functional significance in dimerization and in ligand binding. In the latter, beta 3 flexibility apparently accommodates different binding modes for different ligands resulting in ligand-specific conformational dynamics of the binding site that may impact other processes such as accessibility to phosphorylation.

Publication types

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

MeSH terms

  • Animals
  • Carrier Proteins / chemistry*
  • Dimerization
  • Drosophila Proteins / chemistry*
  • Drosophila Proteins / genetics
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / metabolism
  • Dyneins
  • Hydrogen-Ion Concentration
  • Ligands
  • Models, Molecular*
  • Mutation
  • Peptides / chemistry*
  • Peptides / genetics
  • Peptides / metabolism
  • Protein Binding / physiology
  • Protein Structure, Quaternary / physiology
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism

Substances

  • Carrier Proteins
  • Drosophila Proteins
  • Ligands
  • Peptides
  • RNA-Binding Proteins
  • swa protein, Drosophila
  • Dyneins