Structural modelling of the DNAJB6 oligomeric chaperone shows a peptide-binding cleft lined with conserved S/T-residues at the dimer interface.
Christopher A G SöderbergCecilia MånssonKatja BernfurGudrun RutsdottirJohan HärmarkSreekanth RajanSalam Al-KaradaghiMorten RasmussenPeter HöjrupHans HebertCecilia EmanuelssonPublished in: Scientific reports (2018)
The remarkably efficient suppression of amyloid fibril formation by the DNAJB6 chaperone is dependent on a set of conserved S/T-residues and an oligomeric structure, features unusual among DNAJ chaperones. We explored the structure of DNAJB6 using a combination of structural methods. Lysine-specific crosslinking mass spectrometry provided distance constraints to select a homology model of the DNAJB6 monomer, which was subsequently used in crosslink-assisted docking to generate a dimer model. A peptide-binding cleft lined with S/T-residues is formed at the monomer-monomer interface. Mixed isotope crosslinking showed that the oligomers are dynamic entities that exchange subunits. The purified protein is well folded, soluble and composed of oligomers with a varying number of subunits according to small-angle X-ray scattering (SAXS). Elongated particles (160 × 120 Å) were detected by electron microscopy and single particle reconstruction resulted in a density map of 20 Å resolution into which the DNAJB6 dimers fit. The structure of the oligomer and the S/T-rich region is of great importance for the understanding of the function of DNAJB6 and how it can bind aggregation-prone peptides and prevent amyloid diseases.
Keyphrases
- electron microscopy
- mass spectrometry
- high resolution
- molecularly imprinted
- transcription factor
- heat shock
- binding protein
- heat shock protein
- protein protein
- molecular dynamics
- amino acid
- liquid chromatography
- gas chromatography
- molecular dynamics simulations
- oxidative stress
- single molecule
- heat stress
- ms ms
- tandem mass spectrometry