Molecular dynamics study of ACBP denaturation in alkyl sulfates demonstrates possible pathways of unfolding through fused surfactant clusters

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  • Armen H. Poghosyan, National Academy of Sciences of the Republic of Armenia, Armenia
  • Nicholas Schafer, Rice University
  • ,
  • Jeppe Lyngsø
  • Aram A. Shahinyan, National Academy of Sciences of the Republic of Armenia, Armenia
  • Jan Skov Pedersen
  • Daniel Otzen
Anionic surfactants denature proteins at low millimolar concentrations, yet little is known about the underlying molecular mechanisms. Here, we undertake 1-μs-long atomistic molecular dynamics simulations of the denaturation of acyl coenzyme A binding protein (ACBP) and compare our results with previously published and new experimental data. Since increasing surfactant chain length is known to lead to more rapid denaturation, we studied denaturation using both the medium-length alkyl chain surfactant sodium dodecyl sulfate (SDS) and the long alkyl chain surfactant sodium hexadecyl sulfate (SHS). In silico denaturation on the microsecond timescale was not achieved using preformed surfactant micelles but required ACBP to be exposed to monomeric surfactant molecules. Micellar self-assembly occurred together with protein denaturation. To validate our analyses, we calculated small-angle X-ray scattering spectra of snapshots from the simulations. These agreed well with experimental equilibrium spectra recorded on ACBP-SDS mixtures with similar compositions. Protein denaturation occurs through the binding of partial micelles to multiple preferred binding sites followed by the accretion of surfactant monomers until these partial micelles merge to form a mature micelle and the protein chain is left disordered on the surface of the micelle. While the two surfactants attack in a similar fashion, SHS’s longer alkyl chain leads to a more efficient denaturation through the formation of larger clusters that attack ACBP, a more rapid drop in native contacts, a greater expansion in size, as well as a more thorough rearrangement of hydrogen bonds and disruption of helices.
Original languageEnglish
Article numbergzz037
JournalProtein Engineering, Design and Selection
Volume32
Issue4
Pages (from-to)175-190
Number of pages16
ISSN1741-0126
DOIs
Publication statusPublished - Apr 2019

    Research areas

  • SAXS, simulation, Molecular Dynamics, SDS, Micelles, Surfactant

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