posted on 2016-09-02, 00:00authored byCaitlin
D. Allen, Maria Y. Chen, Alexander Y. Trick, Dan Thanh Le, Andrew L. Ferguson, A. James Link
Lasso peptides are
a class of knot-like polypeptides in which the
C-terminal tail of the peptide threads through a ring formed by an
isopeptide bond between the N-terminal amine group and a side chain
carboxylic acid. The small size (∼20 amino acids) and simple
topology of lasso peptides make them a good model system for studying
the unthreading of entangled polypeptides, both with experiments and
atomistic simulation. Here, we present an in-depth study of the thermal
unthreading behavior of two lasso peptides astexin-2 and astexin-3.
Quantitative kinetics and energetics of the unthreading process were
determined for variants of these peptides using a series of chromatography
and mass spectrometry experiments and biased molecular dynamics (MD)
simulations. In addition, we show that the Tyr15Phe variant of astexin-3
unthreads via an unprecedented “tail pulling”
mechanism. MD simulations on a model ring-thread system coupled with
machine learning approaches also led to the discovery of physicochemical
descriptors most important for peptide unthreading.