jz9b02209_si_001.pdf (1.22 MB)
Revealing Cooperation between Knotted Conformation and Dimerization in Protein Stabilization by Molecular Dynamics Simulations
journal contribution
posted on 2019-09-19, 13:38 authored by Yan Xu, Shixin Li, Zengshuai Yan, Baosheng Ge, Fang Huang, Tongtao YueThe topological knot is thought to
play a stabilizing role in maintaining
the global fold and nature of proteins with the underlying mechanism
yet to be elucidated. Given that most proteins containing trefoil
knots exist and function as homodimers with a large part of the dimer
interface occupied by the knotted region, we reason that the knotted
conformation cooperates with dimerization in protein stabilization.
Here, we take YbeA from Escherichia coli as the knotted
protein model, using molecular dynamics (MD) simulations to compare
the stability of two pairs of dimeric proteins having the same sequence
and secondary structures but differing in the presence or absence
of a trefoil knot in each subunit. The dimer interface of YbeA is
identified to involve favorable contacts among three α-helices
(α1, α3, and α5), one of which (α5) is threaded
through a loop connected with α3 to form the knot. Upon removal
of the knot by appropriate change of the knot-making crossing of the
polypeptide chain, relevant domains are less constrained and exhibit
enhanced fluctuations to decrease contacts at the interface. Unknotted
subunits are less compact and undergo structural changes to ease the
dimer separation. Such a stabilizing effect is evidenced by steered
MD simulations, showing that the mechanical force required for dimer
separation is significantly reduced by removing the knot. In addition
to the knotted conformation, dimerization further improves the protein
stability by restricting the α1−α5 separation,
which is defined as a leading step for protein unfolding. These results
provide important insights into the structure–function relationship
of dimerization in knotted proteins.