Molecular Dynamics Investigation on the Effects of Protonation and Lysyl Hydroxylation on Sulfilimine Cross-links in Collagen IV

Collagen IV networks are an essential component of basement
membranes
that are important for their structural integrity and thus that of
an organism’s tissues. Improper functioning of these networks
has been associated with several diseases. Cross-links, such as sulfilimine
bonds interconnecting NC1 domains, are critical for forming and mechanically
stabilizing these collagen IV networks. More specifically, the sulfilimine
cross-links form between methionine (Met93) and lysine/hydroxylsine
(Lys211/Hyl211) residues of NC1 domains. Therefore, the dynamic nature
of the sulfilimine bond in collagen IV is crucial for network formation.
To understand the dynamic nature of a neutral and protonated sulfilimine
bond in collagen IV, we performed molecular dynamics (MD) simulations
on four sulfilimine cross-linked systems (i.e., Met93S–NLys211, Met93S–NHLys211+, Met93S–NHyl211, and Met93S–NHHyl211+) of collagen IV. The MD
results showed that the neutral Met93S–NLys211 system has the smallest protein backbone and showed the cross-linked
residues’ RMSD value. The conformational change analyses showed
that the conformations of the sulfilimine cross-linked residues take
on a U-shape for the Met93S–NHyl211 and Met93S–HNHyl211+ systems, whereas
the conformations of the sulfilimine cross-linked residues are more
open for the Met93S–NLys211, and Met93S–NHLys211+ systems. Protonation
is a crucial biochemical process to stabilize the protein structure
or the biological cross-links. Furthermore, the protonation of the
sulfilimine bond could potentially influence hydrogen bond interaction
with near amino acid residues, and according to water distribution
analyses, the sulfilimine bond can potentially exist in one or more
protonation states.