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

[Image: see text] 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., (Met93)S–N(Lys211), (Met93)S–NH(Lys211)(+), (Met93)S–N(Hyl211), and (Met93)S–NH(Hyl211)(+)) of collagen IV. The MD results showed that the neutral (Met93)S–N(Lys211) 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 (Met93)S–N(Hyl211) and (Met93)S–HN(Hyl211)(+) systems, whereas the conformations of the sulfilimine cross-linked residues are more open for the (Met93)S–N(Lys211), and (Met93)S–NH(Lys211)(+) 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.