Published December 31, 2024 17:23
Source https://doi.org/10.1021/acs.jcim.4c01479
Amyloidogenic proteins contain short segments (amyloid prone regions) that nucleate formation of large sandwiched β-sheet structures. Analysis of structural properties of interfaces formed between the interacting β-sheets of these oligopeptides is essential for understanding their amyloidogenicity and self-assembly. We developed a tool (ACW plugin for the PyMOL program) for visualization and comparative analysis of amyloid oligopeptide crystal structures and applied it to the database of amyloid oligopeptides derived from the PDB. Our data show that parallel β-sheet structures have higher entanglement and better shape complementarity, probably related to their higher abundance. Our paper was published in the Journal of Chemical Information and Modeling.
