Plastocyanin and Cytochrome Complex Structures Obtained by NMR, Molecular Dynamics, and AlphaFold 3 Methods Compared to Cryo-EM Data.

Plastocyanin is a small mobile protein that facilitates electron transfer through the formation of short-lived protein-protein complexes with cytochrome and photosystem 1. Due to the transient nature of plastocyanin-cytochrome complex, the lack of a long-lived tight complex makes it impossible to determine its structure by X-ray diffraction analysis. Up to today, a number of slightly different structures of such complexes have been obtained by experimental and computer methods. Now, artificial intelligence gives us the possibility to predict the structures of intermolecular complexes. In this study, we compare encounter and final complexes obtained by Brownian and molecular dynamics methods, as well as the structures predicted by AlphaFold 3, with NMR and cryo-EM data. Surprisingly, the best match for the plastocyanin electron density obtained by cryo-EM was demonstrated by an AlphaFold 3 structure. The orientation of plastocyanin in this structure almost completely coincides with its orientation obtained by molecular dynamics calculation, and, at the same time, it is different from the orientation of plastocyanin predicted on the basis of NMR data. This is even more unexpected given that only NMR structures for the plastocyanin-cytochrome complex are available in the PDB database, which was used to train AlphaFold 3.