Dear wise list, I have a question regarding protein oligomers that have multiple, differing axes of symmetry - stimulated by some perplexing but likely real Alphafold models.
I think it's the protein equivalent of this old chestnut: https://en.wikipedia.org/wiki/Three_utilities_problem Consider a trimeric fibre (perhaps collagen a good starting example) - it can have global 3-fold symmetry, and if it breaks from this, it is then able to "re-obey" this symmetry later on, but that axis is approximately the same as the starting one. I.e. a long winding rope with a kink in the middle, and the protein doesn't have to do much to accommodate this. What happens when a long protein has multiple, dissimilar axes of symmetry? I.e. perhaps a trimer with the start and end on the same axis, but the middle domain sits ~90 degrees to this (and is also a 3-fold arrangement of chains A,B & C). I think I'd be correct in assuming that all 3 chains cannot have the same conformation - is this true? I'd argue that the protein has to unwind a little at the junctions and each chain takes a different path in space when migrating from axis 1> axis 2> back to axis 1? (think of 1 as up/down, 2 as left/right). This is because as each chain leaves the centre of mass of axis 1, it is a different distance away from the centre of mass of axis 2....? I hope that makes some sense! So my question is, does anyone have an example PDB that does something similar, and were they able to trace the different chains, demonstrating the different conformations. Thanks in advance - Andy ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
