Hi Dr, Thank you very much for conducting the analysis using various versions of AlphaFold. Based on the AlphaFold criteria, the conclusion appears to be that gp64 is unlikely to form a proper dimer. While I may have some misunderstandings due to my limited expertise in using AlphaFold and ChimeraX, I believe that—considering the following points—it cannot be definitively ruled out that gp64 forms a dimer. Specifically, AlphaFold3 predicts the structure as a "protein moving freely in solution," whereas in reality, gp64 is anchored to the membrane surface via a GPI anchor. 1. A dimer-like band is observed in SDS-PAGE. 2. It contains a Sushi domain (characterized by four disulfide bridges); Sushi domains are known to be involved in protein-protein associations (as seen in "complement-containing proteins"). 3. ChimeraX analysis indicates an interface involving approximately 58 residues. 4. The interface surface area is 1,398 Ų. Given these factors, I would appreciate your opinion on how this should be interpreted. with best regards, Hiroshi Ochiai
2026/07/05 14:29、落合廣 <ochiai3@icloud.com>のメール:
Dear DR. Thank you for using chimeraX. I am very impressed with the development of protein assembly analysis technology. I am an elderly (88-year-old) biochemist. I have a question. ○1. Even if dimer formation is analyzed by AlphaFold 3, dimers with interfaces are not recognized at all (AlphaFold has a list of 19(?) analyzed). Why? ○2. Even though dimer formation (54 or 132 interface residues) can be seen by chimeraX, when looking at ipTM with AlphaFold, a number such as 0.19 is not recognized as a dimer. Do you think that this is because AlphaFold does not take into account that proteins such as GPI membrane proteins are kept in anti-parallel, do you have an opinion? With best Regards
Hiroshi Ochiai Research Institute for Electronic Sciences, Hokkaido University, Sapporo Japan Emeritus Professor