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An Rosetta/AlphaFold model of the interaction between TamB and BamA in Borreliella burgdorferi


To investigate the hypothesis that the TamB DUF490 domain interacts with the BamA POTRA domains in B. burgdorferi, a model of the complex was attempted using AlphaFold v2.2 Multimer, which returns models with a predicted template modeling score (pTM) and an interface pTM (ipTM). Models are scored based on 0.8 ipTM+ 0.2 pTM, where higher values are higher confidence as with pLDDT scores. While individual chains were modeled with high confidence, with a pLDDT of 84.2 for BamA and 68.7 for the N-terminal 2/3 of TamB DUF490, modeled interactions generated low confidence scores with an ipTM+pTM of 0.30 and showed BamA oriented in the wrong direction. However, AlphaFold has been used to model the E. coli TamA-TamB complex, therefore we modeled E. coli TamB DUF490 with TamA. The resulting model was of higher confidence, with an ipTM+pTM 0f 0.59 and pLDDT values of 85.8 for TamA and 73.5 for the N-terminal 2/3 of TamB DUF490. This model was used as a template for homology modeling of B. burgdorferi TamB DUF490 with BamA that depicts B. burgdorferi TamB DUF490 inserted between the B. burgdorferi BamA POTRA domains.

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