Toward Modeling Protein Multimers by Combining AlphaFold 3 Predictions with Secondary Structures from Medium-Resolution Cryo-EM Maps.

AlphaFold 3 (AF3) has recently been shown to offer improved accuracy in predicting the structures of protein multimers. Improved models may lead to new opportunities for fitting them to cryo-electron microscopy (cryo-EM) maps with medium resolution (5-10 Å). Deriving atomic models from such cryo-EM maps is still challenging due to the lack of high-resolution features. Our case study involving four AF3 multimer models and corresponding cryo-EM maps with 7-8 Å resolution showed that the predicted multimer models were partially correct. The predicted models contained fairly accurate domains, secondary structures, and individual chains, since 9 of the 17 chains exhibit TM-scores higher than 0.8 and 16 chains had TM-scores above 0.5 compared with the official atomic structures that were deposited with the cryo-EM maps. However, some cases exhibited incorrect relative positions of individual chains or domains. We observed that the order of cross-correlation (CC) scores between the multimers and their corresponding cryo-EM maps aligned with the order of the TM-scores. This shows that if regions are masked correctly, CC scores are sensitive enough to distinguish among the multimer models. A masking of monomeric chains may not always be attainable, so we also explored the level of accuracy in secondary structure segmentation for one of the cases in greater detail. Although molecular details are not fully visible in cryo-EM maps at medium resolution, the location of major secondary structures, such as α-helices and β-sheets, were detectable using our DeepSSETracer tool. Our analysis illustrates the potential for improvements in the accuracy of AF3-predicted multimer models by combining the density map-model similarity (CC scores) and the secondary structure map-model similarity in a future approach.