Poster abstracts
Poster number 27 submitted by Zachary Drake
Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling
Zachary C. Drake (The Ohio State University), Justin T. Seffernick (The Ohio State University), Steffen Lindert (The Ohio State University)
Abstract:
Covalent labeling (CL) in combination with mass spectrometry can be used as an analytical tool to study and determine structural properties of protein-protein complexes. However, data from these experiments is sparse and does not unambiguously elucidate protein structure. Thus, computational algorithms are needed to deduce structure from the CL data. In this work, we present a hybrid method that combines models of protein complex subunits generated with AlphaFold with differential CL data via a CL-guided protein-protein docking in Rosetta. In a benchmark set, the RMSD (root-mean-square deviation) of the best-scoring models was below 3.6 Å for 5/5 complexes with inclusion of CL data, whereas the same quality was only achieved for 1/5 complexes without CL data. This study suggests that our integrated approach can successfully use data obtained from CL experiments to distinguish between nativelike and non-nativelike models.
References:
Drake, Z.C., Seffernick, J.T. & Lindert, S. Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling. Nat Commun 13, 7846 (2022). https://doi.org/10.1038/s41467-022-35593-8
Keywords: Protein Structure Prediction, Computational Biochemistry, Mass Spectrometry