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. Author manuscript; available in PMC: 2024 Feb 10.
Published in final edited form as: Cell Rep. 2023 Oct 5;42(10):113190. doi: 10.1016/j.celrep.2023.113190

Figure 4. All-atom MD simulations and analysis on example human anti-flu polyreactive vs. monoreactive IgG.

Figure 4.

(A) Workflow of all-atom MD analysis (500 ns), including clustering of CDR conformations via time-lagged independent component analysis (tICA) (1), visual inspection of CDR clusters (2), and RMSD (Å) of Cα backbone movements in CDR loops (3).

(B) From left to right: side view of the crystal structure of the polyreactive human 2G02 Fab shown in cartoon representations; tICA analysis based on 500 ns of all-atom MD simulations, where color dots represent the distinct cluster centers identified in tICA space using a K-means algorithm; representative CDR loop structures from the MD analysis, colored according to the cluster dot color in the tICA analysis; and RMSD (Å) of the Cα backbone movements across the 500-ns MD trajectory of each of the CDR loops.

(C) Same analysis as in (B) of the monoreactive human anti-flu 3B03 Fab structure.