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. 2020 Mar 9;16(3):e1008373. doi: 10.1371/journal.ppat.1008373

Fig 3. Molecular dynamics simulations to dissect the mechanism of Fab668 binding.

Fig 3

Molecular dynamics (MD) simulations were undertaken to dissect binding to a variety of possible repeat epitopes for Fab668. (A) Root mean square fluctuations (RMSF) from 1.2 μs aggregate runs were calculated for each of the modeled peptide-Fab668 structures and plotted (NANPNANP: green, NVDPNANP: orange, NPDPNANP: blue, NANPNVDP: pink and PADGNPDP: lime, see also the graph legend in B). (B) Using the molecular mechanics / generalized Born solvent accessibility (MM/GBSA) approach, free energy contributions were calculated for each peptide and plotted as a function of amino-acid position (color code as in panel A).