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Fig. 6 | BMC Immunology

Fig. 6

From: Conformational flexibility of a free and TCR-bound pMHC-I protein investigated by long-term molecular dynamics simulations

Fig. 6

H-bonds between the peptide and the MHC binding-groove. a Time course and histogram of the total number of H-bonds (mean ± SD) calculated from 10 pooled 400 ns MD simulations each for the free and the bound state. b Cartoon representation of the MHC binding groove with lateral α1- and α2-helices and the β-sheet (grey) together with the peptide (shown as licorice) consisting of nine residues (position 1: Glu, blue; position 9: Tyr, green). Residues with H-bonds of a relative occurrence ≥ 25% in either bound, free or both states are labelled. The figure was prepared using VMD version 1.9.3 [50]

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BMC Immunology

ISSN: 1471-2172

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