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. 2020 Oct 19;153(15):154109. doi: 10.1063/5.0021399

FIG. 2.

FIG. 2.

Free energy profiles and low-energy conformational states of peptide binding to the SH3 domains: (a) 2D PMF profiles regarding the peptide backbone RMSD and the distance between protein Asp19 and peptide Arg10 in the 1SSH structure. (b) 2D PMF profiles regarding the peptide backbone RMSD and the distance between protein Asp150 and peptide Lys8 in the 1CKA structure. (c) 2D PMF profiles regarding the peptide backbone RMSD and the distance between protein Asp150 and peptide Arg7 in the 1CKB structure. [(d)–(f)] Low-energy intermediate conformations (red) as identified from the 2D PMF profiles of the (d) 1SSH, (e) 1CKA, and (f) 1CKB structures, respectively. X-ray structures of the peptide-bound complexes are shown in green and magenta for protein and peptide, respectively. Protein residues Asp19 and Trp40 in the 1SSH structure and Asp150 and Trp169 in the 1CKA and 1CKB structures, and peptide residues Arg10 in the 1SSH structure, Lys8 in the 1CKA structure, and Arg7 in the 1CKB structure are highlighted in sticks. The “N” and “C” labels denote the N-terminus and C-terminus of the peptides.