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. 2015 Jun 24;24(9):1463–1474. doi: 10.1002/pro.2732

Figure 5.

Figure 5

Representative conformations for the WT:BPTI (A) and Y36F:BPTI (B) complexes based on separate 500 ns MD simulations. In the WT:BPTI complex Y39 (shown in green, panel A) is positioned near P4′ I19 and forms a stable hydrogen bond interaction with the backbone amine. In the Y36F complex F39 (shown in green, panel B) moves out of position near I19 toward P2′ R17 in BPTI. This reposition allows R17 to form a new hydrogen bond with H40 of trypsin (blue line, panel B), which is absent in the WT:BPTI complex (panel A). The formation of the new hydrogen bond and the position of F39 against the R17 side chain both stabilize the Y39F:BPTI complex. The binding free energy for the Y39F:BPTI complex is 3.58 kcal/mol lower than the WT:BPTI complex and 17.76 kcal/mol lower than the Y39A:BPTI complex. The improved stability of the Y39F:BPTI complex correlates with the biochemically observed higher sensitivity of Y39F relative to WT and Y39A.