Figure 2
From: Computational model for lipid binding regions in phospholipase (Ves a 1) from Vespa venom
(A) The structural superimposition of Ves a 1 from 290 to 300 ns, the G251-C261, T83-E93 loops, and the catalytic triad are shown in orangish-red, greenish-yellow, and yellow, respectively. (B) The open and close conformation structures of Ves a 1, with the average distance values between T83-E93 and G251-C261 loops of the two conformations being approximately 22.00 Å of open conformation and 19.00 Å of close conformation. (C) Time evolution of Ves a 1’s secondary structural elements (left). The heat map of Ves a 1 RMSF profiles (right), with the highest to lowest RMSF shaded from dark orange to viridian, respectively. (D) The free energy landscape (FEL) of free-ligand Ves a 1 was calculated for each T83-E93 and G251-C261 loop’s distance vs. RMSD. The distance of catalytic gates (T83-E93 to G251-C261 loops) was measured to be approximately 22.00 Å and 19.00 Å for open conformation (D\(_{Open~conformation}\)) and close conformation (D\(_{Close~conformation}\)), respectively, and the highest to lowest FEL are gradually shaded from dark blue to dark orange colour. The FEL was calculated by AMBER16’s CPPTRAJ module and plotted using the OriginPro (trial version) software (https://www.originlab.com) as mentioned in FEL calculation method.
