Fig 1.
Activity sites of angiotensin-converting enzyme.
(a) Organization of the ACE protein. The active sites, located in α13 and α14 of ACE, are indicated by a black rectangle. (b) Zinc-binding motif. The residues that surround the Zn2+are represented by pink sticks. (c) The hydrogen bond interaction between Zn2+ and key residues. The distance between key residues and zinc is shown by aligplot.
Table 1.
Identified bioactive peptides from literature.
Fig 2.
Geometric structure of the inhibitor was optimized by Gaussion09.
(a-c) The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of LIVT, YLVR, and YLVPH are displayed, respectively. The LUMO orbit is colored red and the HOMO orbit is colored blue.
Fig 3.
Results of docking between ACE and inhibitors.
(a-c) The relative positions of LIVT, YLVR, and YLVPH located at ACE protein, respectively. The α1, α2, and α3 helices, surrounding the inhibitors, are indicated in red. The inhibitor molecules are shown as orange sticks. (d) The primary structure sequence of helix α1, α2, and α3.
Fig 4.
3D plots of the frontier molecular orbital of the three inhibitors.
(a-c) Result of binding of the three inhibitors to ACE. The ACE protein is shown as a red cartoon. The hydrogen bonds between protein and inhibitors are indicated by a blue dotted line. The residues that had a weak interaction with inhibitors are colored by the red eyelash.
Fig 5.
Structural stability analysis of three ACE-inhibitor complexes (ACE-YLVPH, ACE-YLVR, and ACE-LIVT).
(a) The plot of root-mean-square deviation (RMSD), (b) the plot of radius of gyration (Rg), (c) and the plot of solvent accessible surface (SASA) for three inhibitor-protein complex systems during 400 ns molecular dynamics (MD) simulations.
Fig 6.
Result of RMSF of three inhibitor-protein complex systems during 400 ns MD simulation.
(a) Total RMSF of three inhibitor-protein complex systems (YLVPH is shown in black, YLVR is shown in red, LIVT is shown in blue). (b-c) Comparison of the effects of different inhibitors on RMSF for α5. (d-e) Comparison of the effects of different inhibitors on RMSF for α10–12.
Fig 7.
Results of covariance of three inhibitor-protein complex systems.
The cross-correlation matrix maps for (a) ACE-YLVPH, (b) ACE-YLVR, and (c) ACE-LIVT systems. The positive regions, marked in cyan, indicate the strongly correlated motions of residues, whereas the negative regions, colored by pink, are associated with the anti-correlated movements.
Fig 8.
Distance variations betweenAsn167 and Met305, Asn167 and Ala319, and Asn167 and Trp336.
(a-c) The relative positions between Asn167, Met305, Ala319 and Trp336 in ACE-YLVPH, ACE-YLVR, and ACE-LIVT complex systems. (d-e) Distance variationsbetweenAsn167 and Met305, Asn167 and Ala319, andAsn167 and Trp336 in three systems during 400 ns simulations. (g-i) Relative frequency between Asn167 and Met305, Asn167 and Ala319, and Asn167 and Trp336 in three systems.
Table 2.
Probability of PC1 to PC5 for YLVPH, YLVR, and LIVT.
Fig 9.
Result of principal component analysis (PCA) for three inhibitor-protein complex systems.
Free energy landscape (FEL) and structures of the two most stable structures of the three systems. The lowest energy structures of PC1 (lift) and PC2 (right) are shown as a cartoon. The α5, α10, α11, and α12 helix are indicated in red. (a) ACE-YLVPH, (b) ACE-YLVR, and (c) ACE-LIVT.
Fig 10.
Computational alanine scanning of residue binding sites.
The analysis was performed using the FoldX approach applied to conformational ensembles obtained from 400 ns MD simulations. Energetic binding hotspots correspond to residues for which alanine scanning resulted in a significant decrease in the binding free energy.