Figure 3.

Principal component analysis (PCA) analysis of 28 snapshots during 30–36 ns MD simulation. (A) Projection of the motion of CsCatD2_free and CsCatD2_bound at neutral (pH 7) and acidic (pH 4) condition in phase space along the eigenvectors 1 (PC1) and 2 (PC2). Color labels were assigned to each snapshot, depending on its assigned cluster. (B) Contribution of each residue of CsCatD2 to the PC2. Residues showing high contribution are marked by a red circle. Secondary structure elements were predicted using DSSP (https://swift.cmbi.umcn.nl/gv/dssp/; accessed on 10 August 2021) and pH-dependent alterations are marked by a blue rectangle. Colors and alphabets identify α-helices (red and black) and β-strands (green and gray). Asterisk symbols indicate the two catalytic aspartic residues, Asp₃₃ and Asp₂₁₉.