(Color online) The MFCC scheme in which (a) a peptide bond is cut along the backbone, (b) a pair of caps that mimics the neighboring environment of the fragment is inserted to cap the fragments, and (c) the caps are fused to form a molecular species (concap).
(Color) The optimized structure of PR complexed with ABT-538 from MD simulation. ABT-538 is shown as stick and the PR residues are in ribbon and ball with stick. ASP25 (in A chain) is deprotonated and (in B chain) is protonated. The hydrogen bonds formed between the W301 and PR/ABT-538 are shown as dashed lines.
“Interaction spectrum” of the PR-W301 complex obtained from MFCC calculation at level for both A and B chains of the protease. The axis denotes the residue and concap number for each chain and the axis denotes the interaction energy between the W301 and specific residues shown in solid lines.
(Color online) Relative orientation of W301 and ILE50 in the A chain (a) and in the B chain (b) of PR. The O atom in (a) points toward the O atom of the water.
Interaction energies (kcal/mol) between W301 and PR including both A and B chains calculated at levels of HF, B3LYP, and MP2 with a fixed basis set. For comparison, the corresponding energies from AMBER force field are also listed.
Interaction energies (kcal/mol) between W301 and two ILE50’s as well as between W301 and the ligand ABT-538. The basis set is at all levels of calculations.
The bond length and bond angle of the hydrogen bond between W301 and ILE50’s.
Article metrics loading...
Full text loading...