The Large Scale Conformational Change of the Human DPP III–Substrate Prefers the “Closed” Form

Abstract

Human dipeptidyl peptidase III (DPP III) is a two domain metallo-peptidase from the M49 family. The wide interdomain cleft and broad substrate specificity suggest that this enzyme could experience significant conformational change. Long (>100 ns) molecular dynamics (MD) simulations of DPP III revealed large range conformational changes of the protein, suggesting the pre-existing equilibrium model for a substrate binding. The binding free energy calculations revealed tighter binding of the preferred synthetic substrate Arg-Arg-2-naphtylamide to the "closed" than to the "open" DPP III conformation. Our assumption that Asp372 plays a crucial role in the large scale interdomain closure was proved by the MD simulations of the Asp372Ala variant. During the same simulation time, the variant remained more "open" than the wild type protein. Apparently, Ala was not as efficient as Asp in establishing the interdomain interactions. According to the MM-PBSA calculations, the electrostatic component of the free energy of solvation turned out to be higher for the "closed" protein than for its less compact form. However, the gain in entropy due to water released from the interdomain cleft nicely balanced this negative effect.

Synthesis, QSAR, and Molecular Dynamics Simulation of Amidino-substituted Benzimidazoles as Dipeptidyl Peptidase III Inhibitors

“…In this position, the inhibitor interacts by means of electrostatic and van der Waals forces with the residues of the "lower" domain (residues Ser108, Phe109, Asp111, Leu161, Tyr318, Glu327) and the "upper" domain (residues Phe556 and Arg669). However, whereas during the simulation of ligand-free protein 35 the domains progressively approached each other and the Rg decreased (the initial value was about 28.5 Å and the final one about 26.5 As a result of the domains motion, several hydrogen bonds were formed between the inhibitor and the residue Ser108, Glu316, Ile386, Ala416, and His565 (Fig. 6).…”

Human DPP III – Keap1 Interactions: A Combined Experimental And Computational Study

“…The ETGE motif of DPP III resides in a loop, on the surface of the catalytic domain (see Figure 1), and we found that it is the most flexible part of the human DPP III. [12] Besides in human, this loop was identified in DPP IIIs found in animals and fungi, as well. However, DPP IIIs from plant and bacteria lack this loop (see Supplemental materials).…”

“…[12] The zinc ion was described with noncovalent parameters only (charge +2.0 e, and parameters for van der Waals interactions: raduis 1.22 Å, and energy minima of 0.250 kcal mol -1 ).…”

“…The prepared complexes were neutralized (29 Na + were added) and solvated in a cubic box using TIP3P water molecules and periodic boundary conditions (details of the system preparation could be find in our earlier publication). [12] Geometry optimized structures were equilibrated for 100 ps (30 ps of temperature + 70 ps of density adjustments were performed using a 1fs time step and NVT and NpT conditions, respectively). Followed the productive NpT MD simulations at 300 K with the time step of 2 fs.…”

“…[10] Extensive investigations of the biochemical properties, structure and dynamics of this protein have been conducted by our group. [11][12][13][14][15][16] An enhanced level of human DPP III activity and protein was found in endometrial carcinomas and in ovarian malignant neoplasms. [17] Moreover, a correlation between DPP III activity and the aggressiveness of ovarian primary carcinomas was shown.…”