Bacterial protease uses distinct thermodynamic signatures for substrate recognition

Abstract

Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme (“entropy reservoirs”). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.

Identification of a new subtype of dipeptidyl peptidase 11 and a third group of the S46-family members specifically present in the genus Bacteroides

“…Therefore, PeDPP11 in complex with a peptide was chosen as a template for the modeling routine. The coordinates of PeDPP11 in complex with the dipeptide Arg-Asp (PDB code: 5JWG) [22] were subjected to structural alignment and further model building.…”

“…We performed 3D modeling of BfDPP11 using the structure of PeDPP11 (PDB code: 5JXK) [22], which indicated that BfDPP11 also has a bilobal architecture with an entirely helical domain capping the catalytic domain bearing a typical chymotrypsin double β-barrel fold. PeDPP11 3D structures in complexes with peptides (5JY0, 5JWG, 5JWI, 4XZY) and PgDPP11 showed that the S1 subsite is formed by Arg 337 , His 649 , Thr 650 , Gly 652 , Asn 670 , Arg 673 , Gly 677 , Gly 680 , Asp 681 , and…”

“…Ser 691 (PgDPP11 numbering) [21,22]. Among the ten residues, Gly 652 , Arg 673 , Gly 677 , Gly 680 , and…”

“…In Shewanella DPP11, Arg 673 is substituted by Ser, then Lys 680 plays the role of S1. Recently, the 3D structure of DPP11 was reported [21,22], and analysis of the complex of di-, tri-, and tetra-peptides suggested that an increase in conformational entropy of DPP11 is the primary driving force for substrate recognition [22].…”

Heterogeneity of active sites in recombinant betaine aldehyde dehydrogenase is modulated by potassium

“…This enthalpy‐entropy compensation effect has been widely discussed as it was originally thought to be an experimental artifact 31 . However, this seems to be a phenomenon that occurs mainly in multimeric proteins when they bind to their ligands 32,33 . Conversely, the differences in affinity of the active sites in multimeric enzymes have been related to dynamic changes at the level of the secondary structure during the formation of the enzyme‐substrate complex.…”