Role of Second Coordination Sphere Amino Acid Residues on the Proton Transfer Mechanism of Human Carbonic Anhydrase II (HCA II)

Molecular determinants of the mechanism and substrate specificity of Clostridium difficile proline-proline endopeptidase-1

Pro-Pro endopeptidase-1 (PPEP-1) is a secreted metalloprotease from the bacterial pathogen Clostridium difficile that cleaves two endogenous adhesion proteins. PPEP-1 is therefore important for bacterial motility and hence for efficient gut colonization during infection. PPEP-1 exhibits a unique specificity for Pro-Pro peptide bonds within the consensus sequence VNP↓PVP. In this study, we combined information from crystal and NMR structures with mutagenesis and enzyme kinetics to investigate the mechanism and substrate specificity of PPEP-1. Our analyses revealed that the substrate-binding cleft of PPEP-1 is shaped complementarily to the major conformation of the substrate in solution. We found that it possesses features that accept a tertiary amide and help discriminate P1' residues by their amide hydrogen bond-donating potential. We also noted that residues Lys-101, Trp-103, and Glu-184 are crucial for proteolytic activity. Upon substrate binding, these residues position a flexible loop over the substrate-binding cleft and modulate the second coordination sphere of the catalytic zinc ion. On the basis of these findings, we propose an induced-fit model in which prestructured substrates are recognized followed by substrate positioning within the active-site cleft and a concomitant increase in the Lewis acidity of the catalytic Zn²⁺ ion. In conclusion, our findings provide detailed structural and mechanistic insights into the substrate recognition and specificity of PPEP-1 from the common gut pathogen C. difficile.

Principles Governing Catalytic Activity of Self-Assembled Short Peptides

Molecular self-assembly provides a chemical strategy for the synthesis of nanostructures by using the principles of nature, and peptides serve as the promising building blocks to construct adaptable molecular architectures. Recently, a series of heptapeptides with alternative hydrophobic and hydrophilic residues were reported to form amyloid-like structures, which are capable of catalyzing acyl ester hydrolysis with remarkable efficiency. However, information remains elusive about the atomic structures of the fibrils. What is the origin of the sequence-dependent catalytic activity? How is the ester hydrolysis catalyzed by the fibrils? In this work, the atomic structures of the aggregates were determined by using molecular modeling and further validated by solid-state NMR experiments, where the fibril with high activity adopts twisted parallel configuration within each layer, and the one with low activity is in flat antiparallel configuration. The polymorphism originates from the interactions between different regions of the building block peptides, where the delicate balance between rigidity and flexibility plays an important role. We further show that the p-nitrophenylacetate ( pNPA) hydrolysis reactions catalyzed by two different fibrils follow a similar mechanism, and the difference in microenvironment at the active site between the natural enzyme and the present self-assembled fibrils should account for the discrepancy in catalytic activities. The present work provides understanding of the structure and function of self-assembled fibrils formed with short peptides at an atomic level and thus sheds new insight on designing aggregates with better functions.

Structure, Spectroscopy, and Bonding within the Zn(q+)-Imidazole(n) (q = 0, 1, 2; n = 1-4) Clusters and Implications for Zeolitic Imidazolate Frameworks and Zn-Enzymes

Using density functional theory (DFT) with dispersion correction and ab initio post Hartree-Fock methods, we treat the bonding, the structure, the stability, and the spectroscopy of the complexes between Zn(q+) and imidazole (Im), Zn(q+)Imn (where q = 0, 1 and 2; n = 1-4). These entities are subunits of zeolitic imidazolate frameworks (ZIFs) and Zn-enzymes, which possess relevant roles in industrial and biological domains, respectively. We also investigate the Imn (n = 2-4) clusters for comparison. For each species, we determine several new structures that were not found previously. Our calculations show a competition between atomic metal solvation, by either σ-type interactions or π-stacking type interaction, and proton transfer through hydrogen bonding (H-bonding) in charged species. This results in several geometrical environments around the metal. These are connected with structural properties and the functional role of Zn cation within ZIFs and Zn-enzymes. Moreover, we show that the Zn(2+)Imn subunits do not absorb in the visible domain, which may be related to the photostability of ZIFs. Our findings are important for the development of new applications of ZIFs and metalloenzymes.

Characterization of Znq+–imidazole (q = 0, 1, 2) organometallic complexes: DFT methods vs. standard and explicitly correlated post-Hartree–Fock methods

Benchmarking DFts for the characterization of the Zn^q+–imidazole (q= 0, 1, 2) complexes.