Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4'-O-Nucleotidyltransferase

Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits

The origin of the enzyme's powerful role in accelerating chemical reactions is one of the most critical and still widely discussed questions. It is already accepted that enzymes impose an electrostatic field onto their substrates by adopting complex three-dimensional structures; therefore, the preorganization of electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanisms and rate constant enhancement. In this work, we focus on three catalytically active β-subunits of 20S proteasomes with low sequence identity (∼30%) whose active sites, although situated in an electrostatically miscellaneous environment, catalyze the same chemical reaction with similar catalytic efficiency. Our in silico experiments reproduce the experimentally observed equivalent reactivity of the three sites and show that obliteration of the electrostatic potential in all active sites would deprive the enzymes of their catalytic power by slowing down the chemical process by a factor of 1035. To regain enzymatic efficiency, besides catalytic Thr1 and Lys33 residues, the presence of aspartic acid in position 17 and an aqueous solvent is required, proving that the electrostatic potential generated by the remaining residues is insignificant for catalysis. Moreover, it was found that the gradual decay of atomic charges on Asp17 strongly correlates with the enzyme's catalytic rate deterioration as well as with a change in the charge distributions due to introduced mutations. The computational procedure used and described here may help identify key residues for catalysis in other biomolecular systems and consequently may contribute to the process of designing enzyme-like synthetic catalysts.

Biochar and Manure Applications Differentially Altered the Class 1 Integrons, Antimicrobial Resistance, and Gene Cassettes Diversity in Paddy Soils

Integrons are genetic components that are critically involved in bacterial evolution and antimicrobial resistance by assisting in the propagation and expression of gene cassettes. In recent decades, biochar has been introduced as a fertilizer to enhance physiochemical properties and crop yield of soil, while manure has been used as a fertilizer for centuries. The current study aimed to investigate the impact of biochar, manure, and a combination of biochar and manure on integrons, their gene cassettes, and relative antimicrobial resistance in paddy soil. Field experiments revealed class 1 (CL1) integrons were prevalent in all samples, with higher concentration and abundance in manure-treated plots than in biochar-treated ones. The gene cassette arrays in the paddy featured a broad pool of cassettes with a total of 35% novel gene cassettes. A majority of gene cassettes encoded resistance to aminoglycosides, heat shock protein, heavy metals, pilus secretory proteins, and twin-arginine translocases (Tat), TatA, TatB, and TatC. Both in combination and solo treatments, the diversity of gene cassettes was increased in the manure-enriched soil, however, biochar reduced the gene cassettes’ diversity and their cassettes array. Manure considerably enhanced CL1 integrons abundance and antimicrobial resistance, whereas biochar amendments significantly reduced integrons and antimicrobial resistance. The results highlighted the differential effects of biochar and manure on integrons and its gene cassette arrays, showing increased abundance of integrons and antibiotic resistance upon manure application and decrease of the same with biochar. The use of biochar alone or in combination with manure could be a beneficial alternative to mitigate the spread of antimicrobial resistance and bacterial evolution in the environment, specifically in paddy soils.

Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism

Ribozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, apparently, they existed in cells of primitive biological systems. Unveiling the details of these “fossils” enzymes can contribute not only to the understanding of the origins of life but also to the development of new simplified artificial enzymes. A computational study of the reactivity of the pistol ribozyme carried out by means of classical MD simulations and QM/MM hybrid calculations is herein presented to clarify its catalytic mechanism. Analysis of the geometries along independent MD simulations with different protonation states of the active site basic species reveals that only the canonical system, with no additional protonation changes, renders reactive conformations. A change in the coordination sphere of the Mg2+ ion has been observed during the simulations, which allows proposing a mechanism to explain the unique mode of action of the pistol ribozyme by comparison with other ribozymes. The present results are at the center of the debate originated from recent experimental and theoretical studies on pistol ribozyme.

Application of phage therapy: Synergistic effect of phage EcSw (ΦEcSw) and antibiotic combination towards antibiotic-resistant Escherichia coli

Bacteriophage therapy is acknowledged as a potential tool to prevent or treat multidrug-resistant bacterial infections. In this study, our major focus was on the bacteriolytic activity of phage EcSw (ΦEcSw) against the emergence of the clinically important Escherichia coli Sw1 and E. coli O157:H7. The amount of the antibiotics was changed in a concentration-dependent manner, and the ΦEcSw susceptibility to antibiotics was determined. The kanamycin and chloramphenicol inhibited the titre of phage, but ampicillin did not show phage inhibition. Though the kanamycin and chloramphenicol controlled the growth of Sw1 in a concentration-dependent manner, the ampicillin did not due to the resistance. The combined activity of the ΦEcSw with antibiotics (kanamycin and chloramphenicol) compared with the antibiotics alone showed significant lytic activity p < .001). In addition, phage-based therapy was evaluated for controlling the multidrug-resistant E. coli Sw1 and E. coli O157:H7 in zebrafish and BALB/c mice, respectively. Our results provide novel advantages of phage therapy and phage-antibiotic therapy to control antibiotic-resistant bacteria.

Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase

Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate tRNAs, an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and the "prokaryotic-like" ProRSs are distinguished from "eukaryotic-like" ProRSs by the presence of an editing domain (INS) inserted between motifs 2 and 3 of the main catalytic domain. Earlier studies suggested the presence of coupled-domain dynamics could contribute to catalysis; however, the role that the distal, highly mobile INS domain plays in catalysis at the synthetic active site is not completely understood. In the present study, a combination of theoretical and experimental approaches has been used to elucidate the precise role of INS domain dynamics. Quantum mechanical/molecular mechanical simulations were carried out to model catalytic Pro-AMP formation by Enterococcus faecalis ProRS. The energetics of the adenylate formation by the wild-type enzyme was computed and contrasted with variants containing active site mutations, as well as a deletion mutant lacking the INS domain. The combined results revealed that two distinct types of dynamics contribute to the enzyme's catalytic power. One set of motions is intrinsic to the INS domain and leads to conformational preorganization that is essential for catalysis. A second type of motion, stemming from the electrostatic reorganization of active site residues, impacts the height and width of the energy profile and has a critical role in fine tuning the substrate orientation to facilitate reactive collisions. Thus, motions in a distal domain can preorganize the active site of an enzyme to optimize catalysis.

"Catch and Release": A Variation of the Archetypal Nucleotidyl Transfer Reaction

Nucleotidyl transfer is an archetypal enzyme reaction central to DNA replication and repair. Here we describe a variation of the nucleotidylation reaction termed "catch and release" that is used by an antibiotic modifying enzyme. The aminoglycoside nucleotidyl transferase 4' (ANT4') inactivates antibiotics such as kanamycin and neomycin through nucleotidylation within an active site that shares significant structural, and inferred underlying catalytic similarity, with human DNA polymerase beta. Here we follow the entire nucleotidyl transfer reaction coordinate of ANT4' covalently inactivating neomycin using X-ray crystallography. These studies show that although the underlying reaction mechanism is conserved with polymerases, a short 2.35 A hydrogen bond is initially formed to facilitate tight binding of the aminoglycoside substrate and is subsequently disrupted by the assembly of the catalytically active ternary complex. This enables the release of products post catalysis due to a lower free energy of the product state compared to the starting substrate complex. We propose that this "catch and release" mechanism of antibiotic turnover observed in ANT4' is a variation of nucleotidyl transfer that has been adapted for the inactivation of antibiotics.