Uncovering an effecient binary system as a chemosensor for visual and fluorescence detection of chromium (VI) in water samples.

There is an urgent requirement for the development of sensitive and quick sensors to monitor chromium (VI) due to its substantial carcinogenic and mutagenic properties. A coexisting system of coumarin 334 and diphenylcarbazide (C334/DPC) was used in this study as a fluorescent chemosensor to detect Cr(VI) ions. Upon the addition of Cr(VI), a purple chelate complex (Cr(III)-diphenylcarbazone) was produced, which resulted from the quantitative reaction between Cr(VI) ions and diphenylcarbazide (DPC), whereas no interaction between Cr(VI) and coumarin 334 took place. More interestingly, the absorption spectra of purple (Cr(III)-diphenylcarbazone) complex (λmax = 540 nm) were overlapped with emission and excitation spectra of coumarin 334 (λex/em = 453/492), resulting in the efficient quenching of coumarin 334 (C334) via the inner filter effect. Furthermore, the semi-quantitative estimation of Cr(VI) ion concentration may be achieved by visually watching the progressive color transformation of the probe from yellow to red after the addition different concentration of Cr(VI). The calibration plot for determination of Cr(VI) by this method is ranging from 0.048 to 268 µM. DFT calculations were conducted to enrich our understanding about the mechanism of action. This approach demonstrates an excellent selectivity and sensitivity for Cr(VI) including a detection limit of 48 nM. The new sensor was successfully applied to water samples (tap, mineral, and waste waters). The accuracy was confirmed by the atomic absorption spectroscopy.

Palladium(ii), platinum(ii), and silver(i) complexes with 3-acetylcoumarin benzoylhydrazone Schiff base: Synthesis, characterization, biomolecular interactions, cytotoxic activity, and computational studies.

New Pd(ii) (C1), Pt(ii) (C2), and Ag(i) (C3) complexes derived from 3-acetylcoumarin benzoylhydrazone (HL) Schiff base were synthesized and characterized by FTIR, 1H NMR, UV-visible spectroscopies along with elemental analysis (C, H, N), magnetic, molar conductivity measurements, and DFT calculations. The obtained results suggested that the ligand had different behaviors in the complexes: mono-negative tridentate (C1) and neutral tridentate (C2) as an ONO-donor and neutral bidentate (C3) as an ON-donor. Quantum chemistry calculations were performed to validate the stability of the suggested geometries and indicated that all the complexes possess tetra-coordinated metal ions. The binding affinity of all the compounds toward calf thymus (ctDNA), yeast (tRNA), and bovine serum albumin (BSA) was evaluated by absorption/emission spectral titration studies, which revealed the intercalative binding to ctDNA and tRNA and static binding upon complex formation with BSA. Molecular insights into the binding affinity of the characterized complexes were provided through conducting molecular docking analysis. Moreover, the cytotoxic activity (in vitro) of the compounds was screened against human cancerous cell lines and a non-cancerous lung fibroblast (WI38) one using cis-platin as a reference drug. The IC50 and selective index (SI) values indicated the higher cytotoxic activity of all the metal complexes compared to their parent ligand. Among all the compounds, the complex C2 showed the highest activity. These results confirmed the improvement of the anticancer activity of the ligand by incorporating the metal ions. In addition, flow cytometry results showed that complexes C1 and C2 induced cell cycle arrest at S and G1/S, respectively.

Luminescent and time-resolved determination of gemifloxacin mesylate in pharmaceutical formulations and spiked blood plasma samples using a lanthanide complex as a probe.

A novel luminescence-based analytical methodology was established employing a europium(III) complex with 3-allyl-2-hydroxybenzohydrazide (HAZ) as the coordinating ligand for the quantification of gemifloxacin mesylate (GMF) in pharmaceutical preparations and human plasma samples spiked with the compound. The stoichiometry of the europium complex with HAZ was determined via the Job plot and exhibited a metal-to-ligand ratio of 1 : 2. The analytical procedure relies on a rapid and significant enhancement of luminescence by the Eu(AZ)2 complex when it interacts with gemifloxacin mesylate, which allowed for the rapid detection of 96 samples within approximately 2 minutes. The thermodynamic parameters of the complexation of GMF with Eu(AZ)2 were evaluated and showed that the complexation of GMF was spontaneous with a negative ΔG. The binding constant K was 4.27 × 105 L mol-1 and DFT calculations supported GMF binding and the formation of Eu(AZ)2-GMF without further ligand exchange. The calibration graph for the luminescence quantitation of GMF was linear over a wide concentration range of 0.11-16 µg mL-1 (2.26 × 10-7 to 3.30 × 10-5 mol L-1), with a limit of quantification (LOQ) of 110 ng mL-1 (230 nmol L-1) and a detection limit (LOD) of 40 ng mL-1 (82 nmol L-1). The proposed method showed good accuracy with an average recovery of 99% with relative standard deviations of less than 5% in spiking experiments, even in complex pharmaceutical dosage forms such as tablets and in human blood plasma. Herein, the ability of the suppression of the luminescence background by using the long lag times of the lanthanide probe in a time-resolved detection scheme provided reliable and precise results, which suggests its potential for use in further real or patient samples.

QM/MM investigation of the discriminatory pre-transfer editing mechanism operated by Lysyl-tRNA synthetase.

Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that remarkable facilitate the aminoacylation process during translation. With a high fidelity, the mischarged tRNA is prevented through implementing pre- and post-transfer proofreading mechanisms. For instance, Lysine-tRNA synthetase charges the native substrate, lysine, to its cognate tRNA. In spite of the great structural similarity between lysine to the noncognate and toxic ornithine, with the side chain of lysine being only one methylene group longer, LysRS is able to achieve this discrimination with a high efficiency. In this work, the hybrid quantum mechanics/molecular mechanics (QM/MM) investigation was applied to probe the pre-transfer editing mechanism catalyzed by lysyl-tRNA synthetase to reject the noncognte aminoacyl, L-ornityl (Orn), compared to the cognate substrate, L-lysyl. Particularly, the self-cyclization pre-transfer editing mechanism was explored for the two substrates. The substrate-assisted self-cyclization editing of Orn-AMP, where its phosphate moiety acts as the catalytic base, is found to be the rate-determining step with an energy barrier of 101.2 kJ mol-1. Meanwhile, the corresponding rate-limiting pathway for the native Lys-AMP lies at 140.2 kJ mol-1. This observation clearly indicated the infeasibility of this catalytic scenario in the presence of the native substrate. Interestingly, a thermodynamically favorable cyclic product of -92.9 kJ mol-1 with respect to the aminoacyl reactant complex demonstrated evidence of a successful pre-transfer editing. This reaction resulted in the discharge of the on-cognate -ornithine derivative from LysU's active site. These valuable mechanistic insights are valuable to enrich our knowledge of this extremely efficient and specific catalytic machinery of LysRS.Communicated by Ramaswamy H. Sarma.

Screening a library of potential competitive inhibitors against bacterial threonyl-tRNA synthetase: DFT calculations.

Due to the growing interest in directing aminoacyl-tRNA synthetases for antimicrobial therapies, evaluating the binding proficiency of potential inhibitors against this target holds significant importance. In this work, we proposed potential ligands that could properly bind to the crucial Zn(II) cofactor located in the active site of Threonyl-tRNA synthetases (ThrRS), potentially functioning as competitive inhibitors. Initially, detailed DFT quantum chemical study was conducted to examine the binding ability of threonine against unnatural amino acids to cofactor Zn(II). Then, the binding energy value for each suggested ligand has been determined and compared to the value determined for the native substrate, threonine. Our screening investigation showed that the native threonine should coordinate in a bidentate fashion to this Zn(II) which lead to the highest (binding energy) BE Thereby, the synthetic site of ThrRS rejects unnatural amino acids that cannot afford this type of coordination to Zn(II) ion which has been supported by our calculations. Moreover, based on their binding to the Zn(II) and the obtained BE values compared to the cognate threonine, many potent ligands have been suggested. Importantly, ligands with deprotonated warheads showed the highest binding ability amongst a list of potential hits. Further investigation on the selected ligands using molecular docking and QM/MM calculations confirmed our findings of the suggested ligands being able to bind efficiently in the active site of ThrRS. The suggested hits from this study should be valuable in paving routs for developing candidates as competitive inhibitors against the bacterial ThrRS.Communicated by Ramaswamy H. Sarma.

Experimental and computational studies of silver(I) dibenzoylmethane-based complexes, interaction with DNA/RNA/BSA biomolecules, and in vitro cytotoxic activity.

Two silver(I) complexes of composition [Ag2(L)2] (1) and [Ag(L)(PPh3)2](2) (HL = dibenzoyl- methane, PPh3 = triphenylphosphine) were synthesized and characterized by elemental analysis, FTIR, NMR, XRPD, and UV-visible spectra. The molecular structures of the studied ligands and Ag(I) complexes have been characterized using Density Function Theory (DFT) calculations. This analysis has enabled us to determine the reactivity and the coordination site(s) for each ligand. Ag(I) ion is found to be coordinated with the ligand's oxygens in almost a linear fashion in complex (1), while in complex (2) it adopts a tetrahedral geometry. The interaction compounds with biomolecules; calf thymus (ct DNA), yeast-tRNA, and bovine serum albumin (BSA) were investigated using both absorption and fluorescence spectroscopy. The in vitro cytotoxic studies of the complexes against normal human lung fibroblast (WI38), cancerous breast (MDA-MB-231), mammary gland breast (MCF7), hepatocellular (HePG2), and prostate (PC3) cell lines indicated that the complexes are highly toxic to the cancer cells but less toxic towards the normal one when compared with the ligand. Flow cytometric results showed that complex (1) induced cell cycle arrest at the G2/M phase, and complex (2) at G2/M and S phases. Moreover, the results of apoptotic genes (caspase3 and p53) and anti-apoptotic (Bcl2) led us to suggest an apoptotic killing mechanism of cells rather than a necrotic one.

The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1.

Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or ß carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.

The metal dependence of single-metal mediated phosphodiester bond cleavage: a QM/MM study of a multifaceted human enzyme.

Nucleases catalyze the cleavage of phosphodiester bonds in nucleic acids using a range of metal cofactors. Although it is well accepted that many nucleases rely on two metal ions, the one-metal mediated pathway is debated. Furthermore, one-metal mediated nucleases maintain activity in the presence of many different metals, but the underlying reasons for this broad metal specificity are unknown. The human apurinic/apyrimidinic endonuclease (APE1), which plays a key role in DNA repair, transcription regulation, and gene expression, is a prototypical example of a one-metal dependent nuclease. Although Mg2+ is the native metal cofactor, APE1 remains catalytically active in the presence of several metals, with the rate decreasing as Mg2+ > Mn2+ > Ni2+ > Zn2+, while Ca2+ completely abolished the activity. The present work uses quantum mechanics-molecular mechanics techniques to map APE1-facilitated phosphodiester bond hydrolysis in the presence of these metals. The structural differences in stationary points along the reaction pathway shed light on the interplay between several factors that allow APE1 to remain catalytically active for various metals, with the trend in the barrier heights correlating with the experimentally reported APE1 catalytic activity. In contrast, Ca2+ significantly changes the metal coordination and active site geometry, and thus completely inhibits catalysis. Our work thereby provides support for the controversial single-metal mediated phosphodiester bond cleavage and clarifies uncertainties regarding the role of the metal and metal identity in this important reaction. This information is key for future medicinal and biotechnological applications including disease diagnosis and treatment, and protein engineering.

Mechanistic insights into the chemistry of compound I formation in heme peroxidases: quantum chemical investigations of cytochrome c peroxidase.

Peroxidases are heme containing enzymes that catalyze peroxide-dependant oxidation of a variety of substrates through forming key ferryl intermediates, compounds I and II. Cytochrome c peroxidase (Ccp1) has served for decades as a chemical model toward understanding the chemical biology of this heme family of enzymes. It is known to feature a distinctive electronic behaviour for its compound I despite significant structural similarity to other peroxidases. A water-assisted mechanism has been proposed over a dry one for the formation of compound I in similar peroxidases. To better identify the viability of these mechanisms, we employed quantum chemistry calculations for the heme pocket of Ccp1 in three different spin states. We provided comparative energetic and structural results for the six possible pathways that suggest the preference of the dry mechanism energetically and structurally. The doublet state is found to be the most preferable spin state for the mechanism to proceed and for the formation of the Cpd I ferryl-intermediate irrespective of the considered dielectric constant used to represent the solvent environment. The nature of the spin state has negligible effects on the calculated structures but great impact on the energetics. Our analysis was also expanded to explain the major contribution of key residues to the peroxidase activity of Ccp1 through exploring the mechanism at various in silico generated Ccp1 variants. Overall, we provide valuable findings toward solving the current ambiguity of the exact mechanism in Ccp1, which could be applied to peroxidases with similar heme pockets.

Comparative QM/MM study on the inhibition mechanism of ß-Hydroxynorvaline to Threonyl-tRNA synthetase.

ß-Hydroxynorvaline (ßHNV) is unnatural amino acid structurally identical to the threonine amino acid with branched ethyl group instead of threonine's methyl. It is a known competitive inhibitor that readily bind to Threonyl-tRNA synthetase's (ThrRS) catalytic site and blocks its function. In this work, we utilized a combination of Molecular Dynamics simulation (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) methodologies to provide mechanistic insights into its inhibition reaction for ThrRS. Due to the presence of Zn(II) with its Lewis acidity character, only the ionized form of ßHNV gives an enzymatically feasible energy barrier. Furthermore, in consistence with the homochirality behavior of this active site, we observed only one conformation of ßHNV that could be acylated in the active site of ThrRS. Considering these new findings together with the recent search for new antibacterial agents, our findings should guide pharmaceutical scientists with further knowledge regarding the chemical nature of this drug. Moreover, benchmarking analysis of the utilized DFT functional has also been performed to identify the impact of various DFT functionals on representing the geometry and kinetics of our system. Notably, our Zn(II) containing chemical models are found to be responsive to the %HF contribution included together with the dispersion correction. Importantly, the BP86(0%HF)-D3 functional is found to display the greatest impact on the rate-limiting step kinetically. The crucial role played by Zn(II) is further enriched when its mutation with the chemically similar Cd(II) led to dramatic difference via obtaining less feasible reaction mechanism from thermodynamic and kinetic perspectives.

Exploring the structure function relationship of heme peroxidases: Molecular dynamics study on cytochrome c peroxidase variants.

Cytochrome c peroxidase (Ccp1) is a mitochondrial heme-containing enzyme that has served for decades as a chemical model to explore the structure function relationship of heme enzymes. Unveiling the impact of its heme pocket residues on the structural behavior, the non-covalent interactions and consequently its peroxidase activity has been a matter of increasing interest. To further probe these roles, we conducted intensive all-atom molecular dynamics simulations on WT and nineteen in-silico generated Ccp1 variants followed by a detailed structural and energetic analysis of H2O2 binding and pairwise interactions. Different structural analysis including RMSD, RMSF, radius of gyration and the number of Hydrogen bonds clearly demonstrate that none of the studied mutants induce a significant structural change relative to the WT behavior. In an excellent agreement with experimental observations, the structural change induced by all the studied mutant systems is found to be very localized only to their surrounding environment. The determined interaction energies between residues and Gibbs binding energies for the WT Ccp1 and the nineteen variants, helped to identify the precise effect of each mutated residues on both the binding of H2O2 and the non-covalent interaction and thus the overall peroxidase activity. The roles of surrounding residues in adopting unique distinctive electronic feature by Ccp1 has been discerned. Our valuable findings have clarified the functions of various residues in Ccp1 and thereby provided novel atomistic insights into its function. Overall, due to the conserved residues of the heme-pocket amongst various peroxidases, the obtained remarks in this work are highly valuable.

Unveiling a Single-Metal-Mediated Phosphodiester Bond Cleavage Mechanism for Nucleic Acids: A Multiscale Computational Investigation of a Human DNA Repair Enzyme.

Despite remarkable stability, the phosphodiester bond of nucleic acids is hydrolytically cleaved in critical biological processes. Although this reaction is commonly accepted to take place via a two-metal-assisted mechanism, recent experimental evidence suggests that several enzymes use a single-metal ion, but the precise catalytic mechanism is unknown. In the present work, we employ a multiscale computational approach to decipher the phosphodiester cleavage mechanism for this unique pathway by focusing on the human APE1 repair enzyme, which catalyzes the incision of phosphodiester bonds adjacent to DNA lesions. To resolve ambiguity in the literature regarding the role of the single-metal (Mg(II)) center, several catalytic mechanisms were carefully examined. Our predicted preferred hydrolysis pathway proceeds in two steps via a pentacovalent phosphorane intermediate in the absence of substrate ligation to Mg(II), with a rate-limiting barrier (19.3 kcal/mol) in close agreement with experiment (18.3 kcal/mol). In this mechanism, D210 promotes catalysis by activating water for nucleophilic attack at the 5'-phosphate group with respect to the damaged site. Subsequently, a Mg(II)-bound water triggers leaving group departure by neutralizing the 3'-hydroxyl of the neighboring nucleotide. Consistent with experimental kinetic and mutational data, several other active site residues (N212, Y171, and H309) play multiple roles throughout the reaction to facilitate this challenging chemistry. In addition to revealing previously unknown mechanistic features of the APE1 catalyzed reaction, our work sets the stage for exploring the phosphodiester bond cleavage catalyzed by other single-metal-dependent enzymes, as well as different pharmaceutical and biotechnological applications.

Acceptor Influence on Thiolate Sensing by Hemicyanine Dyes.

Promoting selective interactions between a nucleophile and electrophilic dye in complex environments is a central goal in nucleophilic chemosensor development. Commonly employed dyes are hemicyanines containing either the N-methylbenzothiazolium (Btz) or the N-methyl-3,3-dimethylindolium (Ind) acceptors. The dyes are related to α,ß-unsaturated carbonyls and contain two sites of reactivity (C2 vs C4) with the C2-site directly attached to the quaternary nitrogen possessing greater electrophilicity. We demonstrate the regioselectivity between reactions of sodium thiomethoxide (NaSMe) with two electrophilic hemicyanine dyes bearing Btz (1) or Ind (2) in dipolar aprotic solvent-water mixtures. Adduct complexation was followed by NMR spectroscopy, and structures were optimized in the gas phase to estimate relative adduct stability. The key results include finding a preference for thiolate attachment at the C4-site to generate an enamine adduct with no evidence for attachment at the more electrophilic C2-position. Equilibration between NaSMe and water also affords NaOH that displays a thermodynamic preference for C2-attachment. Dye 1 containing the Btz moiety exhibits greater selectivity for the thiolate addition, with dye 2 being more reactive toward adventitious water to generate OH-adducts. Our data affords diagnostic 1H/13C NMR adduct signals, regioselectivity for various dye/nucleophile combinations, and suggests use of the Btz acceptor for direct thiolate detection.

Unraveling the Critical Role Played by Ado762'OH in the Post-Transfer Editing by Archaeal Threonyl-tRNA Synthetase.

Archaeal threonyl-tRNA synthetase (ThrRS) possesses an editing active site wherein tRNAThr that has been misaminoacylated with serine (i.e., Ser-tRNAThr) is hydrolytically cleaved to serine and tRNAThr. It has been suggested that the free ribose sugar hydroxyl of Ado76 of the tRNAThr (Ado762'OH) is the mechanistic base, promoting hydrolysis by orienting a nucleophilic water near the scissile Ser-tRNAThr ester bond. We have performed a computational study, involving molecular dynamics (MD) and hybrid ONIOM quantum mechanics/molecular mechanics (QM/MM) methods, considering all possible editing mechanisms to gain an understanding of the role played by Ado762'OH group. More specifically, a range of concerted or stepwise mechanisms involving four-, six-, or eight-membered transition structures (total of seven mechanisms) were considered. In addition, these seven mechanisms were fully optimized using three different DFT functionals, namely, B3LYP, M06-2X, and M06-HF. The M06-HF functional gave the most feasible energy barriers followed by the M06-2X functional. The most favorable mechanism proceeds stepwise through two six-membered ring transition states in which the Ado762'OH group participates, overall, as a shuttle for the proton transfer from the nucleophilic H2O to the bridging oxygen (Ado763'O) of the substrate. More specifically, in the first step, which has a barrier of 25.9 kcal/mol, the Ado762'-OH group accepts a proton from the attacking nucleophilic water while concomitantly transferring its proton onto the substrates C-Ocarb center. Then, in the second step, which also proceeds with a barrier of 25.9 kcal/mol, the Ado762'-OH group transfers its proton on the adjacent Ado763'-oxygen, cleaving the scissile Ccarb-O3'Ado76 bond, while concomitantly accepting a proton from the previously formed C-OcarbH group.

A water-mediated and substrate-assisted aminoacylation mechanism in the discriminating aminoacyl-tRNA synthetase GlnRS and non-discriminating GluRS.

Glutaminyl-tRNA synthetase (GlnRS) catalyzes the aminoacylation of glutamine to the corresponding tRNAGln. However, most bacteria and all archaea lack GlnRS and thus an indirect noncanonical aminoacylation is required. With the assistance of a non-discriminating version of Glutamyl-tRNA synthetases (ND-GluRS) the tRNAGln is misaminoacylated by glutamate. In this study, we have computationally investigated the aminoacylation mechanism in GlnRS and ND-GluRS employing Molecular Dynamics (MD) simulations, Quantum Mechanics (QM) cluster and Quantum Mechanics/Molecular Mechanics (QM/MM) calculations. Our investigations demonstrated the feasibility of a water-mediated, substrate-assisted catalysis pathway with rate limiting steps occurring at energy barriers of 25.0 and 25.4 kcal mol-1 for GlnRS and ND-GluRS, respectively. A conserved lysine residue participates in a second proton transfer to facilitate the departure of the adenosine monophosphate (AMP) group. Thermodynamically stable (-29.9 and -9.3 kcal mol-1 for GlnRS and ND-GluRS) product complexes are obtained only when the AMP group is neutral.

Roles of the Active Site Zn(II) and Residues in Substrate Discrimination by Threonyl-tRNA Synthetase: An MD and QM/MM Investigation.

Threonyl-tRNA synthetase (ThrRS) is a Zn(II) containing enzyme that catalyzes the activation of threonine and its subsequent transfer to the cognate tRNA. This process is accomplished with remarkable fidelity, with ThrRS being able to discriminate its cognate substrate from similar analogues such as serine and valine. Molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) methods have been used to elucidate the role of Zn(II) in the aminoacylation mechanism of ThrRS. More specifically, the role of Zn(II) and active site residues in ThrRS's ability to discriminate between its cognate substrate l-threonine and the noncognate l-serine, l-valine, and d-threonine has been examined. The present results suggest that a role of the Zn(II) ion, with its Lewis acidity, is to facilitate deprotonation of the side chain hydroxyl groups of the aminoacyl moieties of cognate Thr-AMP and noncognate Ser-AMP substrates. In their deprotonated forms, these substrates are able to adopt a conformation preferable for aminoacyl transfer from aa-AMP onto the Ado-3'OH of the tRNAThr cosubstrate. Relative to the neutral substrates, when the substrates are first deprotonated with the assistance of the Zn(II) ion, the barrier for the rate-limiting step is decreased significantly by 42.0 and 39.2 kJ mol-1 for l-Thr-AMP and l-Ser-AMP, respectively. An active site arginyl also plays a key role in stabilizing the buildup of negative charge on the substrate's bridging phosphate oxygen during the mechanism. For the enantiomeric substrate analogue d-Thr-AMP, product formation is highly disfavored, and as a result, the reverse reaction has a very low barrier of 16.0 kJ mol-1.

Substrate-Assisted and Enzymatic Pretransfer Editing of Nonstandard Amino Acids by Methionyl-tRNA Synthetase.

Aminoacyl-tRNA synthetases (aaRSs) are central to a number of physiological processes, including protein biosynthesis. In particular, they activate and then transfer their corresponding amino acid to the cognate tRNA. This is achieved with a generally remarkably high fidelity by editing against incorrect standard and nonstandard amino acids. Using docking, molecular dynamics (MD), and hybrid quantum mechanical/molecular mechanics methods, we have investigated mechanisms by which methionyl-tRNA synthetase (MetRS) may edit against the highly toxic, noncognate, amino acids homocysteine (Hcy) and its oxygen analogue, homoserine (Hse). Substrate-assisted editing of Hcy-AMP in which its own phosphate acts as the mechanistic base occurs with a rate-limiting barrier of 98.2 kJ mol(-1). This step corresponds to nucleophilic attack of the Hcy side-chain sulfur at its own carbonyl carbon (CCarb). In contrast, a new possible editing mechanism is identified in which an active site aspartate (Asp259) acts as the base. The rate-limiting step is now rotation about the substrate's aminoacyl Cß-Cγ bond with a barrier of 27.5 kJ mol(-1), while for Hse-AMP, the rate-limiting step is cleavage of the CCarb-OP bond with a barrier of 30.9 kJ mol(-1). A similarly positioned aspartate or glutamate also occurs in the homologous enzymes LeuRS, IleRS, and ValRS, which also discriminate against Hcy. Docking and MD studies suggest that at least in the case of LeuRS and ValRS, a similar editing mechanism may be possible.