Mechanism Of Catalytic Hydrolysis Research Articles

MOF‐Templated Hierarchical Porous Hollow Core‐Shell Framework Cobalt Oxide for Enhancing Hydrogen Generation from Borohydride‐Based Hydrolysis

AbstractDesigning and fabricating a competent cobalt‐based catalyst for sodium borohydride (NaBH4) hydrolysis is of great importance. The present work reports the synthesis of hierarchical porous hollow core‐shell framework cobalt oxide (HCSCO) via etching and calcination processes, which is then employed for catalyzing NaBH4 hydrolysis. The surface morphology and the hollow core‐shell framework of HCSCO were revealed by scanning electron microscope (SEM) and transmission electron microscope (TEM) analyses; the crystalline structure and the formation of Co3O4 in HCSCO were determined by X‐ray diffraction (XRD) and Raman spectroscopy; the surface area and porosity of HCSCO were verified by N2 adsorption‐desorption isotherm; and X‐ray photoelectron spectroscopy (XPS) was utilized to examine the chemical states of HCSCO. The as‐prepared HCSCO showed prominent catalytic hydrolysis of NaBH4 to generate H2 with a H2 generation rate of 441 ml min−1 gcatalyst−1 and a low activation energy (Ea) of 34.8 kJ mol−1. This Ea value of HCSCO is substantially lower than that of other catalysts, including noble metal catalysts or composites reported in the literature. Besides, HCSCO could remain its superb activity (~100 % H2 generation efficiency) over multiple hydrolysis cycles without significant changes of morphology and microstructure. The catalytic hydrolysis mechanism for H2 generation from NaBH4 using HCSCO is also proposed. This work provides a valuable strategy for the synthesis and fabrication of state‐of‐art catalysts for H2 generation from the hydrolysis of NaBH4.

Efficient nanocatalysis of Ni/Sc2O3@FLG for magnesium hydrolysis of hydrogen generation

Magnesium is one of the most promising candidates of light metal materials for hydrogen production by hydrolysis due to its efficient and economical properties. Various modification methods have been investigated to improve the hydrolytic properties of Mg. However, the direction of the design of efficient catalysts is unclear and needs to be guided by a richer catalytic mechanism of hydrolysis. In this work, a simple approach was used to synthesize Few Layer Graphene (FLG)-loaded ultra-fine highly dispersed Ni/Sc2O3 nanocatalyst, which achieves impressive catalytic hydrolysis results. Here, the addition of 4 wt% Ni/Sc2O3@FLG catalyst allows Mg to produce 833 mL g–1 of H2 in 20 s at 30 °C. There is an initial hydrogen release rate as high as 5942 mL g–1 min–1, a final hydrogen yield of 859 mL g–1 (99.13%), and almost complete conversion of Mg to Mg(OH)2. Furthermore, surprisingly, even with only 0.2 wt% catalysts added, Mg still has an initial hydrogen generation rate of 3627 mL g–1 min–1, which is over 20 times faster than that of Mg. It also produces 690 mL g–1 of H2 in 30 s at 30 °C. Hydrolysis kinetic curves and microscopic morphology tests show that FLG could shape and hold Mg into thin sheets, giving them an ultra-high hydrolysis rate and conversion rate. The formation of micro-galvanic cells between Ni and Mg accelerates the electrochemical corrosion of Mg and greatly enhances electron transfer during hydrolysis. This work provides a new strategy for the preparation of efficient nanocatalysts, which is expected to make “Mg-efficient catalyst” the most ideal light metal-based material for hydrogen production by hydrolysis.

The salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans DSM 6986T is a bifunctional enzyme that inactivates the mycotoxin ochratoxin A by a novel amidohydrolase activity

The salicylate 1,2-dioxygenase from the bacterium Pseudaminobacter salicylatoxidans DSM 6986T (PsSDO) is a versatile metalloenzyme that participates in the aerobic biodegradation of aromatic compounds, such as gentisates and salicylates. Surprisingly, and unrelated to this metabolic role, it has been reported that PsSDO may transform the mycotoxin ochratoxin A (OTA), a molecule that appears in numerous food products that results in serious biotechnological concern. In this work, we show that PsSDO, together with its dioxygenase activity, behaves as an amidohydrolase with a marked specificity for substrates containing a C-terminal phenylalanine residue, similar to OTA, although its presence is not an absolute requirement. This side chain would establish aromatic stacking interactions with the indole ring of Trp104. PsSDO hydrolysed the amide bond of OTA rendering the much less toxic ochratoxin α and L-β-phenylalanine. The binding mode of OTA and of a diverse set of synthetic carboxypeptidase substrates these substrates have been characterized by molecular docking simulations, which has permitted us to propose a catalytic mechanism of hydrolysis by PsSDO that, similarly to metallocarboxypeptidases, assumes a water-induced pathway following a general acid/base mechanism in which the side chain of Glu82 would provide the solvent nucleophilicity required for the enzymatic reaction. Since the PsSDO chromosomal region, absent in other Pseudaminobacter strains, contained a set of genes present in conjugative plasmids, it could have been acquired by horizontal gene transfer, probably from a Celeribacter strain.

Development of a microbial protease for composting swine carcasses, optimization of its production and elucidation of its catalytic hydrolysis mechanism

BackgroundDead swine carcass composting is an excellent method for harmless treatment and resource utilization of swine carcass. However, poor biodegradation ability of traditional composting results in poor harmless treatment effect. Researches report that the biodegradation ability of composting can be improved by inoculation with enzyme-producing microorganisms or by inoculation with enzyme preparations. At present, the researches on improving the efficiency of dead swine carcass composting by inoculating enzyme-producing microorganisms have been reported. However, no work has been reported on the development of enzyme preparations for dead swine carcass composting.MethodologyThe protease-producing strain was isolated by casein medium, and was identified by 16 S rRNA gene sequencing. The optimal fermentation conditions for maximum protease production were gradually optimized by single factor test. The extracellular protease was purified by ammonium sulfate precipitation and Sephadex G-75 gel exclusion chromatography. The potential for composting applications of the purified protease was evaluated by characterization of its biochemical properties. And based on amino acid sequence analysis, molecular docking and inhibition test, the catalytic hydrolysis mechanism of the purified protease was elucidated.ResultsIn this study, a microbial protease was developed for swine carcass composting. A protease-producing strain DB1 was isolated from swine carcass compositing and identified as Serratia marcescen. Optimum fermentation conditions for maximum protease production were 5 g/L glucose, 5 g/L urea, 1.5 mmol/L Mg2+, initial pH-value 8, inoculation amount 5%, incubation temperature 30 °C and 60 h of fermentation time. The specific activity of purified protease reached 1982.77 U/mg, and molecular weight of the purified protease was 110 kDa. Optimum pH and temperature of the purified protease were 8 and 50 °C, respectively, and it had good stability at high temperature and in alkaline environments. The purified protease was a Ser/Glu/Asp triad serine protease which catalyzed substrate hydrolysis by Glu, Arg, Ser, Asp and Tyr active residues.ConclusionsIn general, the microbial protease developed in this study was suitable for industrial production and has the potential to enhance composting at thermophilic stage. Moreover, the catalytic hydrolysis mechanism of the protease was further analyzed in this study.

A novel fluorescent "OFF-ON" sensing strategy for Hg (II) in water based on functionalized gold nanoparticles.

Mercury ion (Hg2+) is a heavy metal pollutant that can affect the safety of water environment and endanger human health. A novel detection strategy (GNPs-L-Cys-Rh6G2) for Hg2+ based on a fluorescence "OFF-ON" was proposed. Gold nanoparticles (GNPs) were assembled with l-cysteine (L-Cys), which was used as a "bridge" to link with rhodamine 6G derivatives (Rh6G2). The fluorescence state transition of GNPs-L-Cys-Rh6G2 switching from "OFF"-"ON" was observed because Hg2+ opened the spirolactam ring through a catalytic hydrolysis mechanism. The fluorescence signal of the GNPs-L-Cys-Rh6G2 system mixed with Hg2+ in the concentration range of 10-100μM was analyzed and determined with a limit of detection (LOD) of 2μM (S/N=3). Moreover, the spiked Hg2+ concentration in real water samples were successfully quantified by GNPs-L-Cys-Rh6G2, which was in line with the ideal average recovery rate and relative standard deviation. The proposed strategy exhibited high specificity, sensitivity and stability, providing a novel sensing platform for heavy metal ions detection in water environment.

Theoretical Analysis of the Catalytic Hydrolysis Mechanism of HCN over Cu-ZSM-5

HCN catalytic hydrolysis mechanism over Cu-ZSM-5 was investigated based on the density functional theory (DFT) with 6-31++g (d, p) basis set. Five paths (A, B, C, D, and E) were designed. For path A and path B, the first step is the nucleophilic attack of water molecule. Next, the hydrogen atom of H2O is transferred to the nitrogen atom first for path A, while in path B, the hydrogen atom of the HCN is first transferred to the nitrogen atom. In path C, HCN isomerizes to HNC initially, and the remaining steps are similar to that of path A. The H atom of HCN shifts to Cu-ZSM-5 initially in path D, and the H atom is transferred to N atom subsequently. The last step is the attack on water molecule. The first step for path E is similar to that of path D. The next step is the attack on water molecule, in which the H atom of water molecule shifts to N atom, and the H on Cu-ZSM-5 shifts to the N atom. Meanwhile, the H atom of oxygen atom is transferred to the N atom. The results show that path C is the most favorable path, with the lowest free energy barrier (35.45 kcal/mol). The results indicate that the Cu-ZSM-5 strongly reduces the energy barrier of HCN and isomerizes to HNC, making it an effective catalyst for HCN hydrolysis.

Theoretical Studies on the Binding Mode and Reaction Mechanism of TLP Hydrolase kpHIUH

In this work, we have investigated the binding conformations of the substrate in the active site of 5-HIU hydrolase kpHIUH and its catalytic hydrolysis mechanism. Docking calculations revealed that the substrate adopts a conformation in the active site with its molecular plane laying parallel to the binding interface of the protein dimer of kpHIUH, in which His7 and His92 are located adjacent to the hydrolysis site C6 and have hydrogen bond interactions with the lytic water. Based on this binding conformation, density functional theory calculations indicated that the optimal catalytic mechanism consists of two stages: (1) the lytic water molecule is deprotonated by His92 and carries out nucleophilic attack on C6=O of 5-HIU, resulting in an oxyanion intermediate; (2) by accepting a proton transferred from His92, C6–N5 bond is cleaved to completes the catalytic cycle. The roles of His7, His92, Ser108 and Arg49 in the catalytic reaction were revealed and discussed in detail.

Catalytic hydrolysis mechanism of aminocarboxylester substrate by human carboxylesterase 1: A theoretical study on methylphenidate hydrolysis

Human carboxylesterase 1 (hCES1) is an important carboxylesterase responsible for the hydrolysis of various esters and amides, and plays very important roles in drug metabolism and pharmacokinetics. In this study, we investigated hCES1-catalyzed hydrolysis mechanism of a common drug, methylphenidate (Ritalin), which bears an amino group at β- position of carboxylester structure. The results show that methylphenidate undergoes an orthoester intermediate, and the free energy barrier of the reaction is thus significantly elevated. These results indicate that orthoester intermediates might exist in hCES1-catalyzed hydrolysis process of other β-aminocarboxylesters. Moreover, our study shows that the enzymatic hydrolysis product of methylphenidate may form a thermodynamically stable internal salt in the catalytic site of hCES1. These findings would be helpful in understanding the related drug metabolism and pharmacokinetics, drug designing, as well as the catalytic mechanism of hCES1 and other carboxylesterases.

Hydrogen Generation by the Hydrolysis of MgH2

Magnesium hydride (MgH2) is a hydrogen-rich compound generating significant amounts of hydrogen in the process of hydrolysis, i.e., in the course of its chemical interaction with water or with aqueous solutions. This process is of great interest for the on-site hydrogen generation aimed at application of H2 as a fuel for PEM fuel cells. We propose a review of recent reference publications in the field and also present the results of our own research. The increase of the rates of H2 release and the completeness of transformation of MgH2 are two important goals, which can be attained by optimizing the size of the powders of MgH2 by ball milling, by using catalysts added to MgH2 and to aqueous solutions, and by increasing the interaction temperature. The effect of these parameters on the degree of conversion and the rates of hydrogen evolution are analyzed in detail and the best systems to reach the efficient hydrolysis performance are identified. The mechanism of catalytic hydrolysis is proposed, while further improvements of the process of hydrolysis are required and additional studies of this important topic are needed.

Catalytic Hydrolysis Mechanism of Cocaine by Human Carboxylesterase 1: An Orthoester Intermediate Slows Down the Reaction.

Human carboxylesterase 1 (hCES1) is a major carboxylesterase in the human body and plays important roles in the metabolism of a wide variety of substances, including lipids and drugs, and therefore is attracting more and more attention from areas including lipid metabolism, pharmacokinetics, drug–drug interactions, and prodrug activation. In this work, we studied the catalytic hydrolysis mechanism of hCES1 by the quantum mechanics computation method, using cocaine as a model substrate. Our results support the four-step theory of the esterase catalytic hydrolysis mechanism, in which both the acylation stage and the deacylation stage include two transition states and a tetrahedral intermediate. The roles and cooperation of the catalytic triad, S221, H468, and E354, were also analyzed in this study. Moreover, orthoester intermediates were found in hCES1-catalyzed cocaine hydrolysis reaction, which significantly elevate the free energy barrier and slow down the reaction. Based on this finding, we propose that hCES1 substrates with β-aminocarboxylester structure might form orthoester intermediates in hCES1-catalyzed hydrolysis, and therefore prolong their in vivo half-life. Thus, this study helps to clarify the catalytic mechanism of hCES1 and elucidates important details of its catalytic process, and furthermore, provides important insights into the metabolism of hCES1 substrates and drug designing.

Insight into the catalytic hydrolysis mechanism of New Delhi metallo-β-lactamase to aztreonam by molecular modeling

The monobactam antibiotic, aztreonam, can be hydrolyzed by some β-lactamases (NDM-1), whereas other β-lactamases, including VIM-1, have no hydrolytic activity on aztreonam. NDM-1 and VIM-1 are both metallo-β-lactamases (MBLs), but they catalyze hydrolysis at different active site residues, which is reflected in their obvious activity difference with aztreonam. In this work, to explore the catalytic hydrolysis mechanism of MBLs at the atomic level, molecular dynamic simulations were performed for NDM-1-aztreonam and VIM-1-aztreonam complexes based on the molecular docking analysis. Molecular modeling revealed the binding of aztreonam to the active regions of NDM-1 and VIM-1. Residues Met67, Phe70, Asp124, Thr190, and His250 play key roles in the binding of aztreonam with NDM-1. His116, Asp118, Cys198, His201, and His240 are the critical residues for the binding of aztreonam with VIM-1. Interestingly, Asp124 displayed the strongest binding energy (ΔEtotal = −11.28 kcal/mol), which was nearly 10 times higher than that of the other residues in the NDM-1-aztreonam complex. A similar result was found for the binding of aztreonam with VIM-1, with Asp118 displaying the strongest binding energy (ΔEtotal = −2.95 kcal/mol). These results implicated aspartic acid as the critical active site in the catalytic hydrolysis pocket of NDM-1 and VIM-1. However, in the VIM-1-aztreonam complex, because of the strong π-π interaction between the thiazol ring group of aztreonam and the imidazole ring groups of His201 and His240, the binding energy obtained from Asp118 become significantly weaker than that of aztreonam with Asp124 of NDM-1. Analysis of the simulation trajectory indicated that the thiazol ring plane of aztreonam is almost parallel to the imidazole ring planes of His201 and His240, implying that they can form a strong π-π interaction, which is consistent with the above results. On the basis of the computational biology results, it was confirmed that aspartic acid in the active pocket of NDM-1 and VIM-1 can effectively promote substrate hydrolysis, while histidine on the other side of the active pocket can block the binding of the substrate with aspartic acid, leading to the loss of hydrolysis.

Substrate-assisted mechanism of catalytic hydrolysis of misaminoacylated tRNA required for protein synthesis fidelity.

d-aminoacyl-tRNA-deacylase (DTD) prevents the incorporation of d-amino acids into proteins during translation by hydrolyzing the ester bond between mistakenly attached amino acids and tRNAs. Despite extensive study of this proofreading enzyme, the precise catalytic mechanism remains unknown. Here, a combination of biochemical and computational investigations has enabled the discovery of a new substrate-assisted mechanism of d-Tyr-tRNATyr hydrolysis by Thermus thermophilus DTD. Several functional elements of the substrate, misacylated tRNA, participate in the catalysis. During the hydrolytic reaction, the 2'-OH group of the А76 residue of d-Tyr-tRNATyr forms a hydrogen bond with a carbonyl group of the tyrosine residue, stabilizing the transition-state intermediate. Two water molecules participate in this reaction, attacking and assisting ones, resulting in a significant decrease in the activation energy of the rate-limiting step. The amino group of the d-Tyr aminoacyl moiety is unprotonated and serves as a general base, abstracting the proton from the assisting water molecule and forming a more nucleophilic ester-attacking species. Quantum chemical methodology was used to investigate the mechanism of hydrolysis. The DFT-calculated deacylation reaction is in full agreement with the experimental data. The Gibbs activation energies for the first and second steps were 10.52 and 1.05 kcal/mol, respectively, highlighting that the first step of the hydrolysis process is the rate-limiting step. Several amino acid residues of the enzyme participate in the coordination of the substrate and water molecules. Thus, the present work provides new insights into the proofreading details of misacylated tRNAs and can be extended to other systems important for translation fidelity.

Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingobium sp. TCM1.

Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phosphotriesterase from Sphingobium sp. TCM1 ( Sb-PTE) is one of the few enzymes known to be able to hydrolyze organophosphorus flame retardants such as triphenyl phosphate and tris(2-chloroethyl) phosphate. The effectiveness of Sb-PTE for the hydrolysis of these organophosphates appears to arise from its ability to hydrolyze unactivated alkyl and phenolic esters from the central phosphorus core. How Sb-PTE is able to catalyze the hydrolysis of the unactivated substituents is not known. To interrogate the catalytic hydrolysis mechanism of Sb-PTE, the pH dependence of the reaction and the effects of changing the solvent viscosity were determined. These experiments were complemented by measurement of the primary and secondary 18-oxygen isotope effects on substrate hydrolysis and a determination of the effects of changing the p Ka of the leaving group on the magnitude of the rate constants for hydrolysis. Collectively, the results indicated that a single group must be ionized for nucleophilic attack and that a separate general acid is not involved in protonation of the leaving group. The Brønsted analysis and the heavy atom kinetic isotope effects are consistent with an early associative transition state with subsequent proton transfers not being rate limiting. A novel binding mode of the substrate to the binuclear metal center and a catalytic mechanism are proposed to explain the unusual ability of Sb-PTE to hydrolyze unactivated esters from a wide range of organophosphate substrates.

Synthesis, crystal structure and hydrolysis activity of a novel heterobinuclear cobalt(ІІІ) sodium(І) Schiff base complex

A novel heterobinuclear complex [CoNa(C15H10NO4F)2(CH3OH)]2 with Schiff base (C15H10NO4F: 2-amino-4-fluorobenzoic acid-3-methoxysalicylaldehyde) was synthesized and characterized by IR and 1H NMR spectroscopy, elemental analysis and single crystal X-ray diffraction. X-ray crystallography reveals that the cobalt atom is six-coordinated by two nitrogen atoms from –CN–, two carboxylate oxygen atoms and two hydroxyl oxygen atoms in different ligands, while the sodium atom is seven-coordinated by two methoxy oxygen atoms, two hydroxyl oxygen atoms in different ligands, two oxygen atoms in the same carboxylate and one oxygen atom of solvent methanol. The reaction results of the complex with the p-nitrophenylphosphate (pNPP) and the adenosine monophosphate (AMP) reveal that the complex can hydrolyze phosphoester bonds. Then the DNA-hydrolysis activity is studied experimentally and theoretically, indicating that the complex can effectively hydrolyze the pBR322 supercoiled plasmid DNA. The molecular docking technology predicts the best binding site and binding affinity between the complex and DNA, and then the catalytic mechanism of hydrolysis is supposed. The study results suggest that the Schiff base metal complex, as a potent artificial enzyme, may find its applications in catalytic hydrolysis and biotechnological areas.

Zeolite-Templated Carbon Catalysts for Adsorption and Hydrolysis of Cellulose-Derived Long-Chain Glucans: Effect of Post-Synthetic Surface Functionalization

This manuscript quantitatively investigates the effect of weak acid site surface density on adsorption and catalytic hydrolysis of long-chain β-glucans, with post-synthetically modified zeolite-templated carbon (ZTC) catalysts. Our approach requires ZTC-surface modification and overcomes previous limitations of pore collapse in accomplishing this, which has previously necessitated electrochemical methods. We demonstrate that mild ZTC treatment in hydrogen peroxide preserves the 1.1 nm micropores of ZTC, which were previously shown to be ideal for β-glucan adsorption, while synthesizing surface-modified ZTC catalysts that hydrolyze adsorbed β-glucans to glucose in up to 87% yield. Our results demonstrate a direct increase in catalytic hydrolysis activity and glucose yield upon increasing acid site density via surface functionalization. Upon investigating the mechanism of catalytic hydrolysis under buffered conditions, we rule out the synthesis of acid sites with stronger acidity as a result of possible gre...

CuxCo1−xO Nanoparticles on Graphene Oxide as A Synergistic Catalyst for High‐Efficiency Hydrolysis of Ammonia–Borane

AbstractAmmonia–borane (AB) is an excellent material for chemical storage of hydrogen. However, the practical utilization of AB for production of hydrogen is hindered by the need of expensive noble metal‐based catalysts. Here, we report CuxCo1−xO nanoparticles (NPs) facilely deposited on graphene oxide (GO) as a low‐cost and high‐performance catalyst for the hydrolysis of AB. This hybrid catalyst exhibits an initial total turnover frequency (TOF) value of 70.0 (H2) mol/(Cat‐metal) mol⋅min, which is the highest TOF ever reported for noble metal‐free catalysts, and a good stability keeping 94 % activity after 5 cycles. Synchrotron radiation‐based X‐ray absorption spectroscopy (XAS) investigations suggested that the high catalytic performance could be attributed to the interfacial interaction between CuxCo1−xO NPs and GO. Moreover, the catalytic hydrolysis mechanism was studied by in situ XAS experiments for the first time, which reveal a significant water adsorption on the catalyst and clearly confirm the interaction between AB and the catalyst during hydrolysis.

Cux Co1-x O Nanoparticles on Graphene Oxide as A Synergistic Catalyst for High-Efficiency Hydrolysis of Ammonia-Borane.

Ammonia-borane (AB) is an excellent material for chemical storage of hydrogen. However, the practical utilization of AB for production of hydrogen is hindered by the need of expensive noble metal-based catalysts. Here, we report Cux Co1-x O nanoparticles (NPs) facilely deposited on graphene oxide (GO) as a low-cost and high-performance catalyst for the hydrolysis of AB. This hybrid catalyst exhibits an initial total turnover frequency (TOF) value of 70.0 (H2 ) mol/(Cat-metal) mol⋅min, which is the highest TOF ever reported for noble metal-free catalysts, and a good stability keeping 94 % activity after 5 cycles. Synchrotron radiation-based X-ray absorption spectroscopy (XAS) investigations suggested that the high catalytic performance could be attributed to the interfacial interaction between Cux Co1-x O NPs and GO. Moreover, the catalytic hydrolysis mechanism was studied by in situ XAS experiments for the first time, which reveal a significant water adsorption on the catalyst and clearly confirm the interaction between AB and the catalyst during hydrolysis.

Ab Initio QM/MM Study Shows a Highly Dissociated SN2 Hydrolysis Mechanism for the cGMP-Specific Phosphodiesterase-5.

Phosphodiesterases (PDEs) are the sole enzymes hydrolyzing the important second messengers cGMP and cAMP and have been identified as therapeutic targets for several diseases. The most successful examples are PDE5 inhibitors (i.e., sildenafil and tadalafil), which have been approved for the treatment of male erectile dysfunction and pulmonary hypertension. However, the side effects mostly due to nonselective inhibition toward other PDE isoforms, set back the clinical usage of PDE5 inhibitors. Until now, the exact catalytic mechanism of the substrate cGMP by PDE5 is still unclear. Herein, the first computational study on the catalytic hydrolysis mechanism of cGMP for PDE5 (catalytic domain) is performed by employing the state-of-the-art ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. Our simulations show a SN2 type reaction procedure via a highly dissociated transition state with a reaction barrier of 8.88 kcal/mol, which is quite different from the previously suggested hydrolysis mechanism of cAMP for PDE4. Furthermore, the subsequent ligand exchange and the release of the product GMP have also been investigated by binding energy analysis and MD simulations. It is deduced that ligand exchange would be the rate-determining step of the whole reaction, which is consistent with many previous experimental results. The obtained mechanistic insights should be valuable for not only the rational design of more specific inhibitors toward PDE5 but also understanding the general hydrolysis mechanism of cGMP-specific PDEs.

Finally! The structural secrets of a HD-GYP phosphodiesterase revealed

The major sessility-motility lifestyle change and additional fundamental aspects of bacterial physiology, behaviour and morphology are regulated by the secondary messenger cyclic di-GMP (c-di-GMP). Although the c-di-GMP metabolizing enzymes and many receptors have been readily characterized upon discovery, the HD-GYP domain c-di-GMP phosphodiesterase family remained underinvestigated. In this issue of Molecular Microbiology, Bellini et al. provide an important step towards functional and structural characterization of the previously neglected HD-GYP domain family by resolving the crystal structure of PmGH, a catalytically active family member from the thermophilic bacterium Persephonella marina. The crystal structure revealed a novel tri-nuclear catalytic iron centre involved in c-di-GMP binding and catalysis and provides the structural basis to subsequently characterize in detail the catalytic mechanism of hydrolysis of c-di-GMP to GMP by HD-GYP domains.

Redox Mechanism of Glycosidic Bond Hydrolysis Catalyzed by 6-Phospho-α-glucosidase: A DFT Study

Glycosidic bonds are remarkably resistant to cleavage by chemical hydrolysis. Glycoside hydrolases catalyze their selective hydrolysis in oligosaccharides, polysaccharides, and glycoconjugates by following nonredox catalytic pathways or a net redox-neutral catalytic pathway using NAD(+) and divalent metal ions as cofactors. GlvA (6-phospho-alpha-glucosidase) is a glycosidase belonging to family GH4 and follows a regioselective redox-neutral mechanism of glycosidic-bond hydrolysis that favors alpha- over beta-glycosides. Its proposed catalytic mechanism can be divided into two half-reactions: the first one activates the glucopyranose ring by successively forming intermediates that are oxidized at the 3-, 2-, and 1-positions of the ring, which ultimately facilitate the heterolytic deglycosylation. The second half-reaction is essentially the reverse of the first half-reaction, beginning with the pyranose ring hydroxylation at the anomeric carbon, and it is followed by 3-reduction and regeneration of the active forms of the catalytic site and its cofactors. We investigated the NAD(+)-dependent redox mechanism of glycosidic bond hydrolysis as catalyzed by GlvA through the combined application of density functional theory and a self-consistent reaction field to a large active-site model obtained from the crystallographic structure of the enzyme, then we applied natural bond orbital and second-order perturbation analyses to monitor the electron flow and change in oxidation state on each atomic center along the reaction coordinate to rationalize the energetics and regioselectivity of this catalytic mechanism. We find that in GlvA, the redox catalytic mechanism of hydrolysis is driven by the gradual strengthening of the axial endo-anomeric component within the hexose ring along the reaction coordinate to facilitate the heterolytic dissociation of the axial C1-O bond. In addition, the combined influence of specific components of the generalized anomeric effect fully explains the regioselectivity observed in the catalytic activity of GlvA.