DFT study on the mechanism of Escherichia coli inorganic pyrophosphatase

The His23 and Lys79 pair determines the high catalytic efficiency of the inorganic pyrophosphatase of the haloacid dehalogenase superfamily

Haloacid dehalogenase (HAD) superfamily members are mainly phosphomonoesterases, while BT2127 from Bacteroides thetaiotaomicron of the HAD superfamily is identified as an inorganic pyrophosphatase. In this study, to explore the roles of the Lys79 and His23 pair in the hydrolysis reaction of inorganic pyrophosphate (PP_i) catalyzed by BT2127, a series of models were designed. Calculations were performed by using the density functional theory (DFT) method with the dispersion energy D3-B3LYP. The His23 and Lys79 pair plays a key role in the high catalytic efficiency of BT2127 with PPi. First, the His23 and Lys79 pair prompts Asp13 to easily provide a proton to the leaving group, which remarkably reduces the energy barrier of the phospho-transfer step; then, Lys79 provides a proton to the first leaving phosphate group via His23, produces a more electrically stabilized phosphate (H₃PO₄), makes this step exothermal, and further promotes the subsequent phospho-enzyme intermediate hydrolysis. The results suggest that the Lys79-His23 pair helps BT2127 reach high catalytic efficiency by strengthening the acid catalysis. Our study provides detailed chemical insights into the evolution of the inorganic pyrophosphatase function of BT2127 from the phosphomonoesterase of the HAD superfamily and the biomimetic enzyme design.

Characterization of an archaeal inorganic pyrophosphatase from Sulfolobus islandicus using a [31P]-NMR-based assay

Inorganic pyrophosphatase catalyzes the conversion of pyrophosphate to phosphate and is often critical for driving reactions forward in cellular processes such as nucleic acid and protein synthesis. Commonly used methods for quantifying pyrophosphatase enzyme activity employ reacting liberated phosphate with a second molecule to produce absorbance changes or employing a second enzyme in coupled reactions to produce a product with a detectable absorbance. In this investigation, a novel [³¹P]-NMR spectroscopy-based assay was used to quantitatively measure the formation of phosphate and evaluate the activity of inorganic pyrophosphatase from the thermoacidophilic Crenarchaeota Sulfolobus islandicus. The enzymatic activity was directly measured via integration of the [³¹P] resonance associated with the phosphate product (δ = 2.1 ppm). Sulfolobus islandicus inorganic pyrophosphatase preferentially utilized Mg²⁺ as divalent cation and had pH and temperature optimums of 6.0 of 50 °C, respectively. The V_max value was 850 μmol/min/mg and the K_m for pyrophosphate was 1.02 mM. Sequence analysis indicates the enzyme is a Family I pyrophosphatase. Sulfolobus islandicus inorganic pyrophosphatase was shown to be inhibited by sodium fluoride with a IC₅₀ of 2.26 mM, compared to a IC₅₀ of 0.066 mM for yeast inorganic pyrophosphatase. These studies reveal that a [³¹P]-NMR spectroscopy-based assay is an effective method for analyzing catalysis by phosphate-producing enzymes.

Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study

The mesophilic inorganic pyrophosphatase from Escherichia coli (EcPPase) retains function at 353 K, the physiological temperature of hyperthermophilic Thermococcus thioreducens, whereas the homolog protein (TtPPase) from this hyperthermophilic organism cannot function at room temperature. To explain this asymmetric behavior, we examined structural and dynamical properties of the two proteins using molecular dynamics simulations. The global flexibility of TtPPase is significantly higher than its mesophilic homolog at all tested temperature/pressure conditions. However, at 353 K, EcPPase reduces its solvent-exposed surface area and increases subunit compaction while maintaining flexibility in its catalytic pocket. In contrast, TtPPase lacks this adaptability and has increased rigidity and reduced protein/water interactions in its catalytic pocket at room temperature, providing a plausible explanation for its inactivity near room temperature.

Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites

Quantum-chemical studies of enzymatic reaction mechanisms sometimes use truncated active-site models as simplified alternatives to mixed quantum mechanics molecular mechanics (QM/MM) procedures. Eliminating the MM degrees of freedom reduces the complexity of the sampling problem, but the trade-off is the need to introduce geometric constraints in order to prevent structural collapse of the model system during geometry optimizations that do not contain a full protein backbone. These constraints may impair the efficiency of the optimization, and care must be taken to avoid artifacts such as imaginary vibrational frequencies. We introduce a simple alternative in which terminal atoms of the model system are placed in soft harmonic confining potentials rather than being rigidly constrained. This modification is simple to implement and straightforward to use in vibrational frequency calculations, unlike iterative constraint-satisfaction algorithms, and allows the optimization to proceed without constraint even though the practical result is to fix the anchor atoms in space. The new approach is more efficient for optimizing minima and transition states, as compared to the use of fixed-atom constraints, and also more robust against unwanted imaginary frequencies. We illustrate the method by application to several enzymatic reaction pathways where entropy makes a significant contribution to the relevant reaction barriers. The use of confining potentials correctly describes reaction paths and facilitates calculation of both vibrational zero-point and finite-temperature entropic corrections to barrier heights.

A seed-mediated growth of gold nanoparticles inside carbon nanotube fibers for fabrication of multifunctional nanohybrid fibers with enhanced mechanical and electrical properties

The seed-mediated growth strategy of Au nanoparticles (Au NPs) inside carbon nanotube (CNT) fibers is demonstrated to greatly improve their mechanical and electrical properties and provide a function for catalytic applications. The resulting Au NP@CNT nanocomposite fibers exhibit 100% knot efficiency, catalytic activity and considerably enhanced modulus, tensile strength, and electrical conductivity from 7 GPa, 109 MPa and 1300 S cm-1 to 24 GPa, 351 MPa and 3600 S cm-1, respectively. The enhancement mechanism is also revealed by systematic characterization and theoretical simulations.

How does Mo-dependent perchlorate reductase work in the decomposition of oxyanions?

The mechanisms of Mo-dependent perchlorate reductase (PcrAB)-catalyzed decomposition of perchlorate, bromate, iodate, and nitrate were revealed by density functional calculations.

Water-Soluble Naked Gold Nanoclusters Are Not Luminescent

Here, the synthesis of water-dispersible naked gold nanoclusters (AuNC_naked ) is reported by a simple reduction of HAuCl₄ with NaOH at room temperature, and it is shown that they are non-luminescent. They are then easily passivated with different thiols and adenosine monophosphate, leading to luminescent NCs. This is an important finding because the photoluminescence of the passivated NCs can now be clearly attributed to the ligand-AuNC surface interaction. These results are also highly relevant from the point of view of the preparation of luminescent NCs from the same NC batch. This strategy can be valuable for the preparation of a broad range of nano(bio)composites.

Improvement of Site-Directed Protein-Polymer Conjugates: High Bioactivity and Stability Using a Soft Chain-Transfer Agent

Protein has been widely applied in biotechnology and biomedicine thanks to its unique properties of high catalytic activity, outstanding receptor-ligand specificity, and controllable sequence mutability. Owing to the easily induced structural variation and thus the inactivation of protein, there has been much effort to improve the structural stability and biological activity of proteins by the use of polymers to modify protein to construct protein-polymer conjugates. However, during the conjugation of polymer to protein active center, the great loss in the original biological activity of the protein is still a serious and so far unsolved question. Here, for the purpose of preparing site-directed and highly structurally stable protein-polymer conjugate, which would possess at least a substantially similar level of biological activity as the original unmodified protein, we proposed a new strategy by using a pyridine chain-transfer agent (CTA-Py) with a soft pyridine-terminated chain for visible-light-induced reversible addition-fragmentation chain transfer (RAFT) polymerization specifically on a number of sites close to the protein active center. The results showed that all the intermediate conjugates PPa-CTA-Py at different modification sites could retain full enzymatic activities (about 110-130% of the unmodified PPa). It was demonstrated by dynamic computer simulation that introducing of CTA-Py had little interference to the protein spatial structure as compared to the popular maleimide chain-transfer agent (CTA-Ma) with rigid maleimide-terminated. Moreover, intermediate conjugates PPa-CTA-Py is facile and ready for further light polymerization under mild conditions. Final PPa-PNIPAAm conjugate produced from CTA-Py exhibited excellent temperature responsiveness and maintained its enzymatic activity even at high temperature. These highly stable and responsive protein-polymer conjugates have great potential and could be widely used in various industrial, chemical, biological, and pharmaceutical applications.

Factors Governing the Bridging Water Protonation State in Polynuclear Mg(2+) Proteins

An aqua ligand bridges metal cations in a wide variety of enzymes, many of which are drug targets for various diseases. However, the factors affecting its protonation state and thus biological roles remain elusive. By computing the free energy for replacing the bridging H2O by OH(-) in various model Mg(2+) sites, we have evaluated how the nature of an aqua bridge depends on the site's net charge (i.e., the number of charged ligands in the first and second shell and the number of metal cations), the site's solvent exposure, the ligand's charge-donating ability, the bridging oxygen's hydrogen-bonding interactions, intramolecular proton transfer from the bridging H2O to a nearby carboxylate, and the metal coordination number. The results reveal the key factors dictating the protonation state of bridging H2O and provide guidelines in predicting whether H2O or OH(-) bridges two Mg(2+) in polynuclear sites. This helps to elucidate the nucleophile in the enzyme-catalyzed reaction and the net charge of the metal complex (metal cation and first-shell ligands), which plays a critical role in binding.

Theoretical study on the chemical mechanism of enoyl-CoA hydratase and the form of inhibitor binding

Enoyl-CoA hydratase (ECH) catalyzes the second step in the vital β-oxidation pathway of fatty acid metabolism. This enzyme catalyzes the syn-addition of a water molecule across the double bond of 4-(N,N-dimethylamino) cinnamoyl-CoA (DAC-CoA). In this work, the reaction mechanisms of ECH were investigated using the density functional theory (DFT) methods. The different protonation states in which the important residues Glu164 and Glu144 are either neutral or ionized were considered. Four models of the active site were designed based on the X-ray crystal structure of the enzyme. The calculations gave strong support to the proposed mechanism and confirmed that both Glu164 and Glu144 are in a deprotonated state in the reaction mechanism of ECH. In addition, we constructed a model of the active site with the inhibitor acetoacetyl-CoA based on the crystal structure. Caomparison of the calculated energy barriers showed that binding of the keto-enol form of the inhibitor is more reasonable than that of the di-keto form in the inhibition process. Moreover, acetoacetyl-CoA was found to exhibit a keto-enol tautomerism when it acts as an inhibitor in the reaction. The present theoretical results indicated that both residues Glu164 and Glu144 are unprotonated in ECH with the substrate bound, while only Glu164 is unprotonated when the inhibitor binds ECH.

Ultrasmall hollow gold-silver nanoshells with extinctions strongly red-shifted to the near-infrared

Hollow gold-silver nanoshells having systematically varying sizes between 40 and 100 nm were prepared. These particles consist of a hollow spherical silver shell surrounded by a thin gold layer. By varying the volume of the gold stock solution added to suspensions of small silver-core templates, we tailored the hollow gold-silver nanoshells to possess strong tunable optical extinctions that range from the visible to the near-IR spectral regions, with extinctions routinely centered at ∼950 nm. The size and morphology of these core/shell nanoparticles were characterized by dynamic light scattering (DLS), field emission scanning electron microscopy (FE-SEM), and transmission electron microscopy (TEM). Separately, X-ray diffraction (XRD), energy-dispersive X-ray spectroscopy (EDS) and X-ray photoelectron spectroscopy (XPS) were used for measuring their elemental composition; UV-vis spectroscopy was used to evaluate their optical properties. Given their relatively small size compared to other nanoparticles that absorb strongly at near IR wavelengths, these easy-to-synthesize particles should find use in applications that require ultrasmall nanoparticles with extinctions comfortably beyond visible wavelengths (e.g., medicinal therapies, diagnostic imaging, nanofluidics, and display technologies).

Quantum Chemical Modeling of Enzymatic Reactions: The Case of Decarboxylation

We present a systematic study of the decarboxylation step of the enzyme aspartate decarboxylase with the purpose of assessing the quantum chemical cluster approach for modeling this important class of decarboxylase enzymes. Active site models ranging in size from 27 to 220 atoms are designed, and the barrier and reaction energy of this step are evaluated. To model the enzyme surrounding, homogeneous polarizable medium techniques are used with several dielectric constants. The main conclusion is that when the active site model reaches a certain size, the solvation effects from the surroundings saturate. Similar results have previously been obtained from systematic studies of other classes of enzymes, suggesting that they are of a quite general nature.

Protonation of a hydroxide anion bridging two divalent magnesium cations in water probed by first-principles metadynamics simulation

The protonation of a hydroxide anion (OH(-)) located between two magnesium cations (Mg(2+)) in aqueous solution has been investigated by first-principles metadynamics simulation. We observe that the complex Mg(2+)-OH(-)-Mg(2+) is stabilized by the coparticipation of the hydroxide anion to the first hydration shells of both the Mg(2+) cations. Contrary to the cases of OH(-) in pure water, the transfer of protons in the presence of the divalent metal ions turns out to be a slow chemical event. This can be ascribed to the decreased proton affinity of the bridging OH(-). Metadynamics simulation, used to overcome the difficulty of the long time scale required by the protonation of the bridging OH(-), has shown that the system possesses a great stability on the reactant state, characterized by a bioctahedral (6,6) solvation structure around the two Mg(2+) cations. The exploration of the free energy landscape shows that this stable bioctahedral configuration converts into a lower coordinated (5,6) structure, leading to a proton transfer from a water molecule belonging to the first solvation shell of the Mg(2+) ion having the lower coordination to the bridging OH(-); the free energy barrier for the protonation reaction is 11 kcal/mol, meaning that the bridging hydroxide is a weak base. During the proton transfer, the bridging OH(-) reverts to an H(2)O molecule, and this breaks the electrostatic coupling of the two Mg(2+) ions, which depart independently with their own hydration shells, one of which is entirely formed by water molecules. The second one carries the newly created OH(-). Our results show that the flexibility in the metal coordination plays a crucial role in both the protonation process of the bridging OH(-) and the separation of the metal cations, providing useful insight into the nature of proton transfer in binuclear divalent metal ions, with several biological implications, such as, for instance, transesterification of catalytic RNA.

The mechanism of cyclization in chromophore maturation of green fluorescent protein: a theoretical study

An intriguing aspect of the green fluorescent protein (GFP) is the autocatalytic post-translational modification that results in the formation of its chromophore. Numerous experimental and theoretical studies indicate that cyclization is the first and the most important step in the maturation process. In this work, two proposed mechanisms for the cyclization were investigated by using the hybrid density functional theory method B3LYP. Cluster models corresponding to the two mechanisms proposed by Wachter et al. [J. Biol. Chem. 2005, 280, 26248-26255] are constructed on the basis of the X-ray crystal structure (PDB entry 2AWJ) and corresponding reaction path potential energy profiles for the two cyclization mechanisms are presented. Our results suggest that the backbone condensation initiated by deprotonation of the Gly67 amide nitrogen is easier than deprotonation of the Tyr66 alpha-carbon. Moreover, Arg96 fulfills the role of stabilizing the enolate moiety, and Glu222 plays the role of a general base. The formation of the cyclized product is found to be 16.0 and 18.6 kcal/mol endothermic with respect to the two models, which is in agreement with experimental observation.