Metal ions binding to NAD-glycohydrolase from the venom of Agkistrodon acutus: regulation of multicatalytic activity

ICP-MS characterization of seven North American snake venoms

Snake venoms are inherently complex. They are mixtures of multiple enzymes, peptides, lipids, carbohydrates, nucleosides, and metal ions. Metal ions make up a small portion of a snake's venom but play outsized roles in enzyme function and stability. Unlike enzyme primary structure, which is easily predicted from genomic sequences, a venom's metal ion content must be measured directly. We leveraged the high throughput and sensitivity of inductively coupled plasma mass spectrometry to analyze the metal ion content of seven North American snake venoms. All venoms were collected from snakes reared at one location, so we could discount variation from environmental or geographical factors. We profiled 71 metal isotopes. Selenium isotopes were consistently high across all venoms tested. When each venom's toxicity was graphed as a function of each different metal isotope, the only strong relationships between metal content and toxicity were for magnesium isotopes.

Mutual influence of piceatannol and bisphenol F on their interaction with pepsin: Insights from spectroscopic, isothermal titration calorimetry and molecular modeling studies

The individual and combined interactions of bisphenol F and piceatannol with pepsin were investigated using spectroscopic methods (fluorescence, UV-vis absorption, and circular dichroism spectroscopy), combined with isothermal titration calorimetry and molecular docking. Thermodynamic data showed that hydrogen bonds and van der Waals forces might play a major role for the binding process. Site marking experiments and molecular docking confirmed the binding sites of these two ligands on pepsin. The discrepancy in the binding constant between the binary and ternary systems indicated the competitive binding of piceatannol and bisphenol F to pepsin. Circular dichroism spectra studies suggested that the binding of the two ligands led to a loosening of pepsin backbone. Enzyme activity assays indicated that the inhibition of pepsin activity by piceatannol and bisphenol F was competitive. These results will be helpful to understand the mechanism of piceatannol and bisphenol F affecting the activity of digestive proteases in the sight of the food security.

Antibodies against Venom of the Snake Deinagkistrodon acutus

Snake venom protein from Deinagkistrodon acutus (DA protein), one of the major venomous species in Taiwan, causes hemorrhagic symptoms that can lead to death. Although horse-derived antivenin is a major treatment, relatively strong and detrimental side effects are seen occasionally. In our study, yolk immunoglobulin (IgY) was purified from eggs, and DA protein was recognized using Western blotting and an enzyme-linked immunosorbent assay (ELISA), similar to therapeutic horse antivenin. The ELISA also indicated that specific IgY antibodies were elicited after the fifth booster, plateaued, and lasted for at least 3 months. To generate monoclonal single-chain variable fragment (scFv) antibodies, we used phage display technology to construct two libraries with short or long linkers, containing 6.24 × 10(8) and 5.28 × 10(8) transformants, respectively. After four rounds of biopanning, the eluted phage titer increased, and the phage-based ELISA indicated that the specific clones were enriched. Nucleotide sequences of 30 individual clones expressing scFv were analyzed and classified into four groups that all specifically recognized the DA venom protein. Furthermore, based on mass spectrometry, the scFv-bound protein was deduced to be snake venom metalloproteinase proteins. Most importantly, both IgY and mixed scFv inhibited the lethal effect in mice injected with the minimum lethal dosage of the DA protein. We suggest that together, these antibodies could be applied to the development of diagnostic agents or treatments for snakebite envenomation in the future.

Purification and partial characterization of a novel fibrinogenase from the venom of Deinagkistrodon acutus: inhibition of platelet aggregation

A novel fibrinogenase, DAnase, was purified from the venom of Deinagkistrodon acutus by a combination of anion and cation exchange chromatography. Unlike other fibrinogenases which are usually single polypeptide chain proteins, the enzyme was a disulfide-linked dimer with an isoelectric point of 6.03 and an apparent molecular weight of 25kDa on SDS-polyacrylamide gel electrophoresis. DAnase showed α-fibrinogenase activity devoid of fibrinolytic activity. It hydrolyzed rapidly the Aα-chain of fibrinogen and followed by the Bβ-chain and did not cleave the γ-chain. It also exhibited arginine esterase activity. The fibrinogenolytic and arginine esterase activities were completely inhibited by phenylmethanesulfonyl fluoride or tris-(2-carboxyethyl)phosphine hydrochloride, but not by EDTA, indicating that DAnase is a serine protease requiring disulfide bridge(s) for its activity. The protease strongly inhibited ADP-induced platelet aggregation in human platelet-rich plasma but was lack of ADPase activity, indicating that its fibrinogenolytic activity is involved in its inhibition of ADP-induced platelet aggregation. DAnase was devoid of hemorrhagic activity and Factor XIII activation activity. DAnase may have a potential clinical application for the therapy of thrombosis disease.

Effects of metal ions and disulfide bonds on the activity of phosphodiesterase from Trimeresurus stejnegeri venom

Obviously different from the other known phosphodiesterases, the phosphodiesterase from Trimeresurus stejnegeri venom (TS-PDE) consists of two different chains linked with disulfide bonds and contains both endogenous Cu(2+) and Zn(2+). Cu(2+) and Zn(2+) are important for its phosphodiesterase activity. In this study, the effects of metal ions and small-molecule reductants on its structure and activity have been investigated by polyacrylamide gel electrophoresis, high performance liquid chromatography, fluorescence and electron paramagnetic resonance spectroscopy. The results show that TS-PDE has one class of Zn(2+) binding site and two classes of Cu(2+) binding site, including the high affinity activator sites and the low affinity sites. Cu(2+) ions function as a switch for its phosphodiesterase activity. The catalytic activity of TS-PDE does not have an absolute requirement for Cu(2+) and Zn(2+). Mg(2+), Mn(2+), Ni(2+), Co(2+) and Ca(2+) are all effective for its phosphodiesterase activity. TS-PDE has seven disulfide bonds and ten free cysteine residues. l-Ascorbate inhibits the phosphodiesterase activity of TS-PDE through reduction of the Cu(2+), while dithiothreitol, glutathione and tris(2-carboxyethyl)phosphine inhibit the phosphodiesterase activity of TS-PDE by reducing both the Cu(2+) and disulfide bonds. The catalytic activity of TS-PDE relies on its disulfide bonds and bimetallic cluster. In addition, biologically-relevant reductants, glutathione and l-ascorbate, have been found to be endogenous inhibitors to the phosphodiesterase activity of TS-PDE.

Spectral studies on the interaction between HSSC and apoCopC

The interaction between HSSC (SSC = salicylaldehyde semicarbazone anion) and apoCopC has been investigated in detail by means of UV, fluorescence and fluorescence lifetime measurement in 10 mM Hepes buffer, at pH 7.4, 25°C. The results suggested that HSSC can form a novel supramolecular system with apoCopC, which can form a 1:1 host-guest inclusion supramolecular complex with HSSC, and the forming constant had been calculated to be (8.83±0.32)×10(5) M(-1). It suggested the strong inclusion ability of apoCopC to the guest molecules. In addition, the stoichiometric ratio of Cu(2+) and HSSC was 1:1, which was the same as Cu(2+) and apoCopC. However, the binding ability between Cu(2+) and HSSC was much weaker than that between Cu(2+) and apoCopC. Moreover, the binding ability of HSSC with Cu(2+) has an effect on the binding ability between HSSC and apoCopC, and vice versa. The reason attributed to this effect was that the formation of hydrogen bond between Met46 in apoCopC and the phenolic hydroxyl of HSSC participated in the copper coordination. Furthermore, it was also found that HSSC quench the fluorescence of apoCopC by the static quenching process and the number of binding site was calculated. The thermodynamic parameters ΔH°, ΔS° and ΔG° at different temperatures were obtained. The formation of apoCopC-HSSC complex depended on the cooperation of the van der Waals force and hydrogen bond, and the binding average distance between apoCopC and HSSC was determined. What is more, the binding site of HSSC to apoCopC was shown vividly by an automated public domain software package ArgusLab 4.0.1.

The binding characteristics of isoniazid with copper-zinc superoxide dismutase and its effect on enzymatic activity

Background

Isoniazid (INH) is front-line anti-tuberculosis (TB) drugs, which are usually prescribed to TB patients for a total period of 6 months. Antituberculosis drug-induced hepatotoxicity (ATDH) is a serious adverse reaction of TB treatment. It is reported that INH-induced hepatotoxicity is associated with oxidative stress. Superoxide dismutase (SOD, EC 1.15.1.1) is the key enzyme for the protection of oxidative stress, which catalyzes the removal of superoxide radical anion, thereby raising the need to better understand the interaction between INH and SOD.

Results

The experimental results showed that the fluorescence intensity of Cu/Zn-SOD regularly decreased owing to form a 1:1 INH-SOD complex. According to the corresponding association constants (K_SV) between INH and SOD obtained from Stern–Volmer plot, it is shown that values of K_A are 1.01 × 10⁴, 5.31 × 10³, 3.33 × 10³, 2.20 × 10³ L · mol⁻¹ at four different temperatures, respectively. The binding constants, binding sites and the corresponding thermodynamic parameters (^ΔH, ^ΔG and ^ΔS) were calculated. A value of 3.93 nm for the average distance between INH and chromophore of Cu/Zn-SOD was derived from Förster theory of non-radiation energy transfer. The conformational investigation showed that the presence of INH resulted in the microenvironment and conformational changes of Cu/Zn-SOD. In addition, Effects of INH on superoxide dismutase activity was examined.

Conclusions

The results show that the hydrogen bonding and van der Waals forces play major roles in stabilizing the 1:1 INH-SOD complex. After addition of INH during the range of the experiment, the conformation and microenvironment of Cu/Zn-SOD are changed, but the activity of Cu/Zn-SOD is not changed.

Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010

Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.

Cu(ii)- and disulfide bonds-induced stabilization during the guanidine hydrochloride- and thermal-induced denaturation of NAD-glycohydrolase from the venom of Agkistrodon acutus

NAD-glycohydrolase (AA-NADase) from Agkistrodon acutus venom is a unique multicatalytic enzyme with both NADase and AT(D)Pase-like activities. Among all identified NADases, only AA-NADase is a disulfide-linked dimer and contains Cu(2+). Cu(2+) and disulfide bonds are essential for its multicatalytic activity. In this study, the effects of Cu(2+) and disulfide-bonds on guanidine hydrochloride (GdnHCl)- and thermal-induced unfolding of AA-NADase have been investigated by fluorescence, circular dichroism (CD) and differential scanning calorimetry (DSC). Cu(2+) and disulfide bonds not only increase the free energy change during the GdnHCl-induced unfolding as determined by fluorescence, but also increase the overall enthalpy change and the transition temperature during the thermal-induced unfolding as determined by CD and DSC. The slope of the GdnHCl-induced unfolding curve at its midpoint and the heat capacity of thermal-induced unfolding are slightly affected by Cu(2+) but significantly decrease after reduction of three disulfide-bonds. This work suggests that Cu(2+) stabilizes the folded state by increasing the enthalpy of unfolding, while disulfide-bonds stabilize the folded state by increasing the enthalpy of unfolding and stabilizing the packing of hydrophobic residues. Thus both Cu(2+) and disulfide bonds play a structural role in its multicatalytic activity.