Rat Liver Arginase Research Articles

Gold Nanoparticle-Based Photoluminescent Nanoswitch Controlled by Host-Guest Recognition and Enzymatic Hydrolysis for Arginase Activity Assay.

The development of simple yet powerful methods for monitoring enzyme activity is of great significance. Herein, a facile, convenient, cost-effective, and continuous fluorescent method for the detection of arginase and its inhibitor has been reported based on a host-guest interaction-controlled and enzymatic hydrolysis-controlled luminescent nanoswitch. The fluorescence intensity of 6-aza-2-thiothymine-stabilized gold nanoparticle (ATT-AuNP) is enhanced by l-arginine, owing to the formation of a supramolecular host-guest assembly between the guanidine group of l-arginine and ATT molecules capped on the AuNP surface. However, hydrolysis of l-arginine, catalyzed by arginase, leads to a decrease in the fluorescence intensity of l-arginine/ATT-AuNPs hybrids. Upon incorporation of the arginase inhibitor l-norvaline, the fluorescence of the ATT-AuNP-based detecting system is restored. The linear range of arginase activity determination is from 0.0625 to 1.15 U/mL and the limit of detection is 0.056 U/mL. The half-maximal inhibition value IC50 of l-norvaline is determined to be 5.6 mM. The practicability of this luminescent nanoswitch is validated by assaying the arginase activity in rat liver and monitoring the response of rat liver arginase to pharmacological agent. Compared to the existing fluorescent method of arginase activity assay, the approach demonstrated here does not involve any complicated technical manipulation, thereby greatly simplifying the detection steps. We propose that this AuNP-based luminescent nanoswitch would find wide applications in the field of life sciences and medicine.

Rat liver arginase system under acetaminophen-induced toxic injury and protein deprivation

Rat liver arginase system under acetaminophen-induced toxic injury and protein deprivation

QM/MM study of hydrolysis of arginine catalysed by arginase

ABSTRACTIn this paper, we have investigated the catalytic mechanism of rat liver arginase using a quantum mechanics/molecular mechanics (QM/MM) approach. The enzyme catalyses the hydrolysis of L-arginine (L-Arg) to generate L-ornithine and urea. The reaction mechanism proposed by the previous experimental studies is well reproduced by the QM/MM computations. The explicit treatment of the protein environment suggests that Glu277 fulfil its role in stabilising and orienting L-Arg before nucleophilic attack by the bridging hydroxide in the first step. We have also found that the proton transfer step involving a hydrogen bond switch is the rate-limiting step. The activation energy is computed to be 9.0 and 5.9 kcal/mol at the UB3LYP-D3/CHARMM22 and UBHandHLYP-D3/CHARMM22 levels, which are comparable to the observed activation barrier of 7.2 kcal/mol.

Inhibition of Leishmania (Leishmania) amazonensis and Rat Arginases by Green Tea EGCG, (+)-Catechin and (−)-Epicatechin: A Comparative Structural Analysis of Enzyme-Inhibitor Interactions

Epigallocatechin-3-gallate (EGCG), a dietary polyphenol (flavanol) from green tea, possesses leishmanicidal and antitrypanosomal activity. Mitochondrial damage was observed in Leishmania treated with EGCG, and it contributed to the lethal effect. However, the molecular target has not been defined. In this study, EGCG, (+)-catechin and (−)-epicatechin were tested against recombinant arginase from Leishmania amazonensis (ARG-L) and rat liver arginase (ARG-1). The compounds inhibit ARG-L and ARG-1 but are more active against the parasite enzyme. Enzyme kinetics reveal that EGCG is a mixed inhibitor of the ARG-L while (+)-catechin and (−)-epicatechin are competitive inhibitors. The most potent arginase inhibitor is (+)-catechin (IC50 = 0.8 µM) followed by (−)-epicatechin (IC50 = 1.8 µM), gallic acid (IC50 = 2.2 µM) and EGCG (IC50 = 3.8 µM). Docking analyses showed different modes of interaction of the compounds with the active sites of ARG-L and ARG-1. Due to the low IC50 values obtained for ARG-L, flavanols can be used as a supplement for leishmaniasis treatment.

Homology modeling, docking and molecular dynamics of the Leishmania mexicana arginase: A description of the catalytic site useful for drug design

The crystallographic structure of the Leishmania mexicana arginase, an attractive target for the design of leishmanicidal agents, is still unknown. For this reason, we report a computer-assisted homology study conducted to build its three-dimensional structure based on the known sequence of amino acids of this enzyme. In this study, the amino acid sequence in the arginase of the parasite was compared with the sequence of the amino acids in the crystallographic structure of rat and human liver arginases. The best similarity was found with the rat liver arginase. The catalytic site of the three-dimensional arginase structure built for L. mexicana has important structural differences as compared with that of the human liver arginase with regard to reasonable design selective compounds against L. mexicana. With this information, a docking study was conducted to find the inhibitors of this enzyme. 1439 molecules were docked and 18 were selective to the L. mexicana arginase. Moreover, molecular dynamics were carried out to study the stability of the homologue protein (including manganeses) and the ligand–enzyme complex. The results indicated that the manganese remains inside the protein throughout the simulation. Besides, hydrogen bonds interactions between the ligand and the arginase were analyzed. These results provide important information for the design of new inhibitors.

Structures of Metal-Substituted Human Histone Deacetylase 8 Provide Mechanistic Inferences on Biological Function,

The metal-dependent histone deacetylases (HDACs) adopt an alpha/beta protein fold first identified in rat liver arginase. Despite insignificant overall amino acid sequence identity, these enzymes share a strictly conserved metal binding site with divergent metal specificity and stoichiometry. HDAC8, originally thought to be a Zn(2+)-metallohydrolase, exhibits increased activity with Co(2+) and Fe(2+) cofactors based on k(cat)/K(M) (Gantt, S. L., Gattis, S. G., and Fierke, C. A. (2006) Biochemistry 45, 6170-6178). Here, we report the first X-ray crystal structures of metallo-substituted HDAC8, Co(2+)-HDAC8, D101L Co(2+)-HDAC8, D101L Mn(2+)-HDAC8, and D101L Fe(2+)-HDAC8, each complexed with the inhibitor M344. Metal content of protein samples in solution is confirmed by inductively coupled plasma mass spectrometry. For the crystalline enzymes, peaks in Bijvoet difference Fourier maps calculated from X-ray diffraction data collected near the respective elemental absorption edges confirm metal substitution. Additional solution studies confirm incorporation of Cu(2+); Fe(3+) and Ni(2+) do not bind under conditions tested. The metal dependence of the substrate K(M) values and the K(i) values of hydroxamate inhibitors that chelate the active site metal are consistent with substrate-metal coordination in the precatalytic Michaelis complex that enhances catalysis. Additionally, although HDAC8 binds Zn(2+) nearly 10(6)-fold more tightly than Fe(2+), the affinities for both metal ions are comparable to the readily exchangeable metal concentrations estimated in living cells, suggesting that HDAC8 could bind either or both Fe(2+) or Zn(2+) in vivo.

EPR spectroscopy and catalase activity of manganese-bound DNA-binding protein from nutrient starved cells

DNA-binding proteins from nutrient-starved cells (DPS) protect cells from oxidative stress by removing H(2)O(2) and iron. A new class of DPS-like proteins has recently been identified, with DPS-like protein from Sulfolobus solfataricus (SsDPS) being the best characterized to date. SsDPS protects cells from oxidative stress and is upregulated in response to H(2)O(2) but also in response to iron depletion. The ferroxidase active site of SsDPS is structurally similar to the active sites of manganese catalase and rat liver arginase. The present work shows that the ferroxidase center in SsDPS binds two Mn(2+) ions with K (D) = (1/K (1) K (2))(1/2) = 48(3) microM. The binding constant of the second Mn(2+) is significantly higher than that of the first, inducing dinuclear Mn(II) cluster formation for all but the lowest concentrations of added Mn(2+). In competition experiments, equimolar amounts of Fe(2+) were unable to displace the bound manganese. EPR spectroscopy of the Mn(2) (2+) cluster showed signals comparable to those of other characterized dimanganese clusters. The exchange coupling for the cluster was determined, J = -1.4(3) cm(-1) (H = -2JS (1) S (2)), and is within the range expected for a mu(1,1)-carboxylato bridge between the manganese ions. Manganese-bound SsDPS showed catalase activity at a rate 10-100 times slower than for manganese catalases. EPR spectra of SsDPS after addition of H(2)O(2) showed the appearance of an intermediate in the reaction with H(2)O(2).

Evolution of the arginase fold and functional diversity.

Novel structural superfamilies can be identified among the large number of protein structures deposited in the Protein Data Bank based on conservation of fold in addition to conservation of amino acid sequence. Since sequence diverges more rapidly than fold in protein Evolution, proteins with little or no significant sequence identity are occasionally observed to adopt similar folds, thereby reflecting unanticipated evolutionary relationships. Here, we review the unique alpha/beta fold first observed in the manganese metalloenzyme rat liver arginase, consisting of a parallel eight-stranded beta-sheet surrounded by several helices, and its evolutionary relationship with the zinc-requiring and/or iron-requiring histone deacetylases and acetylpolyamine amidohydrolases. Structural comparisons reveal key features of the core alpha/beta fold that contribute to the divergent metal ion specificity and stoichiometry required for the chemical and biological functions of these enzymes.

Inhibition of rat liver and kidney arginase by cadmium ion

Cadmium ion activates arginase from many species of organisms but is an inhibitor of arginase from many other species. The purpose of this study was to investigate the inhibition of rat liver and kidney arginase by cadmium ion. Rat kidney arginase was inhibited by much lower concentrations of cadmium ion than rat liver arginase. Cadmium ion was a mixed noncompetitive inhibitor of both rat liver and kidney arginase. Cadmium ion enhanced the substrate activation of rat kidney arginase while still inhibiting the enzyme. Cadmium ion prevented the substrate inhibition of rat kidney arginase by fluoride while still inhibiting the enzyme. Cadmium ion also inhibited rat kidney arginase in the presence of manganese ion.

Probing the role of the hyper-reactive histidine residue of arginase

Rat liver arginase (arginase I) is potently inactivated by diethyl pyrocarbonate, with a second-order rate constant of 113 M −1s −1 for the inactivation process at pH 7.0, 25 °C. Partial protection from inactivation is provided by the product of the reaction, l-ornithine, while nearly complete protection is afforded by the inhibitor pair, l-ornithine and borate. The role of H141 has been probed by mutagenesis, chemical modulation, and X-ray diffraction. The hyper-reactivity of H141 towards diethyl pyrocarbonate can be explained by its proximity to E277. A proton shuttling role for H141 is supported by its conformational mobility observed among the known arginase structures. H141 is proposed to serve as an acid/base catalyst, deprotonating the metal-bridging water molecule to generate the metal-bridging hydroxide nucleophile, and by protonating the amino group of the product to facilitate its departure.

Synthesis and evaluation of new ω-borono-α-amino acids as rat liver arginase inhibitors

Recent studies have demonstrated that arginase plays important roles in pathologies such as asthma or erectile dysfunctions. We have synthesized new ω-borono-α-amino acids that are analogues of the previously known arginase inhibitors S-(2-boronoethyl)- l-cysteine (BEC) and 2-amino-6-boronohexanoic acid (ABH) and evaluated them as inhibitors of purified rat liver arginase (RLA). In addition to the distance between the B(OH) 2 and the α-amino acid functions, the position of the sulfur atom in the side chain also appears as a key determinant for the interaction with the active site of RLA. Furthermore, substitution of the alkyl side chain of BEC by methyl groups and conformational restriction of ABH by incorporation of its side chain in a phenyl ring led to inactive compounds. These results suggest that subtle interactions govern the affinity of inhibitors for the active site of RLA.

Structure and Function of Arginases

The arginases catalyze the divalent cation dependent hydrolysis of L-arginine to produce L-ornithine and urea. Although traditionally considered in terms of its role as the final enzyme of the urea cycle, the enzyme is found in a variety of nonhepatic tissues. These findings suggest that the enzyme may have other functions in addition to its role in nitrogen metabolism. High-resolution crystal structures have been determined for recombinant rat liver (type I) arginase and for recombinant human kidney (type II) arginase, their variants, and complexes with products and inhibitors. Each identical subunit of the trimeric enzyme contains an active site that lies at the bottom of a 15 A deep cleft. The 2 essential Mn(II) ions are located at the bottom of this cleft, separated by approximately 3.3 A and bridged by oxygens derived from 2 aspartic acid residues and a solvent-derived hydroxide. This metal bridging hydroxide is proposed to be the nucleophile that attacks the guanidinium carbon of substrate arginine. On the basis of this proposed mechanism, boronic acid inhibitors of the enzyme have been synthesized and characterized kinetically and structurally. These inhibitors display slow-onset inhibition at the pH optimum of the enzyme, and are found as tetrahedral species at the active site, as determined by X-ray diffraction. The potent inhibition of arginases I and II by these compounds has not only delineated key enzyme-substrate interactions, but has also led to a greater understanding of the role of arginase in nonhepatic tissues.

First principles computational study of the active site of arginase.

Ab initio density functional theory (DFT) methods were used to investigate the structural features of the active site of the binuclear enzyme rat liver arginase. Special emphasis was placed on the crucial role of the second shell ligand interactions. These interactions were systematically studied by performing calculations on models of varying size. It was determined that a water molecule, and not hydroxide, is the bridging exogenous ligand. The carboxylate ligands facilitate the close approach of the Mn (II) ions by attenuating the metal-metal electrostatic repulsion. Of the two metals, Mn(A) was shown to carry a larger positive charge. Analysis of the electronic properties of the active site revealed that orbitals involving the terminal Asp234 residue, as well as the flexible micro-1,1 bridging Asp232, lie at high energies, suggesting weaker coordination. This is reflected in certain structural variability present in our models and is also consistent with recent experimental findings. Finally, implications of our findings for the biological function of the enzyme are delineated.

Substrate inhibition of rat liver and kidney arginase with fluoride

Fluoride is an uncompetitive inhibitor of rat liver arginase. This study has shown that fluoride caused substrate inhibition of rat liver arginase at substrate concentrations above 4 mM. Rat kidney arginase was more sensitive to inhibition by fluoride than liver arginase. For both liver and kidney arginase preincubation with fluoride had no effect on the inhibition. When assayed with various concentrations of l-arginine, rat kidney arginase did not have Michaelis–Menten kinetics. Lineweaver–Burk and Eadie–Hofstee plots were nonlinear. Kidney arginase showed strong substrate activation at concentrations of l-arginine above 4 mM. Within narrow concentrations of l-arginine, the inhibition of kidney arginase by fluoride was uncompetitive. Fluoride caused substrate inhibition of kidney arginase at l-arginine concentrations above 1 mM. The presence of fluoride prevented the substrate activation of rat kidney arginase.

Functional Consequences of the G235R Mutation in Liver Arginase Leading to Hyperargininemia

Hyperargininemia is a rare autosomal disorder that results from a deficiency in hepatic type I arginase. This deficiency is the consequence of random point mutations that occur throughout the gene. The G235R patient mutation has been proposed to affect the catalytic activity and structural integrity of the protein [D. E. Ash, L. R. Scolnick, Z. F. Kanyo, J. G. Vockley, S. D. Cederbaum, and D. W. Christianson (1998) Mol. Genet. Metab. 64, 243–249]. The G235R (patient) and G235A (control) arginase mutants of rat liver arginase have been generated to probe the effects of these point mutations on the structure and function of hepatic type I arginase. Both mutant arginases were trimeric by gel filtration, but the control G235A mutant had 56% of wild-type activity and the G235R mutant had less than 0.03% activity compared to the wild-type enzyme. The G235R mutant contained undetectable levels of tightly bound manganese as determined by electron paramagnetic resonance, while the G235A mutant had a Mn(II) stoichiometry of 2 Mn/subunit. Molecular modeling indicates that the introduction of an arginine residue at position 235 results in a major rearrangement of the metal ligands that compromise Mn(II) binding.

Interaction of anions with rat liver arginase: specific inhibitory effects of fluoride

The inhibitory effects of anions, such as N3−, NO2−, BO43−, SCN−, CH3COO−, SO42−, ClO4−, H2PO4−, CN−, I−, Br−, Cl− and F−, on the hydrolysis of l-arginine (l-Arg) by rat liver arginase (RLA) have been studied. From all these anions, only F− exhibited a clear inhibitory effect at the mM level. Inhibition of RLA by F− is reversible and uncompetitive towards l-Arg binding with a Ki value of 1.3±0.5 mM at pH 7.4. This effect is dependent on pH as the IC50 value of F− towards RLA increases from 1.2 to 19 mM when increasing the pH from 7 to 10. Another specific inhibitor of RLA, Nω-hydroxy-l-nor-arginine (nor-NOHA), that has been recently shown to bind to RLA as a bridging ligand of its (MnII)2 cluster, exhibits some similarities with F− in its inhibitory effects (identical pH dependence). It is thus tempting to propose that the inhibitory effects of F− could be due to its binding as a bridging ligand of the RLA (MnII)2 cluster. However, further studies are required to determine the modes of interaction of F− with RLA.

Molecular dynamics simulations of active site mutants of rat liver arginase

By using molecular dynamics (MD) simulations and crystallographic data for rat liver arginase, the substrate positions in the active sites of native and mutant forms of the enzyme, were compared and correlated with known kinetic consequences of mutations. The mutants compared were His 141 Phe and His 141 Asn. The simulations show that mutation His141 Asn gives the greatest divergence from the atomic coordinates, when compared with the control native enzyme. The mutant Asp128 Asn does not show a change in atomic coordinates in the substrate, in agreement with the concept that a change in the metal coordination is responsible for the loss of catalytic activity in this mutant. Results obtained agree with reported kinetic consequences of mutations in arginase.

Molecular dynamics simulations of active site mutants of rat liver arginase

EJB Electronic Journal of Biotechnology ISSN: 0717-3458 Vol.4 No.3, Issue of December 15, 2001© 2001 by Universidad Catolica de Valparaiso -- Chile Received August 10, 2001 / Accepted November 7, 2001

Subunit-Subunit Interactions in Trimeric Arginase: GENERATION OF ACTIVE MONOMERS BY MUTATION OF A SINGLE AMINO ACID

The structure of the trimeric, manganese metalloenzyme, rat liver arginase, has been previously determined at 2.1-A resolution (Kanyo, Z. F., Scolnick, L. R., Ash, D. E., and Christianson, D. W., (1996) Nature 383, 554-557). A key feature of this structure is a novel S-shaped oligomerization motif at the carboxyl terminus of the protein that mediates approximately 54% of the intermonomer contacts. Arg-308, located within this oligomerization motif, nucleates a series of intramonomer and intermonomer salt links. In contrast to the trimeric wild-type enzyme, the R308A, R308E, and R308K variants of arginase exist as monomeric species, as determined by gel filtration and analytical ultracentrifugation, indicating that mutation of Arg-308 shifts the equilibrium for trimer dissociation by at least a factor of 10(5). These monomeric arginase variants are catalytically active, with k(cat)/K(m) values that are 13-17% of the value for wild-type enzyme. The arginase variants are characterized by decreased temperature stability relative to the wild-type enzyme. Differential scanning calorimetry shows that the midpoint temperature for unfolding of the Arg-308 variants is in the range of 63.6-65.5 degrees C, while the corresponding value for the wild-type enzyme is 70 degrees C. The three-dimensional structure of the R308K variant has been determined at 3-A resolution. At the high protein concentrations utilized in the crystallizations, this variant exists as a trimer, but weakened salt link interactions are observed for Lys-308.

Comparison of the inhibition of rat liver and kidney arginase by metal ions

Comparison of the inhibition of rat liver and kidney arginase by metal ions