Origins of enhanced proton transport in the Y7F mutant of human carbonic anhydrase II

Human carbonic anhydrase II (HCA II), among the fastest enzymes known, catalyzes the reversible hydration of CO 2 to HCO 3 (-). The rate-limiting step of this reaction is believed to be the formation of an intramolecular water wire and transfer of a proton across the active site cavity from a zinc-bound solvent to a proton shuttling residue (His64). X-ray crystallographic studies have shown this intramolecular water wire to be directly stabilized through hydrogen bonds via a small well-defined set of amino acids, namely, Tyr7, Asn62, Asn67, Thr199, and Thr200. Furthermore, X-ray crystallographic and kinetic studies have shown that the mutation of tyrosine 7 to phenylalanine, Y7F HCA II, has the effect of increasing the proton transfer rate by 7-fold in the dehydration direction of the enzyme reaction compared to wild-type (WT). This increase in the proton transfer rate is postulated to be linked to the formation of a more directional, less branched, water wire. To evaluate this proposal, molecular dynamics simulations have been employed to study water wire formation in both the WT and Y7F HCA II mutant. These studies reveal that the Y7F mutant enhances the probability of forming small water wires and significantly extends the water wire lifetime, which may account for the elevated proton transfer seen in the Y7F mutant. Correlation analysis of the enzyme and intramolecular water wire indicates that the Y7F mutant significantly alters the interaction of the active site waters with the enzyme while occupancy data of the water oxygens reveals that the Y7F mutant stabilizes the intramolecular water wire in a manner that maximizes smaller water wire formation. This increase in the number of smaller water wires is likely to elevate the catalytic turnover of an already very efficient enzyme.

Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III

We report the X-ray crystal structures and rate constants for proton transfer in site-specific mutants of human carbonic anhydrase III (HCA III) that place a histidine residue in the active-site cavity: K64H, R67H, and K64H-R67N HCA III. Prior evidence from the exchange of 18O between CO2 and water measured by mass spectrometry shows each mutant to have enhanced proton transfer in catalysis compared with wild-type HCA III. However, His64 in K64H and K64H-R67N HCA III have at most a capacity for proton transfer that is only 13% that of His64 in HCA II. This reduced rate in mutants of HCA III is associated with a constrained side-chain conformation of His64, which is oriented outward, away from the active-site zinc in the crystal structures. This conformation appears stabilized by a prominent pi stacking interaction of the imidazole ring of His64 with the indole ring of Trp5 in mutants of HCA III. This single orientation of His64 in K64H HCA III predominates also in a double mutant K64H-R67N HCA III, indicating that the positive charge of Arg67 does not influence the observed conformation of His64 in the crystal structure. Hence, the structures and catalytic activity of these mutants of HCA III containing His64 account only in small part for the lower activity of this isozyme compared with HCA II. His67 in R67H HCA III was also shown to be a proton shuttle residue, having a capacity for proton transfer that was approximately four times that of His64 in K64H HCA III. This is most likely due to its proximity and orientation inward towards the zinc-bound solvent. These results emphasize the significance of side chain orientation and range of available conformational states as characteristics of an efficient proton shuttle in carbonic anhydrase.

Carbonic Anhydrase Inhibitors: Inhibition of Isozymes I, II, and IX with Triazole-LinkedO-Glycosides of Benzene Sulfonamides

We report the synthesis of a series of benzene sulfonamides containing triazole-O-glycoside tails for evaluation as carbonic anhydrase (CA) inhibitors. These glycoconjugates were synthesized by the 1,3-dipolar cycloaddition reaction of 4-azidobenzenesulfonamide with O-propynyl glycosides. Compounds were assessed for their ability to inhibit the enzymatic activity of the physiologically dominant isozymes hCA I and II and the tumor-associated isozyme hCA IX (h = human). Against hCA I these compounds were either micromolar or low-nanomolar inhibitors, while against hCA II and IX inhibition in the range of 6.8-53 and 9.7-107 nM, respectively, was observed. The most potent inhibitor against hCA IX was the galactose derivative 8 (Ki = 9.7 nM); this is so far the most potent glycoconjugate inhibitor reported for the tumor-associated hCA IX. These carbohydrate-tethered sulfonamides may prove interesting lead candidates to target tumor-associated CA isozymes, wherein the CA domain is located extracellularly.

Human Carbonic Anhydrase III: Structural and Kinetic Study of Catalysis and Proton Transfer,

The residue phenylalanine 198 (Phe 198) is a prominent cause of the lower activity of human carbonic anhydrase III (HCA III) compared with HCA II and other isozymes which have leucine at this site. We report the crystal structures of HCA III and the site-directed mutant F198L HCA III, both at 2.1 A resolution, and the enhancement of catalytic activity by exogenous proton donors containing imidazole rings. Both enzymes had a hexahistidine extension at the carboxy-terminal end, used to aid in purification, that was ordered in the crystal structures bound in the active site cavity of an adjacent symmetry-related enzyme. This observation allowed us to comment on a number of possible binding sites for imidazole and derivatives as exogenous proton donors/acceptors in catalysis by HCA III. Kinetic and structural evidence indicates that the phenyl side chain of Phe 198 in HCA III, about 5 A from the zinc, is a steric constriction in the active site, may cause altered interactions at the zinc-bound solvent, and is a binding site for the activation of catalysis by histidylhistidine. This suggests that sites of activation of the proton-transfer pathway in carbonic anhydrase are closer to the zinc than considered in previous studies.

Molecular determinants of S-glutathionylation of carbonic anhydrase 3

Carbonic anhydrase 3 is easily S-glutathionylated in vivo and in vitro. The protein has two surface-exposed cysteine residues that can be modified. We found that Cys186 is more readily glutathionylated than Cys181. We studied a series of site-specific mutants to identify the residues that interact with Cys186 to make its thiol more reactive. We found that Lys211 is responsible for lowering the pKa of Cys186. We also found that two acidic residues, Asp188 and Glu212, interact with the thiol and actually decrease its reactivity. We speculate that conformational changes that alter the interaction with these three residues provide a mechanistic basis for modulation of the susceptibility of carbonic anhydrase 3 to glutathionylation.

Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models

Proton transport (PTR) processes play a major role in bioenergetics and thus it is important to gain a molecular understanding of these processes. At present the detailed description of PTR in proteins is somewhat unclear and it is important to examine different models by using well-defined experimental systems. One of the best benchmarks is provided by carbonic anhydrase III (CA III), because this is one of the few systems where we have a clear molecular knowledge of the rate constant of the PTR process and its variation upon mutations. Furthermore, this system transfers a proton between several water molecules, thus making it highly relevant to a careful examination of the "proton wire" concept. Obtaining a correlation between the structure of this protein and the rate of the PTR process should help to discriminate between alternative models and to give useful clues about PTR processes in other systems. Obviously, obtaining such a correlation requires a correct representation of the "chemistry" of PTR between different donors and acceptors, as well as the ability to evaluate the free energy barriers of charge transfer in proteins, and to simulate long-time kinetic processes. The microscopic empirical valence bond (Warshel, A., and R. M. Weiss. 1980. J. Am. Chem. Soc. 102:6218-6226; and Aqvist, J., and A. Warshel. 1993. Chem. Rev. 93:2523-2544) provides a powerful way for representing the chemistry and evaluating the free energy barriers, but it cannot be used with the currently available computer times in direct simulation of PTR with significant activation barriers. Alternatively, one can reduce the empirical valence bond (EVB) to the modified Marcus' relationship and use semimacroscopic electrostatic calculations plus a master equation to determine the PTR kinetics (Sham, Y., I. Muegge, and A. Warshel. 1999. Proteins. 36:484-500). However, such an approximation does not provide a rigorous multisite kinetic treatment. Here we combine the useful ingredients of both approaches and develop a simplified EVB effective potential that treats explicitly the chain of donors and acceptors while considering implicitly the rest of the protein/solvent system. This approach can be used in Langevin dynamics simulations of long-time PTR processes. The validity of our new simplified approach is demonstrated first by comparing its Langevin dynamics results for a PTR along a chain of water molecules in water to the corresponding molecular dynamics simulations of the fully microscopic EVB model. This study examines dynamics of both models in cases of low activation barriers and the dependence of the rate on the energetics for cases with moderate barriers. The study of the dependence on the activation barrier is next extended to the range of higher barriers, demonstrating a clear correlation between the barrier height and the rate constant. The simplified EVB model is then examined in studies of the PTR in carbonic anhydrase III, where it reproduces the relevant experimental results without the use of any parameter that is specifically adjusted to fit the energetics or dynamics of the reaction in the protein. We also validate the conclusions obtained previously from the EVB-based modified Marcus' relationship. It is concluded that this approach and the EVB-based model provide a reliable, effective, and general tool for studies of PTR in proteins. Finally in view of the behavior of the simulated result, in both water and the CA III, we conclude that the rate of PTR in proteins is determined by the electrostatic energy of the transferred proton as long as this energy is higher than a few kcal/mol.

Isolation, sequence analysis and expression profile of a novel swine gene differentially expressed in the Longissimus dorsi muscle tissues from LandracexLarge white cross-combination

The mRNA differential display technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from LandracexLarge White cross-combination. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) and its complete cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 260 amino acids that contains the putative conserved domain of the carbonic anhydrase, and this protein has high homology with the carbonic anhydrase III (CA-III) of four species mouse (91%), horse (91%), rat (89%) and human (86%)-so that it can be defined as swine carbonic anhydrase III. The phylogenetic tree analysis revealed that the swine CA-III has a closer genetic relationship with the horse CA-III than with those of mouse, rat and human. The tissue expression analysis indicated that the swine CA-III gene is generally expressed in most tissues. Our experiment is the first to establish the primary foundation for further research on the swine CA-III gene.

QSAR study on carbonic anhydrase inhibitors: aromatic/heterocyclic sulfonamides containing 8-quinoline-sulfonyl moieties, with topical activity as antiglaucoma agents

Quantitative structure-activity-relationship (QSAR) study on aromatic/heterocyclic sulfonamides containing 8-quinoline-sulfonyl carbonic anhydrase (CA) inhibitors has been carried out topologically using first-order valence connectivity index ((1)chi(v)). Excellent results are obtained against all the three isozymes; CA I, II and IV of the zinc enzyme CA by using indicator parameters along with (1)chi(v).

Selective covalent binding of acrylonitrile to Cys 186 in rat liver carbonic anhydrase III in vivo

Covalent binding of reactive chemical species to tissue proteins is a common, but poorly understood, mechanism of toxicity. Identification of the proteins and the specific amino acid residues within the proteins that are chemically modified will aid our understanding of the toxification/detoxification mechanisms involved in covalent binding. Acrylonitrile (AN) is a commercial vinyl monomer that is acutely toxic and readily binds to tissue proteins. Total covalent binding of AN to tissue proteins is highly correlated with acute toxicity. Two-dimensional PAGE and autoradiography were used to locate proteins in male rat liver cytosol that are radiolabeled following administration of [2,3-(14)C]AN in vivo. Four intensely labeled spots were prominent in the autoradiogram and formed an apparent "charge-train" at approximately 30 kDa. Tryptic peptide mapping by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS was used to identify all of the spots as carbonic anhydrase III (CAIII). HPLC of the tryptic digests combined with MALDI-TOF MS was used to localize the radiolabel to tryptic fragment T22 containing amino acids 171-187. This tryptic fragment contains two Cys residues (Cys181 and Cys186) in the rat CAIII sequence. Electrospray ionization ion-trap MS was used to sequence the peptide and establish that only Cys186 was labeled. Thus, although AN is considered to be highly reactive, our data indicate that it does not react indiscriminately with rat CAIII but rather is selective for one out of five Cys residues. Rat liver CAIII has previously been shown to protect cells against oxidative stress. Our data suggest that CAIII is also capable of scavenging reactive xenobiotics and may help prevent covalent binding to more critical macromolecules.

Kinetic analysis of multiple proton shuttles in the active site of human carbonic anhydrase

We have prepared a site-specific mutant of human carbonic anhydrase (HCA) II with histidine residues at positions 7 and 64 in the active site cavity. Using a different isozyme, we have placed histidine residues in HCA III at positions 64 and 67 and in another mutant at positions 64 and 7. Each of these histidine residues can act as a proton transfer group in catalysis when it is the only nonliganding histidine in the active site cavity, except His(7) in HCA III. Using an (18)O exchange method to measure rate constants for intramolecular proton transfer, we have found that inserting two histidine residues into the active site cavity of either isozyme II or III of carbonic anhydrase results in rates of proton transfer to the zinc-bound hydroxide that are antagonistic or suppressive with respect to the corresponding single mutants. The crystal structure of Y7H HCA II, which contains both His(7) and His(64) within the active site cavity, shows the conformation of the side chain of His(64) moved from its position in the wild type and hydrogen-bonded through an intervening water molecule with the side chain of His(7). This suggests a cause of decreased proton transfer in catalysis.

Proton transfer within the active-site cavity of carbonic anhydrase III

The maximal turnover rate of CO2 hydration catalyzed by the carbonic anhydrases is limited by proton transfer steps from the zinc-bound water to solution, steps that regenerate the catalytically active zinc-bound hydroxide. Catalysis of CO2 hydration by wild-type human carbonic anhydrase III (HCA III) (k(cat) = 2 ms (-1)) is the least efficient among the carbonic anhydrases in its class, in part because it lacks an efficient proton shuttle residue. We have used site-directed mutagenesis to test positions within the active-site cavity of HCA III for their ability to carry out proton transfer by replacing various residues with histidine. Catalysis by wild-type HCA III and these six variants was determined from the initial velocity of hydration of CO2 measured by stopped-flow spectrophotometry and from the exchange of 18O between CO2 and H2O at chemical equilibrium by mass spectrometry. The results show that histidine at three positions (Lys64His, Arg67His and Phe131His) have the capacity to transfer protons during catalysis, enhancing maximal velocity of CO2 hydration and 18O exchange from 4- to 15-fold compared with wild-type HCA III. Histidine residues at the other three positions (Trp5His, Tyr7His, Phe20His) showed no firm evidence for proton transfer. These results are discussed in terms of the stereochemistry of the active-site cavity and possible proton transfer pathways.

Dissolution of the Carbonate Minerals of Phosphate Ores: Catalysis by Carbonic Anhydrase II, from Bovine Erythrocytes, in Acid Solutions

In this manuscript we report detailed experimental and theoretical evidence of the effect of carbonic anhydrase II, from bovine erythrocytes, on the dissolution process of carbonate minerals of phosphate ores (Epirus area, Greece) in dilute acetic acid, by recording the pH value of the acid solution as a function of time in the pH range from 2.37 to 6.40. We found that mass transfer makes a significant contribution to the determining step of the overall enzymatic reaction, while we distinguished five separate pH regions within the pH range from 2.37 to 6.40. Two different reaction systems and two model equations fitted perfectly the corresponding experimental data, and were used to evaluate all rate constants and parameters. Subsequently, we proposed the possible mechanisms of action for this enzyme from pH 2.37 to 6.40, within which carbonic anhydrase II was found active.

Crystallization and preliminary X-ray analysis of human carbonic anhydrase III

Carbonic anhydrases catalyze the interconversion of carbon dioxide to bicarbonate. Human carbonic anhydrase isozyme III with a C-terminal hexahistidine tag was overexpressed in Eschericha coli, purified and crystallized. Diffraction data (93.4% completeness) were collected to 2.2 A resolution on an in-house R-AXIS IV++ image-plate system with Osmic mirrors and a Rigaku HU-H3R CU rotating-anode generator operating at 50 kV and 100 mA. A 60 degrees sweep of data were collected from a single crystal with a crystal-to-detector distance of 150 mm and a 0.5 degrees oscillation angle per frame using an exposure of 60 s per frame at 293 K. The crystals were shown to conform to the Laue hexagonal crystal system P6, with unit-cell parameters a = 44.7, c = 222.5 A and a scaling R(sym) of 0.087 for 11 962 unique reflections. Using the known crystal structure of the rat form of carbonic anhydrase isozyme III, a molecular-replacement model was built. This model was used for rotation and translation searches and uniquely defined the space group as P6(5). Rigid-body refinement of the model was used to generate an initial phased electron-density map with an R(work) of 31.17%.

Carbonic anhydrase III in liver and muscle of male rats purification and properties

Cytosolic carbonic anhydrases CAI, CAII, and CAIII from liver, and CAII, and CAIII from muscle of adult male Sprague-Dawley rats were purified to homogeneity. CAIII from liver and muscle had the same amino acid composition and were immunochemically similar. Their kinetic properties at 0 degrees C were also similar. Km(CO2) was 4 mM and kcat 3x105 s(-1). Ki was 0.4 and 0.2 M for acetazolamide and NaCl, respectively. Both CAIIIs ran as single bands on SDS-electrophoresis and high-speed centrifugation, with a mol wt of 29.3 kDa. Their hydrodynamic properties suggest that CAIII is a compact, nearly spherical molecule. It contained 0.9 M zinc per M protein. In both tissues isoelectric focusing identified neutral and acidic isoforms with pIs near 7.0 and 6.3, respectively. These forms were immunologically identical and had the same amino acid composition and mol wts. The acidic forms probably represent subspecies of CAIII in different states of oxidation. CAIII is the major soluble protein in rat liver and muscle. Its function is probably to protect proteins of these tissues from oxidation catalyzed by iron-containing degradation products of haemoglobin and myoglobin. Liver CAI and CAII and muscle CAII were identical to CAI and CAII of rat erythrocytes.

Detection and identification of subcutaneous adipose tissue protein related to obesity in New Zealand obese mouse

New Zealand obese (NZO) mouse, a genetic model of obesity, shows hyperphagia, hyperinsulinemia and leptin resistance. We analyzed subcutaneous adipose tissue proteins in NZO mice with a two-dimensional gel electrophoresis technique followed by protein sequence analysis. NZO mice showed hyperinsulinemia and hyperleptinemia. Abdominal subcutaneous adipose tissue was inspected in NZO and C57BL/6J lean mice. Two-dimensional gel electrophoresis detected 4 spots which were obviously reduced in NZO mice. Those spots were p26, p19, p18 and p15. Internal sequences of the p26 and p15 protein were homologous with those of carbonic anhydrase III, p19 was cytochrome b5, p18 was superoxide dismutase. Serum arachidonic acid level in NZO mice was lower by 80% of C57BL/6J mice. The present study demonstrated the reduction of several enzymes related to lipid metabolism in NZO mice. These data raises the hypothesis that the supposed changes of membrane fluidity caused by altered membrane lipid content may involve central leptin resistance of this model of obesity.