Carbonic anhydrase molecular structures

Z, ] McClarin, T Klein and R Langridge 1985. A Quantitative Structure-Activity Relationship and ecular Graphics Study of Carbonic Anhydrase Inhibitors. Molecular Pharmacology 27 493-498. 

Carbonic anhydrase (CA) exists in three known soluble forms in humans. All three isozymes (CA I, CA II, and CA III) are monomeric, zinc metalloenzymes with a molecular weight of approximately 29,000. The enzymes catalyze the reaction for the reversible hydration of C02. The CA I deficiency is known to cause renal tubular acidosis and nerve deafness. Deficiency of CA II produces osteopetrosis, renal tubular acidosis, and cerebral calcification. More than 40 CA II-defi-cient patients with a wide variety of ethnic origins have been reported. Both syndromes are autosomal recessive disorders. Enzymatic confirmation can be made by quantitating the CA I and CA II levels in red blood cells. Normally, CA I and CAII each contribute about 50% of the total activity, and the CAI activity is completely abolished by the addition of sodium iodide in the assay system (S22). The cDNA and genomic DNA for human CA I and II have been isolated and sequenced (B34, M33, V9). Structural gene mutations, such as missense mutation, nonsense... 

This reaction is essential in maintaining a constant pH in blood by the bicarbonate buffer system. Carbonic anhydrase, which contains a single zinc atom in its structure, has a molecular weight of about 30,000. In this structure, zinc is surrounded tetrahedrally by three histidine molecules and one water molecule. The exact role of the catalyst is not known, but it is believed to involve hydrolysis that can be represented as... 

Menziani, M.C., De Benedetti, P.G., Gago, F. and Richards, W.G. (1989) The binding of benzenesulfonamides to carbonic anhydrase enzyme. A molecular mechanics study and quantitative structure-activity... 

Figure 7.1 (a) The denatured conformation of the zinc metalloenzyme carbonic anhydrase and the ESI mass spectra obtained under acidic denaturing conditions, (b) The ESI mass spectra obtained under native-state conditions. The decon-voluted ESI mass spectra of carbonic anhydrase reveals the protein molecular weight. The three dimensional structure is protein Data Bank ID IBNl. 

K. K. Kannan, I. Vaara, B. Notstrand, S. Lovgren Borell, K. Fridborg, M. Petef (1977). Structure and function of carbonic anhydrase comparative studies of sulfonamide binding to human erythrocyte carbonic anhydrases B and C. In G. C. K. Roberts (Ed.). Drug Action at the Molecular Level. Baltimore University Park Press, pp. 73-91. 

Compounds which enhance the catalytic activities of the CAs are known as activators. Activators of carbonic anhydrases are less studied because CA is one of the most efficient enzymes known. Carbonic anhydrase II activation by phosphorylation in the presence of protein kinase and cAMP has been reported (195,196). Also some anions are activators for CA III (197,198) the catalytic effect is due to the proton shuttling capacities of such activators. Histamine, a well known activator, for native and Co(II)-substituted isoenzymes I and II CA is reported by Briganti et al. (199). Amines [Ar-CH(R3)CH(R2)NH(R1) Ar =Aromatic/heterocyclic group R1 =R2 = H, Me R3 = H, OH, COOH] and amino acids are efficient activators for CA I—III (200-207). These amines possess a bulky aromatic/heterocyclic moiety in their molecular structure and act as proton acceptor (204-207). 

Figure 21 The structure of carbonic anhydrase. Cylinders represent helices, and arrows represent -structure (reproduced with permission from Isozymes I, Molecular Structure , Academic, New York, 1975, p. 575...

The most important aspect of the study of Co(II) metalloenzymes is the possibility of using the metal ion as a functional, built-in reporter of the dynamics of the active site. The spectral and magnetic properties of Co (II) carbonic anhydrase have given valuable clues to the catalytic function of this enzyme. The recent studies of Co(II) alkaline phosphatase and Co (II) carboxypeptidase A indicate the general applicability of this approach to enzymes where the probe properties of the constitutive metal ion are poor. The comparison of the absorption spectra of these enzymes and low-molecular weight models have shown that the proteins provide irregular, and in some cases nearly tetrahedral environments. It is obvious, however, that a knowledge of the crystal structures of the enzymes is necessary before the full potential of this method can be exploited. 

Tapia and Eklund (1986) carried out a Monte Carlo simulation of the substrate channel of liver alcohol dehydrogenase, based on the X-ray diffraction structure for this enzyme. The addition of substrate and the associated conformation change induce an order—disorder transition for the solvent in the channel. A solvent network, connecting the active-site zinc ion and the protein surface, may provide the basis for a proton relay system. A molecular dynamics simulation of carbonic anhydrase showed two proton relay networks connecting the active-site zinc atom to the surrounding solvent (Vedani et ai, 1989). They remain intact when the substrate, HCOf, is bound. 

Carbonic anhydrase is an enzyme of central importance to the production of gastric acid. This enzyme, which contains zinc, accelerates the naturally occurring reversible reaction of CO2 with water. Before considering the mechanism of action of the enzyme, note the resonating structure of CO2. The carbon-to-oxygen bonds are polar the molecular structure can be represented by the resonance hybrids shown in Figure 2.54. Note that in two of the three forms shown the central carbon atom has a positive charge. 

Mendiratta, S. and Madan, A.K. (1994). Structure-Activity Study on Antiviral 5-Vinylpyrimidine Nucleoside Analogs Using Wiener s Topological Index. J.Chem.Inf.Comput.ScL, 34,867-871. Menziani, M.C. and De Benedetti, P.G. (1992). Molecular Mechanics and Quantum Chemical QSAR Analysis in Carbonic Anhydrase Heterocyclic Sulfonamide Interactions. Struct. CherrL,... 

At Merck, the structure-based design of carbonic anhydrase inhibitors was started in the mid-1980s. The first compound with molecular modeling and X-ray structure determination playing an important role in the discovery process was thienothiopyrane-sulfonamide 20 (MK-927). This binds to carbonic anhydrase with a subnanomolar binding constant (Xi = 0.7 nM). 

Hansch C, McClarin J, Klein T, Langridge R. A quantitative structure-activity relationship and molecular graphics study of carbonic anhydrase inhibitors. Mol Pharmacol 1985 27 493-498. 

Figure 12.8 (a) Synthesis of cyclohexane imine-based carbonic anhydrase mimics with a hydro-phobic binding pocket, (b) X-ray molecular structure of the zinc(II) acetate complex of CM-l,3,5-tris [3-(2-furyl)prop-2-enylideneamino]cyclohexane showing the actate coordination, highly reminiscent of Zn-coordinated hydrogen carbonate in carbonic anhydrase. ... 

Another approach to representing the metal center in a molecular-mechanics-based model has been developed for zinc(II) centers and apphed to the modeling of the interaction of natural substrates and inhibitors of the enzyme human carbonic anhydrase [157, 492, 493]. Stmcturally characterized four-, five- and six-coordinate small-molecule complexes of zinc(II) were analyzed to determine the distribution of bond lengths and angles about the zinc ion. A function was developed that was able to reproduce these structural features, and was added to the program YETI [494], developed for modeling smaU-molecule-metalloprotein interactions. 

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