Active site of carbonic anhydrase

The value of the tris(pyrazolyl)hydroborato complexes [TpRR ]ZnOH is that they are rare examples of monomeric four-coordinate zinc complexes with a terminal hydroxide funtionality. Indeed, [TpBut]ZnOH is the first structurally characterized monomeric terminal hydroxide complex of zinc (149). As such, the monomeric zinc hydroxide complexes [TpRR ]ZnOH may be expected to play valuable roles as both structural and functional models for the active site of carbonic anhydrase. Although a limitation of the [TpRR ]ZnOH system resides with their poor solubility in water, studies on these complexes in organic solvents... 

Fig. 42. Comparison of the coordination environment about zinc in the active site of carbonic anhydrase in its deprotonated form with that of [TpRR ]ZnOH. Reprinted with permission from Ref. (151). Copyright 1993 American Chemical Society.

The ligand tris[2-(l-methylbenzimidazol-2-yl)ethyl] nitromethane (25) has been used in the formation of zinc complexes as models of the active site of carbonic anhydrase, and the formed complexes reveal affinity for the sulfonamide-containing enzyme inhibitor acetazolamide.248... 

Theoretical calculations have been carried out on a number of zinc-containing enzymatic systems. For example, calculations on the mechanism of the Cu/Zn enzyme show the importance of the full protein environment to get an accurate description of the copper redox process, i.e., including the electronic effects of the zinc ion.989 Transition structures at the active site of carbonic anhydrase have been the subject of ab initio calculations, in particular [ZnOHC02]+, [ZnHC03H20]+, and [Zn(NH3)3HC03]+.990... 

Fig. 22. Important residues in the active site of carbonic anhydrase II.

Fig. 24. Snapshots of a possible CO2 diffusion pathway into the active site of carbonic anhydrase II, as calculated in a molecular dynamics simulation. Tbe CO2 molecule is represented as a stick, and its diffusion pathway is shown by dashed arrows. [Reprinted with permission from Liang, J.-Y., Lipscomb, W. N. 1990) Proc. Natl. Acad. Sci. U.S.A. 87, 3675-3679.1...

FIGURE 21. Active site of carbonic anhydrase. Adapted with permission from Reference 9. Copyright (2004) ACS... 

Zn-organometallic compound and the complex was synthesized with the aim of modeling the active site of carbonic anhydrase during its first catalytic step, the acquisition of the NMR properties of nucleus at this Zn complex could be further exploited in studies where the zinc ion would be replaced by a Zn nucleus. 

Complexes of the phosphine (90) have been investigated605 as models for the active site of carbonic anhydrase enzymes (see Section 56.1.14.1). 

Ab-initio and density functional theory are used to calculate the probability of proton conduction via a chain of water molecules from Zn+ to its residue in the active site of carbonic anhydrase (Isaev and Scheiner, 2001). They conclude that proton conduction occurs as a concerted process and includes the shortening of each H-bonds as the proton donor and acceptor move towards one other. 

Hg. 19.23 Active site of carbonic anhydrase. resting engine a water molecule (O = > coordinates to the zjnc atom. All hydrogen atoms have been omitled for clarity. 

The molecular components of many buffers are too large to reach the active site of carbonic anhydrase. Carbonic anhydrase II has evolved a proton shuttle to allow buffer components to participate in the reaction from solution. The primary component of this shuttle is histidine 64. This residue transfers protons from the zinc-bound water molecule to the protein surface and then to the buffer (Figure 9.30). Thus, catalytic function has been enhanced through the evolution of an apparatus for controlling proton transfer from and to the active site. Because protons participate in many biochemical reactions, the manipulation of the proton inventory within active sites is crucial to the function of many enzymes and explains the prominence of acid-base catalysis. 

In the presence of human serum albumin, the H spectrum of acetyl-salicyclic acid is specifically shifted and broadened [119]. The interpretation of changes in T, and T2 require several theoretical assumptions. These have been discussed in detail [120] for JV-acetylsulphanilamide and acetate binding to the active site of carbonic anhydrase. It was concluded that the acetyl groups of these inhibitors have a motion additional to that of the enzyme. It can be shown by NMR that acetate binds to two sites on the enzyme, only one of which is inhibitory to esterase activity (methyls are 4.3 and 4.8 A from the metal in the Mn substituted enzyme [121]). Strict care must be taken to avoid paramagnetic impurities when NMR relaxation enhancement by diamagnetic macromolecules is being studied. A preparation of carbonic anhydrase, for example, can contain 0.24 paramagnetic Cu atoms per Zn atom [122]. 

Step 1 A water molecule is attracted to the zinc ion at the active site of carbonic anhydrase. The positively charged zinc ion displaces a proton from the water molecule. The displaced proton finds a new place of residence — the histidine residue. This histidine residue prt>bably aids in the removal of the proton from the water molecule, in concert wdth the action of the zinc ion. Combination of the zinc ion (Zn ) vedth the hydroxyl group does not form a complex with the structure Zn OH. The zinc atom does not change its valence (Its number of charges). Instead, the complex has the structure Zn (OH ). [Calcium ions behave similarly to zinc ions. In contrast, iron and copper ions readily change their valences when they participate in biochemical reactions.)... 

FIGURE 2.5S The active site of carbonic anhydrase and simplified mechanism of action of the enzyme. The enzyme is shown catalyzing the hydration of CO , although the dehydration of bicarbonate also is catalyzed freely by the enz.ymc. 

Biochemical CO2 fixation by mimicking zinc(II) complex for active site of carbonic anhydrase... 

We designed the model complex for the active site of carbonic anhydrase providing (i) imidazole ligand which corresponds to histidine imidazole, (ii) coordinated water molecule and (iii) hydrophobic pocket, as mentioned in Experimental Section. Since the ligand, tris(2-benzimidazolylmethyl)amine L used in this work plays a role of steric hindrance, it will be able to reproduce the tetrahedral geometry which is identical with the active site of carbonic anhydrase. Furthermore, the benzene rings of benzimidazolyl groups can fix a hydrophobic pocket, in which there exists the active site of the native enzymes. 

Figure 28-4 A computer-generated representation of a thienothipyran-2-sulfonamide bound to the active site of carbonic anhydrase. Note that the ribbon has been traced through the protein backbone. Proteins are commonly displayed this way.

Imidazole is apparently small enough to reach the active site of carbonic anhydrase. Buffers with large molecular components cannot do so, and the effects of the mutation are more evident. 

Figure 29.19 The reactant (R), transition state (TS) and product (P) configurations for the rate-determining triple proton transfer step of the 58-atom model used to represent the active site of carbonic anhydrase II [18]. The numbers denote bond distances (in A) calculated at two different levels of theory. The arrows in the insert figure represent the tunneling mode and illustrate the degree of synchronicity of the transfer.

---