Recognition pocket

Small molecule imprinting in sol-gel matrices has received considerable interest in recent years, undoubtedly due to the flexibility offered by the sol-gel process.5 Two different approaches have been utilized covalent assembly and noncovalent self-assembly.9 In the covalent assembly approach, the polymerizable functional group (i.e., the silicon alkoxide group) is covalently attached to the imprint molecule. The functionalized imprint molecule is then mixed with appropriate monomers (i.e., TMOS) to form the imprinted materials. After polymerization, the covalent bonds are cleaved to release the template and leave the molecular recognition pocket. Figure 20.4 shows a diagram of this process. 

An extensive search for new thrombin inhibitors led to a variety of low molecular weight thrombin inhibitors. Screening of small basic molecule for binding in the recognition pocket of thrombin led to selective thrombin inhibitors - derivatives of D-phenylalanyl-3-[(aminomethyl)amidino]piperi-dine (55-58) [113]. For this series of compounds, the correlation obtained... 

L. Serre, G. Verdon, T. Choinowski, N. Hervouet, J.L. Risler, and C. Zelwer. 2001. Ho v methionyl-tRNA synthetase creates its amino acid recognition pocket upon 1-methionine binding J. Mol. Biol. 306 863-876. (PubMed)... 

In general terms, the crystallographic results show that lipases contain several distinct sites, each responsible for a specific function. The hydrolysis of the ester bond is accomplished by the catalytic triad, responsible for nucleophilic attack on the carbonyl carbon of the scissile ester bond, assisted by the oxyanion hole, which stabilizes the tetrahedral intermediates. The fatty acid recognition pocket defines the specificity of the leaving acid. There is also one or more interface activation sites, responsible for the conformational change in the enzyme. In this section the discussion is on the available structural data relevant to the function of all these sites. 

The specificity for cleavage after arginine or lysine is mediated by a recognition pocket with an aspartate side chain at the bottom. This pocket accommodates the positively charged side chain by forming a salt bridge with the carboxylate of the aspartic acid. 

Figure 3. Cartoon of the binding mode of fibrinogen 2 in thrombin with the arginine side chain in the recognition pocket, the valine side chain in the P-pocket and the leucine and phenylalanine side chains in the D-pocket.

Serre, L.. Verdon, G.. Choinowski, T., Hervouct, N., Risler, J. L, and Zelwer, C. 2001. How methionyl-tRNA. synthetase creates its amino acid recognition pocket upon l,-methionine binding./. Mol Biol 306 863-876. 

Fig. 7.2 Thrombin active site regions as defined by the binding of D-Phe-Pro-Arg analogues, e.g., PPACK. The recognition pocket (SI) is clear. The proximal (P) hydrophobic pocket binds the proline side chain and thus corresponds to S2. The distal (D) hydrophobic pocket binds the D-Phe side chain. For PPACK 1 Rl= CO.CHjCI.

First, the needle itself, amidino-piperidine, has Kj for thrombin of 150 pM and for trypsin 360 pM and thus is 2.4 x selective for thrombin. This contrasts with the classical needle benzamidine, which has fQ for thrombin of 300 pM and 31 pM for trypsin and thus is 10 X selective for trypsin. This is perhaps unexpected, as it could be argued that benzamidine, being planar, is a much better analogue of the substrate arginine guanidinium group. The width of the recognition pocket (measured from... 

Fig. 7.9 Interactions at the bottom of the S, (recognition) pocket. (Left) The canonical benzamidine hydrogen-bonding scheme with two hydrogen bonds to Aspl89, one to the carbonyl of Cly219 and one to the conserved...

We further observe that it is possible to obtain low nanomolar inhibition without making the canonical benzamidine hydrogen bonds (Fig. 7.9). For a detailed discussion of non-canonical needles and recognition pocket and P pocket flexibility, the reader should consult ]41, 42, 45]. 

The FRET process that occurs between QDs and a dye-labeled substrate bound to the recognition pocket of a protein, may provide a general means for following the recognition events that occur between the proteins and their native substrates, by a displacement mechanism or a competitive assay. For example, when CdSe/ZnS QDs... 

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