Mapping of Active Sites

Amino acids of the natural (S) configuration, that is the building blocks 

FIGURE 1 Molecular formulas of some sweet molecules, representative of the major natural classes carbohydrates (sucrose), polyols (glycerol, sorbitol), amino acids (glycine, tryptophan), peptides (aspartame, monatin). 

FIGURE 2 Molecular formulas of further typical natural sweet molecules, mainly related to terpenes stevioside, glycyrrhizin, neohesperidine i y rochalcone, and 

FIGURE 3 Molecular models of some representative synthetic sweeteners saccharin, 6Cl-saccharin, cyclamate, nitrothiophene, dulcin, P4000 (orfho-propoxy-mcfo-nitro aniline), and SSN (3-anilino-2-styryl-3H-naphtho[l,2-d]imidazole-5-sulphonate). 

FIGURE 4 Three of the most popular indirect models of the active site of the sweet taste receptor. (A) Main contour ofthe active site proposed by Temussi and coworkers (Kamphuis et al., 1992 Temussi et al., 1978,1984,1991), hosting a molecular model of aspartame in an extended conformation. (B) A topological model, developed by Goodman et al. (1987). The L -shaped model and an L -shaped conformation of aspartame are superimposed. The hydrophobic side chain of Phe is denoted X, since it corresponds to the Kier s dispersion point. (C) 3D model of an idealized sweetener proposed by Tinti and Nofre (1991). Besides the AH-B entity, the model has six additional interaction points connected by a complex network of distances. 

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Kutsenko AS, Kuznetsov DA, Poroikov VV, Tumanian VG. Mapping of active site of alcohol dehydrogenase with low-molecular ligands. Bioorg Khim 2000 26 179-86. 

From a map at low resolution (5 A or higher) one can obtain the shape of the molecule and sometimes identify a-helical regions as rods of electron density. At medium resolution (around 3 A) it is usually possible to trace the path of the polypeptide chain and to fit a known amino acid sequence into the map. At this resolution it should be possible to distinguish the density of an alanine side chain from that of a leucine, whereas at 4 A resolution there is little side chain detail. Gross features of functionally important aspects of a structure usually can be deduced at 3 A resolution, including the identification of active-site residues. At 2 A resolution details are sufficiently well resolved in the map to decide between a leucine and an isoleucine side chain, and at 1 A resolution one sees atoms as discrete balls of density. However, the structures of only a few small proteins have been determined to such high resolution. 

One common deficiency in the sites reviewed was the lack of an accurate, up-to-date site work zone map. Of the sites reviewed, only the Site H contractor had established site work zones that were clearly marked on a site zone map. The SSAHP for Site G contained a general discussion of the types of work zones established at the site and the kinds of activities that took place within each zone although the SSAHP... 

Fig. 6 Biomonitoring of pollution in the Ebro Delta with Daphnia magna and Corbicula fluminea. (a) Map of sampling sites. Site 1 is out of the figure limits, close to Amposta (see Fig. 1). (b) Assays for neurotoxic activity (ChE and CbE) and D. magna feeding). Note the different pattern for the microcrustacean (sensitive to insecticides), which show a maximal toxic (inhibitory) effect in May and June, and the mollusk (relatively resistant), (c) Oxidative stress markers. These markers showed a similar response for both species with maximal effects (activation) in May (month 5) and August (month 8). Data from [43] and [44], Dm and Cf identify markers from D. magna and C. fluminea, respectively...

Cai, K., Itoh, Y., and Khorana, H. G. (2001). Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking Use of a photoactivatable reagent. Proc. Natl. Acad. Sci. USA 98, 4877-4882. 

Mayer, M. and Meyer, B. (2000) Mapping the active site of angiotensin-converting enzyme by transferred NOE spectroscopy../. Med. Chem. 43,2093-2099. 

I. SCHECHTEE, A. Bergee On the active site of proteases. 3. Mapping the active site of papain specific peptide inhibitors... 

Mapping between Chemistry Spaces of Active Sites and Ligands... 

Figure 1. Stereoviews of active sites of ASV IN complexed with metals, la. Electron density map of coordinated with four water molecules. Two active site carboxylate oxygens and four waters create the octahedral coordination for the metal cation, lb. Electron density map of two Zt ions with coordinating two water molecules. Four active site carboxylate oxygens and two water molecules coordinate the metal cations.

A. Berger and I. Schechter. Mapping the active site of papain with the aid of peptide substrates and inhibitors. Phil. Trans. R. Soc. Land. B. 257 249 (1970). 

McRae, B.J., Kurachi, K., Heimark, R. L, Fujikawa, K., Davie, E.W., Powers, J.C. 1981. Mapping the active sites of bovine thrombin, factor IXa, factor Xa, factor XIa, factor XI la, plasma kallikrein and trypsin with amino acid and peptide thioesters development of new sensitive substrates. Biochemistry 20, 7196-7206. 

Adam, G. C., Burbaum, J., Kozarich,J. W., Patricelli, M. P., Cravatt, B. F. (2004). Mapping enzyme active sites in complex proteomes. Journal of the American Chemical Society, 126, 1363—1368. 

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