Molecular recognition modeling

Fig. 6.3 Molecular model of the domains of the chimeric nuclease (constituted by an hybrid between a non-specific DNA cleavage domain and a zinc finger recognition domain) and DNA. The cleavage domain sits behind...

Another hypothesis was provided by Mikio Shimitso (1982) on the basis of studies of steric effects in molecular models. It had been noted years previously that the fourth nucleotide at the 3 end of the tRNA molecules (referred to as the discrimination base) might have a recognition function. In the case of certain amino acids (i.e., their tRNA-amino acid complexes) this base pair, in combination with the anticodon of the tRNA molecule, can select the amino acid corresponding to the tRNA species in question this is done on the basis of the stereochemical properties of the molecule. Since the anticodon of a tRNA molecule and the fourth nucleotide of the acceptor stem are far apart in space, two tRNA molecules must complex in a head-to-tail manner. The pocket thus formed can then fit specifically to the corresponding amino acid. 

Combining 2D-NOESY and 2D-ROESY NMR experiments with molecular modelling protocols, Kuhn and Kunz32 have been able to study the saccharide-induced peptide conformational behaviour of the recognition region of Ll-Cadherin. The detailed conformational analysis of this key biomolecule not only proves that the saccharide side chain exerts a marked influence on the conformation of the peptide chain, but also that the size and type of the saccharide indeed strongly affects the conformation of the main chain. 

The data for these oligosaccharides have been incorporated into the molecular models shown in Figs. 3 and 4. The conformation and molecular recognition of sialylated oligosaccharides are an important area for future investi-... 

Finally, we consider the effects on recognition and binding of single site replacements [34] of the individual charged residues which have been emphasized in molecular modeling studies. These residues include Lys (18, 32, 77) in cytochrome c and Asp (37, 79, 217) in ccp. 

Various endeavors have been undertaken to get insight into the 3D selector-selectand complex structures and to elucidate chiral recognition mechanisms of cinchonan carbamate selectors for a few model selectands (in particular, DNB-Leu). Such studies comprised NMR [92-94], ET-IR [94-96], X-ray diffraction [33,59,92,94], and molecular modeling investigations (the latter focusing on molecular dynamics [92,93,97], and 3D-QSAR CoMFA studies [98]). 

In summary, molecular modeling when used in combination with instrumental techniques, especially 1D-ROESY and X-ray crystallography, may significantly contribute to understanding the nature of the intermolecular forces responsible for chiral drug-cyclodextrin interactions and chiral recognition. 

Many researchers have put a considerable amount of effort into studies of the chiral recognition mechanisms (using, e.g., NMR and molecular modeling), but yet the choice of chiral selector or chiral phase for a new compound is often based on trial and error. Different strategies for chiral method development have been presented by many of the retailers of chiral columns as a service for the customers. In addition to the information supplied by these retailers, another source of knowledge is Chirbase, a database that contains more than 50,000 HPLC separations of more than 15,000 different chiral substances [61], which also can provide guidance to the analytical chemist. 

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