Amino acids molecular recognition

ABSTRACT. The copper(n) complexes of p-cyclodextrins functionalized with aliphatic or pseudoaromatic amines were used for the chiral recognition of unmodified amino acids. Molecular recognition, assisted by non-covalent interactions, was proved by means of thermodynamic and spectroscopic (c.d., e.p.r. and fluorescence) measurements. A cis-disposition of amino groups seems to assist enantiomeric selectivity. The copper(II)-p-cyclodextrin complexes can be used as mobile phase additives in HPLC to separate enantiomeric mixtures of unmodified aromatic amino acids. 

Fig. 4.1 Topological organization of the vanilloid receptor TRP VI. Highlighted are the molecular determinants of TRPVl regulation, such as recognition (binding) domains for capsaicin and acids, and phosphorylation sites for protein kinases. Numbers designate the key amino acid residues deduced from the rTRPVl primary sequence. Adapted from Ferrer-Montaniel, A. et al. (2004) Fur. J. Biochem. 271, 1820—1826.

Seel, C., Galan, A., de Mendoza, J. Molecular Recognition of Organic Acids and Anions -Receptor Models for Carboxylates, Amino Acids, and Nucleotides. 175, 101-132 (1995). 

Finally, the third level of molecular description can be illustrated by the complex formed between a transcription factor and the DNA molecule. In such a complex, the atoms involved in the interaction, the hydrogen bonds formed between the amino acids and the bases are shown, because this description, is necessary to explain the specificity of molecular recognition. 

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. 

Archontis, G. Simonson, T. Karplus, M., Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase, J. Mol. Biol. 2001, 306, 307-327... 

Polytopic macrocyclic receptors 1, 2 (Figure 10.1) are able to complex the zwitterionic form of the amino acids by a double non-covalent charge interaction [28,29]. The unsymmetrical benzocrown sulfonamide derivative, 2 which contains benzo-18-crown-6 and benzo-15-crown-5 moieties was used as a ditopic receptor for multiple molecular recognition of the amino acids, by combining two non-covalent interactions ammonium-crown hydrogen bonding and carboxylate- complexed Na+-benzo-15-crown-5 charge interactions [28,33]. 

Fig. 10.1 Multiple molecular recognition of the zwitterionic amino acids by macrocyclic polytopic receptors 1,2 [28,33],...

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