Selectivity in molecular recognition

Wilcox. C.S. Webb. T.H. Zawacki, F.J. Glagovich. N. Chemistry of synthetic receptors and functional group arrays. 21. Selectivity in molecular recognition of steroids, alkanes and alicyclic substrates in aqueous media. Supra-mol. Chem. 1993. 1. 129-137. 

Selectivity In molecular recognition, the ratio of the stability constants for a pair of guests with a given host. In chromatography, the capacity factor of a stronger retained species divided by the capacity factor of a weaker retained species. In membranes, the fiux of one species divided by that of another. 

The racemic mixture of all four components LP2, LU2, DP2, and DU2 yielded long superhelices of opposite handedness that coexisted in the same sample, pointing to the occurrence of spontaneous resolution through chiral selection in molecular recognition-directed self-assembly of supramolecular liquid-crystalline polymers. Such chiral selection features of self-organized entities are of general significance in connection with the questions of spontaneous resolution and of chirality amplification. This was confirmed by subsequent studies on a variety of helical supramolecular polymers (see Chapters 2, 3, and 6). 

Cation-TT interactions play a crucial role in molecular recognition. For example, Na /K cation interactions with aromatic rings of some amino acids are implicated in the biological functions of specific enzymes and in the selectivity of Na" /K channels. " The same factors are responsible of the relative stability of the charge-solvated vs. zwitterionic structure of amino acids. " ... 

Zimmermann, Shapes, Selectivity, and Complementarity in Molecular Recognition, in Frontiers in Supramolecular Chemistry, H.-J. Schneider. H. Durr, Eds., VCH. Weinheim. 1991, p. 29. 

With the seven-helix bundle construct in hand, we turned our attention to incorporation of the three extracellular (EC) loops. The cytoplasmic loops were disregarded because they would not be involved in molecular recognition between the receptor and the SFLLRN ligand. Extracellular loop 3, the smallest of the three EC loops, was added first via the loop-search routine in the Biopolymer mode of Sybyl. The loop backbone choices found in the Brookhaven PDB were examined in 3-D and selected on the basis of their fit to the overall protein structure. After the side chains were added to EC3, some of them had to be rotated to avoid unfavorable steric interactions with other parts of the protein. Then, the entire protein was energy minimized. Extracellular loop 1 was then added, followed by EC2, and each time the loop selection was made after analyzing the protein in 3-D. Side chains of amino... 

Eiichi Kimura is retired from the Department of Medicinal Chemistry at Hiroshima University in Japan. His recent research interests have included the supramolecular chemistry of macrocyclic polyamines and their use in molecular recognition and as zinc-enzyme models. These interests have led to the development of fluorophore sensors for Zn(II) [8] use of macrocycles to effect selective recognition of anions [9], nucleobases in polynucleotides [10], thymidine mono- and diphosphate nucleotides (11), carbonic anhydrase and carboxypeptidase [12], and development of Zn(II)-macrocycle anti-HIV agents [13], In May 2004, he received a Purple Ribbon Award from the Emperor of Japan. 

Figure 1. The selectivity of molecular recognition addresses two steps The equilibrium binding between the host and the competing guest species A and B and their subsequent conversion. Either step may be dominant in selectivity generation.

Molecular Interactions in Molecular Recognition Molecular recognition occurs due to various molecular interactions such as electrostatic interaction and hydrogen bonding. Selective and efficient recognition is sometimes achieved by cooperative contributions from these interactions. 

In molecular recognition, a molecule selectively recognizes its partner through various molecular interactions. In this section, these interactions are briefly overviewed. 

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