Bindings properties of small molecules

Various biological molecules, including peptides, proteins, and nucleic acids, generate vast chemical diversity that can be used as hosts in competition assays. One weU-known protocol is the fluorescent intercalator displacement assay for targeting nucleic acids binding properties of small molecules and proteins, pioneered by... 

Perhaps the simplest two-site cooperative systems are small molecules having two binding sites for protons, such as dicarboxylic acids and diamines. Despite their molecular simplicity, most of these molecules do not conform with the modelistic assumptions made in this chapter. Therefore, their theoretical treatment is much more intricate. The main reasons for this are (1) there is, in general, a continuous range of macrostates (2) the direct and indirect correlations are both strong and intertwined, so that factorization of the correlation function is impossible. In addition, as with any real biochemical system, the solvent can have a major effect on the binding properties of these molecules. 

QUANTUM-MECHANICAL STUDIES ON THE BINDING PROPERTIES OF SMALL ATMOSPHERE MOLECULES... 

According to current understanding, binding by an induced-fit mechanism seems to be a unique property of small-molecule-binding RNA aptamers. This property of aptamers might have inspired the idea of fusing aptamer sequences with known catalytic RNAs to introduce the principle of allosteric regulation into ribozyme catalysis. None of the ribo-zymes described so far was known to operate as allosteric enzymes in vitro or in vivo. 

Experimental techniques based on the application of mechanical forces to single molecules in small assemblies have been applied to study the binding properties of biomolecules and their response to external mechanical manipulations. Among such techniques are atomic force microscopy (AFM), optical tweezers, biomembrane force probe, and surface force apparatus experiments (Binning et al., 1986 Block and Svoboda, 1994 Evans et ah, 1995 Israelachvili, 1992). These techniques have inspired us and others (see also the chapters by Eichinger et al. and by Hermans et al. in this volume) to adopt a similar approach for the study of biomolecules by means of computer simulations. 

I cannot but agree with Professor Klotz that the influence of the binding of small molecules on the properties of these molecules and the conformational properties of the polymer must follow from thermodynamics. Of course such effects, when observed, must follow the rules... 

Both enzymes and antibodies are proteins. Antibodies consist of subunits with multiple domains, just as do some enzymes. Both enzymes and antibodies have binding sites for small molecules between domains or subunits. In view of such similarities it isn t surprising that some antibodies have catalytic properties. The possibility was suggested in 1969 by Jencks 3 He also proposed that injection of a mouse with a hapten, that resembled a transition state for an enzyme, might induce formation of antibodies complementary to the transition-state structure. These might be catalytic. By the early 1980s such antibodies were discovered.1 d Some of the first catalytic antibodies (also dubbed abzymes) had esterase activity. The haptens used to induce antibody formation were phosphonates such as the following.e f... 

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