Functional binding sites

These examples show that binding site formation is governed by physical, chemical, and evolutionary constraints and that these principles can be used for uncovering functional binding sites. 

Recently, some more advanced methods have been reported that integrate the disparate features used for the characterization of functional binding sites. It can be expected that the cooperative effect of using all the information available will greatly enhance the reliability of binding site prediction and detection tools. 

Nguyen TV, Paterson IA, Juorio AV, Greenshow AJ, Boulton AA (1989) Trypt-amine receptors neurochemical and electrophysiological evidence for post-synaptic and functional binding sites. Brain Res 476 85-93... 

G-actin is very highly conserved, both across actin genes within a species and across species. Apparently, the need for so many functional binding sites in a molecule of that size leaves few options for nonlethal mutations. Among the actins sequenced from 30 widely divergent species, there were only 32 amino acid substitutions. One implication of this is that when differences in contractile properties are observed between various types of muscle, those differences must be due to the motor protein (myosin) or to the various regulatory proteins. 

However, IUPAC consensus sequences strongly depend on the sequence set used for definition. The final IUPAC consensus sequence remains arbitrary depending on the rules used to determine the consensus. Cavener defined some rules that we have used at GSF for several years now and, in our experience, IUPAC consensus sequences defined that way can be useful [29]. However, IUPAC consensus sequences may reject biologically functional binding sites due to a single mismatch (or an ill-defined IUPAC sequence). 

Chen, D., Lepar, G., and Kemper, B. (1994) A transcriptional regulatory element common to a large family of hepatic cytochrome P450 genes is a functional binding site of the orphan receptor HNF-4. J. Biol. Chem. 269, 5420-5427. 

Since P-endorphin is located within the hypothalamus and the pituitary, and has a relatively longer duration of action, it tends to be viewed as a neurohormone. Enkephalins, on the other hand, are more extensively distributed, are very rapidly degraded, and are primarily located in synaptosomal areas. The additional observation that enkephalin release following depolarization of brain (and intestinal) tissues is calcium dependent makes it more realistic to categorize them as neurotransmitters or modulators of synaptic function. Binding sites (receptors) for opioids are found, particularly in synaptosomal brain fractions. The enkephalins are located in neurons whose distribution correlates well with that of the receptors. In fact, regional distribution of peptides and their receptors are closely parallel, as would be predicted for a neurotransmitter system. 

Through the addition of multi-functional binding sites, additional function for sensing, or some other form of responsive behaviour, can be incorporated without having to redesign template or receptor sites [25,26,34,35]. 

Not only the components of the sensing layer are important but also the strategies of integration between them and with the primary transducer are of paramount importance. Passive adsorption is one of the simplest and most frequently used immobilization techniques, based mainly on weak noncovalent bindings. However, random protein orientation can lead to the obstruction of functional binding sites and can result in the loss of affinity or activity. Thus, covalent attachment of a protein layer on a chemically functionalized surface produces a more stable layer with correct orientation. This influences sensitivity and specificity of the immunoassay as density of immobilized protein can be better controlled and nonspecific adsorption may be decreased [155]. On the other hand, covalent procedures are usually longer and more tedious and are less justified when disposable surfaces can be used. 

It is interesting to notice how these three types of lipids cooperate to provide a functional binding site on the surface of a lipid raft. Cholesterol, although dipped in the membrane and out of reach of PrP, plays a critical role in this process. Indeed, cholesterol constrains the... 

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