Ion channels are specialized proteins not known to Fischer (1894). They are proteins with a hole down their middle that allow the movement of specific solutes across otherwise impermeable membranes. Ion channels ‘catalyze’ (Eisenberg 1990
) the selective movement of ions moving through a dielectric barrier—from outside a cell to inside a cell, for example—but they do so without conventional chemistry. The ‘catalysis’ of ion channels does not involve the breaking or making of chemical bonds or the use of chemical energy. The catalytic active sites of ion channel proteins are the selectivity filters of the channel. The selectivity filter distinguishes between ions as the channel protein speeds (i.e., ‘catalyzes’) their movement across cell membranes—without the hydrolysis of ATP. Ion channels are nearly enzymes (Eisenberg 1990
) and have been studied extensively in that tradition (Hille 2001
The idea of catalytic active sites has been important in the history of enzymology (Dixon and Webb 1979
; Kyte 1995
; Segel 1993
) but the idea is not as prominent as it once was, perhaps because the notion of an active site seems vague. After all the image of an active site is rather dim when compared to structures seen in the bright light of modern x-ray sources. The phrases ‘active site’ and ‘catalytic active site’ are not even in the index of one of the more widely used textbooks of biochemistry (Voet and Voet 2004
Here, we use the computational power of CASTp to define active sites objectively, avoiding vagueness. CASTp identifies and measures all the concavities in enzymes, both pockets and voids, using a computer code involving little human subjectivity. It identifies and measures both pockets and voids. First, we examine these concavities to see if they contain amino acids that participate in the chemical reaction catalyzed by the enzyme. Then, we further examine the concavities that are catalytic active sites to see if they have large densities of acid and base side chains in a small volume, as in calcium and sodium channel proteins.
We find that 573 catalytic active sites of enzymes of known structure and function are easily distinguished by their large numbers of acid and base side chains: Acid and base side chains are reliable markers of catalytic active sites. These enzymes have 4 acid and 5 basic side chains, on the average, in their catalytic active sites. The volume of the catalytic active sites is tiny so the number densities (in chemical units) of acid and base side chains is some 20 molar. In comparison, the number density of solid
sodium chloride is 37 molar. The phrase number density is used, as it is in mathematics, to make clear that no assumptions about the properties of the system are made. The number density is simply the number of objects found in a region, divided by the volume of that region. We fear (and find) that the use of the word ‘concentration’ causes confusion because ‘concentration’ is often treated as if it is the (thermodynamic) ‘activity’, but concentration does not well approximate activity in the ionic solutions found in biology (Eisenberg 2011b
; Eisenberg 2011c
It seems likely that enzymes use the special properties of such concentrated mixtures of charges to promote catalysis one way or the other, for example, by crowding ions into the special electrostatic environment identified by Warshel (Warshel et al. 2006
We imagine it will be useful to view catalytic activity of enzymes as a property of an ionic liquid of substrate and (tethered) side chains in the special electrostatic environment of the catalytic active site. Analysis that neglects interactions between ions seems unlikely to be useful, no matter how common in the classical literature of enzymology.