I offer the hypothesis that those amino-acid residues that are not part of the active-site, and particularly those found on the outside of the active protein, may perhaps have a role in the construction of structural elements to the organised cell. For instance, perhaps some molecules can provide pathways for the transport of other molecules, acting as signposts. Or, perhaps, acting as attractors or repellers of some classes of other molecules. This is to suggest that the chemistries of the outer surfaces of proteins, may be conserved due to beneficial side effects of these molecules upon the biochemistry of the cell.
These are interesting ideas and can certainly get one thinking.
One can suggest a great number of possible functions for the surface, non-catalytic amino acids of enzymes including the roles suggested by William. Properties that seem to be important include surface glycosylation which can be crucial in targeting an enzyme to specific regions of the cell and other amino acids may interact with the surface amino acids of other proteins to bring enzymes close together or tether an enzyme in an appropriate location. If the enzyme is subject to regulation by kinases catalysing phosphorylation for example, serine/threonine residues exposed to solvent will be of immense importance physiologically. Also there are other regulatory mechanisms involving covalent modification of selective amino acid residues.
William's idea of an enzyme acting as a transporter around the cell does not get a lot of favour by me because such transport systems within cells (e.g. GLUT) seem to have evolved as non-catalytic proteins.
Peter
Let's give a few more details. Often, proteins are embedded within lipid bi-layers, with portions sticking outside of the lipid bi-layer. Perhaps these are arranged in Poisson fashion (a sense of maximal disorder), and perhaps not. Perhaps they are instead found in organised patterns that are by some degree removed from a Poisson or other similar distribution. I well understand that large scale organisation is one means to transport necessary molecules the superstructure of the cell. I also understand that mechanisms evocative of Belousov Zhabotinsky can provide other means of cyclic behavior. Yet, it has always seemed dis-satisfactory that much of biochemistry might be the yield of random molecular motion. When concerned with large scale motion, often cilia are employed but that is a bit higher scale than the molecular, and it seems to me that there might be a few scales in between. How is molecular motion controlled within the cytoplasm, between the scales of immediate interaction between molecules, and large scale motion based upon vesicle transport? And, upon what part of related molecules is conservation attendant? Might it be that the spatial organisation of generally stationary molecules provide "grooves" in the surface that act as venturi, to affect eddy currents and so drive molecules in a preferred spatial direction?
Dear William,
It is really an interesting hypothesis that deserves deep consideration. However, I found my ideas very similar to those presented above by Peter J. Butterworth in his detailed answer about possible roles of the mentioned amino acids.
Wishing you all the success.
SM Najim
Ah. A degree of consistency in the answers. This encourages me to investigate deeply the suggested mechanisms. Thank you all, Drs. Al-Manhel, Najim, and Butterworth. Please, should any other notion come to mind, point me the way.
Also, please address the notion of spatial placement of macromolecules over a lipid bi-layer, and how that will or will not yield super-molecular scale charge surfaces, or even complex arrangements of electromagnetic field lines.
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