Computational or Information Processing Proteins
Proteins as information processing units.
Proteins are probably the most special and functional substance in the universe. It is because they can respond delicately and sensitively to external chemical and physical changes such as temperature, pressure and pH. It is the "semiconductor of the universe", analogically speaking.
The reason why semiconductor is critical in information/electronics technology is that it is right in the middle of conducting and non-conducting behaviour. A tiny change of electron density can change a non-conductor to be a conductor causing information switching.
Protein is special as it lies right in the center of states: gas, liquid and solid. Not only that, it has special edge property to electricity, chemistry, and physics. Various types of special protein switches respond to environment to act as catalysts, transporters, conductors, solid structure, anti-freeze, and signal processors. Their networks, whether small or large, function as information processors in life. They produce oscillatiing signals as crystals in radios. Their complex network using other ligand components can build a gigantic network of information called brains.
For proteins to elucidate their special property, they need layers and modules. These layers are provided by lipids in life. By encapsulating these proteins and hence producing information processing modules, cells can achieve a remarkable degree of computation. This encapsulation is fractal. It occurs in all the levels of life. From small vesicles to a huge canopy of atmosphere on Earth.
Phosphorylation is the addition of a phosphate (PO4) group to a protein or other organic molecule. Protein phosphorylation in particular plays a significant role in a wide range of cellular processes. Its prominent role in biochemistry is the subject of a very large body of research (as of March 2009, the Medline database returns nearly 160,000 articles on the subject, largely on protein phosphorylation). Reversible phosphorylation of proteins is an important regulatory mechanism that occurs in both prokaryotic and eukaryotic organisms. Enzymes called kinases (phosphorylation) and phosphatases (dephosphorylation) are involved in this process. Many enzymes and receptors are switched "on" or "off" by phosphorylation and dephosphorylation. Reversible phosphorylation results in a conformational change in the structure in many enzymes and receptors, causing them to become activated or deactivated.
The Chemistry of Vision
In the rod and cone cells in the retina of the eye, retinal in rhodopsin is found “at rest” in the cis form. When it absorbs a photon (hν) of light, one of the π-bonds is broken, causing the molecule to rotate and lock into the trans form, which has a completely different shape. This starts a long chain of chemical processes which eventually results in a visual image in the brain. The transretinal molecule is then twisted back into the cis form by another enzyme. When you look directly at a very bright light, the “afterimage” that you see in front of your eyes is the result of a large amount of cis-retinal having been
transformed into trans-retinal all at once; the enzymes take a little bit of time to go through and “reset” all of these molecules.
Protein function in Neurons (and glial cells)
Neurons are cells that are specialized for a purely information processing function. It is therefore likely that some proteins within these cells may have evolved to be purely information processing in function. The Histone proteins as well as the DNA in these cells combined with protein scaffolds and other proteins undoubtedly provide powerfull information processing power and learning mechanisms within these cells. This model should also shed light on the functioning of the mysterious glial cells which have heretofore been thought to provide metabollic support to the neurons. It is unlikely that the purely information processing potential of these cells, which outnumber the neurons should not be used in some manner.
The Neurotransmitter System-
This is the system evolved to optimize speed, probably including the five senses, the fight or flight impulse, consciousness. Breathing and dreaming are somehow a hybrid part also.
The Brain has two two classes of cells: The neurons and the glial cells. The neurons operate at the outer level at the speed of electricity. Receiving information at the dendritic end and passing along information at the axonal ends. As the information passes along at about 250 miles per hour from one cell to the other, at a possibly lesser speed (?), the Histone-DNA complex in the nucleus monitors this activity. There are at least two possible systems in use here: Enzymatic pathways and signal conduction along protein scaffolds. Note how these molecules have a branching structure similar to electrical circuits.
The Glial Cell System-
The glial cells have been til now somewhat mysterious in their function. It is easy however to imagine information processing potential. Clearly they would be involved in those functions with the least time constraints.