The phosphorylation code

I can not go here into the details of the phosphorylation code but let me only enunciate its nature as a digital-analogical code for the creation of complex systems of specificities, comparable in this sense to the Ca²⁺ code with which it ”cross-talks” and co-operates in a modular fashion to participate in higher emerging codes.

In this case, some effector proteins - kinases and phosphorilases - create patterns of phosphorylation by cyclically phosphorylating and de-phosphorylating specific

residues in substrate proteins leading to sensitisation or desensitisation of cells to various stimuli. The phosphorylated form of some proteins is active, whereas the dephosphorylated form of other proteins is active.

Protein kinases modulate the activity or the binding properties of one or more substrate proteins by phosphorylating serine, threonine, or tyrosine residues. On the other hand, protein phosphatases remove phosphate groups from specific substrate proteins, i.e.: they de-phosphorylate them. The combined action of kinases and protein phosphatases can cycle proteins between active and inactive states.

In other words kinases and phosphorilases “sculpt” specific (digital)

“differences” on their substrates, providing them with a specific (analogical) recognition pattern, i.e.: phosphorylation and/or desphophorylation of specific substrates produce meaningful patterns, a compound analogical message out of different single digital phosphorilated sites. So what may change, i.e.: what becomes relevant, is not the concentration of the substrate itself but the concentration of those with a specific phosphorylation pattern.

There are many possibilities for second messenger codes and the phosphorylation code to interface with each other, before, during and after the production of the second messenger and conversely before, during and after the production of phosphorylation patterns. When the concentration of the second messenger is de-coded, the message is transformed into the phosphorylation code.

3.1.14 Amplification

The term “amplification” also deserves to be further specified in this context.

According to Lodish et. al. (2000: 887) the “overcomplication” of cascades - a series of reactions in which the enzyme catalysing one step is activated, or inhibited, by the product of the previous step - has at least two advantages:

1) A cascade allows an entire group of enzyme-catalysed reactions to be

“regulated” by a single type of molecule. Some metabolic pathways are regulated by hormone-induced cascades, some mediated by cAMP and some by other second messengers. Such a single type of “regulating molecule” would then be viewed as the coordinator of an integrated set of enzymes, something analogous to the role of a

regulon in genome architecture, i. e.: a repetitive element that insures the simultaneous activation of cooperative elements in the required concentrations.

2) It is said that a cascade provides a huge amplification of an initially small signal. For example, blood levels of epinephrine as low as 10^-10 M can stimulate liver glycogenolysis and release glucose, resulting in an increase of blood glucose levels by as much as 50 percent. An epinephrine stimulus of this magnitude generates an intracellular cAMP concentration of 10^-6 M, an amplification of 10⁴. Because three more catalytic steps precede the release of glucose, another 10⁴ amplification can occur. In striated muscle, the concentrations of the three successive enzymes in the glycogenolytic cascade (i.e.: cAPK, GPK, and GP) are in a 1:10:240 ratio, which

“dramatically illustrates the amplification of the effects of epinephrine and cAMP”

(Lodish et. al., 2000: 887).

In a sense it would be wrong to talk here about amplification. The signal is not really amplified in spite of the fact that subsequent steps of the cascade build up higher concentrations of intermediaries. The signal may be said to be just “normally”

transduced (i.e. not amplified) because those ratios of higher concentrations are implicit in the semantic value of the original signal. An amplification would rather imply concentration ratios much higher than what the “average” cascade would yield (granting that such increments could effect a proportional increment of response).

What is called amplification in this context is rather the transformation of a sign - constituted by a threshold concentration of a certain signal - into another sign -

constituted by the threshold concentration of another molecule. In turn, these threshold concentrations combine to originate subsequent signs. An amplification would presuppose a meta-kind of sensibility in which by some kind of arrangement the original message would be sensed as being more drastic or urgent than “usual”

and therefore a different arrangement of ratios could be useful for speeding or slowing the cascade, or for giving extra output (if possible) under special conditions.

Amplification would be more similar to certain autoinductive processes with one or more positive feedback loops in the network. For example, one of the different effects of adrenaline is higher contraction rate of the heart, and thus higher blood pressure, which in turn enhances the circulation of adrenaline. This could more properly be considered an amplification.

When the system has a built-in potentiality to amplify a signal it means that it can be differentially more or less sensible to that signal, prompting in this way the

necessary response before the concentration of what the signal refers to reaches intolerable levels, or escapes away, depending on the case. When on the other hand the system is capable of diversifying a signal, it means that the difference created by it is relevant to a related “cross-talking” pathway. A way for diversification may be the modulation of specific threshold concentration levels.

The amount of a particular receptor expressed in a cell at a given moment may be relatively low. Hormone receptors are present in minute amounts: the surface of a typical cell bears 10,000-20,000 receptors for a particular hormone representing only

≈10^-6 of the total protein in the cell or ≈ 10^-4 of the plasma membrane protein. The specificity of a receptor is a function of its binding affinity for the ligand. Changes in hormone concentration are reflected in proportional changes in the fraction of

receptors occupied. At a rise of hormone concentration, the rise of receptor-hormone complex concentration will rise proportionally, according to its affinity constant. And usually the cellular responses will increase in the same proportion. But for many hormone receptors, the ligand concentration needed to induce maximal cellular response is lower than that needed to saturate all the receptor molecules in a cell i.e.:

the maximal response of a cell to a ligand is generally achieved at concentrations at which most of its receptors are still not occupied (Lodish et. al., 2000: 859-860).

This discussion about amplification evidences the importance of considering the signal-sign-system in its triadic logic and not just exclusively in its dyadic workings.

Dyadically, an increase in concentration levels of each subsequent enzyme may look as an amplification, a quantitative event, because we see how fewer molecules hierarchically mobilise higher quantities of other molecules. But triadically, it is the regularity of these ratios that gives coherence to the semiotic network in which the cascade is immersed. Triadic relations do not build up by an additive process of always increasing numbers of the next step molecule, as it is so clearly evident in the Ca²⁺ code. They result from the logical products produced by combinations of

threshold concentrations of successive and/or simultaneous and adjacent steps. So the fact that there seems to be more materials downstream of the cascade does not

necessarily mean an amplification of the logical result in the entire semiotic network.

i.e.: the signal produces the “right” result, not more result. So it is the fractionating effect of the logical products that matters, not necessarily the additive effect of matter.

Given that in communicational systems we deal with sequences which resemble stimulus-and-response rather than cause-and-effect, much before we encounter

energetic or material restraints we may encounter other types of limiting factors which are semiotic in nature. There is for example an economics of probability of the

possible logical products that are present at a given moment and of the finite number of alternatives available to the system, which are context-dependent. This economics differs from the material budget in that probability - being a ratio - is not subject to addition or subtraction but only to multiplicative processes, such as fractionation (Bateson, 1972: 403). Let me try to provide an example of how such “fractionating effect” may work. When buffer molecules capture a necessary given number of free Ca²⁺ ions, keeping the cytosolic concentration under a certain threshold, the

probabilities of activating the different pathways that are sensible to concentrations above such a threshold remain low. This can be compared to the example given by Bateson (1972: 403) in which a telephone exchange at a time of emergency may be

“jammed” when a large fraction of its alternative pathways are busy. There is, then, a low probability of any given message getting through. Since the sign (or rather a part of it) that may prescribe a certain transcriptional response is a precise concentration of Ca²⁺ ions (plus of course a whole battery of other consensus parameters), all the individual Ca²⁺ dependent signal pathways of the network may contribute or not to the formation of the analogical sign. A Ca²⁺ ion bound to the buffer molecule is a busy line. The fractionating effect is not limited to that level. The threshold

concentration of Ca²⁺ (as a compound analogue), by being or not being at a certain location and at a certain time is also a digital sign in a larger analogical message that leads for example to the transcription of a gene, whose product participates (by being or not being present) in other analogical products that give rise to complex emergent traits.