An Information Theoretical Analysis of Kinase Activated Phosphorylation Dephosphorylation Cycle

Abstract

Signal transduction, the information processing mechanism in biological cells, is carried out by a network of biochemical reactions. The dynamics of driven biochemical reactions can be studied in terms of nonequilibrium statistical physics. Such systems may also be studied in terms of Shannon's information theory. We combine these two perspectives in this study of the basic units (modules) of cellular signaling: the phosphorylation dephosphorylation cycle (PdPC) and the guanosine triphosphatase (GTPase). We show that the channel capacity is zero if and only if the free energy expenditure of biochemical system is zero. In fact, a positive correlation between the channel capacity and free energy expenditure is observed. In terms of the information theory, a linear signaling cascade consisting of multiple steps of PdPC can function as a distributed "multistage code." With increasing number of steps in the cascade, the system trades channel capacity with the code complexity. Our analysis shows that while a static code can be molecular structure based, a biochemical communication channel has to have energy expenditure.

Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics

“…Since our framework accounts for time-dependent drivings and transient dynamics, it could be used to represent the transmission of signals through CRNs or their response to external modulations in the environment. These features become crucial when considering problems such as signal transduction and biochemical switches [24,109,110], biochemical oscillations [28,111], growth and self-organization in evolving bio-systems [112,113], or sensory mechanisms [85,87,[114][115][116][117]. Also, since transient signals in CRNs can be used for computation [118] and have been shown to display Turing-universality [119][120][121][122], one should be able to study the thermodynamic cost of chemical computing [123].…”

Universal ideal behavior and macroscopic work relation of linear irreversible stochastic thermodynamics

“…It will be the origin of a Maxwellʼs demon [40]. For an isothermal system, one can introduce Helmholtzʼs free energy function A E TS = − , then equation (49) becomes…”

“…This is where the 'information' in Maxwellʼs demon enters thermodynamics. Equations (49) and (50), thus, are a grander First Law which now includes feedback information as a part of the conservation [39] with 'informatic energy' F dα α , on a par with heat energy T S d , mechanical energy p V d , and Gibbs' chemical energy N d μ . Equation (49) is the theory of absolute information in connection to controlling α.…”

Nonequilibrium Thermodynamics of Cell Signaling

“…Some particular cases of signaling dynamics have been studied, even at the nonequilibrium statistical physics level of description, for instance, by means of information theoretical approaches [14]. In such studies, a positive correlation between the channel capacity (i.e., the informationcarrying capacity of the signaling networks) and freeenergy expenditure has been observed.…”

“…Performance of biomolecular switches can be sensibly tuned via mutations that alter their switching thermodynamics [7]. Thermodynamic conditions in the intracellular medium hence alter sensitivity, control, and effective information transfer in signaling networks [14].…”