Non-Equilibrium Thermodynamics of Gene Expression and Transcriptional Regulation

Abstract

In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to phenotypic diversity and disease. A wide variety of methods of quantitative analysis have been developed to cope with high throughput data sets generated by gene expression profiling experiments. Due to the complexity associated with transcriptomics, specially in the case of gene regulation phenomena, most of these methods are of a probabilistic or statistical nature. Even if these methods have reached a central status in the development of an integrative, systematic understanding of the associated biological processes, they very rarely constitute a concrete guide to the actual physicochemical mechanisms behind biological function and the role of these methods is more on a hypotheses generating line. An important improvement could be done with the development of a thermodynamic theory for gene expression and transcriptional regulation that will build the foundations for a proper integration of the vast amount of molecular biophysical data and could lead, in the future, to a systemic view of genetic transcription and regulation. . * ehernandez@inmegen.gob.mx

Nonequilibrium thermodynamics modeling of coupled biochemical cycles in living cells

“…Focusing on measurement technologies will rely on an iterative relationship with computational modeling approaches that are capable of dealing with the gradients and discontinuities of biological systems. New modeling approaches, on the other hand, will be required to represent the nonlinearity, adaptive, and collective behavior of biological systems by using the responses as assets of a biological network rather than simply the programmed responses of cells [53][54][55][56][57][58][59].…”

“…Consequently, biochemical cycles emerge from collective and functional efforts to devise a cyclic flow of optimal energy degradation rate, which can only be described by nonequilibrium thermodynamics [6,21,29,31,32,36,[38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53]. For example, as a major part of organization, the thermodynamic coupling in the membranes of living cells plays major role in the respiratory electron transport chain leading to synthesizing of ATP [31].…”