System to simulate the activity of living organism - construction of proteome

摘要

The living organism maintains homeostasis despite being a thermodynamically open system in constant inter action with its environment. Only a system which implements automatic control mechanisms can meet these criteria. The negative feedback loop provides a way to implement such mechanisms.While the organism is thermodynamically open, feedback loops active on the level of cells and the organism as a whole maintain specific substrate concentrations and functions which we refer to as "normal" or "physiological". Each automatically controlled process constitutes a distinct unit associated with a specific metabilism. This unit encompasses all components which enables a specific function - it may therefore be referred to as a "functional unit" or a "functional-structural unit". Individual units which control specific processes may be further linked with one another, forming a complex network of dependencies.Receptors play a crucial role in feedback systems. By detecting deviations from the predefined norm - within the scope of a given process - they can trigger counterbalancing actions. They are also involved in inter-process communications. Such communications can be either cooperative - where the product of one process becomes the substrate of another - or coordinative - where the product of one process modulates the behavior of another by affecting the operation of its control function. The latter type introduces a hierarchy of processes.Proteins are the basic building blocks of biological systems. Their mutual interactions are represented in the form of proteomes, in which they represent structural components. It is, however, difficult to determine what the role a given protein plays in a metabolic process purely by analyzing its structure. Treating proteins as elements of feedback loops provides far greater insight into their functional characteristics. This is why the presented study focuses on functional units rather than on individual proteins.