Despite the diversity in biological form and function, there is a surprising similarity in the ways that cells function. For example; the process that converts DNA information into proteins is largely the same for all living organisms. Similarly, the motile behaviors of cells are often shared across different cell types. This suggests that all cells have a limited number of “functions” that are utilized under particular circumstances or states. For details on the principles underlying these diverse functions, see Common themes in mechanotransduction.
The multi-protein modules that orchestrate these functions can be considered general tools and can be shared across functions. Their classification as Functional Modules is based upon critical assumptions that are unifying principles of this resource:
i) Mechanical functions are performed by meso-scale “machines” composed of modular protein complexes that communicate with each other through biophysical and biochemical signals.
ii) These machines are digital in nature, i.e. they are either ‘on’ or ‘off’. Intermediate states may arise from physical feedback mechanisms, due to the fraction of time that the machine is ‘on’ or the fraction of the cell membrane that is ‘on’.
iii) These machines assemble, perform a function and then disassemble for reuse at other sites and are therefore recyclable.
The collective activity of the functional modules in operation at any given time will drive specific, complex processes, in a highly regulated manner that ultimately contributes to the global state of the cell. Behaviors specific to certain cell types results from the variable regulation of alternate control and signaling pathways.
Cellular behaviors cannot be viewed in isolation, as they are impacted by their surroundings. To address the integrated nature of complex cellular activities, this manual starts by setting the wider context for the function. This is followed by a basic description of the function and finally moves towards a physical and chemical understanding of how the function works at a molecular level:
1. Identify wider contexts that lead to one or more cellular functions
2. Define the cellular functions/processes
3. Describe the steps that contribute to each process
4. Discuss the functional modules that contribute to the steps