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How Cells Build a Solid Skeleton and Move Actively

Interestingly, cells also need a solid skeleton to be able to move actively. This is composed

of various structural proteins, in particular actin, tubulin and myosin. Bioinformatically,

structural proteins can be identified by the fact that only a few amino acids are always

repeated, resulting in a stable structure in that protein. Such repeats can be found with the

help of repeat recognition software (available, for example, on the ExPASy website).

Protein-specific signatures can also be detected using PROSITE software, which, for

example, displays actin signatures when the actin sequence is entered. Similarly, one can

recognize structural proteins again using protein domains and matching databases, for

example, the ProDom domain database. Equally important for active movement is enough

energy. This energy is available in the form of ATP, which is provided from metabolism.

To calculate the resulting metabolic fluxes, we naturally use metabolic modeling software

(see penultimate chapter). An orderly and efficient metabolism in the cell is essential for

survival. Its “design” is quickly queried via databases such as KEGG or calculated more

precisely via metabolic modelling (e.g. with YANA or Metatool).

How Do Cells Communicate?

The considerations and algorithms from Chap. 5 are particularly useful here. However, the

messages that cells exchange are also subject to the principles of Chap. 7. And, of course, each

passing of messages from one protein to the next (for example, in a signalling cascade with

kinases to switch on and phosphatases to switch off) can also be analysed with the aid of

interactome software and databases (e.g. STRING database at EMBL, “information hyper­

linked over proteins” website, iHOP), for example, checked for completeness and function of

the components and simulated with a mathematical model (e.g. SQUAD, Jimena).

Looking a little closer at the communication of individual organisms, bacterial cells

have quite direct communication, with mRNAs mostly being translated directly into pro­

teins. Besides the standard promoter, there is a second binding site (PRODORIC is a very

good database for bacterial promoters for this), the sigma factor, which determines whether

“everything is fine” (70-S sigma factor) or whether different types of stress or lack of food

are present and then other raw factors are used.

Eukaryotic cells in higher organisms, on the other hand, have much more complex

communication. First, hormones circulate in the bloodstream. These in turn excite recep­

tors in specific organs. Now a second messenger is often sent off, e.g. cAMP, which then

sends signals into the nucleus. There, a complex combination of transcription factors

(three and more) first determines the cell type, then the metabolic situation and then the

general transcription (a good software for the analysis of such promoters is the Genomatix

software).

Differentiation as well as all switching processes in the nervous system are based on

the fact that cellular communication first determines the cell types and tissues involved.

Subsequently, different brain regions, but also all different differentiation pathways, result

starting from stem cells (and again this can be modeled fully dynamically or semiquanti­

tatively, see Chap. 10).

11  Design Principles of a Cell