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I am trying to find out how these networks can be linked together. I know that Protein-protein interaction networks and metabolic networks both fall under the Intra-cellular type of biological networks that describe the cellular functioning. But what is the relationship between them?

Thank you very much.

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closed as too broad by March Ho, AliceD, WYSIWYG, James, p.s.w.g Feb 23 '15 at 23:20

Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. Avoid asking multiple distinct questions at once. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

  • $\begingroup$ Metabolic processes are carried out by enzymes and regulated by hormones. Both enzymes and many hormones are proteins. You may have to specify your question further. $\endgroup$ – AliceD Feb 22 '15 at 19:44
  • $\begingroup$ Did you find answer helpful? $\endgroup$ – aaaaaa Feb 23 '15 at 11:34
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Proteins interact with each other often for regulation purposes and for localization of several enzymatic reactions for increased efficiency. For example, some proteins inhibit their binding partners. Or DNA replication complex is made of bunch of proteins, many of which do different jobs, but they are in physical complex (e.g. helicase with DNA polymerase).

Metabolic networks are sets of chemical reactions, they might even happen in different compartments inside the cell. While you can try to investigate protein interaction network by cross-linking proteins and then analyzing complexes you extract, metabolic networks are constructed by deciphering sequences of chemical reactions (e.g. metabolic cycles) and finding appropriate enzymes for each reaction.

Metabolic process (e.g. DNA replication) can be run by interacting proteins, but also might include proteins that don't directly interact with each other. For example, DNA polymerase complex does not produce nucleotides, but they are necessary for it's function.

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In short, proteins in Protein-protein interaction networks perform a function by directly interacting with one another. They may for instance bind to one another forming permanent or momentary complexes (e.g. insulin binding to insulin receptor or the pieces of F0-F1 ATPase combining), or they may chemically modify one another (e.g. protein kinases adding a phosphate to the residue of another protein).

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Proteins in a Metabolic network might never be in physical contact one another. They effect one another by producing chemical compounds which are utilized by other enzymes, forming a network of chemical transformations.

Of course an enzyme in a metabolic network might also have its activity modulated through interacting with other proteins in a protein-protein network. The two terms are of course not mutually exclusive, but describe different sorts of relationships between proteins.

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  • $\begingroup$ I think you should try to connect the figure more clearly to your answer. $\endgroup$ – fileunderwater Mar 3 '15 at 9:55
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The basic struture of the metabolic networks (MN) is like this: molecule1 -> molecule2, where the edges are enzymes.

And the basic structure of the PPIN is like this: Protein1 - Protein2, where the edges are van der Waals forces between proteins.

There are some diferences, PPIN isnt directional and MN is directional in the way of the spontaneous reaction. PPIN has two modes of interaction date interactions (1-1) and party interactions (many-many).

One easy way to combine both is to invert the MN so the enzymes are now the nodes and the metabolites are now the edges, like this: enzyme1 -> enzyme2, and then add the proteins in the PPIN, like this: enzyme1(protein1) -> enzyme(protein2). But in this way you need to demostrate that some properties of the network are conserved.

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