What are the experiments that demonstrate proteins "working" together?

Question

I'm trying to figure out how bacteria got started. Viruses offer some promise, but I can't find any data on how proteins will come together to form some sort of chemical "machine" if you will.

Answer 1

I assume by "working together" you mean interacting.

Some well established techniques used to detect protein-protein interactions are:

1. The yeast two-hybrid system: http://www.staff.kvl.dk/~dacoj3/resource...

2. The yeast three hybrid system:

PNAS November 12, 1996 vol. 93 no. 23 12817-12821

3. Co-immunoprecipitation: http://www.protocol-online.org/prot/Mole...

4. Tandem affinity purification: http://www.ncbi.nlm.nih.gov/pubmed/11403...

A more complete list can be found here:

http://en.wikipedia.org/wiki/Protein-pro...

The article below is an old review article, but is still good (and available for free).

http://mmbr.asm.org/cgi/reprint/59/1/94....

Here are some papers that actually discuss protein-protein interactions in bacteria. You will likely need access to a library at a university to access most of them:

Chembiochem. 2008 Apr 14;9(6):826-48.

Biochem Soc Trans. 2007 Nov;35(Pt 5):970-3

J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Jan 15;861(2):160-70. Epub 2007 Jul 3

Curr Protein Pept Sci. 2007 Jun;8(3):293-310.

Nat Rev Microbiol. 2007 May;5(5):343-54.  

Answer 2

The experiments are innumerable, but if you want a lot of proteins (and RNA) coming together to form a molecular machine, take a look at a ribosome.