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The article on Wikiomics:Protein function prediction states that "there are now plenty of proteins which have an unknown function," raising the question of what Wikiomics:Protein functions are known. // Netesq 18:25, 17 August 2006 (PDT)
That's a good subject for a biology exam :-) We could start by asking ourselves what "protein function" means. The function of something is well-defined in the case of machines, which are normally designed to fulfill some specific functions. In the case of natural things like proteins, you never know if they actually have a function. They may also have several functions, some of which being possibly turned on or off depending on the situation. Here again, the analogy with machines is not always clear. The activation of a protein by some cofactor or the inhibition by the interaction with another protein can be seen either as a modification of the machine itself, or just a switch being activated. Then, should the protein itself be considered as a machine, or just a piece in a bigger machine? Usually both views make sense, e.g. a given enzyme such as the chymotrypsin has a catalytic function ("machine" which cuts other proteins) and is a part of the digestive system, itself being a part the organism.
This leaves us with many possible answers which depend on what we are studying. Anyway, you can browse the GO tree to get an idea of a possible classification of protein functions. --Martin 19:47, 17 August 2006 (PDT)
The question of protein function is really interesting. Before the GO came along Monica Riley did a lot of very good work on classifying the functions of gene products in E. coli. From some very interesing later work (recently reviewed in Giandani et al., 2006. TIBS 31(5) 284-291) it seems likely that a good proportion of proteins are multifunctional.
Function can be looked at in two principal ways: it's either what something is designed to do or what it gets used for. e.g. we could use a screwdriver to remove screws or to bang in nails. Evolution mostly works on the "first past the post" principle so there are quite a few proteins which seem to have ended up with a particular function because they were convenient somehow. e.g. lens crystallins. This is in spite of having been optimized (preferable to "designed" I think) for a different purpose originally and still retaining that molecular function.
Finding putative binding residues for protein-protein interaction
given: - a protein X (member of a family with two domains) - protein alignment of X to other members of the family - related (detected by pdb-blast) to X protein Y with 3D structure find: -residues to mutate to keep the structure of X but break its ability to bind a ligand/protein (== conserved surface residues in around pockets/binding surfaces ??)
Darked 09:25, 24 May 2006 (PDT)