If someone isolates a new protein/enzyme what are the main steps in finding its function? Are there programmes that help you for this? I don't mean its characteristics such as molecular weight, solubility, isoelectric point etc. , but its role in the organism, supposing no similar structures were found using BLAST or other programmes. Thank you.

you first look at its mRNA expression (northern blotting and in-situ hybridization) to see where the gene is expressed and in which cell types. You then raise antibodies to confirm the expression at the protein level with immunocytochemistry and Western blotting. Then once you know where it is expressed and in which cells that gives you some idea of what it might do and you then use various functional read outs and manipulate its expression (micro RNA, viral gene transfer, transgenic mice) in-vitro and then in-vivo to see how that alters function using those readouts. These sorts of analysis when one has no idea what the protein does are long, time consuming and very expensive!

Of course David is quite right, but only gave one answer to a very complex question.

One alternative approach is to look at genome context, which might give you clues about function; for example comparison with other genomes might reveal conserved proximity of your gene to certain know genes or regulatory elements, which can imply a guilt-by-association relationship. This is a broad-brush approach and can be most useful with large datasets.

As a masters student I was involved in a "structural genomics" project, where crystal structures were solved of unknown ORFs from Micobacterium tuberculosis. Possible functions were extrapolated from the structures by looking for motifs or conserved folds, which are not necessarily visible using only sequence information.

But like David said, it a very time consuming and therefore expensive exercise regardless of the method.

As John points out genome comparisons can be very useful, although the function of a hormone or neurotransmitter in one animal (e.g., a snail) can obviously be quite different for the same or similar protein in a mammal. That being said scientists are finding chemicals in plants that might act say, as an insecticide, that in humans could have therapeutic value for some condition(s).