We are working with soybean proteins that are subjected to various outside stresses (pH, temp., ionic strength, etc.) and we'd like to know a tool to assess changes in structure.
That would be CD/ORD, visit: http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=0ahUKEwjwxY2R0q_KAhVGNj4KHYLwBA0QFggwMAI&url=http%3A%2F%2Fiupac.org%2Fpolyedu%2Fpage36%2Fpage19%2Fpage25%2Ffiles%2F5_Circular%2520Dicroism_a.doc&usg=AFQjCNFlhm5uombb0Qi22YXE9PAlbu49iQ
For more specific information you would need protein NMR spectroscopy, visit: https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy_of_proteins
Circular dichroism (CD) - gives information about the "foldedness" of a protein, as well as the proportions of different secondary structural elements within the protein (relative presence of alpha-helix, beta-sheet, and/or random coil). With the right accessories you can also generate "melting curves" which can tell you about the thermodynamic stability of the protein, in terms of Tm values (the transition temperature at which your protein unfolds) from which you can calculate the free energy of unfolding (deltaG) as well as other thermodynamic quantities. If you're looking at a variety of conditions, mutants, etc, comparison of CD-derived thermal melt data can tell you quite a bit about relative effects on stability.
A bit less informative, but still useful, is intrinsic tryptophan fluorescence. If the tertiary structure of a protein is significantly altered, then this can be reflected in the fluorescence emission spectra of tryptophan (a shift in the emission peak wavelength and/or intensity). This method provides less secondary structure information than CD, but still can be an easy qualitative tool.
Bruce mentioned NMR, which indeed is a very powerful and diverse method of inquiry, but often requires high micromolar to mM concentrations of pure & labeled protein (along with MW constraints, etc). Perhaps for simple 1D 1H-NMR experiments it could be fairly straightforward, but I'm not sure how much tertiary structure information you could extract from experiments of that sort.
Of course, I'm assuming that you're talking about specific, highly purified proteins. Is this the case?
Changes in sensitivity to digestion by proteases such as trypsin, chymotrypsin, and V8 protease can be used to assess changes in tertiary structure using SDS-PAGE.
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