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Beside energy and heat, I don't know any useful physical information of a protein. Can you help me list some of it. Somethings like Fourier-transform infrared spectroscopy to provide protein structure aren't what I'm looking for.

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  • $\begingroup$ What about the sequence and the 3D-structure? This is important information... $\endgroup$
    – Chris
    Jun 24 '14 at 12:06
  • $\begingroup$ Please clarify what kind of information you are looking for. $\endgroup$
    – WYSIWYG
    Jun 24 '14 at 12:28
  • $\begingroup$ Somethings like energy, heat, entropy, which are physical measurable things. The structure is a good point, I don't know what the sequence information are. $\endgroup$
    – Ooker
    Jun 24 '14 at 12:33
  • $\begingroup$ sounds like you mean 'typical means of monitoring the folding of a protein' or something like that? such a question would work... $\endgroup$
    – shigeta
    Jun 24 '14 at 13:42
  • $\begingroup$ Something like that. I need some new conceptions to research deeper. $\endgroup$
    – Ooker
    Jun 24 '14 at 13:46
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I'll make a list, by wavelength then 'others'. This is only the most common techniques list. i'd be here all week if I tried to get all the applications. Scientists are crafty and are always coming up with stuff.

Electro magnetic protein derived measurements:

  • NMR spectroscopy (radio) - can detect the structural variations in the individual amino acids allowing a protein structure with the dynamics of the peptide chain to be modeled.
  • IR spectroscopy - can look at bond-bond vibrations. Mostly used to observe for non-peptide moities and cofactors of the protein like heme in hemoglobin for instance.
  • RAMAN spectroscopy - also an IR spectroscopy, but which can look for dynamic qualities of the interatomic vibrations. Like IR this is used with cofactors usually and not the protein, which looks very much the same over most of a peptide.
  • UV/visible spectroscopy - on the low end, examine the behavior or concentration of chromophores associated with the protein. used for kinetics - study of enzymes in the act of catalysis. On the high end can also be used for things like watching photon-energy transduction in photosynthetic systems and things like this. The peptide itself has no Visible absorption, but the colored molecules are often used as a probe to watch the peptide in action - like folding.
    FRET is a technique that can measure how far apart two colored labels are - two separate points of a protein are labelled and a distance measurement obtained.
  • UV circular dichroism. the aromatic side chains of Phe, Trp, Tyr, His etc absorb in the UV and are directly observed to follow folding some times. Circular dichroism looks for differences in the absorption of right and left circularly polarized light and can show secondary structure.
  • X-ray. Scattering of proteins in solution can measure the so called 'radius of gyration' which profiles the overall shape of the protein. X-ray scattering off of 2D and 3D crystals can reveal the molecular protein structure.

Others:

  • Calorimetry. By tracking the heat capacity/heat given off/taken in by a protein, its folding state, binding and other structural characteristics of a protein sample can be measured.
  • Mass Spectroscopy - generally this just measures whether a protein is present, by fragmenting it and measuring the mass of the fragments. useful for mixtures of many proteins (like a living cell).
  • Peptide sequencing - like Mass Spec, but often used when there is just one protein in a pure sample.

There's lots more - just depends on where you want to cut off the list. Hopefully this is a good start.

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All the information about a protein, biochemical or functional is encoded in its structure, which are primary (Amino Acid (AA) sequence), secondary (alpha helix or beta pleated sheet), tertiary (overall 3D structure of a single peptide) and quaternary (overall 3D-structure of a protein composed of multiple peptides which are attached together through various different bonds) structures (http://en.wikipedia.org/wiki/Protein_structure).

Obviously, the key determinants for all these structures is the AA sequence of a protein, since that determines the biochemical property of a protein as well as its function (e.g. enzymatic residues and active sites, functional domains, motifs, whether it is post-translationally modified or not by phosphorylation and whether that causes its activation or inactivation through conformational changes or its interaction with other proteins etc).

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