Can one monitor dynamics of a specific protein domain (helix, strand etc) by Raman Sp? If one labels a specific residue with an isotope, like in NMR, can one use that to monitor the dynamics of the region that encompasses this residue?
From my understanding (or lack thereof), you do not need any specific modifications to a protein in order to study a specific area in dynamic raman spec. studies (provided that the area(s) of interest are identifiable and show strong enough absorbance/signal). However, more often than not dynamics studies in proteins that monitor specific areas of a protein utilize some form of mutant proteins (some truncated, a residue here and/or there swapped, etc.).
Perhaps, this study of the folded and unfolded states of OmpA may be of use to you http://galileo.ucsd.edu/pdf/sanchez_jpcb_08.pdf [Broken]
Therefore, if i have 2 mutants to a WT protein I should be able to measure dynamics of these 3 proteins. Can I localize the analysis of the dynamics to a specific domain? Say a single helix? Can one perform a differential analysis to compare WT->mutant 1 and WT->mutant2? Simply put, can one subtract spectra in a statistically significant manner?
Fianlly, I understand that residues with aromatic sidechains like tryptophans are more significant spectra. Will it be an issue of the domains in question do not have such aromatic residues?