Diffusion coefficient measurement inconsistency as a parameter to monitor structural conformational changes in biomolecules

Residue specific measurement of translational diffusion coefficient involving labile amide protons of a protein molecule is known to give inconsistent result due to multiple solute-solvent exchange events during the diffusion encoding period. The residues accessible to solvent often overestimates the diffusion coefficient due to the contribution by fast diffusing solvent molecules to the measured values. It has been, however, shown that this apparent drawback of overestimation can become a valuable source of information about the exchange rates. An associated exchange related drawback that has never been perceived in a similar positive manner is the high repetition inaccuracy. The exchanging residues not only overestimate, they do so in an inconsistent way as the contribution of exchange differs from one measurement to the next. We show here how measurement uncertainty can become another useful tool in recognizing the sections of the polypeptide chain that are exposed to solvent. Additionally, we show that the uncertainty is more sensitive a marker than the overestimation in detecting small changes in solvent accessibility of a residue due to structural changes of a protein molecule.