Amide HX in Folded Polypeptides

The primary contributor to exchange of the folded form of a protein is fully solvated (nonhydrogen bonded) amides located on the surface of unstructured parts of the protein. These will exchange rapidly at rates approaching the chemical HX rate constant, (Eq. 1.6)  

Under native state conditions, proteins typically return rapidly to the folded state after unfolding thus, and Equation 1.8 approximates to Equation 1.9 (for an exact treatment of the kinetics 

An improved quantitative understanding of the aggregate of fundamental factors that govern the HX of individual amides in proteins is needed to fully harness the wealth of information on local stmcture and d5mamics that is resident in protein HX kinetics. Thus, a direct and simple structural interpretation of observed HX rates in native proteins should be approached with utmost caution. This latter point was also recently highlighted by Englander et al. [40,41]. 

From Equation 1.11, it follows that the rate of exchange is proportional to the equilibrium between open and closed protein states and thus the local stability of the structural environment of the exchanging amide. Hence, the free energy of opening or the structural stabilization free energy (AG ) can be determined by Equation 1.12  

Time (min) Centroid (m/z) Centroid (Da) Reiative deuterium uptake  

---