Protection Factor

Several features affect the rate of amide hydrogen exchange, which reflect the protein's structure and dynamic properties. These include an amide's participation in hydrogen bonding [36], its distance from the protein surface [3], and the flexibility of the peptide chain [37]. The degree of retardation in amide hydrogen exchange rate that results from the amide's physical environment is termed its ''protection factor (pf)'':

where kex is the observed exchange rate and kch is the ''intrinsic'' exchange rate calculated at a given pH and temperature in unstructured peptide chain [34].

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