Achieving a realistic native protein ensemble by HDX-MS and computational modeling

Abstract

Amide hydrogen-deuterium exchange (HDX) measurements pioneered in the 1950s and developed extensively by Englander in the 1980s (1), still give us more information than we understand about protein motions. Some backbone amides exchange within milliseconds, whereas others may take months. How amides exchange in a folded protein and why some exchange so quickly and others so slowly has puzzled biophysicists for several generations. What exactly are the underlying physicochemical phenomena that result in amide exchange and how do the rates of exchange relate to structural dynamics? Early investigators, including Ken Dill and Hue Sun Chan, worked in statistical mechanical lattice models of proteins to try to answer this question (2,3).