Hydrogen exchange and the dynamic structure of proteins

Abstract

In native proteins, buried, labile protons undergo isotope exchange with solvent hydrogens, but the kinetics of exchange are markedly slower than in unfolded polypeptides. This indicates that, whereas buried protein atoms are shielded from solvent, the protein fluctuates around the time average structure and occasionally exposes buried sites to solvent. Generally, hydrogen exchange studies are designed to characterize the nature of the fluctuations between conformational substates, to monitor the shift in conformational equilibria among protein substates due to ligand binding or other factors, or to monitor the major cooperative denaturation transition. In this article, we review the recent reports of hydrogen exchange in proteins, focusing on recent advances in methodology, especially with regard to the implications of the results for the mechanism of hydrogen exchange in folded proteins.

Determinants of protein hydrogen exchange studied in equine cytochrome c

“…This condition has been verified for cyt c under the conditions used here (Bai et al, ACHx in Equation 1 can be understood in terms of a preequilibrium structural unfolding when exchange is dominated by large unfolding reactions that fully expose all the NHs measured. When exposure is less than complete, as may occur when exchange is dominated by local fluctuations, terms that include a rate for solvent species penetration and internal diffusion may then enter (Richards, 1979;Woodward et al, 1982). In this case some reinterpretation in terms of an activation energy contribution may also be required (see chapter 2 in (Englander & Kallenbach, 1984)).…”

“…Much prior work has tended to focus on burial itself as the cause of slow exchange (Lumry & Rosenberg, 1975;Richards, 1979;Woodward et al, 1982) with the assumption that contact with solvent is sufficient to accomplish exchange. All the slowly exchanging hydrogens measured here are involved in H-bonding, including some side chains and water molecules as acceptors.…”

Mapping the lifetimes of local opening events in a native state protein

“…Many models describing the protein dynamics that lead to hydrogen exchange in folded proteins have been proposed. These have all been described extensively in several reviews including the breathing model, the penetration model, the mobile defect model, the local unfolding model, and the global unfolding model (Hvidt & Nielsen, 1966;Englander et al, 1972;Englander, 1975: Richards, 1979Wagner & Wuthrich, 1979;Wood-ward & Hilton, 1979;Barksdale & Rosenberg, 1982;Wagner, 1982;Woodward et al, 1982).…”

Substrate binding and conformational changes of Clostridium glutamicum diaminopimelate dehydrogenase revealed by hydrogen/deuterium exchange and electrospray mass spectrometry

“…Keywords: amide hydrogen exchange; diaminopimelate dehydrogenase; electrospray ionization mass spectrometry; protein conformational change; substrate binding Isotopic exchange rates of amide hydrogens have been used for many years to provide information about the high-order structure, structural changes, and structural dynamics of proteins (Englander et al, 1979;Woodward et al, 1982). With the advent of electrospray ionization mass spectrometry (ESI-MS) has come the ability to investigate intact protein structures using mass spectrometry.…”