The hydrogen exchange core and protein folding
- 1 January 1999
- journal article
- review article
- Published by Wiley in Protein Science
- Vol. 8 (8), 1571-1590
- https://doi.org/10.1110/ps.8.8.1571
Abstract
A database of hydrogen‐deuterium exchange results has been compiled for proteins for which there are published rates of out‐exchange in the native state, protection against exchange during folding, and out‐exchange in partially folded forms. The question of whether the slow exchange core is the folding core (Woodward C, 1993, Trends Biochem Sci 18:359–360) is reexamined in a detailed comparison of the specific amide protons (NHs) and the elements of secondary structure on which they are located. For each pulsed exchange or competition experiment, probe NHs are shown explicitly; the large number and broad distribution of probe NHs support the validity of comparing out‐exchange with pulsed‐exchange/competition experiments. There is a strong tendency for the same elements of secondary structure to carry NHs most protected in the native state, NHs first protected during folding, and NHs most protected in partially folded species. There is not a one‐to‐one correspondence of individual NHs. Proteins for which there are published data for native state out‐exchange and ϕ values are also reviewed. The elements of secondary structure containing the slowest exchanging NHs in native proteins tend to contain side chains with high ϕ values or be connected to a turn/loop with high ϕ values. A definition for a protein core is proposed, and the implications for protein folding are discussed. Apparently, during folding and in the native state, nonlocal interactions between core sequences are favored more than other possible nonlocal interactions. Other studies of partially folded bovine pancreatic trypsin inhibitor (Barbar E, Barany G, Woodward C, 1995, Biochemistry 34:11423–11434; Barber E, Hare M, Daragan V, Barany G, Woodward C, 1998, Biochemistry 37:7822–7833), suggest that developing cores have site‐specific energy barriers between microstates, one disordered, and the other(s) more ordered.Keywords
This publication has 127 references indexed in Scilit:
- Defining Protein Ensembles with Native-state NH Exchange: Kinetics of Interconversion and Cooperative Units from Combined NMR and MS AnalysisJournal of Molecular Biology, 1999
- The origin of the α-domain intermediate in the folding of hen lysozymeJournal of Molecular Biology, 1998
- Amide hydrogen exchange and internal dynamics the chemotactic protein CheY from Escherichia coliJournal of Molecular Biology, 1997
- Hydrogen-exchange kinetics in the cold denatured state of ribonuclease ABiochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, 1996
- Temperature and pH Dependences of Hydrogen Exchange and Global Stability for Ovomucoid Third DomainBiochemistry, 1996
- A Comparison of the pH, Urea, and Temperature-denatured States of Barnase by Heteronuclear NMR: Implications for the Initiation of Protein FoldingJournal of Molecular Biology, 1995
- Different Subdomains are Most Protected From Hydrogen Exchange in the Molten Globule and Native States of Human α-LactalbuminJournal of Molecular Biology, 1995
- Investigation of ribonuclease T1 folding intermediates by hydrogen-deuterium amide exchange-two-dimensional NMR spectroscopyBiochemistry, 1993
- The folding of an enzyme: V. solH2H exchange-nuclear magnetic resonance studies on the folding pathway of barnase: Complementarity to and agreement with protein engineering studiesJournal of Molecular Biology, 1992
- Determination of the secondary structure and molecular topology of interleukin-1.beta. by use of two- and three-dimensional heteronuclear nitrogen-15-proton NMR spectroscopyBiochemistry, 1990