Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects

TitleUnderstanding protein hydrogen bond formation with kinetic H/D amide isotope effects
Publication TypeJournal Article
Year of Publication2002
AuthorsKrantz, B. A., Srivastava A. K., Nauli S., Baker D., Sauer R. T., & Sosnick T. R.
JournalNature structural biology
Volume9
Issue6
Pagination458-63
Date Published2002 Jun
ISSN1072-8368
KeywordsAcid Anhydride Hydrolases, Amides, Bacterial Proteins, Circular Dichroism, Collaborative Publication, DNA-Binding Proteins, Hydrogen Bonding, Isotopes, Kinetics, Models, Chemical, Models, Molecular, Peptides, Plant Proteins, Protein Folding, Protein Structure, Secondary, Proteins, Repressor Proteins, Thermodynamics, Viral Proteins, Viral Regulatory and Accessory Proteins
Abstract

Through the development of a procedure to measure when hydrogen bonds form under two-state folding conditions, alpha-helices have been determined to form proportionally to denaturant-sensitive surface area buried in the transition state. Previous experiments assessing H/D isotope effects are applied to various model proteins, including lambda and Arc repressor variants, a coiled coil domain, cytochrome c, colicin immunity protein 7, proteins L and G, acylphosphatase, chymotrypsin inhibitor II and a Src SH3 domain. The change in free energy accompanied by backbone deuteration is highly correlated to secondary structure composition when hydrogen bonds are divided into two classes. The number of helical hydrogen bonds correlates with an average equilibrium isotope effect of 8.6 +/- 0.9 cal x mol(-1) x site(-1). However, beta-sheet and long-range hydrogen bonds have little isotope effect. The kinetic isotope effects support our hypothesis that, for helical proteins, hydrophobic association cannot be separated from helix formation in the transition state. Therefore, folding models that describe an incremental build-up of structure in which hydrophobic burial and hydrogen bond formation occur commensurately are more consistent with the data than are models that posit the extensive formation of one quantity before the other.

Alternate JournalNat. Struct. Biol.
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