Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects.
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.
Krantz
Bryan A
BA
Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA.
Srivastava
Alok K
AK
Nauli
Sehat
S
Baker
David
D
Sauer
Robert T
RT
Sosnick
Tobin R
TR
D017766:Acid Anhydride Hydrolases / Q000737:chemistry / Q000378:metabolism; D000577:Amides / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D002942:Circular Dichroism; D004268:DNA-Binding Proteins; D006860:Hydrogen Bonding; D007554:Isotopes / Q000378:metabolism; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D010940:Plant Proteins; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics; D014764:Viral Proteins / Q000737:chemistry / Q000378:metabolism; D054334:Viral Regulatory and Accessory Proteins; D000097024:Acylphosphatase
D017766:Acid Anhydride Hydrolases; D000577:Amides; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D007554:Isotopes; D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; D000097024:Acylphosphatase; C034284:IgG Fc-binding protein, Streptococcus; C093336:chymotrypsin inhibitor 2; C016649:phage repressor proteins