title: Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes.
abstract: The time scale for ordering of the polypeptide backbone relative to the side chains is a critical issue in protein folding. The interplay between ordering of the backbone and ordering of the side chains is particularly important for the formation of β-sheet structures, as the polypeptide chain searches for the native stabilizing cross-strand interactions. We have studied these issues in the N-terminal domain of protein L9 (NTL9), a model protein with mixed α/β structure. We have developed a general approach for introducing site-specific IR probes for the side chains (azide) and backbone ((13)C═(18)O) using recombinant protein expression. Temperature-jump time-resolved IR spectroscopy combined with site-specific labeling enables independent measurement of the respective backbone and side-chain dynamics with single residue resolution. We have found that side-chain ordering in a key region of the β-sheet structure occurs on a slower time scale than ordering of the backbone during the folding of NTL9, likely as a result of the transient formation of non-native side-chain interactions.
authors: Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
authors: Sureshbabu
authors: S
authors: Nagarajan
authors: Humeyra
authors: H
authors: Taskent-Sezgin
authors: Dzmitry
authors: D
authors: Parul
authors: Isaac
authors: I
authors: Carrico
authors: Daniel P
authors: DP
authors: Raleigh
authors: R Brian
authors: RB
authors: Dyer
mesh_terms: D015335:Molecular Probes; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013055:Spectrophotometry, Infrared / Q000379:methods
chemical_list: D015335:Molecular Probes; D011506:Proteins