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 ?-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 ?/? 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 ?-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.

SUBMITTER: Nagarajan S 

PROVIDER: S-EPMC3241911 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature