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Differential Ordering of the Protein Backbone and Side Chains during Protein Folding Revealed by Site-Specific Recombinant Infrared Probes

2011; American Chemical Society; Volume: 133; Issue: 50 Linguagem: Inglês

10.1021/ja2071362

1943-2984

Sureshbabu Nagarajan, Humeyra Taskent‐Sezgin, Dzmitry Parul, Isaac S. Carrico, Daniel P. Raleigh, R. Brian Dyer,

Enzyme Structure and Function

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.