The folding energy landscape of the dimerization domain of Escherichia coli trp repressor:: A joint experimental and theoretical investigation

JOURNAL OF MOLECULAR BIOLOGY

卷:363

Article

Simler, B. Robert ; Levy, Yaakov ; Onuchic, Jose N. ; Matthews, C. Robert

关键词: protein folding;    hydrogen exchange;    segment swapping;    mass spectrometry;    Go model;   

DOI  :  10.1016/j.jmb.2006.07.080

来源: Elsevier

【 摘 要 】

Enhanced structural insights into the folding energy landscape of the N-terminal dimerization. domain of Escherichia coli tryptophan repressor, [2-66](2) TR, were obtained from a combined experimental and theoretical analysis of its equilibrium folding reaction. Previous studies have shown that the three intertwined helices in [2-66](2) TR are sufficient to drive the formation of a stable dimer for the full-length protein, [2107](2) TR. The monomeric and dimeric folding intermediates that appear during the folding reactions of [2-66](2) TR have counterparts in the folding mechanism of the full-length protein. The equilibrium unfolding energy surface on which the folding and dimerization reactions occur for [2-66](2) TR was examined with a combination of native-state hydrogen exchange analysis, pepsin digestion and matrix-assisted laser/ desorption mass spectrometry performed at several concentrations of protein and denaturant. Peptides corresponding to all three helices in [2-66](2) TR show multi-layered protection patterns consistent with the relative stabilities of the climeric and monomeric folding intermediates. The observation of protection exceeding that offered by the dimeric intermediate in segments from all three helices implies that a segment-swapping mechanism may be operative in the monomeric intermediate. Protection greater than that expected from the global stability for a single amide hydrogen in a peptide from the C-hehx possibly and another from the A-helix may reflect nonrandom structure, possibly a precursor for segment swapping, in the ureadenatured state. Native topology-based model simulations that correspond to a funnel energy landscape capture both the monomeric and dimeric intermediates suggested by the HX MS data and provide a rationale for the progressive acquisition of secondary structure in their conformational ensembles. (c) 2006 Elsevier Ltd. All rights reserved.

【 授权许可】

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