A Combinatorial NMR and EPR Approach for Evaluating the Structural Ensemble of Partially Folded Proteins

• Published in: Journal of the American Chemical Society Vol. 132; no. 25; pp. 8657 - 8668
• Main Authors: Rao, Jampani Nageswara, Jao, Christine C, Hegde, Balachandra G, Langen, Ralf, Ulmer, Tobias S
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 30.06.2010
• Subjects: alpha-Synuclein - chemistry; Electron Spin Resonance Spectroscopy - methods; Humans; Micelles; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular - methods; Protein Folding; Protein Structure, Tertiary; Sarcosine - chemistry
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja100646t

Partially folded proteins, characterized as exhibiting secondary structure elements with loose or absent tertiary contacts, represent important intermediates in both physiological protein folding and pathological protein misfolding. To aid in the characterization of the structural state(s) of such proteins, a novel structure calculation scheme is presented that combines structural restraints derived from pulsed EPR and NMR spectroscopy. The methodology is established for the protein α-synuclein (αS), which exhibits characteristics of a partially folded protein when bound to a micelle of the detergent sodium lauroyl sarcosinate (SLAS). By combining 18 EPR-derived interelectron spin label distance distributions with NMR-based secondary structure definitions and bond vector restraints, interelectron distances were correlated and a set of theoretical ensemble basis populations was calculated. A minimal set of basis structures, representing the partially folded state of SLAS-bound αS, was subsequently derived by back-calculating correlated distance distributions. A surprising variety of well-defined protein−micelle interactions was thus revealed in which the micelle is engulfed by two differently arranged antiparallel αS helices. The methodology further provided the population ratios between dominant ensemble structural states, whereas limitation in obtainable structural resolution arose from spin label flexibility and residual uncertainties in secondary structure definitions. To advance the understanding of protein−micelle interactions, the present study concludes by showing that, in marked contrast to secondary structure stability, helix dynamics of SLAS-bound αS correlate with the degree of protein-induced departures from free micelle dimensions.