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Native and nonnative conformational preferences in the urea-unfolded state of barstar

¹ Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005, India
² National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560 065, India

(RECEIVED April 8, 2004; FINAL REVISION July 12, 2004; ACCEPTED August 14, 2004)

The refolding of barstar from its urea-unfolded state has been studied extensively using various spectroscopic probes and real-time NMR, which provide global and residue-specific information, respectively, about the folding process. Here, a preliminary structural characterization by NMR of barstar in 8 M urea has been carried out at pH 6.5 and 25°C. Complete backbone resonance assignments of the urea-unfolded protein were obtained using the recently developed three-dimensional NMR techniques of HNN and HN(C)N. The conformational propensities of the polypeptide backbone in the presence of 8 M urea have been estimated by examining deviations of secondary chemical shifts from random coil values. For some residues that belong to helices in native barstar, ¹³C and ¹³CO secondary shifts show positive deviations in the urea-unfolded state, indicating that these residues have propensities toward helical conformations. These residues are, however, juxtaposed by residues that display negative deviations indicative of propensities toward extended conformations. Thus, segments that are helical in native barstar are unlikely to preferentially populate the helical conformation in the unfolded state. Similarly, residues belonging to -strands 1 and 2 of native barstar do not appear to show any conformational preferences in the unfolded state. On the other hand, residues belonging to the -strand 3 segment show weak nonnative helical conformational preferences in the unfolded state, indicating that this segment may possess a weak preference for populating a helical conformation in the unfolded state.

Keywords: unfolded state; HNN; HN(C)N; secondary chemical shifts

Abbreviations: NMR, nuclear magnetic resonance • HSQC, hetero-nuclear single-quantum coherence

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04805204.

Reprint requests to: Jayant B. Udgaonkar, National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560 065, India; e-mail: jayant{at}ncbs.res.in; fax: +91-80-23636662; or Ramakrishna V. Hosur, Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India; e-mail: hosur{at}tifr.res.in; fax: +91-22-22804610.

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