Extensive formation of off-pathway species during folding of an alpha-beta parallel protein is due to docking of (non)native structure elements in unfolded molecules

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Abstract

Detailed information about unfolded states is required to understand how proteins fold. Knowledge about folding intermediates formed subsequently is essential to get a grip on pathological aggregation phenomena. During folding of apoflavodoxin, which adopts the widely prevalent ¿¿ß parallel topology, most molecules fold via an off-pathway folding intermediate with helical properties. To better understand why this species is formed, guanidine hydrochloride-unfolded apoflavodoxin is characterized at the residue level using heteronuclear NMR spectroscopy. In 6.0 M denaturant, the protein behaves as a random coil. In contrast, at 3.4 M denaturant, secondary shifts and 1H¿15N relaxation rates report four transiently ordered regions in unfolded apoflavodoxin. These regions have restricted flexibility on the (sub)nanosecond time scale. Secondary shifts show that three of these regions form ¿-helices, which are populated about 10% of the time, as confirmed by far-UV CD data. One region of unfolded apoflavodoxin adopts non-native structure. Of the ¿-helices observed, two are present in native apoflavodoxin as well. A substantial part of the third helix becomes ß-strand while forming native protein. Chemical shift changes due to amino acid residue replacement show that the latter ¿-helix has hydrophobic interactions with all other ordered regions in unfolded apoflavodoxin. Remarkably, these ordered segments dock non-natively, which causes strong competition with on-pathway folding. Thus, rather than directing productive folding, conformational preorganization in the unfolded state of an ¿¿ß parallel-type protein promotes off-pathway species formation.
Original languageEnglish
Pages (from-to)16914-16920
JournalJournal of the American Chemical Society
Volume130
Issue number50
DOIs
Publication statusPublished - 2008

Keywords

  • azotobacter-vinelandii apoflavodoxin
  • nmr chemical-shifts
  • 8 m urea
  • secondary structure
  • denatured state
  • hydrogen-exchange
  • energy landscape
  • intermediate
  • topology
  • conformations

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