Structure and dynamics of a denatured 131-residue fragment of staphylococcal nuclease: a heteronuclear NMR study

Abstract

A partially folded form of staphylococcal nuclease has been obtained by deleting residues 4-12 and 141-149 of the 149-residue wild-type protein. Sequence-specific NMR resonance assignments have been obtained for 106 of the 131 residues in this protein fragment by using multi-dimensional triple resonance NMR of samples enriched with 13C and 15N. Residues corresponding to helix 2 (residues 98-106) and helix 1 (residues 54-68) of the native state give chemical shifts and NOE effects characteristic of helical structure. These same residues, however, give coupling constants and NOE effects indicative of fast conformational averaging between helical and extended conformations. The residual helix structure observed in the nuclease fragment is thus considerably less persistent than the corresponding structure in the native state. Based on H alpha chemical shifts, we estimate the fractional population of helical conformers to be 30% for helix 2 and 10% for helix 1. Two segments, 83-86 and 94-97, show NOE effects, coupling constants, and lowered amide temperature coefficients consistent with a native-like reverse-turn structure. The C-terminal alpha-helix as well as the fourth and fifth strands of the 5-strand beta-barrel show little evidence for ordered structure. The first three strands of the beta-sheet, part of the catalytic loop, and the first turn of helix 3 give significantly poorer NMR data than the rest of the protein, possibly as a result of exchange broadening, and could not be characterized in detail. That the most persistent elements of structure in the fragment are native-like suggests that nuclease may fold by a hierarchical mechanism.