Yw. Bai et al., Structural and dynamic characterization of an unfolded state of poplar apo-plastocyanin formed under nondenaturing conditions, PROTEIN SCI, 10(5), 2001, pp. 1056-1066
Plastocyanin is a predominantly beta -sheet protein containing a type I cop
per center. The conformational ensemble of a denatured state of apo-plastoc
yanin formed in solution under conditions of low salt and neutral pH has be
en investigated by multidimensional heteronuclear NMR spectroscopy. Chemica
l shift assignments were obtained by using three-dimensional triple-resonan
ce NMR experiments to trace through-bond heteronuclear connectivities along
the backbone and side chains. The (3)J(HN,H alpha) coupling constants, N-1
5-edited proton-proton nuclear Overhauser effects (NOEs), and N-15 relaxati
on parameters were also measured for the purpose of structural and dynamic
characterization Most of the residues corresponding to beta -strands in the
folded protein exhibit small upfield shifts of the C-13(alpha) and (CO)-C-
13 resonances relative to random coil values, suggesting a slight preferenc
e for backbone dihedral angles in the beta region of (phi,psi) space. This
is further supported by the presence of strong sequential d(alphaN)(i, i +1
) NOEs throughout the sequence. The few d(NN)(i, i + 1) proton NOEs that ar
e observed are mostly in regions that form loops in the native plastocyanin
structure. No medium or long-range NOEs were observed. A short sequence, b
etween residues 59 and 63, was found to populate a nonnative helical confor
mation in the unfolded state, as indicated by the shift of the C-13(alpha),
(CO)-C-13, and H-1(alpha) resonances relative to random coil values and by
the decreased values of the (3)J(HN,H alpha) coupling constants. The N-15
relaxation parameters indicate restriction of motions on a nanosecond times
cale in this region. Intriguingly, this helical conformation is present in
a sequence that is close to but not in the same location as the single shor
t helix in the native folded protein. The results are consistent with earli
er NMR studies of peptide fragments of plastocyanin and confirm that the re
gions of the sequence that form beta -strands in the native protein spontan
eously populate the beta -region of (phi,psi) space under folding condition
s, even in the absence of stabilizing tertiary interactions. We conclude th
at the state of apo-plastocyanin present under nondenaturing conditions is
a noncompact unfolded state with some evidence of nativelike and nonnative
local structuring that may be initiation sites for folding of the protein.