Probing the folding capacity and residual structures in 1-79 residues fragment of staphylococcal nuclease by biophysical and NMR methods.
1-79 residues SNase fragment (SNase79) has chain length containing a sequence for helix alpha(1), omega-loop, beta(I)-sheet, and partial beta(II)-sheet of native SNase. The incomplete "beta-barrel" structural region of SNase79 makes this fragment to be interested in investigation of its conformation. For this study, we use CD, fluorescence, and NMR spectroscopy to probe the folding capacity and the residual structures in SNase79. The optical spectra obtained for SNase79 and its mutants reveal the presence of retained capacity for folding of the fragment. The NMR derived (13)C(alpha) secondary chemical shifts, (3)J(NH-Halpha) coupling constants, amide-proton temperature coefficients, interresidue NOEs, and (15)N relaxation data determine the intrinsic propensities for helix- and turn- or beta-sheet-like conformations of SNase79, which is not the result of stabilizing inter-molecular interactions by oligomerization effects. The residual turn- and helix-like structures may serve as potential local nucleation sites, whereas the residual beta(I)-sheet-like structure can be regarded as a potential non-local nucleation site in the folding of SNase79. The intrinsic local and non-local interactions in these potential initiation sites are insufficient to stabilize the folding of SNase79 due to the shortage of relevant long-range interactions from other part of the fragment. The conformational ensemble of SNase79 is a highly heterogeneous collection of interconverting conformations having transiently populated helix- and beta-sheet- or turn-like structures.
Wang
Xu
X
National Laboratory of Biomacromolecules, Center for Structural and Molecular Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People's Republic of China.
Wang
Min
M
Tong
Yufeng
Y
Shan
Lu
L
Wang
Jinfeng
J
D000595:Amino Acid Sequence; D002942:Circular Dichroism; D009682:Magnetic Resonance Spectroscopy; D008836:Micrococcal Nuclease / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011522:Protons; D013050:Spectrometry, Fluorescence; D013696:Temperature; D014508:Urea / Q000378:metabolism
D011522:Protons; D014508:Urea; D008836:Micrococcal Nuclease