Accretion of structure in staphylococcal nuclease: an 15N NMR relaxation study.
15N main-chain dynamics are compared in four forms of staphylococcal nuclease with different stabilities to unfolding: (1) SN-T, the ternary complex of the protein, Ca2+, and the inhibitor thymidine 3', 5'-bisphosphate; (2) SN, the protein in the absence of added ligands; (3) SN-OB, a folded fragment that corresponds to an "OB-fold" subdomain; (4) delta 131 delta, a denatured 131-residue fragment. SN-T exhibits very little internal motion on the nanosecond timescale. In SN, a moderate increase in flexibility is observed for the first three strands of the five-stranded beta-sheet, and for a loop between strands 4 and 5. In SN-OB, the loops between strands 3 and 4, and between strands 4 and 5, are extremely flexible on the nanosecond timescale. While the beta-sheets of SN-OB and SN have comparable dynamics on the nanosecond timescale, the beta-sheet in SN-OB experiences additional motion on a slower timescale of 330(+/-170) microseconds. We attribute the latter to interconversion between a major folded (> or = 98%) and a minor unfolded (> or = 2%) conformation. In delta 131 delta, the first three strands of beta-sheet experience conformational averaging on the millisecond timescale. Most of the remainder of the polypeptide chain is highly flexible on the nanosecond timescale. When all four forms of nuclease are considered, there is an increase in the proportion of residues with large amplitude internal motions (low order parameters) as the stability of the folded state is decreased. Residues with low order parameters cluster to distinct regions of the chain, and have H alpha chemical shifts and 3JHN-H alpha coupling constants that tend towards "random coil" values. Conversely, a trend towards uniformly high order parameters suggests a consolidation of structure with increasing stability to denaturation.
Alexandrescu
A T
AT
Department of Structural Biology, University of Basel, Switzerland.
Jahnke
W
W
Wiltscheck
R
R
Blommers
M J
MJ
D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008836:Micrococcal Nuclease / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding
D008836:Micrococcal Nuclease