Backbone dynamics of a highly disordered 131 residue fragment of staphylococcal nuclease

Andrei T. Alexandrescu, David Shortle

Research output: Contribution to journalArticlepeer-review


In order to characterize the dynamic properties of the denatured state of staphylococcal nuclease, R1, R2, and NOE relaxation parameters have been measured for the backbone 15N nuclei of a 131 residue fragment that serves as a model of the denatured state under non-denaturing conditions. The relaxation data indicate a wide range of amplitudes for segmental motion and are inconsistent with a random coil conformation. An optimal value of 7.8 ns was obtained for the molecular rotational correlation time τ(m), based on the analysis of the 79 residues for which R1, R2, and NOE relaxation data could be obtained. This value corresponds roughly to the slowest detectable motion on the nanosecond time scale and is of a magnitude consistent with global tumbling of a large portion of the molecule. For the majority of residues, experimental data could be described most adequately in terms of a modified 'model-free' formalism which includes contributions from internal motions on both an intermediate (τ(e)) and a fast time scale (τ(f)) in the context of Slow overall tumbling (τ(m)). The generalized order parameter S2, which gives the amplitude of motions on time scales faster than τ(m), correlates with sequence hydrophobicity and suggests a relationship between chain flexibility and sequence propensity for hydrophobic collapse. The fractional populations of three α-helices in the protein show a stronger correlation with S2 values and hydrophobicities than with intrinsic helix propensities. These observations suggest that secondary structure may be preferentially stabilized in hydrophobic segments of the sequence.

Original languageEnglish (US)
Pages (from-to)527-546
Number of pages20
JournalJournal of molecular biology
Issue number4
StatePublished - Sep 29 1994


  • Backbone dynamics
  • Multinuclear NMR
  • N relaxation
  • Order-disorder transitions
  • Protein folding

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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