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Research Article

Measurement of water–amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique

  1. Susumu Mori1,*,
  2. Peter C.M. van Zijl1,2,
  3. David Shortle1,2

Article first published online: 7 DEC 1998

DOI: 10.1002/(SICI)1097-0134(199707)28:3<325::AID-PROT3>3.0.CO;2-B

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 28, Issue 3, pages 325–332, July 1997

Additional Information

How to Cite

Mori, S., van Zijl, P. C.M. and Shortle, D. (1997), Measurement of water–amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique. Proteins, 28: 325–332. doi: 10.1002/(SICI)1097-0134(199707)28:3<325::AID-PROT3>3.0.CO;2-B

Author Information

  1. 1

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland

  2. 2

    Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland

*Johns Hopkins University School of Medicine, Department of Radiology, 217 Traylor Bldg, 720 Rutland Avenue, Baltimore, MD 21205

Publication History

  1. Issue published online: 7 DEC 1998
  2. Article first published online: 7 DEC 1998
  3. Manuscript Accepted: 23 JAN 1997
  4. Manuscript Received: 26 SEP 1996

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Keywords:

  • hydrogen exchange;
  • denatured state;
  • staphylococcal nuclease;
  • NMR;
  • magnetization transfer

Abstract

The rates of hydrogen exchange were measured in a “physiological” denatured state of staphylococcal nuclease using a NMR magnetization transfer experiment suitable for the measurement of exchange rates faster than 0.5 s−1. The results are compared with predicted exchange rates (kex) for the random coil state (Bai et al., Proteins 17:75–86, 1993). No protection factors (· predicted rate/measured rate) larger than 2.4 were observed, consistent with other NMR data which strongly suggest only small amounts of residual secondary structure in this denatured state. Systematically low protection factors (0.51 · 0.23) were found for Asp and Glu residues, while high protection factors were observed for Gly (1.60 · 0.60). We conclude that the predicted exchange rates (kex) may have an uncertainty of 2- to 3-fold. Thus, for denatured proteins only protection factors with a value of 5 or larger can be assigned structural significance. These results also demonstrate that multidimensional magnetization transfer NMR techniques are powerful tools in this research field due to its ability to measure rapidly exchanging protons (·05 s−1) with high accuracy. Proteins 28:325–332, 1997. © 1997 Wiley-Liss, Inc.

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