How Experiments See Fluctuations of Native Proteins: Perspective from an Exact Model KAREN E. S. TANG, 1,  KEN A. DILL 2 1 Graduate Group in Biophysics, University of California, San Francisco, California, 94143-1204 2 Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143- 1204 Received 16 September 1998; accepted 18 November 1998 ABSTRACT: Proteins undergo fluctuations under native conditions. Many lines of evidence are usually interpreted as implying that fluctuations are small excursions away from the native structure. By definition, fluctuations from the native conformation are small increases in free energy. But if protein folding energy landscapes are bumpy, such fluctuations could involve highly nonnative but compact ‘‘misfolded’’ structures, even while the excursions in energy are small. Using a model in which we can rigorously study fluctuations and rugged energy landscapes, we ask whether current experimental measures of structure, such as X-ray crystallographic Patterson maps and Debye  Waller Ž . Ž . factors or nuclear magnetic resonance NMR nuclear Overhauser effect NOE spectra, could detect bumpy landscapes. We find that even a substantial population of highly nonnative transients will generally be masked by the heavy averaging implicit in current experiments. This means that, in contrast to current interpretations, very nonnative or Misfold Fluctuations of native proteins may exist but are escaping experimental detection. A positive implication is that structure determination is robust to the presence of much conformational noise.  1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 147164, 1999 Key words: rugged energy landscape; conformational plasticity; NMR NOESY; X-ray crystallography; Debye  Waller factor * Current address: Department of Biochemistry, 140 Gortner Lab, University of Minnesota, St Paul, MN 55108-1022. Correspondence to: Ken A. Dill. Project grant sponsors: NIH; ONR; USCF Graduate Dean’s Health Science Fellowship; UCSF Regent’s Fellowship. ( ) International Journal of Quantum Chemistry, Vol. 75, 147 164 1999  1999 John Wiley & Sons, Inc. CCC 0020-7608 / 99 / 030147-18