W0167

Burst Phase Collapse Studies and the Initial Barrier Mechanism in Protein Folding. Jaby Jacob^1,2, Bryan Krantz¹, Leland Mayne³, Shane Dothager¹, John Rumbley³, P. Thiyagarajan², S. Walter Englander³, and Tobin R. Sosnick^1,3, ¹Dept. of Biochemistry and Molecular Biology, The Univ. of Chicago, Chicago, IL 60637, ²Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, IL 60439, ²Dept. of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia, PA 19104, ⁴Institute for Biophysical Dynamics, The Univ.of Chicago, Chicago, IL 60637.

Do stable, collapsed intermediates form very early in the protein folding process? When a protein is transferred from high denaturant to low denaturant conditions, fluorescent techniques can exhibit sub-millisecond signal changes, which have been interpreted as the formation of structured intermediate states. An alternative interpretation of this behavior is a solvent-dependent response of the denatured molecule to the new solvent condition. To investigate this issue, we have performed time-resolved synchrotron small-angle scattering measurements on ubiquitin and common-type acylphosphatase. Upon dilution to lower than 1 M denaturant, the two proteins fail to exhibit any appreciable chain contraction at very early folding times. This lack of contraction indicates that collapse under aqueous conditions is not an obligate event for proteins, implying that water is a “good solvent” for polypeptides. The lack of contraction also suggests that burst phase fluorescent signals may be sensing a local environmental change of the fluorophore. In summary, these and previous results provide little support for early intermediate accumulation before an initial time-consuming conformational search that is necessary to find a nucleating transition state.