Fast Photochemical Oxidation of Proteins and Mass Spectrometry Follow Submillisecond Protein Folding at the Amino-Acid Level

We report a study of submillisecond protein folding with amino-acid residue resolution achieved with a two-laser pump/probe experiment with analysis by mass spectrometry. The folding of a test., protein,,barstar, can be triggered by a laser-induced temperature jump (T jump) from similar to 0 degrees C to similar to room temperature. Subsequent reactions' via fast photochemical oxidation of proteins (FPOP) at various fractional millisecond points after the T jump lead to oxidative modification of solvent-accessible side chains whose "protection" changes with time and extent of folding. The modifications are identified and quantified by LC-MS/MS.following proteolysis. Among all the segments that form secondary structure in the 'native State, helix(1) shows a decreasing Arend of oxidative modification during the first 0.1-1 ms of folding while others do not change in this time range: Residues I5, H17, L20, L24 and F74 are modified less in the intermediate state than the denatured state, likely due.. to full or partial protection of these residues as folding occurs. We propose. that in the early folding stage, barstar forms a partially solvent-accessible hydrophobic core consisting of several residues that have long-range. interaction with other, more remote residues in the protein sequence. Our data not only are consistent with the previous conclusion that barstar fist folding follows the nucleation-condensation mechanism with the nucleus centered on helix(1) formed in a folding intermediate but also show the efficacy Of this new approach to following protein folding on the submilliseeond time range.