Method of Rapid Mix EPR Applied to the Folding of Bi−Spin-Labeled Protein as a Probe for the Dynamic Onset of Interaction between Sequentially Distant Side Chains

The time scale over which an interaction between distant residues is established impacts the nature of protein folding. Our method for probing the interaction between distant residues is the result of newly developed rapid-mix flow EPR apparatus and of cysteine-directed spin labeling. In our method, entire spectra of bi-labeled protein have been acquired with better than millisecond time resolution after the start of folding. To do this, we use an ultra rapid ball-mixer interfaced to a mini dielectric resonator and combined with simultaneous rapid field scanning. Details of the specialized mixer, resonant structure, and the field sweep/data gathering are presented. This initial application focused on iso-1-cytochrome c cysteine-specifically bi-labeled at the cysteine-mutated sites, Ser47Cys and Lys79Cys. These are sequentially distant sites whose unmutated side chains in folded protein are less than 10 Å away from each other and whose spin labels are ∼14 Å distant as evidenced by spin−spin dipolar broadening of the EPR spectrum from the folded bi-labeled protein. During flow, we observed entire EPR spectra of folding protein with ages of 380 μs and 1.2 ms, referenced to the start of folding. Absence of dipolar-broadening showed that folding had not sufficiently proceeded at 380 microseconds or 1.2 milliseconds to cause the sequentially distant spin labeled side chains of residues 47 and 79 to achieve the conformation they have in folded protein, although diminishment of the EPR peak intensities was consistent with local probe enfolding/immobilization. Spectra obtained with rapid field scans triggered 1 s after the start of folding in the stopped-flow EPR mode showed significant, albeit incomplete, onset of the dipolar broadening interaction between the labels on Ser47Cys and Lys79Cys.