Direct observation of multiple and stochastic transition states by a feedback-controlled single-molecule force measurement.

To overcome the ensemble-averaging barrier, single-molecule experiments have been performed, but energy landscapes comprising multiple intermediates have not yet been defined. We performed mechanical unfolding of staphylococcal nuclease using intermolecular force microscopy, modified AFM with high resolution and feedback control of the positioning. The force dropped vertically just after its peak, and multiple transition states were detected as force peaks. The multiple and stochastic intermediates found in the present study provide new important information on protein folding.

Stochastic emergence of multiple intermediates detected by single-molecule quasi-static mechanical unfolding of protein.

Experimental probing of a protein-folding energy landscape can be challenging, and energy landscapes comprising multiple intermediates have not yet been defined. Here, we quasi-statically unfolded single molecules of staphylococcal nuclease by constant-rate mechanical stretching with a feedback positioning system. Multiple discrete transition states were detected as force peaks, and only some of the multiple transition states emerged stochastically in each trial. This finding was confirmed by molecular dynamics simulations, and agreed with another result of the simulations which showed that individual trajectories took highly heterogeneous pathways. The presence of Ca2+ did not change the location of the transition states, but changed the frequency of the emergence. Transition states emerged more frequently in stabilized domains. The simulations also confirmed this feature, and showed that the stabilized domains had rugged energy surfaces. The mean energy required per residue to disrupt secondary structures was a few times the thermal energy (1-3 kBT), which agreed with the stochastic feature. Thus, single-molecule quasi-static measurement has achieved notable success in detecting stochastic features of a huge number of possible conformations of a protein.

Alignment of glycolipid nanotubes on a planar glass substrate using a two-step microextrusion technique.

We have developed a two-step microextrusion technique to align lipid nanotubes of 200 nm in diameter in parallel on planar glass substrates. This technique is useful to align self-assembled molecular nanofibers or nanotubes with diameters ranging from 100 to 300 nm. In the first step, we applied relatively large air pressure (approximately 40 hPa) onto a microcapillary filled with aqueous dispersion of lipid nanotubes to push them out. An aqueous droplet with 60 microm diameter was then extruded from the tip of the microcapillary. After one end of the lipid nanotube moved out, we changed the air pressure to be smaller, approximately 20 hPa to reduce the flow rate of the dispersion. The decrease in size of the droplet allowed us to fix the exposed end of the lipid nanotube onto the planar substrate. By dragging the microcapillary along the planar surface, we were able to align the whole nanotube onto the substrate. Using this technique, we have achieved the parallel alignment of the lipid nanotubes on the glass substrate.