Protein hydrophobic collapse and early folding steps observed in a microfluidic mixer.

We demonstrate that the sub-millisecond protein folding process referred to as "collapse" actually consists of at least two separate processes. We observe the UV fluorescence spectrum from naturally occurring tryptophans in three well-studied proteins, cytochrome c, apomyoglobin, and lysozyme, as a function of time in a microfluidic mixer with a dead time of approximately 20 mus. Single value decomposition of the time-dependent spectra reveal two separate processes: 1), a spectral shift which occurs within the mixing time; and 2), a fluorescence decay occurring between approximately 100 and 300 micros. We attribute the first process to hydrophobic collapse and the second process to the formation of the first native tertiary contacts.

Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy.

We have used the combination of single-molecule Förster resonance energy transfer and kinetic synchrotron radiation circular dichroism experiments to probe the conformational ensemble of the collapsed unfolded state of the small cold shock protein CspTm under near-native conditions. This regime is physiologically most relevant but difficult to access experimentally, because the equilibrium signal in ensemble experiments is dominated by folded molecules. Here, we avoid this problem in two ways. One is the use of single-molecule Förster resonance energy transfer, which allows the separation of folded and unfolded subpopulations at equilibrium and provides information on long-range intramolecular distance distributions. From experiments with donor and acceptor chromophores placed at different positions within the chain, we find that the distance distributions in unfolded CspTm agree surprisingly well with a Gaussian chain not only at high concentrations of denaturant, where the polypeptide chain is expanded, but also at low denaturant concentrations, where the chain is collapsed. The second, complementary approach is synchrotron radiation circular dichroism spectroscopy of collapsed unfolded molecules transiently populated with a microfluidic device that enables rapid mixing. The results indicate a beta-structure content of the collapsed unfolded state of approximately 20% compared with the folded protein. This suggests that collapse can induce secondary structure in an unfolded state without interfering with long-range distance distributions characteristic of a random coil, which were previously found only for highly expanded unfolded proteins.

Optimization of a microfluidic mixer for studying protein folding kinetics.

We have applied an optimization method in conjunction with numerical simulations to minimize the mixing time of a microfluidic mixer developed for protein folding studies. The optimization method uses a semideterministic algorithm to find the global minimum of the mixing time by varying the mixer geometry and flow conditions. We describe the minimization problem and constraints and give a brief overview of the optimization algorithm. We present results of the optimization, including the optimized geometry and parameter sensitivities, and we demonstrate the improvement in mixing performance with experiments using microfabricated mixers. The dye-quenching experiments of the original and optimized mixer designs show respective mixing times of 7 and 4 mus, a 40% reduction. The new design also provides more uniform mixing across streamlines that enter the mixer. The optimized mixer is the fastest reported continuous flow mixer for protein folding.

Femtomole mixer for microsecond kinetic studies of protein folding.

We have developed a microfluidic mixer for studying protein folding and other reactions with a mixing time of 8 mus and sample consumption of femtomoles. This device enables us to access conformational changes under conditions far from equilibrium and at previously inaccessible time scales. In this paper, we discuss the design and optimization of the mixer using modeling of convective diffusion phenomena and a characterization of the mixer performance using microparticle image velocimetry, dye quenching, and Forster resonance energy-transfer (FRET) measurements of single-stranded DNA. We also demonstrate the feasibility of measuring fast protein folding kinetics using FRET with acyl-CoA binding protein.

Porous glass electroosmotic pumps: design and experiments.

An analytical model for electroosmotic flow rate, total pump current, and thermodynamic efficiency reported in a previous paper has been applied as a design guideline to fabricate porous-structure EO pumps. We have fabricated sintered-glass EO pumps that provide maximum flow rates and pressure capacities of 33 ml/min and 1.3 atm, respectively, at applied potential 100 V. These pumps are designed to be integrated with two-phase microchannel heat exchangers with load capacities of order 100 W and greater. Experiments were conducted with pumps of various geometries and using a relevant, practical range of working electrolyte ionic concentration. Characterization of the pumping performance are discussed in the terms of porosity, tortuosity, pore size, and the dependence of zeta potential on bulk ion density of the working solution. The effects of pressure and flow rate on pump current and thermodynamic efficiency are analyzed and compared to the model prediction. In particular, we explore the important tradeoff between increasing flow rate capacity and obtaining adequate thermodynamic efficiency. This research aims to demonstrate the performance of EOF pump systems and to investigate optimal and practical pump designs. We also present a gas recombination device that makes possible the implementation of this pumping technology into a closed-flow loop where electrolytic gases are converted into water and reclaimed by the system.