A simple three-dimensional-focusing, continuous-flow mixer for the study of fast protein dynamics

In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning

Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.

Chips for Biomaterials and Biomaterials for Chips: Recent Advances at the Interface between Microfabrication and Biomaterials Research

In recent years, the use of microfabrication techniques has allowed biomaterials studies which were originally carried out at larger length scales to be miniaturized as so-called "on-chip" experiments. These miniaturized experiments have a range of advantages which have led to an increase in their popularity. A range of biomaterial shapes and compositions are synthesized or manufactured on chip. Moreover, chips are developed to investigate specific aspects of interactions between biomaterials and biological systems. Finally, biomaterials are used in microfabricated devices to replicate the physiological microenvironment in studies using so-called "organ-on-chip," "tissue-on-chip" or "disease-on-chip" models, which can reduce the use of animal models with their inherent high cost and ethical issues, and due to the possible use of human cells can increase the translation of research from lab to clinic. This review gives an overview of recent developments at the interface between microfabrication and biomaterials science, and indicates potential future directions that the field may take. In particular, a trend toward increased scale and automation is apparent, allowing both industrial production of micron-scale biomaterials and high-throughput screening of the interaction of diverse materials libraries with cells and bioengineered tissues and organs.

Analysis of biomolecular condensates and protein phase separation with microfluidic technology

An increasing body of evidence shows that membraneless organelles are key components in cellular organization. These observations open a variety of outstanding questions about the physico-chemical rules underlying their assembly, disassembly and functions. Some molecular determinants of biomolecular condensates are challenging to probe and understand in complex in vivo systems. Minimalistic in vitro reconstitution approaches can fill this gap, mimicking key biological features, while maintaining sufficient simplicity to enable the analysis of fundamental aspects of biomolecular condensates. In this context, microfluidic technologies are highly attractive tools for the analysis of biomolecular phase transitions. In addition to enabling high-throughput measurements on small sample volumes, microfluidic tools provide for exquisite control of self-assembly in both time and space, leading to accurate quantitative analysis of biomolecular phase transitions. Here, with a specific focus on droplet-based microfluidics, we describe the advantages of microfluidic technology for the analysis of several aspects of phase separation. These include phase diagrams, dynamics of assembly and disassembly, rheological and surface properties, exchange of materials with the surrounding environment and the coupling between compartmentalization and biochemical reactions. We illustrate these concepts with selected examples, ranging from simple solutions of individual proteins to more complex mixtures of proteins and RNA, which represent synthetic models of biological membraneless organelles. Finally, we discuss how this technology may impact the bottom-up fabrication of synthetic artificial cells and for the development of synthetic protein materials in biotechnology.

On the competition between mixing rate and uniformity in a coaxial hydrodynamic focusing mixer

Fast microfluidic mixers for use with line-of-sight integrating detection schemes pose unique challenges. Such detectors typically cannot discriminate signal from slow moving (e.g. near internal walls) and fast-moving portions of the fluid stream. This convolves reaction rate dynamics with fluid flow residence time dynamics. Further, the small cross sections of typical three-dimensional hydrodynamic focusing devices lead to lower detection signals. The current study focuses on achieving both small time scales of mixing and homogenous residence times. This is achieved by injecting sample through a center capillary and hydrodynamically focusing using a sheath flow within a tapered second capillary. The current design also features a third, larger coaxial capillary. The mixed stream flows into the large cross-section of this third capillary to decelerate and expand the stream by up to 14-fold to improve line-of-sight signal strength of reaction products. Hydrodynamic focusing, mixing, and expansion are studied using analytical and numerical models and also studied experimentally using a fluorescein-iodide quenching reaction. The experimentally validated models are used to explore trade-offs between mixing rate and uniformity. For the first time, this work presents detailed analysis of the Lagrangian time history of species transport during mixing inside coaxial capillaries to measure mixing nonuniformity. The mixing region enables order 100 μs mixing times and residence time widths of the same order (140 μs).

Droplet-based optofluidic systems for measuring enzyme kinetics

The study of enzyme kinetics is of high significance in understanding metabolic networks in living cells and using enzymes in industrial applications. To gain insight into the catalytic mechanisms of enzymes, it is necessary to screen an enormous number of reaction conditions, a process that is typically laborious, time-consuming, and costly when using conventional measurement techniques. In recent times, droplet-based microfluidic systems have proved themselves to be of great utility in large-scale biological experimentation, since they consume a minimal sample, operate at high analytical throughput, are characterized by efficient mass and heat transfer, and offer high levels of integration and automation. The primary goal of this review is the introduction of novel microfluidic tools and detection methods for use in high-throughput and sensitive analysis of enzyme kinetics. The first part of this review focuses on introducing basic concepts of enzyme kinetics and describing most common microfluidic approaches, with a particular focus on segmented flow. Herein, the key advantages include accurate control over the flow behavior, efficient mass and heat transfer, multiplexing, and high-level integration with detection modalities. The second part describes the current state-of-the-art platforms for high-throughput and sensitive analysis of enzyme kinetics. In addition to our categorization of recent advances in measuring enzyme kinetics, we have endeavored to critically assess the limitations of each of these detection approaches and propose strategies to improve measurements in droplet-based microfluidics. Graphical abstract.

Resolution of Submillisecond Kinetics of Multiple Reaction Pathways for Lactate Dehydrogenase

Enzymes are known to exhibit conformational flexibility. An important consequence of this flexibility is that the same enzyme reaction can occur via multiple reaction pathways on a reaction landscape. A model enzyme for the study of reaction landscapes is lactate dehydrogenase. We have previously used temperature-jump (T-jump) methods to demonstrate that the reaction landscape of lactate dehydrogenase branches at multiple points creating pathways with varied reactivity. A limitation of this previous work is that the T-jump method makes only small perturbations to equilibrium and may not report conclusively on all steps in a reaction. Therefore, interpreting T-jump results of lactate dehydrogenase kinetics has required extensive computational modeling work. Rapid mixing methods offer a complementary approach that can access large perturbations from equilibrium; however, traditional enzyme mixing methods like stopped-flow do not allow for the observation of fast protein dynamics. In this report, we apply a microfluidic rapid mixing device with a mixing time of <100 μs that allows us to study these fast dynamics and the catalytic redox step of the enzyme reaction. Additionally, we report UV absorbance and emission T-jump results with improved signal-to-noise ratio at fast times. The combination of mixing and T-jump results yields an unprecedented view of lactate dehydrogenase enzymology, confirming the timescale of substrate-induced conformational change and presence of multiple reaction pathways.

Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR

The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate.

Sandwich-format 3D printed microfluidic mixers: a flexible platform for multi-probe analysis

We report on a microfluidic mixer fabrication platform that increases the versatility and flexibility of mixers for biomolecular applications. A sandwich-format design allows the application of multiple spectroscopic probes to the same mixer. A polymer spacer is 'sandwiched' between two transparent windows, creating a closed microfluidic system. The channels of the mixer are defined by regions in the polymer spacer that lack material and therefore the polymer need not be transparent in the spectral region of interest. Suitable window materials such as CaF₂ make the device accessible to a wide range of optical probe wavelengths, from the deep UV to the mid-IR. In this study, we use a commercially available 3D printer to print the polymer spacers to apply three different channel designs into the passive, continuous-flow mixer, and integrated them with three different spectroscopic probes. All three spectroscopic probes are applicable to each mixer without further changes. The sandwich-format mixer coupled with cost-effective 3D printed fabrication techniques could increase the applicability and accessibility of microfluidic mixing to intricate kinetic schemes and monitoring chemical synthesis in cases where only one probe technique proves insufficient.

Submillisecond mixing in a continuous-flow, microfluidic mixer utilizing mid-infrared hyperspectral imaging detection

We report a continuous-flow, microfluidic mixer utilizing mid-infrared hyperspectral imaging detection, with an experimentally determined, submillisecond mixing time. The simple and robust mixer design has the microfluidic channels cut through a polymer spacer that is sandwiched between two IR transparent windows. The mixer hydrodynamically focuses the sample stream with two side flow channels, squeezing it into a thin jet and initiating mixing through diffusion and advection. The detection system generates a mid-infrared hyperspectral absorbance image of the microfluidic sample stream. Calibration of the hyperspectral image yields the mid-IR absorbance spectrum of the sample versus time. A mixing time of 269 μs was measured for a pD jump from 3.2 to above 4.5 in a D2O sample solution of adenosine monophosphate (AMP), which acts as an infrared pD indicator. The mixer was further characterized by comparing experimental results with a simulation of the mixing of an H2O sample stream with a D2O sheath flow, showing good agreement between the two. The IR microfluidic mixer eliminates the need for fluorescence labeling of proteins with bulky, interfering dyes, because it uses the intrinsic IR absorbance of the molecules of interest, and the structural specificity of IR spectroscopy to follow specific chemical changes such as the protonation state of AMP.

An "off-the-shelf" capillary microfluidic device that enables tuning of the droplet breakup regime at constant flow rates

The fabrication of glass capillary microfluidic devices is technically challenging, often hampering use of the design. We describe a new technique, based on commercially available components, for assembling flow focusing capillary devices that can readily be taken apart and cleaned between uses. This design strategy allows for generation of both water-in-oil and oil-in-water emulsions in the same device after an ethanol rinse. The modularity of the device enables the adjustment of the tip separation between the two inner capillaries during droplet generation, which enables tuning of the age of the interface. Time-dependent surfactant diffusion to the interface changes the interfacial tension, thus providing an approach for adjusting the capillary number in addition to the usual method of changing flow rates. This design enables the tuning of the mode of breakup and the droplet size.