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Biology subjects

Jacquat, R. P. B.

Publications and source records attributed to Jacquat, R. P. B..

5 recordsLinked to original sources

Enhancement of Enzymatic Activity by Biomolecular Condensates through pH Buffering

Biomolecular condensates can affect enzymatic reactions by locally changing not only concentrations of molecules but also their environment. Since protein conformations can differ between the dense and dilute phase, phase separation can particularly modulate enzymes characterized by a conformation-dependent activity. Here, we generate enzymatic condensates based on a lipase from Bacillus thermocatenulatus, which exhibits an equilibrium between a closed, inactive state, and an open, active conformation. We show that the activity of the enzyme increases inside the dense phase, leading to an enhancement of the overall reaction rate in the phase-separated system. Moreover, we demonstrate that these condensates can generate a more basic environment compared to the surrounding solution. As a consequence, the phase-separated system maintains a high enzymatic activity even in acidic conditions that would be otherwise less favourable for the lipase. We further show that the formation of two phases with distinct pH values optimizes a cascade reaction involving two enzymes with different optimal pH conditions. Our results demonstrate that biomolecular condensates can also affect the dependence of enzymatic rates on solution pH, thereby expanding the accessible pH interval and enabling network reactions with enzymes that require distinct pH values. These findings have crucial implications in biology and biotechnology for biocatalytic engineering.

biochemistry↗

Single-molecule digital sizing of proteins in solution

Proteins constitute the molecular machinery of life and exert their biological function by interacting with other proteins, as well as by assembling into biomolecular complexes and higher order structures. Characterizing the sizes, interactions, and assembly states of proteins is thus key for understanding the normal functional behavior of proteins and for elucidating aberrant processes and interactions that can lead to dysfunction and disease. However, the physical characterization of proteins has remained a challenging problem due to the inherent compositional heterogeneity of protein mixtures as well as the polydisperse nature of protein complexes. Here, we address this challenge by demonstrating measurements of molecular diffusivity of single proteins and protein assemblies in microchannels using single-molecule fluorescence detection. The approach, termed single-molecule microfluidic diffusional sizing (smMDS), allows individual molecules to be counted directly, that is, in a digital manner, to enable calibration-free single-molecule diffusional-sizing-based monitoring of protein hydrodynamic radii even within heterogenous multicomponent mixtures. Applying smMDS to a variety of protein systems, we show that the high sensitivity provided by smMDS enables ultrasensitive sizing of proteins down to the femtomolar concentration range. We further demonstrate the applicability of the approach towards affinity profiling of protein interactions at the single-molecule level and illustrate the potential of smMDS in resolving different assembly states of high- and low-molecular weight protein oligomers. Furthermore, we highlight the digital nature of the detection process by sizing multiple protein species within complex aggregation mixtures. Finally, we apply the approach to characterize nanoscale clusters of a phase separating protein system. Taken together, smMDS constitutes a versatile approach for digital, in-solution characterization of the sizes, interactions, and assembly states of proteins. We anticipate that smMDS will facilitate the discovery of new biomolecular mechanisms of proteins and will find broad applicability in the analysis of protein complexes in the biological, biophysical, and biomedical sciences, and beyond.

biophysics↗

Single-molecule sizing through nano-cavity confinement

An approach relying on nano-cavity confinement is developed in this paper for the sizing of nanoscale particles and single biomolecules in solution. The approach, termed nano-cavity diffusional sizing (NDS), measures particle residence times within fluidic nano-cavities to determine their hydrodynamic radii. Using theoretical modeling and simulation, we show that the residence time of particles within nano-cavities above a critical timescale depends on the diffusion coefficient of the particle, which allows estimation of the particles size. We demonstrate this approach experimentally through measurement of particle residence times within nano-fluidic cavities using single-molecule confocal microscopy. Our data show that the residence times scale linearly with the sizes of nanoscale colloids, protein aggregates and single DNA oligonucleotides. NDS thus constitutes a new single molecule optofluidic approach that allows rapid and quantitative sizing of nanoscale particles for potential application in nanobiotechnology, biophysics, and clinical diagnostics. Table of content graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/472369v2_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@15abf7eorg.highwire.dtl.DTLVardef@d2180dorg.highwire.dtl.DTLVardef@1290f57org.highwire.dtl.DTLVardef@ae2087_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

2-photon-fabricated nano-fluidic traps for extended detection of single macromolecules and colloids in solution

The analysis of nanoscopic species, such as proteins and colloidal assemblies, at the single-molecule level has become vital in many areas of fundamental and applied research. Approaches to increase the detection timescales for single molecules in solution without immobilising them onto a substrate surface and applying external fields are much sought after. Here we present an easy-to-implement and versatile nanofluidics-based approach that enables increased observational-timescale analysis of single biomacromolecules and nanoscale colloids in solution. We use two-photon-based hybrid lithography in conjunction with soft lithography to fabricate nanofluidic devices with nano-trapping geometries down to 100 nm in height. We provide a rigorous description and characterisation of the fabrication route that enables the writing of nanoscopic 3D structures directly in photoresist and allows for the integration of nano-trapping and nano-channel geometries within micro-channel devices. Using confocal fluorescence burst detection, we validated the functionality of particle confinement in our nano-trap geometries through measurement of particle residence times. All species under study, including nanoscale colloids, -synuclein oligomers, and double-stranded DNA, showed a three to five-fold increase in average residence time in the detection volume of nano-traps, due to the additional local steric confinement, in comparison to free space diffusion in a nearby micro-channel. Our approach thus opens-up the possibility for single-molecule studies at prolonged observational timescales to analyse and detect nanoparticles and protein assemblies in solution without the need for surface immobilisation.

biophysics↗

Direct digital sensing of proteins through single-molecule optofluidics

The detection of proteins is of central importance to biomolecular analysis and diagnostics, yet fundamental limitations due to the surface-based nature of most sensing approaches persist, and limited improvements have been designed to integrate multimodal information beyond concentration measurements. Here we present a single-molecule microfluidic sensing platform for digital protein biomarker detection in solution, termed digital immunosensor assay (DigitISA). DigitISA is based on microchip electrophoretic separation combined with single-molecule detection and enables absolute number-concentrations quantification of proteins in a single, solution-phase step. Applying DigitISA to a range of targets including amyloid aggregates, exosomes, and biomolecular condensates, we demonstrate that the assay provides information beyond stoichiometric interactions, and enables characterization of immunochemistry, binding affinity, and protein biomarker abundance. Together, DigitISA constitutes a new experimental paradigm for the digital sensing of protein biomarkers, and enables analyses of targets that would otherwise be hard or impossible to address by conventional immuno-sensing techniques.

biophysics↗