Movements of the epsilon-subunit during catalysis and activation in single membrane-bound H(+)-ATP synthase

F0F1-ATP synthases catalyze proton transport-coupled ATP synthesis in bacteria, chloroplasts, and mitochondria. In these complexes, the epsilon-subunit is involved in the catalytic reaction and the activation of the enzyme. Fluorescence-labeled F0F1 from Escherichia coli was incorporated into liposomes. Single-molecule fluorescence resonance energy transfer (FRET) revealed that the epsilon-subunit rotates stepwise showing three distinct distances to the b-subunits in the peripheral stalk. Rotation occurred in opposite directions during ATP synthesis and hydrolysis. Analysis of the dwell times of each FRET state revealed different reactivities of the three catalytic sites that depended on the relative orientation of epsilon during rotation. Proton transport through the enzyme in the absence of nucleotides led to conformational changes of epsilon. When the enzyme was inactive (i.e. in the absence of substrates or without membrane energization), three distances were found again, which differed from those of the active enzyme. The three states of the inactive enzyme were unequally populated. We conclude that the active-inactive transition was associated with a conformational change of epsilon within the central stalk.

Revealing dynamics of helicase translocation on single-stranded DNA using high-resolution nanopore tweezers

Enzymes that operate on DNA or RNA perform the core functions of replication and expression in all of biology. To gain high-resolution access to the detailed mechanistic behavior of these enzymes, we developed single-molecule picometer-resolution nanopore tweezers (SPRNT), a single-molecule technique in which the motion of polynucleotides through an enzyme is measured by a nanopore. SPRNT reveals two mechanical substates of the ATP hydrolysis cycle of the superfamily 2 helicase Hel308 during translocation on single-stranded DNA (ssDNA). By analyzing these substates at millisecond resolution, we derive a detailed kinetic model for Hel308 translocation along ssDNA that sheds light on how superfamily 1 and 2 helicases turn ATP hydrolysis into motion along DNA. Surprisingly, we find that the DNA sequence within Hel308 affects the kinetics of helicase translocation.

Engineering and Modeling the Electrophoretic Trapping of a Single Protein Inside a Nanopore

The ability to confine and to study single molecules has enabled important advances in natural and applied sciences. Recently, we have shown that unlabeled proteins can be confined inside the biological nanopore Cytolysin A (ClyA) and conformational changes monitored by ionic current recordings. However, trapping small proteins remains a challenge. Here, we describe a system where steric, electrostatic, electrophoretic, and electro-osmotic forces are exploited to immobilize a small protein, dihydrofolate reductase (DHFR), inside ClyA. Assisted by electrostatic simulations, we show that the dwell time of DHFR inside ClyA can be increased by orders of magnitude (from milliseconds to seconds) by manipulation of the DHFR charge distribution. Further, we describe a physical model that includes a double energy barrier and the main electrophoretic components for trapping DHFR inside the nanopore. Simultaneous fits to the voltage dependence of the dwell times allowed direct estimates of the cis and trans translocation probabilities, the mean dwell time, and the force exerted by the electro-osmotic flow on the protein (≅9 pN at -50 mV) to be retrieved. The observed binding of NADPH to the trapped DHFR molecules suggested that the engineered proteins remained folded and functional inside ClyA. Contact-free confinement of single proteins inside nanopores can be employed for the manipulation and localized delivery of individual proteins and will have further applications in single-molecule analyte sensing and enzymology studies.

Plasmon-Enhanced Single-Molecule Enzymology

We present a numerical study on plasmon-enhanced single-molecule enzymology. We combine Brownian dynamics and electromagnetic simulations to calculate the enhancement of fluorescence signals of fluorogenic substrate converted by an enzyme conjugated to a plasmonic particle. We simulate the Brownian motion of a fluorescent product away from the active site of the enzyme, and calculate the photon detection rate taking into account modifications of the excitation and emission processes by coupling to the plasmon. We show that plasmon enhancement can boost the signal-to-noise ratio (SNR) of single turnovers by up to 100 fold compared to confocal microscopy. This enhancement factor is a trade-off between the reduced residence time in the near-field of the particle, and the enhanced emission intensity due to coupling to the plasmon. The enhancement depends on the size, shape and material of the particle and the photophysical properties of the fluorescent product. Our study provides guidelines on how to enhance the SNR of single-molecule enzyme studies and may aid in further understanding and quantifying static and dynamic heterogeneity.

AFM for Studying the Functional Activity of Enzymes

The conventional approach to investigating enzyme systems involves the simultaneous investigation of a large number of molecules and observing ensemble-averaged properties. However, modern science allows us to study the properties of single molecules and to obtain data on biochemical systems at a fundamentally new level, significantly expanding our understanding of the mechanisms of biochemical processes. Imaging of single biomolecules with high spatial and temporal resolution is among such modern research tools. To effectively image the individual steps or intermediates of biochemical reactions in single-molecule experiments, we need to develop a methodology for data acquisition and analysis. Its development will make it possible to solve the problem of separating the static and dynamic disorder present in the parameters identified by traditional proteomic methods. Such a methodology may be based on AFM imaging, the high-resolution microscopic visualization of enzymes. This review focuses on this direction of research, including the relevant methodological and practical solutions related to the potential of developing a single-molecule approach to the study of enzyme systems using AFM-based techniques. We focus on the results of enzyme reaction studies, as there are still few such studies, as opposed to the AFM studies of the mechanical properties of individual enzyme molecules.

AFM-Based Monitoring of Enzymatic Activity of Individual Molecules of Cytochrome CYP102A1

Herein, we report the use of a nanotechnology-based approach for the study of enzyme-functionalized mica surfaces. Atomic force microscopy (AFM) has been employed for the determination of the catalytic activity of single molecules of heme-containing cytochrome P450 CYP102A1 (CYP102A1) enzyme, which was immobilized on the surface of a mica chip. Height fluctuations in individual molecules of the enzyme were measured under near-native conditions by AFM measurements in liquid using a cantilever with a 10 to 20 nm tip curvature radius. We have found that in the process of enzymatic catalysis, the mean amplitude of height fluctuations in individual enzyme molecules is 1.4-fold higher than that of enzyme molecules in an inactive state. The temperature dependence of the mean amplitude of height fluctuations in cytochrome CYP102A1 has been revealed, and the maximum of this dependence has been observed at 22 °C. The proposed nanotechnology-based approach can be employed in studies of a wide variety of enzymes, which are important for the development of novel diagnostic tests and systems for pharmaceutical analysis. The approach developed in our work will favor further miniaturization of enzyme-based biosensors and the transition from traditional sensors to nanobiosensors.