Systematic Kinetics Study of FoF1-ATPase: Analytic Results and Comparison with Experiments

Modeling control and transduction of electrochemical gradients in acid-stressed bacteria

Transmembrane electrochemical gradients drive solute uptake and constitute a substantial fraction of the cellular energy pool in bacteria. These gradients act not only as "homeostatic contributors," but also play a dynamic and keystone role in several bacterial functions, including sensing, stress response, and metabolism. At the system level, multiple gradients interact with ion transporters and bacterial behavior in a complex, rapid, and emergent manner; consequently, experiments alone cannot untangle their interdependencies. Electrochemical gradient modeling provides a general framework to understand these interactions and their underlying mechanisms. We quantify the generation, maintenance, and interactions of electrical, proton, and potassium potential gradients under lactic acid-stress and lactic acid fermentation. Further, we elucidate a gradient-mediated mechanism for intracellular pH sensing and stress response. We demonstrate that this gradient model can yield insights on the energetic limitations of membrane transport, and can predict bacterial behavior across changing environments.

The dynamic evaporation process of the deep eutectic solvent LiTf2N:N-methylacetamide at ambient temperature

The dynamic evaporation process of the lithium-based deep eutectic solvent LiTf₂N:NMA under ambient conditions can be divided into three stages.

Structural conditions on complex networks for the Michaelis-Menten input-output response

The Michaelis-Menten (MM) fundamental formula describes how the rate of enzyme catalysis depends on substrate concentration. The familiar hyperbolic relationship was derived by timescale separation for a network of three reactions. The same formula has subsequently been found to describe steady-state input-output responses in many biological contexts, including single-molecule enzyme kinetics, gene regulation, transcription, translation, and force generation. Previous attempts to explain its ubiquity have been limited to networks with regular structure or simplifying parametric assumptions. Here, we exploit the graph-based linear framework for timescale separation to derive general structural conditions under which the MM formula arises. The conditions require a partition of the graph into two parts, akin to a "coarse graining" into the original MM graph, and constraints on where and how the input variable occurs. Other features of the graph, including the numerical values of parameters, can remain arbitrary, thereby explaining the formula's ubiquity. For systems at thermodynamic equilibrium, we derive a necessary and sufficient condition. For systems away from thermodynamic equilibrium, especially those with irreversible reactions, distinct structural conditions arise and a general characterization remains open. Nevertheless, our results accommodate, in much greater generality, all examples known to us in the literature.

Highly sensitive detection of NT-proBNP by molecular motor

F_oF₁-ATPase is an active rotary motor, and generates three-ATP for each rotation. At saturated substrate concentration, the motor can achieve about 10³ r.p.m, which means one motor can generate about 10⁵ ATP molecules during 30 min. Here, we constituted a novel nanodevice with a molecular rotary motor and a “battery”, F_oF₁-ATPase and chromatophore, and presented a novel method of sandwich type rotary biosensor based on ε subunit with one target-to-one motor, in which one target corresponds 10⁵ ATP molecules as detection signals during 30 min. The target such as NT-proBNP detection demonstrated that this novel nanodevice has potential to be developed into an ultrasensitive biosensor to detect low expressed targets.

Monte Carlo simulation from proton slip to "coupled" proton flow in ATP synthase based on the bi-site mechanism

ATP synthase couples proton flow to ATP synthesis, but is leaky to protons at very low nucleotide concentration. Based on the bi-site mechanism, we simulated the proton conduction from proton slip to "coupled" proton flow in ATP synthase using the Monte Carlo method. Good agreement is obtained between the simulated and available experimental results. Our model provides deeper insight into the nucleotide dependence of ATP catalysis, and the kinetic cooperativity in three catalysis subunits. The results of simulation support the bi-site mechanism in ATP synthesis.

FoF1-ATPase, rotary motor and biosensor

F(o)F(1)-ATPase is an amazing molecular rotary motor at the nanoscale. Single molecule technologies have contributed much to the understanding of the motor. For example, fluorescence imaging and spectroscopy revealed the physical rotation of isolated F(1) and F(o), or F(o)F(1) holoenzyme. Magnetic tweezers were employed to manipulate the ATP synthesis/hydrolysis in F(1), and proton translation in F(o). Here, we briefly review our recent works including a systematic kinetics study of the holoenzyme, the mechanochemical coupling mechanism, reconstituting the delta-free F(o)F(1)-ATPase, direct observation of F(o) rotation at single molecule level and activity regulation through external links on the stator.

F0F1-ATPase activity regulated by external links on beta subunits

F(o)F(1)-ATPase activity is regulated by external links on beta subunits with different molecular weight. It is inhibited when anti-beta subunit antibody, streptavidin and H9 antibody link on the beta subunits successively, but is activated when virus was binded. Western blotting indicated that the employed anti-beta antibody target was on the non-catalytic site of the beta subunit. Furthermore, an ESR study of spin-labeled ATP (SL-ATP) showed that the affinity of ATP to the holoenzyme increases with increasing external links on the beta subunits. This simple regulation method may have great potential in the design of rapid, free labeled, sensitive and selective biosensors.