Estimating Kinetic and Thermodynamic Parameters from Single Molecule Enzyme−Inhibitor Interactions

Kinetic parameters from detection probability in single molecule force spectroscopy.

The detection probability of rupture events in AFM force spectroscopy measurements presents a viable alternative to standard methods for extracting kinetic parameters of dissociation. The detection probability has a maximum as a function of the probe velocity where (1) the probability to form a molecular bond is independent of the probe velocity and (2) the detection of rupture events is limite...

Single-Molecule Kinetic and Thermodynamic Studies of Cation-Facilitated RNA Folding: Isolated Tertiary Interactions

Kinetic and thermodynamic characterization of single-mismatch discrimination using single-molecule imaging

A single-molecule detection setup based on total internal reflection fluorescence (TIRF) microscopy has been used to investigate association and dissociation kinetics of unlabeled 30mer DNA strands. Single-molecule sensitivity was accomplished by letting unlabeled DNA target strands mediate the binding of DNA-modified and fluorescently labeled liposomes to a DNA-modified surface. The liposomes,...

Estimating Enzyme Kinetic Parameters from Apparent KMs and Vmaxs

The kinetic properties of enzymes are often reported using the apparent KM and Vmax appropriate to the standard Michaelis-Menten enzyme. However, this model is inappropriate to enzymes that have more than one substrate or where the rate expression does not apply for other reasons. Consequently, it is desirable to have a means of estimating the appropriate kinetic parameters from the apparent va...

Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension.

We use mesoscopic nonequilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yie...