Characterization of Viscous and Excluded Volume effects on the Folding Kinetics of the Tetraloop-Receptor Motif: Single Molecule Tests of Kramer's Theory
Characterization of Viscous and Excluded Volume effects on the Folding Kinetics of the Tetraloop-Receptor Motif: Single Molecule Tests of Kramer's Theory
It is widely known that there exists a strong relationship between the solvent, including co-solutes (e.g. cations, proteins, nucleic acids), and RNA that cooperatively defines the kinetics of tertiary structure formation. Viscosity, a solvent property that is coupled to dynamics, is critical in RNA folding due to the propensity for populating kinetically trapped species on a rough free energy landscape. Also of importance is the role of macromolecular co-solutes that limit the volume available for molecules to sample (excluded volume effects). The effects of these properties are highlighted by observed in vivo diffusion coefficients that are 4-200x smaller than in aqueous solvents. In this work, Kramers' rate theory is used to describe the viscosity dependence of tetraloop-receptor docking kinetics at the single molecule level. Both rate constants, kfold and kunfold, decrease with increasing viscosity (increasing glycerol %), trends that are predicted by Kramers' theory in the over-damped limit. However, the same measurements made in high molecular weight PEG solutions showed folding rate constants are accelerated by 1-2 orders of magnitude. Scaled particle theory, describing a hard spheres PEG-RNA interaction, quantitatively predicts the stabilizing effect of excluded volume. Temperature dependent measurements show that the thermodynamics of docking are not perturbed (ΔH°= −23(2) kcal/mol and ΔS°= −76(6) cal/mol∗K) even in up to 50% glycerol (∼6 cP) and that solvent activation accounts for 4-6 kcal/mol of the folding enthalpy. In PEG solutions thermodynamics reveal that the folding is stabilized by a reduction in the entropy of the unfolded RNA ensemble (ΔΔS°>0). Thus, these studies validate physical models describing characteristic kinetic and thermodynamic trends for intramolecular structure formation attributed to viscosity and excluded volume.
- University of Colorado Boulder United States
- Joint Institute for Laboratory Astrophysics United States
Biophysics
Biophysics
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