Dissipation at the angstrom scale: Probing the surface and interior of an enzyme

Abstract

Pursuing a materials science approach to understanding the deformability of enzymes, we introduce measurements of the phase of the mechanical response function within the nanorheology paradigm. Driven conformational motion of the enzyme is dissipative as characterized by the phase measurements. The dissipation originates both from the surface hydration layer and the interior of the molecule, probed by examining the effect of point mutations on the mechanics. We also document changes in the mechanics of the enzyme examined, guanylate kinase, upon binding its four substrates. GMP binding stiffens the molecule, ATP and ADP binding softens it, while there is no clear mechanical signature of GDP binding. A hyperactive two-Gly mutant is found to possibly trade specificity for speed. Global deformations of enzymes are shown to be dependent on both hydration layer and polypeptide chain dynamics.

Mechanical properties of BiP protein determined by nano‐rheology

“…Finally to close the chamber, a gold‐coated cover slip was arranged at 200 µm distance, constituting the upper part of the chamber, closing it and acting like a capacitor arrangement (Fig. S1) . After this a fresh chamber that last 8 h is ready to be used.…”

“…Protein's viscoelastic transition is a universal mechanical property of the folded state, and it is relevant for the large conformational changes, which often accompany substrate binding in proteins . Nano‐rheology is a novel ensemble technique that allows studying the mechanical properties of enzymes in their folded state, determining changes in their mechanical behavior as a function of an applied force . In this study, we used nano‐rheology to study the mechanical properties of the folded state of BiP protein, trying to determine changes in mechanical properties as consequence of force application and ligand binding (nucleotides and peptide substrate).…”

Thermoelectric effects at a Germanium-electrolyte interface: measuring 100 nK temperature oscillations at room temperature

“…As an example, take a globular protein of typical size ∼ 5 nm. The protein can be deformed by the large electric field at the Debye layer [24]; deformations beyond the linear elasticity regime can be achieved [25,26], which are then dissipative [9,10]. If n is the number of molecules per unit surface and the energy per molecule dissipated per cycle of the electric field, then the power dissipated per unit surface at the gold -elec-trolyte interface is P = n 2πω .…”

“…We are also interested in the temperature oscillation averaged over the Ge thickness; the corresponding amplitude is, using (10) :…”

“…Here we show that in our geometry, one can measure driven temperature oscillations of the solid-liquid interface of order 100 nK at room temperature. This resolution should allow to investigate by this method dissipative phenomena such as the internal dissipation of a driven molecular layer [9,10], and in general hydrodynamic dissipative phenomena down to the molecular scale.…”