Intramolecular Diffusion in α-Synuclein: It Depends on How You Measure It

Abstract

Intramolecular protein diffusion, the motion of one part of the polypeptide chain relative to another part, is a fundamental aspect of protein folding and may modulate amyloidogenesis of disease-associated intrinsically disordered proteins. Much work has determined such diffusion coefficients using a variety of probes, but there has been an apparent discrepancy between measurements using long-range probes, such as fluorescence resonance energy transfer, and short-range probes, such as Trp-Cys quenching. In this work, we make both such measurements on the same protein, α-synuclein, and confirm that such discrepancy exists. Molecular dynamics simulations suggest that such differences result from a diffusion coefficient that depends on the spatial distance between probes. Diffusional estimates in good quantitative agreement with experiment are obtained by accounting for the distinct distance ranges probed by fluorescence resonance energy transfer and Trp-Cys quenching.

Segmental Motions of Proteins under Non-native States Evaluated Using Quasielastic Neutron Scattering

“…The intramolecular diffusion coefficients have been estimated using the fluorescence-based techniques for unfolded proteins and IDPs. The values obtained are on the order of 10 –7 cm 2 /s and, in some cases, 10 –6 cm 2 /s. − These values are consistent with the values of D seg obtained here. In particular, the intramolecular diffusion coefficients of RNase A under the MG and unfolded states were estimated from the time-resolved fluorescence measurements to be 1.5 × 10 –7 and 4.7 × 10 –7 cm 2 /s, respectively .…”

Dynamical Behavior of Disordered Regions in Disease-Related Proteins Revealed by Quasielastic Neutron Scattering

“…On the other hand, the D seg values of αSyn are 14.3 ± 0.9 × 10 −7 cm 2 /s and 15.1 ± 0.8 × 10 −7 cm 2 /s for the low-and high-salt conditions, respectively. These values are consistent with the values of the intramolecular diffusion coefficients obtained by other techniques [42][43][44], indicating the usefulness of D seg . The hydrodynamic radius, R H , corresponding to D seg, can be calculated using the Stokes-Einstein equation, D = k B T/6πηR H , where k B is the Boltzmann constant, η is the viscosity.…”

Kinetics of Loop Closure in Disordered Proteins: Theory vs Simulations vs Experiments

“…37 The key parameter that is reported by such studies is thus the intrachain diffusion coefficient D. Experimental studies however suggest that, for the same system, the measured value of D may be different for short-range and long-range probes. 63 Polymer theory similarly indicates that the apparent value of the diffusion coefficient should generally be dependent on the time and length scale of the process. 20,39 One way to interpret this is that memory effects in the intrachain dynamics cause the diffusion coefficient to be a frequencydependent quantity, with its apparent value being dependent on the characteristic frequency or time scale of the process.…”