Local and Global Dynamics in Intrinsically Disordered Synuclein

Abstract

Intrinsically disordered proteins (IDPs) experience a diverse spectrum of motions that are difficult to characterize with a single experimental technique. Herein we combine high- and low-field nuclear spin relaxation, nanosecond fluorescence correlation spectroscopy (nsFCS), and long molecular dynamics simulations of alpha-synuclein, an IDP involved in Parkinson disease, to obtain a comprehensive picture of its conformational dynamics. The combined analysis shows that fast motions below 2 ns caused by local dihedral angle fluctuations and conformational sampling within and between Ramachandran substates decorrelate most of the backbone N-H orientational memory. However, slow motions with correlation times of up to ca. 13 ns from segmental dynamics are present throughout the alpha-synuclein chain, in particular in its C-terminal domain, and global chain reconfiguration occurs on a timescale of ca. 60 ns. Our study demonstrates a powerful strategy to determine residue-specific protein dynamics in IDPs at different time and length scales.

Sequence-dependent correlated segments in the intrinsically disordered region of ChiZ

“…Still, the demand for more accurate IDP force fields remains unabated, especially regarding dynamic properties. In several MD simulation studies, the CNH(t) correlation functions were fitted to a sum of exponentials, but either the fitting parameters or the trajectories used for the fitting had to be adjusted in order to reach agreement with experimental data (46)(47)(48)(49)(50)(51). It is thus notable that, using the AMBER14SB (52) / TIP4PD (43) force field and without adjusting CNH(t), Kämpf et al (53) were able to reproduce experimental relaxation data for the 26-residue N-terminal fragment of histone H4.…”

A facile oxygen-17 NMR method to determine effective viscosity in dilute, molecularly crowded and confined aqueous media

“…7 Protein dynamics generally occur at multiple time and length scales, which are best characterized through combination of several experimental techniques. 8,9 Due to differences in the inherent sensitivity of various experimental techniques, protein samples at different concentrations are often used for protein dynamical studies. It is therefore essential to quantify pure viscosity effects on protein dynamics before any reasonable comparison of experimental data obtained at different protein concentrations can be made.…”

“…NMR-based dynamical studies are frequently performed at high protein concentrations, where concentration-dependent changes in viscosity influence the timescale of different motional modes of proteins. In particular, low-field proton relaxometry, a powerful technique monitoring slow reorientational dynamics in disordered proteins, 9 requires millimolar protein concentrations. As exemplified by the ubiquitin and GB3 data above, the viscosity determination through 17 O R 1 of water enables direct evaluation of the viscosity effects on protein dynamics and allows disentangling pure viscosity effects from potential concentration-dependent phenomena such as protein self-association events.…”

Behavior of Protein-Inspired Synthetic Random Heteropolymers

“…For proteins, the reports of IDP relaxation timescales range from under a nanosecond to several microseconds for various molecular components, and full conformational interconversion likely takes tens of nanoseconds to microseconds. 35,76,77 78 With this information, we can see that our RHP is more dense and has slower remodeling than many IDPs, although is likely still more dynamic than most globular ordered proteins which configure slowly and exhibit greater compaction. In the future, it would be interesting to calculate the free energy barrier for remodeling, which will give direct kinetic information, at least for a single sequence.…”