Internal Nanosecond Dynamics in the Intrinsically Disordered Myelin Basic Protein

Abstract

Intrinsically disordered proteins lack a well-defined folded structure and contain a high degree of structural freedom and conformational flexibility, which is expected to enhance binding to their physiological targets. In solution and in the lipid-free state, myelin basic protein belongs to that class of proteins. Using small-angle scattering, the protein was found to be structurally disordered similar to Gaussian chains. The combination of structural and hydrodynamic information revealed an intermediary compactness of the protein between globular proteins and random coil polymers. Modeling by a coarse-grained structural ensemble gave indications for a compact core with flexible ends. Neutron spin-echo spectroscopy measurements revealed a large contribution of internal dynamics to the overall diffusion. The experimental results showed a high flexibility of the structural ensemble. Displacement patterns along the first two normal modes demonstrated that collective stretching and bending motions dominate the internal modes. The observed dynamics represent nanosecond conformational fluctuations within the reconstructed coarse-grained structural ensemble, allowing the exploration of a large configurational space. In an alternative approach, we investigated if models from polymer theory, recently used for the interpretation of fluorescence spectroscopy experiments on disordered proteins, are suitable for the interpretation of the observed motions. Within the framework of the Zimm model with internal friction (ZIF), a large offset of 81.6 ns is needed as an addition to all relaxation times due to intrachain friction sources. The ZIF model, however, shows small but systematic deviations from the measured data. The large value of the internal friction leads to the breakdown of the Zimm model.

Membrane Association Landscape of Myelin Basic Protein Portrays Formation of the Myelin Major Dense Line

“…The ab initio model (Fig. 1b) is elongated and similar to previously described models 20, 21 . Ensemble optimisation analysis (EOM) revealed distinct subpopulations of both R g and maximum particle dimension ( D max ), suggesting the presence of different rMBP conformational species in solution (Fig.…”

“…A notable amount of past MBP research has been performed using C-terminally His 6 -tagged recombinant MBP (MBP-His) 12, 14, 15, 19, 20 or MBP purified from nerve tissue 4, 9, 10, 16, 17, 21 . To overcome problems arising from construct design or contaminants and heterogeneity in tissue extracts, we used untagged recombinant murine MBP (rMBP) corresponding to the major 18.5-kDa isoform, similarly to other recent studies 18, 22–24 .…”

Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins

“…These observations may at least partially explain why the two different definitions of friction, internal friction (operationally defined as solvent viscosity independent component of reconfiguration time) and barrier friction (stemming from hindered dihedral rotations) may coincide 27 . Experimental studies that probed not only the slowest relaxation time but also the entire spectrum of relaxation times 27, 32 further suggest that the dynamics of unfolded proteins can be interpreted in terms of the Rouse or Zimm models with internal friction 18, 24, 33, 34 (RIF and ZIF), whose physical foundation is the Kuhn picture of barrier friction 35 . RIF and ZIF provide a semi-phenomenological description of internal friction effects and build on the classic Rouse and Zimm models of polymer dynamics.…”

Perspective: Chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single-molecule FRET

“…119 Neutron spin echo spectroscopy 120 may be the only other method besides nsFCS currently available for probing (bio)polymer chain dynamics in the tens of nanosecond range; it can reveal a large spectrum of relaxation modes and has been used to identify internal friction. 121,122 Arguably the most popular technique for IDPs is nuclear magnetic resonance (NMR) spectroscopy: While the time scales of global chain dynamics are difficult to access with NMR because of rotational decorrelation, the technique is ideal for obtaining a wealth of information on local dynamics, especially on the level of individual residues or segments forming secondary structures. 123,124 With such combined data acting as stringent benchmarks or restraints, it should ultimately be possible to use the framework of MD simulations to describe the complete structural and dynamic properties of unfolded and intrinsically disordered proteins from picoseconds to microseconds and beyond.…”