Radially softening diffusive motions in a globular protein

Area of Science:

• Biophysics
• Structural Biology
• Computational Biology

Background:

• Proteins exhibit complex atomic motions crucial for their function.
• Understanding these dynamics, especially in hydrated environments, is key to deciphering protein mechanisms.
• Previous studies suggest temperature-dependent transitions in protein dynamics.

Purpose of the Study:

• To characterize the diffusive motions within a hydrated protein, C-phycocyanin.
• To correlate atomic motion geometry and timescales with protein depth.
• To investigate the implications for protein function and temperature-induced transitions.

Main Methods:

• Combined molecular dynamics simulations, quasielastic neutron scattering, and analytical theory.
• Decomposition of simulation-derived scattering functions to identify key motion contributions.
• Modeling atomic motion geometry as diffusion in spheres with a distribution of radii.

Main Results:

• Atomic motions modeled as diffusion in spheres with a distribution of radii.
• Dynamics exhibit stretched exponential behavior, indicating a distribution of relaxation times.
• Side chain and backbone dynamics show smooth variation with distance from the protein core, with increasing flexibility outwards.

Conclusions:

• Protein dynamics exhibit a "radially softening" behavior, with increasing flexibility away from the core.
• This depth-dependent dynamics may influence protein function.
• Protein dynamical or glass transitions might be depth-dependent, with freezing occurring progressively further from the core as temperature decreases.