&Bullet; physics 14, s32
How fast a protein diffuses in a liquid depends directly on its radius, which changes when the conformation of the protein fluctuates.
Proteins are constantly changing their shape. These changes, which can be caused, for example, by temperature shifts, change the radius of the protein and impair its ability to move through a cell membrane. With the help of molecular dynamic simulations, Eiji Yamamoto from Keio University, Japan, and colleagues are now showing that changes in the radius can also directly influence the “instantaneous” diffusivity of a protein, ie its diffusivity at any point in time  . The finding could help explain more recent experimental measurements of the randomly fluctuating diffusivities of tracer particles such as colloids, quantum dots or fluorescence-labeled proteins in supercooled liquids, soft materials and biological systems.
A tracer moves in a liquid by colliding with and ricocheting off liquid molecules. The diffusivity of the tracer is traditionally determined by its radius and the viscosity of the liquid. In some systems, such as B. polymers in dilute solutions, where both the viscosity of the liquid and the radius of the tracer are believed to remain constant, the diffusivity has been observed to vary over time.
To investigate the origin of these fluctuations, Yamamoto and his team simulated the movement of proteins suspended in water under various pressure and temperature conditions. From these simulations, they calculated the time-dependent radius and the diffusivity of each protein.
The team found that the measured diffusivity decreased when conditions caused the protein radius to increase, and vice versa. They derived a relationship between radius and diffusivity and showed that it follows a time-dependent version of the classical diffusivity relationship for a spherical particle. The team speculates that the relationship holds for proteins more complex than those they studied, for other tracers found in cells, and for other deformable macromolecules and polymers.
Rachel Berkowitz is Corresponding Editor for physics based in Vancouver, Canada.
- E. Yamamoto et al., “Universal relationship between instantaneous diffusivity and radius of gyration of proteins in aqueous solution” Phys. Rev. Lett.126128101 (2021).