Using inelastic neutron scattering (INS) and quasi-elastic neutron scattering (QENS), an international group of researchers have carried out a series of studies looking at the behaviour of protein molecules and their interaction with water both in model systems and in bacterial cells.
This information is important for understanding many biological processes as the internal dynamics of proteins, and the way they interact with water, are crucial to their function. Water also behaves differently inside biological cells than in bulk, suggesting other interactions are occurring.
The low-energy vibrational modes of proteins play an important role in the transportation of energy inside the molecules themselves, and facilitate their enzymatic function and binding to ligands and other biomolecules. However, the details of these modes have remained largely unknown because of limitations of the experimental techniques.
For their series of studies, this group relied on their synthesis of perdeuterated proteins, enabling the group to use neutron scattering to study the hydrogen atoms in the water without the “noise" created by the hydrogen atoms in the protein molecules. Perdeuterated proteins are particularly useful for exploring the collective motion of the protein molecules.
The group's initial study on this work, published in Physical Review Research, used inelastic neutron scattering on the LET instrument at ISIS alongside molecular dynamics simulations. They found that the protein vibrational modes are correlated mainly through the peptide bonds rather than noncovalent interactions such as hydrogen bonds.
They also found that their results could be produced using a simple one-dimensional model, which could then also be used for future investigations into the behaviour of other biomacromolecules, and other polymers.
In addition to the work on the protein vibrations, the group also studied the behaviour of water molecules surrounding the protein molecules. Previous experiments into the behaviour of the water have used a wide range of experimental techniques, but produced a similarly wide range of results.
To shed light on the cause of these contradictory results, the group did neutron scattering studies of a perdeuterated protein at a series of hydration levels using Osiris at ISIS, and BASIS at the Oak Ridge National laboratory, publishing their work in PCCP.
They found that both the translational and rotational motions of water are slowed down with decreasing protein hydration, with the two motions decoupling, and the translational mobility decreasing more dramatically.
Using molecular dynamics simulations, they suggest that this is likely to be due to the translational motion being restricted by spatial constraints, and the interaction between the water molecules and the charged, or polar, areas of the protein surface.
Their work also rationalises the previous contradictory results, by considering the timescales under which the experiments took place. They suggest that future work should use one technique across the full range of timescales to explore the motion decoupling in more detail.
Continuing their work combining neutron scattering and isotopic labelling, the group carried out a further study, published in Structural Dynamics, which characterised the translational motion of water on a biomolecular surface in a hydrated protein powder, a concentrated protein solution and in living Escherichia coli (E. coli) cells.
They found that the behaviour of the water in all three systems was similar, exhibiting the slower 'sub-diffusive' character seen in biological cells.
“By combining neutron and selective deuteration we have been able to video the motions of protein and its surface water, giving us new insights into their behaviour," explains study author Liang Hong.
One-dimensional nature of protein low-energy vibrations, https://doi.org/10.1103/PhysRevResearch.2.032050
Decoupling between the translation and rotation of water in the proximity of a protein molecule, https://doi.org/10.1039/D0CP02416C
Anomalous sub-diffusion of water in biosystems: From hydrated protein powders to concentrated protein solution to living cells, https://aca.scitation.org/doi/full/10.1063/4.0000036