Molecular dynamics simulation combined with small-angle X-ray/neutron scattering defining solution-state protein structures

Protein crystallography is frequently used to obtain the atomic-resolution structure of a particular protein by x-ray diffraction of its crystallized form. Nevertheless, a single static structure cannot represent the sequence structural dynamics of a protein's function. Based on our previous study (J. Phys. Chem. B 2017, 121 (50), 11229-11240 and ACS Catal. 2018, 8 (3), 2534-2545), we herein introduce a strategy of determining the protein hydration structures by small-angle X-ray and neutron scattering (SAXS and SANS) with contrast variation techniques, in combination with molecular dynamics simulation (MD), to describe hydrodynamics conformation transitions of biomacromolecules. Water is a partner that conducts the dynamics of proteins, and hydration interactions with proteins affect their dynamics. To shed light on the way of the chemical constitution of a protein, the water interactions, and the dynamics of its structure underlie the specific mechanisms of enzyme functions, we review an integrated approach using small-angle X-ray and neutron scattering (SAXS and SANS) in combination with molecular dynamics (MD) simulation to probe the structural dynamics of a given protein, thus shedding light on its function.

Automated summary

This article introduces a strategy for determining protein hydration structures using small-angle X-ray and neutron scattering in combination with molecular dynamics simulation, to describe the hydrodynamics conformation transitions of biomacromolecules.