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Molecular dynamics simulation combined with small‐angle X‐ray/neutron scattering defining solution‐state protein structures
Author(s) -
Lin ShangWei,
Su KuanHsuan,
Yeh YiQi,
Jeng USer,
Wu ChunMing,
Yang HsiaoChing
Publication year - 2021
Publication title -
journal of the chinese chemical society
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.329
H-Index - 45
eISSN - 2192-6549
pISSN - 0009-4536
DOI - 10.1002/jccs.202000498
Subject(s) - chemistry , small angle x ray scattering , molecular dynamics , neutron scattering , crystallography , neutron diffraction , scattering , chemical physics , protein dynamics , protein structure , computational chemistry , crystal structure , physics , optics , biochemistry
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.