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Improving Coarse-Grained Protein Force Fields with Small-Angle X-ray Scattering Data

Author:
Latham, Andrew P., Zhang, Bin
Source:
TheJournal of physical chemistry 2019 v.123 no.5 pp. 1026-1034
ISSN:
1520-5207
Subject:
biochemical compounds, energy, models, protein structure, small-angle X-ray scattering
Abstract:
Small-angle X-ray scattering (SAXS) experiments provide valuable structural data for biomolecules in solution. We develop a highly efficient maximum entropy approach to fit SAXS data by introducing minimal biases to a coarse-grained protein force field, the associative memory, water mediated, structure, and energy model (AWSEM). We demonstrate that the resulting force field, AWSEM-SAXS, succeeds in reproducing scattering profiles and models protein structures with shapes that are in much better agreement with experimental results. Quantitative metrics further reveal a modest, but consistent, improvement in the accuracy of modeled structures when SAXS data are incorporated into the force field. Additionally, when applied to a multiconformational protein, we find that AWSEM-SAXS is able to recover the population of different protein conformations from SAXS data alone. We, therefore, conclude that the maximum entropy approach is effective in fine-tuning the force field to better characterize both protein structure and conformational fluctuation.
Agid:
6303215