Fitting high-resolution electron density maps from atomic models to solution scattering data

doi:10.1016/j.bpj.2023.10.034

2023-12-01

Sarah Chamberlain

Moore, Stephen

Thomas D. Grant *

DOI：10.1016/j.bpj.2023.10.034

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摘要

En 中文

Solution scattering techniques, such as small-and wide-angle X-ray scattering (SWAXS), provide valuable in-sights into the structure and dynamics of biological macromolecules in solution. In this study, we present an approach to accu-rately predict solution X-ray scattering profiles at wide angles from atomic models by generating high-resolution electron density maps. Our method accounts for the excluded volume of bulk solvent by calculating unique adjusted atomic volumes directly from the atomic coordinates. This approach eliminates the need for one of the free fitting parameters commonly used in existing al-gorithms, resulting in improved accuracy of the calculated SWAXS profile. An implicit model of the hydration shell is generated that uses the form factor of water. Two parameters, namely the bulk solvent density and the mean hydration shell contrast, are adjusted to best fit the data. Results using eight publicly available SWAXS profiles show high-quality fits to the data. In each case, the optimized parameter values show small adjustments demonstrating that the default values are close to the true solu-tion. Disabling parameter optimization produces significantly more accurate predicted scattering profiles compared to the lead-ing software. The algorithm is computationally efficient, comparable to the leading software and up to 10 times faster for large molecules. The algorithm is encoded in a command line script called denss.pdb2mrc.py and is available open source as part of the DENSS v1.7.0 software package. In addition to improving the ability to compare atomic models to experimental SWAXS data, these developments pave the way for increasing the accuracy of modeling algorithms using SWAXS data and decreasing the risk of overfitting.

Keyword:

X-RAY-SCATTERING

SMALL-ANGLE SCATTERING

WEB SERVER

BIOLOGICAL MACROMOLECULES

HYDRATION LAYER

COMPUTATION

SAXS

PROTEINS

PROFILES

SOLVENT