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Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse...

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Autores principales: Su, Zhen, Dasgupta, Medhanjali, Poitevin, Frédéric, Mathews, Irimpan I., van den Bedem, Henry, Wall, Michael E., Yoon, Chun Hong, Wilson, Mark A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Crystallographic Association 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8270650/
https://www.ncbi.nlm.nih.gov/pubmed/34258328
http://dx.doi.org/10.1063/4.0000087
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author Su, Zhen
Dasgupta, Medhanjali
Poitevin, Frédéric
Mathews, Irimpan I.
van den Bedem, Henry
Wall, Michael E.
Yoon, Chun Hong
Wilson, Mark A.
author_facet Su, Zhen
Dasgupta, Medhanjali
Poitevin, Frédéric
Mathews, Irimpan I.
van den Bedem, Henry
Wall, Michael E.
Yoon, Chun Hong
Wilson, Mark A.
author_sort Su, Zhen
collection PubMed
description Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.
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spelling pubmed-82706502021-07-12 Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters Su, Zhen Dasgupta, Medhanjali Poitevin, Frédéric Mathews, Irimpan I. van den Bedem, Henry Wall, Michael E. Yoon, Chun Hong Wilson, Mark A. Struct Dyn ARTICLES Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments. American Crystallographic Association 2021-07-08 /pmc/articles/PMC8270650/ /pubmed/34258328 http://dx.doi.org/10.1063/4.0000087 Text en © 2021 Author(s). https://creativecommons.org/licenses/by/4.0/All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle ARTICLES
Su, Zhen
Dasgupta, Medhanjali
Poitevin, Frédéric
Mathews, Irimpan I.
van den Bedem, Henry
Wall, Michael E.
Yoon, Chun Hong
Wilson, Mark A.
Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters
title Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters
title_full Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters
title_fullStr Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters
title_full_unstemmed Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters
title_short Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters
title_sort reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters
topic ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8270650/
https://www.ncbi.nlm.nih.gov/pubmed/34258328
http://dx.doi.org/10.1063/4.0000087
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