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...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
AIP Publishing LLC and ACA
2021-07-01
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| Series: | Structural Dynamics |
| Online Access: | http://dx.doi.org/10.1063/4.0000087 |
| _version_ | 1818730005922840576 |
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| author | Zhen Su Medhanjali Dasgupta Frédéric Poitevin Irimpan I. Mathews Henry van den Bedem Michael E. Wall Chun Hong Yoon Mark A. Wilson |
| author_facet | Zhen Su Medhanjali Dasgupta Frédéric Poitevin Irimpan I. Mathews Henry van den Bedem Michael E. Wall Chun Hong Yoon Mark A. Wilson |
| author_sort | Zhen Su |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-17T22:54:55Z |
| format | Article |
| id | doaj.art-83899f132e8540bdb34658d93de4e3e7 |
| institution | Directory Open Access Journal |
| issn | 2329-7778 |
| language | English |
| last_indexed | 2024-12-17T22:54:55Z |
| publishDate | 2021-07-01 |
| publisher | AIP Publishing LLC and ACA |
| record_format | Article |
| series | Structural Dynamics |
| spelling | doaj.art-83899f132e8540bdb34658d93de4e3e72022-12-21T21:29:34ZengAIP Publishing LLC and ACAStructural Dynamics2329-77782021-07-0184044701044701-1810.1063/4.0000087Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parametersZhen Su0Medhanjali Dasgupta1Frédéric Poitevin2Irimpan I. Mathews3Henry van den Bedem4Michael E. Wall5Chun Hong Yoon6Mark A. Wilson7 Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, USAProtein 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.http://dx.doi.org/10.1063/4.0000087 |
| spellingShingle | Zhen Su Medhanjali Dasgupta Frédéric Poitevin Irimpan I. Mathews Henry van den Bedem Michael E. Wall Chun Hong Yoon Mark A. Wilson Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters Structural Dynamics |
| 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 |
| url | http://dx.doi.org/10.1063/4.0000087 |
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