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Title: Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

Abstract

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where largermore » dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.« less

Authors:
ORCiD logo; ; ORCiD logo
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
DOE - BIOLOGICAL AND ENVIRONMENTAL RESEARCH
OSTI Identifier:
1439620
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D. Structural Biology; Journal Volume: 74; Journal Issue: 5
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Thompson, Michael C., Cascio, Duilio, and Yeates, Todd O. Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism. United States: N. p., 2018. Web. doi:10.1107/S2059798318003479.
Thompson, Michael C., Cascio, Duilio, & Yeates, Todd O. Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism. United States. doi:10.1107/S2059798318003479.
Thompson, Michael C., Cascio, Duilio, and Yeates, Todd O. Tue . "Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism". United States. doi:10.1107/S2059798318003479.
@article{osti_1439620,
title = {Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism},
author = {Thompson, Michael C. and Cascio, Duilio and Yeates, Todd O.},
abstractNote = {Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.},
doi = {10.1107/S2059798318003479},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 5,
volume = 74,
place = {United States},
year = {Tue Apr 24 00:00:00 EDT 2018},
month = {Tue Apr 24 00:00:00 EDT 2018}
}