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Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle

Time-resolved x-ray solution scattering (TR-XSS) is a sub-field of structural biology, which observes secondary structural changes in proteins as they evolve along their functional pathways. While the number of distinct conformational states and their rise and decay can be extracted directly from TR...

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Autores principales: Sarabi, Daniel, Ostojić, Lucija, Bosman, Robert, Vallejos, Adams, Linse, Johanna-Barbara, Wulff, Michael, Levantino, Matteo, Neutze, Richard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Crystallographic Association 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9625836/
https://www.ncbi.nlm.nih.gov/pubmed/36329868
http://dx.doi.org/10.1063/4.0000157
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author Sarabi, Daniel
Ostojić, Lucija
Bosman, Robert
Vallejos, Adams
Linse, Johanna-Barbara
Wulff, Michael
Levantino, Matteo
Neutze, Richard
author_facet Sarabi, Daniel
Ostojić, Lucija
Bosman, Robert
Vallejos, Adams
Linse, Johanna-Barbara
Wulff, Michael
Levantino, Matteo
Neutze, Richard
author_sort Sarabi, Daniel
collection PubMed
description Time-resolved x-ray solution scattering (TR-XSS) is a sub-field of structural biology, which observes secondary structural changes in proteins as they evolve along their functional pathways. While the number of distinct conformational states and their rise and decay can be extracted directly from TR-XSS experimental data recorded from light-sensitive systems, structural modeling is more challenging. This step often builds from complementary structural information, including secondary structural changes extracted from crystallographic studies or molecular dynamics simulations. When working with integral membrane proteins, another challenge arises because x-ray scattering from the protein and the surrounding detergent micelle interfere and these effects should be considered during structural modeling. Here, we utilize molecular dynamics simulations to explicitly incorporate the x-ray scattering cross term between a membrane protein and its surrounding detergent micelle when modeling TR-XSS data from photoactivated samples of detergent solubilized bacteriorhodopsin. This analysis provides theoretical foundations in support of our earlier approach to structural modeling that did not explicitly incorporate this cross term and improves agreement between experimental data and theoretical predictions at lower x-ray scattering angles.
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spelling pubmed-96258362022-11-02 Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle Sarabi, Daniel Ostojić, Lucija Bosman, Robert Vallejos, Adams Linse, Johanna-Barbara Wulff, Michael Levantino, Matteo Neutze, Richard Struct Dyn ARTICLES Time-resolved x-ray solution scattering (TR-XSS) is a sub-field of structural biology, which observes secondary structural changes in proteins as they evolve along their functional pathways. While the number of distinct conformational states and their rise and decay can be extracted directly from TR-XSS experimental data recorded from light-sensitive systems, structural modeling is more challenging. This step often builds from complementary structural information, including secondary structural changes extracted from crystallographic studies or molecular dynamics simulations. When working with integral membrane proteins, another challenge arises because x-ray scattering from the protein and the surrounding detergent micelle interfere and these effects should be considered during structural modeling. Here, we utilize molecular dynamics simulations to explicitly incorporate the x-ray scattering cross term between a membrane protein and its surrounding detergent micelle when modeling TR-XSS data from photoactivated samples of detergent solubilized bacteriorhodopsin. This analysis provides theoretical foundations in support of our earlier approach to structural modeling that did not explicitly incorporate this cross term and improves agreement between experimental data and theoretical predictions at lower x-ray scattering angles. American Crystallographic Association 2022-10-31 /pmc/articles/PMC9625836/ /pubmed/36329868 http://dx.doi.org/10.1063/4.0000157 Text en © 2022 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
Sarabi, Daniel
Ostojić, Lucija
Bosman, Robert
Vallejos, Adams
Linse, Johanna-Barbara
Wulff, Michael
Levantino, Matteo
Neutze, Richard
Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle
title Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle
title_full Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle
title_fullStr Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle
title_full_unstemmed Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle
title_short Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle
title_sort modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle
topic ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9625836/
https://www.ncbi.nlm.nih.gov/pubmed/36329868
http://dx.doi.org/10.1063/4.0000157
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