Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle
(2022) In Structural Dynamics 9(5).- Abstract
- 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... (More)
- 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. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/e5db8ead-e183-4c7b-95b5-c73820e082d6
- author
- Sarabi, Daniel LU ; Ostojić, Lucija ; Bosman, Robert ; Vallejos, Adams ; Linse, Johanna-Barbara ; Wulff, Michael ; Levantino, Matteo and Neutze, Richard
- publishing date
- 2022-10-31
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Structural Dynamics
- volume
- 9
- issue
- 5
- article number
- 054102
- publisher
- American Institute of Physics (AIP)
- external identifiers
-
- scopus:85141828931
- ISSN
- 2329-7778
- DOI
- 10.1063/4.0000157
- language
- English
- LU publication?
- no
- id
- e5db8ead-e183-4c7b-95b5-c73820e082d6
- date added to LUP
- 2023-10-26 15:33:43
- date last changed
- 2023-10-27 08:27:42
@article{e5db8ead-e183-4c7b-95b5-c73820e082d6,
abstract = {{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.}},
author = {{Sarabi, Daniel and Ostojić, Lucija and Bosman, Robert and Vallejos, Adams and Linse, Johanna-Barbara and Wulff, Michael and Levantino, Matteo and Neutze, Richard}},
issn = {{2329-7778}},
language = {{eng}},
month = {{10}},
number = {{5}},
publisher = {{American Institute of Physics (AIP)}},
series = {{Structural Dynamics}},
title = {{Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle}},
url = {{http://dx.doi.org/10.1063/4.0000157}},
doi = {{10.1063/4.0000157}},
volume = {{9}},
year = {{2022}},
}