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Sarabi D, Ostojić L, Bosman R, Vallejos A, Linse JB, Wulff M, Levantino M, Neutze R. Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054102. [PMID: 36329868 PMCID: PMC9625836 DOI: 10.1063/4.0000157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
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.
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Affiliation(s)
- Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Lucija Ostojić
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Johanna-Barbara Linse
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michael Wulff
- European Synchrotron Radiation Facility, 38043 Grenoble Cedex 9, France
| | - Matteo Levantino
- European Synchrotron Radiation Facility, 38043 Grenoble Cedex 9, France
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
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2
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Jeong H, Ki H, Kim JG, Kim J, Lee Y, Ihee H. Sensitivity of
time‐resolved
diffraction data to changes in internuclear distances and atomic positions. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Haeyun Jeong
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Jungmin Kim
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
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3
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Marcellini M, Nasedkin A, Zietz B, Petersson J, Vincent J, Palazzetti F, Malmerberg E, Kong Q, Wulff M, van der Spoel D, Neutze R, Davidsson J. Transient isomers in the photodissociation of bromoiodomethane. J Chem Phys 2018; 148:134307. [PMID: 29626862 DOI: 10.1063/1.5005595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The photochemistry of halomethanes is fascinating for the complex cascade reactions toward either the parent or newly synthesized molecules. Here, we address the structural rearrangement of photodissociated CH2IBr in methanol and cyclohexane, probed by time-resolved X-ray scattering in liquid solution. Upon selective laser cleavage of the C-I bond, we follow the reaction cascade of the two geminate geometrical isomers, CH2I-Br and CH2Br-I. Both meta-stable isomers decay on different time scales, mediated by solvent interaction, toward the original parent molecule. We observe the internal rearrangement of CH2Br-I to CH2I-Br in cyclohexane by extending the time window up to 3 μs. We track the photoproduct kinetics of CH2Br-I in methanol solution where only one isomer is observed. The effect of the polarity of solvent on the geminate recombination pathways is discussed.
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Affiliation(s)
- Moreno Marcellini
- Department of Chemistry-Ångström Laboratory, Uppsala University, P.O. Box 462, SE-751 20 Uppsala, Sweden
| | - Alexandr Nasedkin
- Department of Chemistry-Ångström Laboratory, Uppsala University, P.O. Box 462, SE-751 20 Uppsala, Sweden
| | - Burkhard Zietz
- Department of Chemistry-Ångström Laboratory, Uppsala University, P.O. Box 462, SE-751 20 Uppsala, Sweden
| | - Jonas Petersson
- Department of Chemistry-Ångström Laboratory, Uppsala University, P.O. Box 462, SE-751 20 Uppsala, Sweden
| | - Jonathan Vincent
- Department of Chemistry-Ångström Laboratory, Uppsala University, P.O. Box 462, SE-751 20 Uppsala, Sweden
| | - Federico Palazzetti
- Universitá di Perugia, Dipartimento di Chimica, Biologia e Biotecnologie, 06123 Perugia, Italy
| | - Erik Malmerberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Qingyu Kong
- Argonne National Laboratory's, Xray Science Division, 9700 S Cass Ave., Argonne, Illinois 60439, USA
| | - Michael Wulff
- European Synchrotron Radiation Facility, B.P. 220, F-380 43 Grenoble Cedex, France
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, P.O. Box 596, SE-751 24 Uppsala, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Jan Davidsson
- Department of Chemistry-Ångström Laboratory, Uppsala University, P.O. Box 462, SE-751 20 Uppsala, Sweden
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4
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Oang KY, Yang C, Muniyappan S, Kim J, Ihee H. SVD-aided pseudo principal-component analysis: A new method to speed up and improve determination of the optimum kinetic model from time-resolved data. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044013. [PMID: 28405591 PMCID: PMC5382018 DOI: 10.1063/1.4979854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/24/2017] [Indexed: 05/22/2023]
Abstract
Determination of the optimum kinetic model is an essential prerequisite for characterizing dynamics and mechanism of a reaction. Here, we propose a simple method, termed as singular value decomposition-aided pseudo principal-component analysis (SAPPA), to facilitate determination of the optimum kinetic model from time-resolved data by bypassing any need to examine candidate kinetic models. We demonstrate the wide applicability of SAPPA by examining three different sets of experimental time-resolved data and show that SAPPA can efficiently determine the optimum kinetic model. In addition, the results of SAPPA for both time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) data of the same protein reveal that global structural changes of protein, which is probed by TRXSS, may occur more slowly than local structural changes around the chromophore, which is probed by TA spectroscopy.
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Affiliation(s)
| | | | | | - Jeongho Kim
- Department of Chemistry, Inha University , Incheon 22212, South Korea
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Kim J, Kim KH, Oang KY, Lee JH, Hong K, Cho H, Huse N, Schoenlein RW, Kim TK, Ihee H. Tracking reaction dynamics in solution by pump–probe X-ray absorption spectroscopy and X-ray liquidography (solution scattering). Chem Commun (Camb) 2016; 52:3734-49. [DOI: 10.1039/c5cc08949b] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
TRXL and TRXAS are powerful techniques for real-time probing of structural and electronic dynamics of photoinduced reactions in solution phase.
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6
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Ponikvar-Svet M, Liebman JF. Interplay of thermochemistry and Structural Chemistry, the journal (volume 21, 2010) and the discipline. Struct Chem 2011. [DOI: 10.1007/s11224-011-9769-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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