| 1. |
- Sarabi, Daniel, 1987, et al.
(författare)
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Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle
- 2022
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Ingår i: Structural Dynamics-Us. - : AIP Publishing. - 2329-7778. ; 9:5
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Tidskriftsartikel (refereegranskat)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. (C) The Author(s) 2022. Published by Baishideng Publishing Group Inc. All rights reserved.
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| 2. |
- Gruhl, T., et al.
(författare)
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Ultrafast structural changes direct the first molecular events of vision
- 2023
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 615, s. 939-944
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Tidskriftsartikel (refereegranskat)abstract
- Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)(1). A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation(2), thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature(3) to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.
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| 3. |
- Karim, Alavi, 1986, et al.
(författare)
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Carbon's Three-Center, Four-Electron Tetrel Bond, Treated Experimentally
- 2018
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 140:50, s. 17571-17579
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Tidskriftsartikel (refereegranskat)abstract
- © 2018 American Chemical Society. Tetrel bonding is the noncovalent interaction of group IV elements with electron donors. It is a weak, directional interaction that resembles hydrogen and halogen bonding yet remains barely explored. Herein, we present an experimental investigation of the carbon-centered, three-center, four-electron tetrel bond, [N-C-N]+, formed by capturing a carbenium ion with a bidentate Lewis base. NMR-spectroscopic, titration-calorimetric, and reaction-kinetic evidence for the existence and structure of this species is reported. The studied interaction is by far the strongest tetrel bond reported so far and is discussed in comparison with the analogous halogen bond. The necessity of the involvement of a bidentate Lewis base in its formation is demonstrated by providing spectroscopic and crystallographic evidence that a monodentate Lewis base induces a reaction rather than stabilizing the tetrel bond complex. A vastly decreased Lewis basicity of the bidentate ligand or reduced Lewis acidity of the carbenium ion weakens - or even prohibits - the formation of the tetrel bond complex, whereas synthetic modifications facilitating attractive orbital overlaps promote it. As the geometry of the complex resembles the SN2 transition state, it provides a model system for the investigation of fundamental reaction mechanisms and chemical bonding theories.
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| 4. |
- Sarabi, Daniel, 1987
(författare)
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Structural Dynamics of Rhodopsins using Time-Resolved X-ray Solution Scattering
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Light is one of the most important sources of energy and environmental signals, and many organisms adapt in response to the presence of light. This is made possible through specialised proteins called photoreceptors. Rhodopsins are made light-sensitive via the addition of a retinal chromophore, and activated by specific wavelengths of light, which propagates a cascade of structural changes, allowing the protein to carry out it’s function. Microbial rhodopsins have been found to act as light-driven proton pumps, light-gated ion channels or receptors for phototaxis, whereas rhodopsin in higher eukaryotes such as the human eye, is responsible for low-light vision. Time-resolved X-ray solution scattering (TR-XSS) is a sub-field of structural biology which can detect secondary structural changes in proteins as they evolve along their functional pathways in real time. The method addresses many of the limitations of serial crystallography, however, structural modelling is more challenging due to the measured information being one-dimensional. Further challenges arise in structural interpretation of TR-XSS data recorded from integral membrane proteins, due to the presence of a detergent micelle surrounding the protein. In our previous modelling, the interference between the protein and micelle was not addressed, and in this thesis we utilize molecular dynamics simulations to explicitly incorporate the X-ray scattering cross-term between an integral membrane protein and it’s surrounding micelle when modelling against TR-XSS data from photo-activated rhodopsins within a detergent micelle. The influence of the detergent micelle and micelle size on difference X-ray scattering was determined, correction for the solvent excluded volume was made and candidate motions were identified using these protocols for modelling against TR-XSS data of bacteriorhodopsin, SRII in isolation and in complex with it’s transducer protein HrII, and Channelrhodopsin 2. The analysis tools and protocols developed in this thesis should provide a framework for the analysis and structural modelling of light-activated integral membrane proteins as a powerful complement to other biophysical methods.
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