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Dsouza L, Li X, Erić V, Huijser A, Jansen TLC, Holzwarth AR, Buda F, Bryant DA, Bahri S, Gupta KBSS, Sevink GJA, de Groot HJM. An integrated approach towards extracting structural characteristics of chlorosomes from a bchQ mutant of Chlorobaculum tepidum. Phys Chem Chem Phys 2024; 26:15856-15867. [PMID: 38546236 DOI: 10.1039/d4cp00221k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Chlorosomes, the photosynthetic antenna complexes of green sulfur bacteria, are paradigms for light-harvesting elements in artificial designs, owing to their efficient energy transfer without protein participation. We combined magic angle spinning (MAS) NMR, optical spectroscopy and cryogenic electron microscopy (cryo-EM) to characterize the structure of chlorosomes from a bchQ mutant of Chlorobaculum tepidum. The chlorosomes of this mutant have a more uniform composition of bacteriochlorophyll (BChl) with a predominant homolog, [8Ethyl, 12Ethyl] BChl c, compared to the wild type (WT). Nearly complete 13C chemical shift assignments were obtained from well-resolved homonuclear 13C-13C RFDR data. For proton assignments heteronuclear 13C-1H (hCH) data sets were collected at 1.2 GHz spinning at 60 kHz. The CHHC experiments revealed intermolecular correlations between 132/31, 132/32, and 121/31, with distance constraints of less than 5 Å. These constraints indicate the syn-anti parallel stacking motif for the aggregates. Fourier transform cryo-EM data reveal an axial repeat of 1.49 nm for the helical tubular aggregates, perpendicular to the inter-tube separation of 2.1 nm. This axial repeat is different from WT and is in line with BChl syn-anti stacks running essentially parallel to the tube axis. Such a packing mode is in agreement with the signature of the Qy band in circular dichroism (CD). Combining the experimental data with computational insight suggests that the packing for the light-harvesting function is similar between WT and bchQ, while the chirality within the chlorosomes is modestly but detectably affected by the reduced compositional heterogeneity in bchQ.
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Affiliation(s)
- Lolita Dsouza
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands.
| | - Xinmeng Li
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands.
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, 0315, Oslo, Norway
| | - Vesna Erić
- Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, The Netherlands
| | - Annemarie Huijser
- MESA+ Institute for Nanotechnology, University of Twente, 7500 AE, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, The Netherlands
| | - Alfred R Holzwarth
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Francesco Buda
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands.
| | - Donald A Bryant
- Department for Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Salima Bahri
- NMR Spectroscopy, Bijvoet center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | | | - G J Agur Sevink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands.
| | - Huub J M de Groot
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands.
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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Pandit A. Structural dynamics of light harvesting proteins, photosynthetic membranes and cells observed with spectral editing solid-state NMR. J Chem Phys 2022; 157:025101. [DOI: 10.1063/5.0094446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photosynthetic light-harvesting complexes have a remarkable capacity to perform robust photo physics at ambient temperatures and in fluctuating environments. Protein conformational dynamics and membrane mobility are processes that contribute to the light-harvesting efficiencies and control photoprotective responses. This short review describes the application of Magic Angle Spinning (MAS) NMR spectroscopy for characterizing the structural dynamics of pigment, protein and thylakoid membrane components related to light harvesting and photoprotection. I will discuss the use of dynamics-based spectral editing solid-state NMR for distinguishing rigid and mobile components and assessing protein, pigment and lipid dynamics on sub-nanosecond to millisecond timescales. Dynamic spectral editing NMR has been applied to investigate Light-Harvesting Complex II (LHCII) protein conformational dynamics inside lipid bilayers and in native membranes. Furthermore, we used the NMR approach to assess thylakoid membrane dynamics. Finally, it is shown that dynamics-based spectral editing NMR, for reducing spectral complexity, by filtering motion-dependent signals, enabled us to follow processes in live photosynthetic cells.
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van Aalst EJ, Borcik CG, Wylie BJ. Spectroscopic signatures of bilayer ordering in native biological membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183891. [PMID: 35217001 PMCID: PMC10793244 DOI: 10.1016/j.bbamem.2022.183891] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Membrane proteins and polycyclic lipids like cholesterol and hopanoids coordinate phospholipid bilayer ordering. This phenomenon manifests as partitioning of the liquid crystalline phase into liquid-ordered (Lo) and liquid-disordered (Ld) regions. In Eukaryotes, microdomains are rich in cholesterol and sphingolipids and serve as signal transduction scaffolds. In Prokaryotes, Lo microdomains increase pathogenicity and antimicrobial resistance. Previously, we identified spectroscopically distinct chemical shift signatures for all-trans (AT) and trans-gauche (TG) acyl chain conformations, cyclopropyl ring lipids (CPR), and hopanoids in prokaryotic lipid extracts and used Polarization Transfer (PT) SSNMR to investigate bilayer ordering. To investigate how these findings relate to native bilayer organization, we interrogate whole cell and whole membrane extract samples of Burkholderia thailendensis to investigate bilayer ordering in situ. In 13C-13C 2D SSNMR spectra, we assigned chemical shifts for lipid species in both samples, showing conservation of lipids of interest in our native membrane sample. A one-dimensional temperature series of PT SSNMR and transverse relaxation measurements of AT versus TG acyl conformations in the membrane sample confirm bilayer ordering and a broadened phase transition centered at a lower-than-expected temperature. Bulk protein backbone Cα dynamics and correlations consistent with lipid-protein contacts within are further indicative of microdomain formation and lipid ordering. In aggregate, these findings provide evidence for microdomain formation in vivo and provide insight into phase separation and transition mechanics in biological membranes.
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Affiliation(s)
- Evan J van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79415, USA
| | - Collin G Borcik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79415, USA
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79415, USA.
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Nami F, Ferraz MJ, Bakkum T, Aerts JMFG, Pandit A. Real‐Time NMR Recording of Fermentation and Lipid Metabolism Processes in Live Microalgae Cells. Angew Chem Int Ed Engl 2022; 61:e202117521. [PMID: 35103372 PMCID: PMC9305762 DOI: 10.1002/anie.202117521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 11/10/2022]
Abstract
Non‐invasive and real‐time recording of processes in living cells has been limited to detection of small cellular components such as soluble proteins and metabolites. Here we report a multiphase NMR approach using magic‐angle spinning NMR to synchronously follow microbial processes of fermentation, lipid metabolism and structural dynamic changes in live microalgae cells. Chlamydomonas reinhardtii green algae were highly concentrated, introducing dark fermentation and anoxia conditions. Single‐pulse NMR experiments were applied to obtain temperature‐dependent kinetic profiles of the formed fermentation products. Through dynamics‐based spectral editing NMR, simultaneous conversion of galactolipids into TAG and free fatty acids was observed and rapid loss of rigid lipid structures. This suggests that lipolysis under dark and anoxia conditions finally results in the breakdown of cell and organelle membranes, which could be beneficial for recovery of intracellular microbial useful products.
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Affiliation(s)
- Faezeh Nami
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Maria Joao Ferraz
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas Bakkum
- Dept. of Bio Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anjali Pandit
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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Nami F, Ferraz MJ, Bakkum T, Aerts JMFG, Pandit A. Real‐Time NMR Recording of Fermentation and Lipid Metabolism Processes in Live Microalgae Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Faezeh Nami
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Maria Joao Ferraz
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas Bakkum
- Dept. of Bio Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anjali Pandit
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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Nami F, Tian L, Huber M, Croce R, Pandit A. Lipid and protein dynamics of stacked and cation-depletion induced unstacked thylakoid membranes. BBA ADVANCES 2021; 1:100015. [PMID: 37082020 PMCID: PMC10074959 DOI: 10.1016/j.bbadva.2021.100015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chloroplast thylakoid membranes in plants and green algae form 3D architectures of stacked granal membranes interconnected by unstacked stroma lamellae. They undergo dynamic structural changes as a response to changing light conditions that involve grana unstacking and lateral supramolecular reorganization of the integral membrane protein complexes. We assessed the dynamics of thylakoid membrane components and addressed how they are affected by thylakoid unstacking, which has consequences for protein mobility and the diffusion of small electron carriers. By a combined nuclear and electron paramagnetic-resonance approach the dynamics of thylakoid lipids was assessed in stacked and cation-depletion induced unstacked thylakoids of Chlamydomonas (C.) reinhardtii. We could distinguish between structural, bulk and annular lipids and determine membrane fluidity at two membrane depths: close to the lipid headgroups and in the lipid bilayer center. Thylakoid unstacking significantly increased the dynamics of bulk and annular lipids in both areas and increased the dynamics of protein helices. The unstacking process was associated with membrane reorganization and loss of long-range ordered Photosystem II- Light-Harvesting Complex II (PSII-LHCII) complexes. The fluorescence lifetime characteristics associated with membrane unstacking are similar to those associated with state transitions in intact C. reinhardtii cells. Our findings could be relevant for understanding the structural and functional implications of thylakoid unstacking that is suggested to take place during several light-induced processes, such as state transitions, photoacclimation, photoinhibition and PSII repair.
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Affiliation(s)
- Faezeh Nami
- Institute of Chemistry, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Lijin Tian
- Institute of Chemistry, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Roberta Croce
- Department of Physics and Astronomy, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Anjali Pandit
- Institute of Chemistry, Leiden University, 2333 CC, Leiden, The Netherlands
- Corresponding author:
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Conformational Dynamics of Light-Harvesting Complex II in a Native Membrane Environment. Biophys J 2020; 120:270-283. [PMID: 33285116 DOI: 10.1016/j.bpj.2020.11.2265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/17/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Photosynthetic light-harvesting complexes (LHCs) of higher plants, moss, and green algae can undergo dynamic conformational transitions, which have been correlated to their ability to adapt to fluctuations in the light environment. Herein, we demonstrate the application of solid-state NMR spectroscopy on native, heterogeneous thylakoid membranes of Chlamydomonas reinhardtii (Cr) and on Cr light-harvesting complex II (LHCII) in thylakoid lipid bilayers to detect LHCII conformational dynamics in its native membrane environment. We show that membrane-reconstituted LHCII contains selective sites that undergo fast, large-amplitude motions, including the phytol tails of two chlorophylls. Protein plasticity is also observed in the N-terminal stromal loop and in protein fragments facing the lumen, involving sites that stabilize the xanthophyll-cycle carotenoid violaxanthin and the two luteins. The results report on the intrinsic flexibility of LHCII pigment-protein complexes in a membrane environment, revealing putative sites for conformational switching. In thylakoid membranes, fast dynamics of protein and pigment sites is significantly reduced, which suggests that in their native organelle membranes, LHCII complexes are locked in specific conformational states.
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Kim M, Son J, Song Y, Kim Y. Analysis of Plant Metabolites Damaged in Chemical Accidents Using
NMR
Spectroscopy. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Minseon Kim
- Department of Chemistry Hankuk University of Foreign Studies Yong‐In 17035 Republic of Korea
| | - Jinyoung Son
- Department of Chemistry Hankuk University of Foreign Studies Yong‐In 17035 Republic of Korea
| | - Yuyoung Song
- Department of Chemistry Hankuk University of Foreign Studies Yong‐In 17035 Republic of Korea
| | - Yongae Kim
- Department of Chemistry Hankuk University of Foreign Studies Yong‐In 17035 Republic of Korea
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