1
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Mannen K, Nagata T, Rozenberg A, Konno M, Del Carmen Marín M, Bagherzadeh R, Béjà O, Uchihashi T, Inoue K. Multiple Roles of a Conserved Glutamate Residue for Unique Biophysical Properties in a New Group of Microbial Rhodopsins Homologous to TAT Rhodopsin. J Mol Biol 2024; 436:168331. [PMID: 37898385 DOI: 10.1016/j.jmb.2023.168331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/02/2023] [Accepted: 10/21/2023] [Indexed: 10/30/2023]
Abstract
TAT rhodopsin, a microbial rhodopsin found in the marine SAR11 bacterium HIMB114, uniquely possesses a Thr-Ala-Thr (TAT) motif in the third transmembrane helix. Because of a low pKa value of the retinal Schiff base (RSB), TAT rhodopsin exhibits both a visible light-absorbing state with the protonated RSB and a UV-absorbing state with the deprotonated RSB at a neutral pH. The UV-absorbing state, in contrast to the visible light-absorbing one, converts to a long-lived photointermediate upon light absorption, implying that TAT rhodopsin functions as a pH-dependent light sensor. Despite detailed biophysical characterization and mechanistic studies on the TAT rhodopsin, it has been unknown whether other proteins with similarly unusual features exist. Here, we identified several new rhodopsin genes homologous to the TAT rhodopsin of HIMB114 (TATHIMB) from metagenomic data. Based on the absorption spectra of expressed proteins from these genes with visible and UV peaks similar to that of TATHIMB, they were classified as Twin-peaked Rhodopsin (TwR) family. TwR genes form a gene cluster with a set of 13 ORFs conserved in subclade IIIa of SAR11 bacteria. A glutamic acid in the second transmembrane helix, Glu54, is conserved in all of the TwRs. We investigated E54Q mutants of two TwRs and revealed that Glu54 plays critical roles in regulating the RSB pKa, oligomer formation, and the efficient photoreaction of the UV-absorbing state. The discovery of novel TwRs enables us to study the universality and individuality of the characteristics revealed so far in the original TATHIMB and contributes to further studies on mechanisms of unique properties of TwRs.
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Affiliation(s)
- Kentaro Mannen
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Andrey Rozenberg
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - María Del Carmen Marín
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Reza Bagherzadeh
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya 464-8602, Japan; Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Institute for Glyco-core Research, Nagoya University, Nagoya 464-8602, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
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2
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Fang J, Zhang Y, Zhu T, Li Y. Scramblase activity of proteorhodopsin confers physiological advantages to Escherichia coli in the absence of light. iScience 2023; 26:108551. [PMID: 38125024 PMCID: PMC10730872 DOI: 10.1016/j.isci.2023.108551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/11/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Microbial rhodopsins are widely distributed in the aqua-ecosystem due to their simple structure and multifaceted functions. Conventionally, microbial rhodopsins are considered to be exclusively light active. Here, we report the discovery of light-independent function of a proteorhodopsin from a psychrophile Psychroflexus torquis (ptqPR). ptqPR could improve the growth and viability of Escherichia coli cells under stressful conditions in the absence of light, and this was achieved by improving the energy maintenance, membrane potential, membrane fluidity, and membrane integrity. We further show that this non-canonical function of PR is related to its scramblase activity. PR mutants which lost scramblase activities also lost their ability to confer physiological advantages in E. coli. These findings shed light on why microbial rhodopsins are widely distributed in ecological systems where light is inaccessible.
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Affiliation(s)
- Jiayu Fang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Taicheng Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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3
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Lends A, Birlirakis N, Cai X, Daskalov A, Shenoy J, Abdul-Shukkoor MB, Berbon M, Ferrage F, Liu Y, Loquet A, Tan KO. Efficient 18.8 T MAS-DNP NMR reveals hidden side chains in amyloid fibrils. JOURNAL OF BIOMOLECULAR NMR 2023:10.1007/s10858-023-00416-5. [PMID: 37289306 DOI: 10.1007/s10858-023-00416-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Amyloid fibrils are large and insoluble protein assemblies composed of a rigid core associated with a cross-β arrangement rich in β-sheet structural elements. It has been widely observed in solid-state NMR experiments that semi-rigid protein segments or side chains do not yield easily observable NMR signals at room temperature. The reasons for the missing peaks may be due to the presence of unfavorable dynamics that interfere with NMR experiments, which result in very weak or unobservable NMR signals. Therefore, for amyloid fibrils, semi-rigid and dynamically disordered segments flanking the amyloid core are very challenging to study. Here, we show that high-field dynamic nuclear polarization (DNP), an NMR hyperpolarization technique typically performed at low temperatures, can circumvent this issue because (i) the low-temperature environment (~ 100 K) slows down the protein dynamics to escape unfavorable detection regime, (ii) DNP improves the overall NMR sensitivity including those of flexible side chains, and (iii) efficient cross-effect DNP biradicals (SNAPol-1) optimized for high-field DNP (≥ 18.8 T) are employed to offer high sensitivity and resolution suitable for biomolecular NMR applications. By combining these factors, we have successfully established an impressive enhancement factor of ε ~ 50 on amyloid fibrils using an 18.8 T/ 800 MHz magnet. We have compared the DNP efficiencies of M-TinyPol, NATriPol-3, and SNAPol-1 biradicals on amyloid fibrils. We found that SNAPol-1 (with ε ~ 50) outperformed the other two radicals. The MAS DNP experiments revealed signals of flexible side chains previously inaccessible at conventional room-temperature experiments. These results demonstrate the potential of MAS-DNP NMR as a valuable tool for structural investigations of amyloid fibrils, particularly for side chains and dynamically disordered segments otherwise hidden at room temperature.
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Affiliation(s)
- Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Nicolas Birlirakis
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Asen Daskalov
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Jayakrishna Shenoy
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Muhammed Bilal Abdul-Shukkoor
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Mélanie Berbon
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France.
| | - Kong Ooi Tan
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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4
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Kriebel CN, Asido M, Kaur J, Orth J, Braun P, Becker-Baldus J, Wachtveitl J, Glaubitz C. Structural and functional consequences of the H180A mutation of the light-driven sodium pump KR2. Biophys J 2023; 122:1003-1017. [PMID: 36528791 PMCID: PMC10111219 DOI: 10.1016/j.bpj.2022.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 12/04/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Krokinobacter eikastus rhodopsin 2 (KR2) is a light-driven pentameric sodium pump. Its ability to translocate cations other than protons and to create an electrochemical potential makes it an attractive optogenetic tool. Tailoring its ion-pumping characteristics by mutations is therefore of great interest. In addition, understanding the functional and structural consequences of certain mutations helps to derive a functional mechanism of ion selectivity and transfer of KR2. Based on solid-state NMR spectroscopy, we report an extensive chemical shift resonance assignment of KR2 within lipid bilayers. This data set was then used to probe site-resolved allosteric effects of sodium binding, which revealed multiple responsive sites including the Schiff base nitrogen and the NDQ motif. Based on this data set, the consequences of the H180A mutation are probed. The mutant is silenced in the presence of sodium while in its absence proton pumping is observed. Our data reveal specific long-range effects along the sodium transfer pathway. These experiments are complemented by time-resolved optical spectroscopy. Our data suggest a model in which sodium uptake by the mutant can still take place, while sodium release and backflow control are disturbed.
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Affiliation(s)
- Clara Nassrin Kriebel
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marvin Asido
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jagdeep Kaur
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jennifer Orth
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Philipp Braun
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany.
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5
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Han CT, Nguyen KDQ, Berkow MW, Hussain S, Kiani A, Kinnebrew M, Idso MN, Baxter N, Chang E, Aye E, Winslow E, Rahman M, Seppälä S, O'Malley MA, Chmelka BF, Mertz B, Han S. Lipid membrane mimetics and oligomerization tune functional properties of proteorhodopsin. Biophys J 2023; 122:168-179. [PMID: 36352784 PMCID: PMC9822798 DOI: 10.1016/j.bpj.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 08/01/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2022] Open
Abstract
The functional properties of proteorhodopsin (PR) have been found to be strongly modulated by oligomeric distributions and lipid membrane mimetics. This study aims to distinguish and explain their effects by investigating how oligomer formation impacts PR's function of proton transport in lipid-based membrane mimetic environments. We find that PR forms stable hexamers and pentamers in both E. coli membranes and synthetic liposomes. Compared with the monomers, the photocycle kinetics of PR oligomers is ∼2 and ∼4.5 times slower for transitions between the K and M and the M and N photointermediates, respectively, indicating that oligomerization significantly slows PR's rate of proton transport in liposomes. In contrast, the apparent pKa of the key proton acceptor residue D97 (pKaD97) of liposome-embedded PR persists at 6.2-6.6, regardless of cross-protomer modulation of D97, suggesting that the liposome environment helps maintain PR's functional activity at neutral pH. By comparison, when extracted directly from E. coli membranes into styrene-maleic acid lipid particles, the pKaD97 of monomer-enriched E50Q PR drastically increases to 8.9, implying that there is a very low active PR population at neutral pH to engage in PR's photocycle. These findings demonstrate that oligomerization impacts PR's photocycle kinetics, while lipid-based membrane mimetics strongly affect PR's active population via different mechanisms.
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Affiliation(s)
- Chung-Ta Han
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Khanh Dinh Quoc Nguyen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California
| | - Maxwell W Berkow
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Sunyia Hussain
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Ahmad Kiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Maia Kinnebrew
- College of Creative Studies, Biology Department, University of California, Santa Barbara, Santa Barbara, California
| | - Matthew N Idso
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Naomi Baxter
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California
| | - Evelyn Chang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California
| | - Emily Aye
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California
| | - Elsa Winslow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California
| | - Mohammad Rahman
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Bradley F Chmelka
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California; Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California.
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6
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Sumikawa M, Abe-Yoshizumi R, Uchihashi T, Kandori H. Mechanism of the Irreversible Transition from Pentamer to Monomer at pH 2 in a Blue Proteorhodopsin. Biochemistry 2022; 61:1936-1944. [PMID: 36007110 DOI: 10.1021/acs.biochem.2c00328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteorhodopsin (PR) is a light-driven proton pump found in marine bacteria, and thousands of PRs are classified as blue-absorbing PRs (BPR; λmax ∼ 490 nm) and green-absorbing PRs (GPR; λmax ∼ 525 nm). We previously converted BPR into GPR using an anomalous pH effect, which was achieved by an irreversible process at around pH 2. Recent size-exclusion chromatography (SEC) and atomic force microscopy (AFM) analyses of BPR from Vibrio califitulae (VcBPR) revealed the anomalous pH effect owing to the irreversible transition from pentamer to monomer. Different pKa values of the Schiff base counterion between pentamer and monomer lead to different colors at the same pH. Here, we incorporate systematic mutation into VcBPR and examine the anomalous pH effect. The anomalous pH effect was observed for the mutants of key residues near the retinal chromophore such as D76N, D206N, and Q84L, indicating that the Schiff base counterions and the L/Q switch do not affect the irreversible transition from pentamer to monomer at pH ∼ 2. We then focus on the two specific interactions at the intermonomer interface in a pentamer, E29/R30/D31 and W13/H54. Single mutants such as E29Q, R30A, W13A, and H54A and the wild type (WT) exhibited an anomalous pH effect. In contrast, the anomalous pH effect was lost for E29Q/H54A, R30A/H54A, and W13A/E29Q. Size-exclusion chromatography (SEC) and atomic force microscopy (AFM) measurements showed monomer forms in the original states of the double mutants, being a clear contrast to the pentamer forms of all single mutants in the original states. It was concluded that the pentamer structure of VcBPR was stabilized by an electrostatic interaction in the E29/R30/D31 region and a hydrogen-bonding interaction in the W13/H54 region, which was disrupted at pH 2 and converted into monomers.
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Affiliation(s)
- Mizuki Sumikawa
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | | | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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7
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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8
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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9
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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10
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Abstract
Microbial rhodopsins represent the most abundant phototrophic systems known today. A similar molecular architecture with seven transmembrane helices and a retinal cofactor linked to a lysine in helix 7 enables a wide range of functions including ion pumping, light-controlled ion channel gating, or sensing. Deciphering their molecular mechanisms therefore requires a combined consideration of structural, functional, and spectroscopic data in order to identify key factors determining their function. Important insight can be gained by solid-state NMR spectroscopy by which the large homo-oligomeric rhodopsin complexes can be studied directly within lipid bilayers. This chapter describes the methodological background and the necessary sample preparation requirements for the study of photointermediates, for the analysis of protonation states, H-bonding and chromophore conformations, for 3D structure determination, and for probing oligomer interfaces of microbial rhodopsins. The use of data extracted from these NMR experiments is discussed in the context of complementary biophysical methods.
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Affiliation(s)
- Clara Nassrin Kriebel
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johanna Becker-Baldus
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany.
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11
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Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin. Nat Commun 2021; 12:4107. [PMID: 34226545 PMCID: PMC8257665 DOI: 10.1038/s41467-021-24429-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
The green-light absorbing proteorhodopsin (GPR) is the archetype of bacterial light-driven proton pumps. Here, we present the 2.9 Å cryo-EM structure of pentameric GPR, resolving important residues of the proton translocation pathway and the oligomerization interface. Superposition with the structure of a close GPR homolog and molecular dynamics simulations reveal conformational variations, which regulate the solvent access to the intra- and extracellular half channels harbouring the primary proton donor E109 and the proposed proton release group E143. We provide a mechanism for the structural rearrangements allowing hydration of the intracellular half channel, which are triggered by changing the protonation state of E109. Functional characterization of selected mutants demonstrates the importance of the molecular organization around E109 and E143 for GPR activity. Furthermore, we present evidence that helices involved in the stabilization of the protomer interfaces serve as scaffolds for facilitating the motion of the other helices. Combined with the more constrained dynamics of the pentamer compared to the monomer, these observations illustrate the previously demonstrated functional significance of GPR oligomerization. Overall, this work provides molecular insights into the structure, dynamics and function of the proteorhodopsin family that will benefit the large scientific community employing GPR as a model protein.
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12
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Sefah E, Mertz B. Bacterial Analogs to Cholesterol Affect Dimerization of Proteorhodopsin and Modulates Preferred Dimer Interface. J Chem Theory Comput 2021; 17:2502-2512. [PMID: 33788568 DOI: 10.1021/acs.jctc.0c01174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hopanoids, the bacterial analogues of sterols, are ubiquitous in bacteria and play a significant role in organismal survival under stressful environments. Unlike sterols, hopanoids have a high degree of variation in the size and chemical nature of the substituent attached to the ring moiety, leading to different effects on the structure and dynamics of biological membranes. While it is understood that hopanoids can indirectly tune membrane physical properties, little is known on the role that hopanoids may play in affecting the organization and behavior of bacterial membrane proteins. In this work we used coarse-grained molecular dynamics simulations to characterize the effects of two hopanoids, diploptene (DPT) and bacteriohopanetetrol (BHT), on the oligomerization of proteorhodopsin (PR) in a model membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phophoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-3-phosphoglycerol (POPG). PR is a bacterial membrane protein that functions as a light-activated proton pump. We chose PR based on its ability to adopt a distribution of oligomeric states in different membrane environments. Furthermore, the efficiency of proton pumping in PR is intimately linked to its organization into oligomers. Our results reveal that both BHT and DPT indirectly affect dimerization by tuning membrane properties in a fashion that is concentration-dependent. Variation in their interaction with PR in the membrane-embedded and the cytoplasmic regions leads to distinctly different effects on the plasticity of the dimer interface. BHT has the ability to intercalate between monomers in the dimeric interface, whereas DPT shifts dimerization interactions via packing of the interleaflet region of the membrane. Our results show a direct relationship between hopanoid structure and lateral organization of PR, providing a first glimpse at how these bacterial analogues to eukaryotic sterols produce very similar biophysical effects within the cell membrane.
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Affiliation(s)
- Eric Sefah
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States.,WVU Cancer Institute, West Virginia University, Morgantown, West Virginia 26506, United States
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13
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Inoue K. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:89-126. [PMID: 33398809 DOI: 10.1007/978-981-15-8763-4_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.
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Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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14
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LILBID laser dissociation curves: a mass spectrometry-based method for the quantitative assessment of dsDNA binding affinities. Sci Rep 2020; 10:20398. [PMID: 33230224 PMCID: PMC7683618 DOI: 10.1038/s41598-020-76867-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/28/2020] [Indexed: 11/20/2022] Open
Abstract
One current goal in native mass spectrometry is the assignment of binding affinities to noncovalent complexes. Here we introduce a novel implementation of the existing laser-induced liquid bead ion desorption (LILBID) mass spectrometry method: this new method, LILBID laser dissociation curves, assesses binding strengths quantitatively. In all LILBID applications, aqueous sample droplets are irradiated by 3 µm laser pulses. Variation of the laser energy transferred to the droplet during desorption affects the degree of complex dissociation. In LILBID laser dissociation curves, laser energy transfer is purposely varied, and a binding affinity is calculated from the resulting complex dissociation. A series of dsDNAs with different binding affinities was assessed using LILBID laser dissociation curves. The binding affinity results from the LILBID laser dissociation curves strongly correlated with the melting temperatures from UV melting curves and with dissociation constants from isothermal titration calorimetry, standard solution phase methods. LILBID laser dissociation curve data also showed good reproducibility and successfully predicted the melting temperatures and dissociation constants of three DNA sequences. LILBID laser dissociation curves are a promising native mass spectrometry binding affinity method, with reduced time and sample consumption compared to melting curves or titrations.
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15
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Hirschi S, Kalbermatter D, Ucurum Z, Fotiadis D. Cryo-electron microscopic and X-ray crystallographic analysis of the light-driven proton pump proteorhodopsin reveals a pentameric assembly. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100024. [PMID: 32647827 PMCID: PMC7337067 DOI: 10.1016/j.yjsbx.2020.100024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/30/2022]
Abstract
Affinity tag-free isolation of proteorhodopsin (PR) by ion exchange and size exclusion chromatography. Biochemical and computational analysis indicate a single, pentameric PR population. Highly pure and homogeneous PR enables growth of 3D crystals. X-ray crystallography and cryo-electron microscopy reveal pentameric assembly of PR.
The green-light absorbing proteorhodopsin (GPR) is the prototype of bacterial light-driven proton pumps. It has been the focus of continuous research since its discovery 20 years ago and has sparked the development and application of various biophysical techniques. However, a certain controversy and ambiguity about the oligomeric assembly of GPR still remains. We present here the first tag-free purification of pentameric GPR. The combination of ion exchange and size exclusion chromatography yields homogeneous and highly pure untagged pentamers from GPR overexpressing Escherichia coli. The presented purification procedure provides native-like protein and excludes the need for affinity purification tags. Importantly, three-dimensional protein crystals of GPR were successfully grown and analyzed by X-ray crystallography. These results together with data from single particle cryo-electron microscopy provide direct evidence for the pentameric stoichiometry of purified GPR.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - David Kalbermatter
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
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16
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Ganapathy S, Opdam L, Hontani Y, Frehan S, Chen Q, Hellingwerf KJ, de Groot HJ, Kennis JT, de Grip WJ. Membrane matters: The impact of a nanodisc-bilayer or a detergent microenvironment on the properties of two eubacterial rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183113. [DOI: 10.1016/j.bbamem.2019.183113] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 12/29/2022]
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17
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Exploring Protein Structures by DNP-Enhanced Methyl Solid-State NMR Spectroscopy. J Am Chem Soc 2019; 141:19888-19901. [DOI: 10.1021/jacs.9b11195] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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18
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Goldbourt A. Structural characterization of bacteriophage viruses by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:192-210. [PMID: 31779880 DOI: 10.1016/j.pnmrs.2019.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/03/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Magic-angle spinning (MAS) solid-state NMR has provided structural insights into various bacteriophage systems including filamentous, spherical, and tailed bacteriophage viruses. A variety of methodologies have been utilized including elementary two and three-dimensional assignment experiments, proton-detection techniques at fast spinning speeds, non-uniform sampling, structure determination protocols, conformational dynamics revealed by recoupling of anisotropic interactions, and enhancement by dynamic nuclear polarization. This review summarizes most of the studies performed during the last decade by MAS techniques and makes comparisons with prior knowledge obtained from static and solution NMR techniques. Chemical shifts for the capsids of the various systems are reported and analyzed, and DNA shifts are reported and discussed in the context of general high molecular-weight DNA molecules. Chemical shift and torsion angle prediction techniques are compared and applied to the various phage systems. The structures of the intact M13 filamentous bacteriophage and that of the Acinetobacter phage AP205 capsid, determined using MAS-based experimental data, are presented. Finally, filamentous phages, which are highly rigid systems, show interesting dynamics at the interface of the capsid and DNA, and their mutual electrostatic interactions are shown to be mediated by highly mobile positively charged residues. Novel results obtained from recoupling the chemical shift anisotropy of a single arginine in IKe phage, which is in contact with its DNA, further demonstrate this point. MAS NMR thus provides many new insights into phage structure, and on the other hand the richness, complexity and variety of bacteriophage systems provide opportunities for new NMR methodologies and technique developments.
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Affiliation(s)
- Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
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19
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Morizumi T, Ou WL, Van Eps N, Inoue K, Kandori H, Brown LS, Ernst OP. X-ray Crystallographic Structure and Oligomerization of Gloeobacter Rhodopsin. Sci Rep 2019; 9:11283. [PMID: 31375689 PMCID: PMC6677831 DOI: 10.1038/s41598-019-47445-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/24/2019] [Indexed: 01/27/2023] Open
Abstract
Gloeobacter rhodopsin (GR) is a cyanobacterial proton pump which can be potentially applied to optogenetics. We solved the crystal structure of GR and found that it has overall similarity to the homologous proton pump from Salinibacter ruber, xanthorhodopsin (XR). We identified distinct structural characteristics of GR’s hydrogen bonding network in the transmembrane domain as well as the displacement of extracellular sides of the transmembrane helices relative to those of XR. Employing Raman spectroscopy and flash-photolysis, we found that GR in the crystals exists in a state which displays retinal conformation and photochemical cycle similar to the functional form observed in lipids. Based on the crystal structure of GR, we selected a site for spin labeling to determine GR’s oligomerization state using double electron–electron resonance (DEER) spectroscopy and demonstrated the pH-dependent pentamer formation of GR. Determination of the structure of GR as well as its pentamerizing propensity enabled us to reveal the role of structural motifs (extended helices, 3-omega motif and flipped B-C loop) commonly found among light-driven bacterial pumps in oligomer formation. Here we propose a new concept to classify these pumps based on the relationship between their oligomerization propensities and these structural determinants.
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Affiliation(s)
- Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Wei-Lin Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Keiichi Inoue
- The Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 464-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 464-8555, Japan
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. .,Department of Molecular Genetics, University of Toronto, Ontario, M5S 1A8, Canada.
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20
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Good DB, Voinov MA, Bolton D, Ward ME, Sergeyev IV, Caporini M, Scheffer P, Lo A, Rosay M, Marek A, Brown LS, I Smirnov A, Ladizhansky V. A biradical-tagged phospholipid as a polarizing agent for solid-state MAS Dynamic Nuclear Polarization NMR of membrane proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 100:92-101. [PMID: 31029957 PMCID: PMC6709687 DOI: 10.1016/j.ssnmr.2019.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/29/2019] [Accepted: 04/12/2019] [Indexed: 06/01/2023]
Abstract
A novel Dynamic Nuclear Polarization (DNP) NMR polarizing agent ToSMTSL-PTE representing a phospholipid with a biradical TOTAPOL tethered to the polar head group has been synthesized, characterized, and employed to enhance solid-state Nuclear Magnetic Resonance (SSNMR) signal of a lipid-reconstituted integral membrane protein proteorhodopsin (PR). A matrix-free PR formulation for DNP improved the absolute sensitivity of NMR signal by a factor of ca. 4 compared to a conventional preparation with TOTAPOL dispersed in a glassy glycerol/water matrix. DNP enhancements measured at 400 MHz/263 GHz and 600 MHz/395 GHz showed a strong field dependence but remained moderate at both fields, and comparable to those obtained for PR covalently modified with ToSMTSL. Additional continuous wave (CW) X-band electron paramagnetic resonance (EPR) experiments with ToSMTSL-PTE in solutions and in lipid bilayers revealed that an unfavorable conformational change of the linker connecting mononitroxides could be one of the reasons for moderate DNP enhancements. Further, differential scanning calorimetry (DSC) and CW EPR experiments indicated an inhomogeneous distribution and/or a possibility of a partial aggregation of ToSMTSL-PTE in DMPC:DMPA bilayers when the concentration of the polarizing agent was increased to 20 mol% to maximize the DNP enhancement. Thus, conformational changes and an inhomogeneous distribution of the lipid-based biradicals in lipid bilayers emerged as important factors to consider for further development of this matrix-free approach for DNP of membrane proteins.
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Affiliation(s)
- Daryl B Good
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Maxim A Voinov
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - David Bolton
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Meaghan E Ward
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Peter Scheffer
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Andy Lo
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | | | - Antonin Marek
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA; Bruker Biospin, Billerica, MA, USA.
| | - Vlad Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada; Bruker Biospin, Billerica, MA, USA.
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21
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Salnikov ES, Aussenac F, Abel S, Purea A, Tordo P, Ouari O, Bechinger B. Dynamic Nuclear Polarization / solid-state NMR of membranes. Thermal effects and sample geometry. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 100:70-76. [PMID: 30995597 DOI: 10.1016/j.ssnmr.2019.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Whereas specially designed dinitroxide biradicals, reconstitution protocols, oriented sample geometries and NMR probes have helped to much increase the DNP enhancement factors of membrane samples they still lag considerably behind those obtained from glasses made of protein solutions. Here we show that not only the MAS rotor material but also the distribution of the membrane samples within the NMR rotor have a pronounced effect on the DNP enhancement. These observations are rationalized with the cooling efficiency and the internal properties of the sample, monitored by their T1 relaxation, microwave ON versus OFF signal intensities and DNP effect. The data are suggestive that for membranes the speed of cooling has a pronounced effect on the membrane properties and concomitantly the distribution of biradicals within the sample.
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Affiliation(s)
| | | | - Sebastian Abel
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | | | - Paul Tordo
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | - Olivier Ouari
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | - Burkhard Bechinger
- Institute of Chemistry, University of Strasbourg / CNRS, UMR7177, 67070, Strasbourg, France.
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22
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Mandala VS, Hong M. High-sensitivity protein solid-state NMR spectroscopy. Curr Opin Struct Biol 2019; 58:183-190. [PMID: 31031067 DOI: 10.1016/j.sbi.2019.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 03/17/2019] [Accepted: 03/21/2019] [Indexed: 10/27/2022]
Abstract
The sensitivity of solid-state nuclear magnetic resonance (SSNMR) spectroscopy for structural biology is significantly increased by 1H detection under fast magic-angle spinning (MAS) and by dynamic nuclear polarization (DNP) from electron spins to nuclear spins. The former allows studies of the structure and dynamics of small quantities of proteins under physiological conditions, while the latter permits studies of large biomolecular complexes in lipid membranes and cells, protein intermediates, and protein conformational distributions. We highlight recent applications of these two emerging SSNMR technologies and point out areas for future development.
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Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States.
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23
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Photocycle-dependent conformational changes in the proteorhodopsin cross-protomer Asp-His-Trp triad revealed by DNP-enhanced MAS-NMR. Proc Natl Acad Sci U S A 2019; 116:8342-8349. [PMID: 30948633 DOI: 10.1073/pnas.1817665116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteorhodopsin (PR) is a highly abundant, pentameric, light-driven proton pump. Proton transfer is linked to a canonical photocycle typical for microbial ion pumps. Although the PR monomer is able to undergo a full photocycle, the question arises whether the pentameric complex formed in the membrane via specific cross-protomer interactions plays a role in its functional mechanism. Here, we use dynamic nuclear polarization (DNP)-enhanced solid-state magic-angle spinning (MAS) NMR in combination with light-induced cryotrapping of photointermediates to address this topic. The highly conserved residue H75 is located at the protomer interface. We show that it switches from the (τ)- to the (π)-tautomer and changes its ring orientation in the M state. It couples to W34 across the oligomerization interface based on specific His/Trp ring orientations while stabilizing the pKa of the primary proton acceptor D97 within the same protomer. We further show that specific W34 mutations have a drastic effect on D97 and proton transfer mediated through H75. The residue H75 defines a cross-protomer Asp-His-Trp triad, which potentially serves as a pH-dependent regulator for proton transfer. Our data represent light-dependent, functionally relevant cross talk between protomers of a microbial rhodopsin homo-oligomer.
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24
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Kaur J, Kriebel CN, Eberhardt P, Jakdetchai O, Leeder AJ, Weber I, Brown LJ, Brown RC, Becker-Baldus J, Bamann C, Wachtveitl J, Glaubitz C. Solid-state NMR analysis of the sodium pump Krokinobacter rhodopsin 2 and its H30A mutant. J Struct Biol 2019; 206:55-65. [DOI: 10.1016/j.jsb.2018.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/05/2018] [Accepted: 06/02/2018] [Indexed: 12/26/2022]
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25
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Pinto C, Mance D, Julien M, Daniels M, Weingarth M, Baldus M. Studying assembly of the BAM complex in native membranes by cellular solid-state NMR spectroscopy. J Struct Biol 2019; 206:1-11. [DOI: 10.1016/j.jsb.2017.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 12/31/2022]
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26
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Idso MN, Baxter NR, Narayanan S, Chang E, Fisher J, Chmelka BF, Han S. Proteorhodopsin Function Is Primarily Mediated by Oligomerization in Different Micellar Surfactant Solutions. J Phys Chem B 2019; 123:4180-4192. [DOI: 10.1021/acs.jpcb.9b00922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Global response of diacylglycerol kinase towards substrate binding observed by 2D and 3D MAS NMR. Sci Rep 2019; 9:3995. [PMID: 30850624 PMCID: PMC6408475 DOI: 10.1038/s41598-019-40264-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/11/2019] [Indexed: 01/01/2023] Open
Abstract
Escherichia coli diacylglycerol kinase (DGK) is an integral membrane protein, which catalyses the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatic acid (PA). It is a unique trimeric enzyme, which does not share sequence homology with typical kinases. It exhibits a notable complexity in structure and function despite of its small size. Here, chemical shift assignment of wild-type DGK within lipid bilayers was carried out based on 3D MAS NMR, utilizing manual and automatic analysis protocols. Upon nucleotide binding, extensive chemical shift perturbations could be observed. These data provide evidence for a symmetric DGK trimer with all of its three active sites concurrently occupied. Additionally, we could detect that the nucleotide substrate induces a substantial conformational change, most likely directing DGK into its catalytic active form. Furthermore, functionally relevant interprotomer interactions are identified by DNP-enhanced MAS NMR in combination with site-directed mutagenesis and functional assays.
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28
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Kaur H, Abreu B, Akhmetzyanov D, Lakatos-Karoly A, Soares CM, Prisner T, Glaubitz C. Unexplored Nucleotide Binding Modes for the ABC Exporter MsbA. J Am Chem Soc 2018; 140:14112-14125. [PMID: 30289253 DOI: 10.1021/jacs.8b06739] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ATP-binding cassette (ABC) transporter MsbA is an ATP-driven lipid-A flippase. It belongs to the ABC protein superfamily whose members are characterized by conserved motifs in their nucleotide binding domains (NBDs), which are responsible for ATP hydrolysis. Recently, it was found that MsbA could catalyze a reverse adenylate kinase (rAK)-like reaction in addition to ATP hydrolysis. Both reactions are connected and mediated by the same conserved NBD domains. Here, the structural foundations underlying the nucleotide binding to MsbA were therefore explored using a concerted approach based on conventional- and DNP-enhanced solid-state NMR, pulsed-EPR, and MD simulations. MsbA reconstituted into lipid bilayers was trapped in various catalytic states corresponding to intermediates of the coupled ATPase-rAK mechanism. The analysis of nucleotide-binding dependent chemical shift changes, and the detection of through-space contacts between bound nucleotides and MsbA within these states provides evidence for an additional nucleotide-binding site in close proximity to the Q-loop and the His-Switch. By replacing Mg2+ with Mn2+ and employing pulsed EPR spectroscopy, evidence is provided that this newly found nucleotide binding site does not interfere with the coordination of the required metal ion. Molecular dynamic (MD) simulations of nucleotide and metal binding required for the coupled ATPase-rAK mechanism have been used to corroborate these experimental findings and provide additional insight into nucleotide location, orientation, and possible binding modes.
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Affiliation(s)
- Hundeep Kaur
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Bárbara Abreu
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , 2780-157 Oeiras , Portugal
| | - Dmitry Akhmetzyanov
- Institute for Physical and Theoretical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Andrea Lakatos-Karoly
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Cláudio M Soares
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , 2780-157 Oeiras , Portugal
| | - Thomas Prisner
- Institute for Physical and Theoretical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
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Jaudzems K, Polenova T, Pintacuda G, Oschkinat H, Lesage A. DNP NMR of biomolecular assemblies. J Struct Biol 2018; 206:90-98. [PMID: 30273657 DOI: 10.1016/j.jsb.2018.09.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/13/2018] [Accepted: 09/27/2018] [Indexed: 11/30/2022]
Abstract
Dynamic Nuclear Polarization (DNP) is an effective approach to alleviate the inherently low sensitivity of solid-state NMR (ssNMR) under magic angle spinning (MAS) towards large-sized multi-domain complexes and assemblies. DNP relies on a polarization transfer at cryogenic temperatures from unpaired electrons to adjacent nuclei upon continuous microwave irradiation. This is usually made possible via the addition in the sample of a polarizing agent. The first pioneering experiments on biomolecular assemblies were reported in the early 2000s on bacteriophages and membrane proteins. Since then, DNP has experienced tremendous advances, with the development of extremely efficient polarizing agents or with the introduction of new microwaves sources, suitable for NMR experiments at very high magnetic fields (currently up to 900 MHz). After a brief introduction, several experimental aspects of DNP enhanced NMR spectroscopy applied to biomolecular assemblies are discussed. Recent demonstration experiments of the method on viral capsids, the type III and IV bacterial secretion systems, ribosome and membrane proteins are then described.
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Affiliation(s)
- Kristaps Jaudzems
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, 163 The Green, DE 19716, USA
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP), Campus Berlin-Buch Robert-Roessle-Str. 10 13125 Berlin, Germany
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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30
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Jawurek M, Dröden J, Peter B, Glaubitz C, Hauser K. Lipid-induced dynamics of photoreceptors monitored by time-resolved step-scan FTIR spectroscopy. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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31
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Jaudzems K, Bertarello A, Chaudhari SR, Pica A, Cala-De Paepe D, Barbet-Massin E, Pell AJ, Akopjana I, Kotelovica S, Gajan D, Ouari O, Tars K, Pintacuda G, Lesage A. Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kristaps Jaudzems
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Bertarello
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Sachin R. Chaudhari
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Pica
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia I-80126 Naples Italy
| | - Diane Cala-De Paepe
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Emeline Barbet-Massin
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrew J. Pell
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
- Present address: Department of Materials and Environmental Chemistry; Arrhenius Laboratory; Stockholm University; Svante Arrhenius Väg 16 C SE-106 91 Stockholm Sweden
| | - Inara Akopjana
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | | | - David Gajan
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, ICR UMR 7273; 13397 Marseille cedex 20 France
| | - Kaspars Tars
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | - Guido Pintacuda
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Anne Lesage
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
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32
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Jaudzems K, Bertarello A, Chaudhari SR, Pica A, Cala-De Paepe D, Barbet-Massin E, Pell AJ, Akopjana I, Kotelovica S, Gajan D, Ouari O, Tars K, Pintacuda G, Lesage A. Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning. Angew Chem Int Ed Engl 2018; 57:7458-7462. [DOI: 10.1002/anie.201801016] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/06/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Kristaps Jaudzems
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Bertarello
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Sachin R. Chaudhari
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Pica
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia I-80126 Naples Italy
| | - Diane Cala-De Paepe
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Emeline Barbet-Massin
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrew J. Pell
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
- Present address: Department of Materials and Environmental Chemistry; Arrhenius Laboratory; Stockholm University; Svante Arrhenius Väg 16 C SE-106 91 Stockholm Sweden
| | - Inara Akopjana
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | | | - David Gajan
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, ICR UMR 7273; 13397 Marseille cedex 20 France
| | - Kaspars Tars
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | - Guido Pintacuda
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Anne Lesage
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
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Jahnke JP, Idso MN, Hussain S, Junk MJ, Fisher JM, Phan DD, Han S, Chmelka BF. Functionally Active Membrane Proteins Incorporated in Mesostructured Silica Films. J Am Chem Soc 2018; 140:3892-3906. [PMID: 29533066 PMCID: PMC6040920 DOI: 10.1021/jacs.7b06863] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A versatile synthetic protocol is reported that allows high concentrations of functionally active membrane proteins to be incorporated in mesostructured silica materials. Judicious selections of solvent, surfactant, silica precursor species, and synthesis conditions enable membrane proteins to be stabilized in solution and during subsequent coassembly into silica-surfactant composites with nano- and mesoscale order. This was demonstrated by using a combination of nonionic ( n-dodecyl-β-d-maltoside or Pluronic P123), lipid-like (1,2-diheptanoyl- s n-glycero-3-phosphocholine), and perfluoro-octanoate surfactants under mild acidic conditions to coassemble the light-responsive transmembrane protein proteorhodopsin at concentrations up to 15 wt % into the hydrophobic regions of worm-like mesostructured silica materials in films. Small-angle X-ray scattering, electron paramagnetic resonance spectroscopy, and transient UV-visible spectroscopy analyses established that proteorhodopsin molecules in mesostructured silica films exhibited native-like function, as well as enhanced thermal stability compared to surfactant or lipid environments. The light absorbance properties and light-activated conformational changes of proteorhodopsin guests in mesostructured silica films are consistent with those associated with the native H+-pumping mechanism of these biomolecules. The synthetic protocol is expected to be general, as demonstrated also for the incorporation of functionally active cytochrome c, a peripheral membrane protein enzyme involved in electron transport, into mesostructured silica-cationic surfactant films.
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Affiliation(s)
- Justin P. Jahnke
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106 U.S.A
| | - Matthew N. Idso
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106 U.S.A
| | - Sunyia Hussain
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106 U.S.A
| | - Matthias J.N. Junk
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106 U.S.A
| | - Julia M. Fisher
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106 U.S.A
| | - David D. Phan
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106 U.S.A
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106 U.S.A
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106 U.S.A
| | - Bradley F. Chmelka
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106 U.S.A
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Abstract
Solid-state nuclear magnetic resonance (SSNMR) spectroscopy elucidates membrane protein structures and dynamics in atomic detail to yield mechanistic insights. By interrogating membrane proteins in phospholipid bilayers that closely resemble biological membranes, SSNMR spectroscopists have revealed ion conduction mechanisms, substrate transport dynamics, and oligomeric interfaces of seven-transmembrane helix proteins. Research has also identified conformational plasticity underlying virus-cell membrane fusions by complex protein machineries, and β-sheet folding and assembly by amyloidogenic proteins bound to lipid membranes. These studies collectively show that membrane proteins exhibit extensive structural plasticity to carry out their functions. Because of the inherent dependence of NMR frequencies on molecular orientations and the sensitivity of NMR frequencies to dynamical processes on timescales from nanoseconds to seconds, SSNMR spectroscopy is ideally suited to elucidate such structural plasticity, local and global conformational dynamics, protein-lipid and protein-ligand interactions, and protonation states of polar residues. New sensitivity-enhancement techniques, resolution enhancement by ultrahigh magnetic fields, and the advent of 3D and 4D correlation NMR techniques are increasingly aiding these mechanistically important structural studies.
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Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Jonathan K Williams
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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35
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The molecular basis of subtype selectivity of human kinin G-protein-coupled receptors. Nat Chem Biol 2018; 14:284-290. [PMID: 29334381 DOI: 10.1038/nchembio.2551] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 11/21/2017] [Indexed: 12/16/2022]
Abstract
G-protein-coupled receptors (GPCRs) are the most important signal transducers in higher eukaryotes. Despite considerable progress, the molecular basis of subtype-specific ligand selectivity, especially for peptide receptors, remains unknown. Here, by integrating DNP-enhanced solid-state NMR spectroscopy with advanced molecular modeling and docking, the mechanism of the subtype selectivity of human bradykinin receptors for their peptide agonists has been resolved. The conserved middle segments of the bound peptides show distinct conformations that result in different presentations of their N and C termini toward their receptors. Analysis of the peptide-receptor interfaces reveals that the charged N-terminal residues of the peptides are mainly selected through electrostatic interactions, whereas the C-terminal segments are recognized via both conformations and interactions. The detailed molecular picture obtained by this approach opens a new gateway for exploring the complex conformational and chemical space of peptides and peptide analogs for designing GPCR subtype-selective biochemical tools and drugs.
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36
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Ji L, Ma B, Meng Q, Li L, Liu K, Chen D. Detergent-resistant oligomeric Leptosphaeria rhodopsin is a promising bio-nanomaterial and an alternative to bacteriorhodopsin. Biochem Biophys Res Commun 2017; 493:352-357. [PMID: 28887035 DOI: 10.1016/j.bbrc.2017.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/05/2017] [Indexed: 01/10/2023]
Abstract
Bacteriorhodopsin has attracted remarkable attention as a photoactive bio-nanomaterial in the last decades. However, its instability in the presence of detergents has restricted the extent to which bacteriorhodopsin may be applied. In this study, we investigated the oligomerization of a eukaryotic light-driven H+-pump, Leptosphaeria rhodopsin, using circular dichroism spectroscopy and other biophysical and biochemical methods. Our findings revealed that Leptosphaeria rhodopsin assembled into oligomers in the cell membrane and also in 0.05% DDM detergent micelles. Moreover, unlike bacteriorhodopsin in purple membrane, Leptosphaeria rhodopsin retained its oligomeric structure in 1% Triton X-100 and demonstrated strong resistance to other common detergents. A maximal photocurrent density of ∼85 nA/cm2 was consistently generated, which was substantially larger than that of solubilized bacteriorhodopsin (∼10 nA/cm2). Therefore, oligomeric Leptosphaeria rhodopsin may be a promising bio-nanomaterial, and an alternative to bacteriorhodopsin, especially with the use of detergents.
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Affiliation(s)
- Liangliang Ji
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baofu Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Meng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longjie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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37
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Mehler M, Eckert CE, Leeder AJ, Kaur J, Fischer T, Kubatova N, Brown LJ, Brown RCD, Becker-Baldus J, Wachtveitl J, Glaubitz C. Chromophore Distortions in Photointermediates of Proteorhodopsin Visualized by Dynamic Nuclear Polarization-Enhanced Solid-State NMR. J Am Chem Soc 2017; 139:16143-16153. [PMID: 29027800 DOI: 10.1021/jacs.7b05061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteorhodopsin (PR) is the most abundant retinal protein on earth and functions as a light-driven proton pump. Despite extensive efforts, structural data for PR photointermediate states have not been obtained. On the basis of dynamic nuclear polarization (DNP)-enhanced solid-state NMR, we were able to analyze the retinal polyene chain between positions C10 and C15 as well as the Schiff base nitrogen in the ground state in comparison to light-induced, cryotrapped K- and M-states. A high M-state population could be achieved by preventing reprotonation of the Schiff base through a mutation of the primary proton donor (E108Q). Our data reveal unexpected large and alternating 13C chemical shift changes in the K-state propagating away from the Schiff base along the polyene chain. Furthermore, two different M-states have been observed reflecting the Schiff base reorientation after the deprotonation step. Our study provides novel insight into the photocycle of PR and also demonstrates the power of DNP-enhanced solid-state NMR to bridge the gap between functional and structural data and models.
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Affiliation(s)
- Michaela Mehler
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Carl Elias Eckert
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Alexander J Leeder
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Jagdeep Kaur
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Tobias Fischer
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Nina Kubatova
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Lynda J Brown
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Richard C D Brown
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
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Lilly Thankamony AS, Wittmann JJ, Kaushik M, Corzilius B. Dynamic nuclear polarization for sensitivity enhancement in modern solid-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:120-195. [PMID: 29157490 DOI: 10.1016/j.pnmrs.2017.06.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/03/2017] [Accepted: 06/08/2017] [Indexed: 05/03/2023]
Abstract
The field of dynamic nuclear polarization has undergone tremendous developments and diversification since its inception more than 6 decades ago. In this review we provide an in-depth overview of the relevant topics involved in DNP-enhanced MAS NMR spectroscopy. This includes the theoretical description of DNP mechanisms as well as of the polarization transfer pathways that can lead to a uniform or selective spreading of polarization between nuclear spins. Furthermore, we cover historical and state-of-the art aspects of dedicated instrumentation, polarizing agents, and optimization techniques for efficient MAS DNP. Finally, we present an extensive overview on applications in the fields of structural biology and materials science, which underlines that MAS DNP has moved far beyond the proof-of-concept stage and has become an important tool for research in these fields.
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Affiliation(s)
- Aany Sofia Lilly Thankamony
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Johannes J Wittmann
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Monu Kaushik
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany.
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39
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The effect of drug binding on specific sites in transmembrane helices 4 and 6 of the ABC exporter MsbA studied by DNP-enhanced solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:833-840. [PMID: 29069570 DOI: 10.1016/j.bbamem.2017.10.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/09/2017] [Accepted: 10/15/2017] [Indexed: 02/05/2023]
Abstract
MsbA, a homodimeric ABC exporter, translocates its native substrate lipid A as well as a range of smaller, amphiphilic substrates across the membrane. Magic angle sample spinning (MAS) NMR, in combination with dynamic nuclear polarization (DNP) for signal enhancement, has been used to probe two specific sites in transmembrane helices 4 and 6 of full length MsbA embedded in lipid bilayers. Significant chemical shift changes in both sites were observed in the vanadate-trapped state compared to apo state MsbA. The reduced spectral line width indicates a more confined conformational space upon trapping. In the presence of substrates Hoechst 33342 and daunorubicin, further chemical shift changes and line shape alterations mainly in TM6 in the vanadate trapped state were detected. These data illustrate the conformational response of MsbA towards the presence of drugs during the catalytic cycle. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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40
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Visscher KM, Medeiros-Silva J, Mance D, Rodrigues JPGLM, Daniëls M, Bonvin AMJJ, Baldus M, Weingarth M. Supramolekulare Organisation und funktionale Auswirkungen von Ballungen von K +
-Kanälen in Membranen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Koen M. Visscher
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - João P. G. L. M. Rodrigues
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Mark Daniëls
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Alexandre M. J. J. Bonvin
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
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41
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Visscher KM, Medeiros‐Silva J, Mance D, Rodrigues JPGLM, Daniëls M, Bonvin AMJJ, Baldus M, Weingarth M. Supramolecular Organization and Functional Implications of K + Channel Clusters in Membranes. Angew Chem Int Ed Engl 2017; 56:13222-13227. [PMID: 28685953 PMCID: PMC5655921 DOI: 10.1002/anie.201705723] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/29/2017] [Indexed: 11/19/2022]
Abstract
The segregation of cellular surfaces in heterogeneous patches is considered to be a common motif in bacteria and eukaryotes that is underpinned by the observation of clustering and cooperative gating of signaling membrane proteins such as receptors or channels. Such processes could represent an important cellular strategy to shape signaling activity. Hence, structural knowledge of the arrangement of channels or receptors in supramolecular assemblies represents a crucial step towards a better understanding of signaling across membranes. We herein report on the supramolecular organization of clusters of the K+ channel KcsA in bacterial membranes, which was analyzed by a combination of DNP-enhanced solid-state NMR experiments and MD simulations. We used solid-state NMR spectroscopy to determine the channel-channel interface and to demonstrate the strong correlation between channel function and clustering, which suggests a yet unknown mechanism of communication between K+ channels.
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Affiliation(s)
- Koen M. Visscher
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - João Medeiros‐Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - João P. G. L. M. Rodrigues
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Mark Daniëls
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Alexandre M. J. J. Bonvin
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
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42
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Molugu TR, Lee S, Brown MF. Concepts and Methods of Solid-State NMR Spectroscopy Applied to Biomembranes. Chem Rev 2017; 117:12087-12132. [PMID: 28906107 DOI: 10.1021/acs.chemrev.6b00619] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Concepts of solid-state NMR spectroscopy and applications to fluid membranes are reviewed in this paper. Membrane lipids with 2H-labeled acyl chains or polar head groups are studied using 2H NMR to yield knowledge of their atomistic structures in relation to equilibrium properties. This review demonstrates the principles and applications of solid-state NMR by unifying dipolar and quadrupolar interactions and highlights the unique features offered by solid-state 2H NMR with experimental illustrations. For randomly oriented multilamellar lipids or aligned membranes, solid-state 2H NMR enables direct measurement of residual quadrupolar couplings (RQCs) due to individual C-2H-labeled segments. The distribution of RQC values gives nearly complete profiles of the segmental order parameters SCD(i) as a function of acyl segment position (i). Alternatively, one can measure residual dipolar couplings (RDCs) for natural abundance lipid samples to obtain segmental SCH order parameters. A theoretical mean-torque model provides acyl-packing profiles representing the cumulative chain extension along the normal to the aqueous interface. Equilibrium structural properties of fluid bilayers and various thermodynamic quantities can then be calculated, which describe the interactions with cholesterol, detergents, peptides, and integral membrane proteins and formation of lipid rafts. One can also obtain direct information for membrane-bound peptides or proteins by measuring RDCs using magic-angle spinning (MAS) in combination with dipolar recoupling methods. Solid-state NMR methods have been extensively applied to characterize model membranes and membrane-bound peptides and proteins, giving unique information on their conformations, orientations, and interactions in the natural liquid-crystalline state.
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Affiliation(s)
- Trivikram R Molugu
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Soohyun Lee
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Michael F Brown
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
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43
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Recent advances in biophysical studies of rhodopsins - Oligomerization, folding, and structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1512-1521. [PMID: 28844743 DOI: 10.1016/j.bbapap.2017.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/06/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022]
Abstract
Retinal-binding proteins, mainly known as rhodopsins, function as photosensors and ion transporters in a wide range of organisms. From halobacterial light-driven proton pump, bacteriorhodopsin, to bovine photoreceptor, visual rhodopsin, they have served as prototypical α-helical membrane proteins in a large number of biophysical studies and aided in the development of many cutting-edge techniques of structural biology and biospectroscopy. In the last decade, microbial and animal rhodopsin families have expanded significantly, bringing into play a number of new interesting structures and functions. In this review, we will discuss recent advances in biophysical approaches to retinal-binding proteins, primarily microbial rhodopsins, including those in optical spectroscopy, X-ray crystallography, nuclear magnetic resonance, and electron paramagnetic resonance, as applied to such fundamental biological aspects as protein oligomerization, folding, and structure.
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44
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Rogawski R, McDermott AE. New NMR tools for protein structure and function: Spin tags for dynamic nuclear polarization solid state NMR. Arch Biochem Biophys 2017; 628:102-113. [PMID: 28623034 PMCID: PMC5815514 DOI: 10.1016/j.abb.2017.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/05/2017] [Accepted: 06/12/2017] [Indexed: 12/13/2022]
Abstract
Magic angle spinning solid state NMR studies of biological macromolecules [1-3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in DNP experiments.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University, NY, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, NY, NY 10027, United States.
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45
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Lalli D, Idso MN, Andreas LB, Hussain S, Baxter N, Han S, Chmelka BF, Pintacuda G. Proton-Based Structural Analysis of a Heptahelical Transmembrane Protein in Lipid Bilayers. J Am Chem Soc 2017; 139:13006-13012. [PMID: 28724288 PMCID: PMC5741281 DOI: 10.1021/jacs.7b05269] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
structures and properties of membrane proteins in lipid bilayers are
expected to closely resemble those in native cell-membrane environments,
although they have been difficult to elucidate. By performing solid-state
NMR measurements at very fast (100 kHz) magic-angle spinning rates
and at high (23.5 T) magnetic field, severe sensitivity and resolution
challenges are overcome, enabling the atomic-level characterization
of membrane proteins in lipid environments. This is demonstrated by
extensive 1H-based resonance assignments of the fully protonated
heptahelical membrane protein proteorhodopsin, and the efficient identification
of numerous 1H–1H dipolar interactions,
which provide distance constraints, inter-residue proximities, relative
orientations of secondary structural elements, and protein–cofactor
interactions in the hydrophobic transmembrane regions. These results
establish a general approach for high-resolution structural studies
of membrane proteins in lipid environments via solid-state NMR.
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Affiliation(s)
- Daniela Lalli
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 69100 Villeurbanne, France
| | - Matthew N Idso
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 69100 Villeurbanne, France
| | - Sunyia Hussain
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Naomi Baxter
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States.,Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Bradley F Chmelka
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 69100 Villeurbanne, France
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46
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Applications of solid-state NMR to membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1577-1586. [PMID: 28709996 DOI: 10.1016/j.bbapap.2017.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022]
Abstract
Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Salnikov ES, Abel S, Karthikeyan G, Karoui H, Aussenac F, Tordo P, Bechinger B, Ouari O. Dynamic Nuclear Polarization/Solid-State NMR Spectroscopy of Membrane Polypeptides: Free-Radical Optimization for Matrix-Free Lipid Bilayer Samples. Chemphyschem 2017; 18:2103-2113. [PMID: 28574169 DOI: 10.1002/cphc.201700389] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/24/2017] [Indexed: 01/07/2023]
Abstract
Dynamic nuclear polarization (DNP) boosts the sensitivity of NMR spectroscopy by orders of magnitude and makes investigations previously out of scope possible. For magic-angle-spinning (MAS) solid-state NMR spectroscopy studies, the samples are typically mixed with biradicals dissolved in a glass-forming solvent and are investigated at cryotemperatures. Herein, we present new biradical polarizing agents developed for matrix-free samples such as supported lipid bilayers, which are systems widely used for the investigation of membrane polypeptides of high biomedical importance. A series of 11 biradicals with different structures, geometries, and physicochemical properties were comprehensively tested for DNP performance in lipid bilayers, some of them developed specifically for DNP investigations of membranes. The membrane-anchored biradicals PyPol-C16, AMUPOL-cholesterol, and bTurea-C16 were found to exhibit improved g-tensor alignment, inter-radical distance, and dispersion. Consequently, these biradicals show the highest signal enhancement factors so far obtained for matrix-free membranes or other matrix-free samples and may potentially shorten NMR acquisition times by three orders of magnitude. Furthermore, the optimal biradical-to-lipid ratio, sample deuteration, and membrane lipid composition were determined under static and MAS conditions. To rationalize biradical performance better, DNP enhancement was measured by using the 13 C and 15 N signals of lipids and a peptide as a function of the biradical concentration, DNP build-up time, resonance line width, quenching effect, microwave power, and MAS frequency.
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Affiliation(s)
- Evgeniy S Salnikov
- Institut de chimie, UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Sébastien Abel
- Aix Marseille Univ, CNRS, ICR UMR 7273, 13013, Marseille, France
| | | | - Hakim Karoui
- Aix Marseille Univ, CNRS, ICR UMR 7273, 13013, Marseille, France
| | - Fabien Aussenac
- Bruker Biospin, 34, rue de l'industrie, 67166, Wissembourg, France
| | - Paul Tordo
- Aix Marseille Univ, CNRS, ICR UMR 7273, 13013, Marseille, France
| | - Burkhard Bechinger
- Institut de chimie, UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, ICR UMR 7273, 13013, Marseille, France
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48
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Oligomeric Structure of Anabaena Sensory Rhodopsin in a Lipid Bilayer Environment by Combining Solid-State NMR and Long-range DEER Constraints. J Mol Biol 2017; 429:1903-1920. [DOI: 10.1016/j.jmb.2017.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/27/2017] [Accepted: 05/06/2017] [Indexed: 11/22/2022]
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49
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From Gene to Function: Cell-Free Electrophysiological and Optical Analysis of Ion Pumps in Nanodiscs. Biophys J 2017; 113:1331-1341. [PMID: 28450130 DOI: 10.1016/j.bpj.2017.03.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022] Open
Abstract
Nanodiscs that hold a lipid bilayer surrounded by a boundary of scaffold proteins have emerged as a powerful tool for membrane protein solubilization and analysis. By combining nanodiscs and cell-free expression technologies, even completely detergent-free membrane protein characterization protocols can be designed. Nanodiscs are compatible with various techniques, and due to their bilayer environment and increased stability, they are often superior to detergent micelles or liposomes for membrane protein solubilization. However, transport assays in nanodiscs have not been conducted so far, due to limitations of the two-dimensional nature of nanodisc membranes that offers no compartmentalization. Here, we study Krokinobacter eikastus rhodopsin-2 (KR2), a microbial light-driven sodium or proton pump, with noncovalent mass-spectrometric, electrophysiological, and flash photolysis measurements after its cotranslational insertion into nanodiscs. We demonstrate the feasibility of adsorbing nanodiscs containing KR2 to an artificial bilayer. This allows us to record light-induced capacitive currents that reflect KR2's ion transport activity. The solid-supported membrane assay with nanodisc samples provides reliable control over the ionic condition and information of the relative ion activity of this promiscuous pump. Our strategy is complemented with flash photolysis data, where the lifetimes of different photointermediates were determined at different ionic conditions. The advantage of using identical samples to three complementary approaches allows for a comprehensive comparability. The cell-free synthesis in combination with nanodiscs provides a defined hydrophobic lipid environment minimizing the detergent dependence often seen in assays with membrane proteins. KR2 is a promising tool for optogenetics, thus directed engineering to modify ion selectivity can be highly beneficial. Our approach, using the fast generation of functional ion pumps incorporated into nanodiscs and their subsequent analysis by several biophysical techniques, can serve as a versatile screening and engineering platform. This may open new avenues for the study of ion pumps and similar electrogenic targets.
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50
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Rogawski R, Sergeyev IV, Li Y, Ottaviani MF, Cornish V, McDermott AE. Dynamic Nuclear Polarization Signal Enhancement with High-Affinity Biradical Tags. J Phys Chem B 2017; 121:1169-1175. [PMID: 28099013 DOI: 10.1021/acs.jpcb.6b09021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Dynamic nuclear polarization is an emerging technique for sensitizing solid-state NMR experiments by transferring polarization from electrons to nuclei. Stable biradicals, the polarization source for the cross effect mechanism, are typically codissolved at millimolar concentrations with proteins of interest. Here we describe the high-affinity biradical tag TMP-T, created by covalently linking trimethoprim, a nanomolar affinity ligand of dihydrofolate reductase (DHFR), to the biradical polarizing agent TOTAPOL. With TMP-T bound to DHFR, large enhancements of the protein spectrum are observed, comparable to when TOTAPOL is codissolved with the protein. In contrast to TOTAPOL, the tight binding TMP-T can be added stoichiometrically at radical concentrations orders of magnitude lower than in previously described preparations. Benefits of the reduced radical concentration include reduced spectral bleaching, reduced chemical perturbation of the sample, and the ability to selectively enhance signals for the protein of interest.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Ivan V Sergeyev
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Yongjun Li
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - M Francesca Ottaviani
- Department of Pure and Applied Sciences, University of Urbino , Loc. Crocicchia, 61029 Urbino, Italy
| | - Virginia Cornish
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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