1
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Umegawa Y, Kato S, Seo S, Shinoda W, Kawatake S, Matsuoka S, Murata M. Protein-lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin. Biophys Chem 2024; 308:107204. [PMID: 38412762 DOI: 10.1016/j.bpc.2024.107204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
Boundary lipids surrounding membrane proteins play an essential role in protein function and structure. These protein-lipid interactions are mainly divided into electrostatic interactions between the polar amino acids of proteins and polar heads of phospholipids, and hydrophobic interactions between protein transmembrane sites and phospholipid acyl chains. Our previous report (Kawatake et al., Biochim. Biophys. Acta 1858 [2016] 2106-2115) covered a method for selectively analyzing boundary lipid interactions and showed differences in membrane protein-peripheral lipid interactions due to differences in their head group. Interactions in the hydrophobic acyl chains of phospholipids are relatively consistent among proteins, but the details of these interactions have not been elucidated. In this study, we reconstituted bacteriorhodopsin as a model protein into phospholipid membranes labeled with 2H and 13C for solid-state NMR measurement to investigate the depth-dependent effect of the head group structure on the lipid bilayer. The results showed that the position of the phospholipid near the carbonyl carbon was affected by the head group in terms of selectivity for protein surfaces, whereas in the deep interior of the bilayer near the leaflet interface, there was little difference between the head groups, indicating that the dependence of their interactions on the head group was much reduced.
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Affiliation(s)
- Yuichi Umegawa
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Sho Kato
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Division of Supercomputing, Korea Institute of Science and Technology Information, 245 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Institute for Interdisciplinary Science, Okayama University, 3-1-1, Tsushima-naka, Okayama 700-8530, Japan
| | - Satoshi Kawatake
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Matsuoka
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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2
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Vugmeyster L, Au DF, Frazier B, Qiang W, Ostrovsky D. Rigidifying of the internal dynamics of amyloid-beta fibrils generated in the presence of synaptic plasma vesicles. Phys Chem Chem Phys 2024; 26:5466-5478. [PMID: 38277177 PMCID: PMC10956644 DOI: 10.1039/d3cp04824a] [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] [Indexed: 01/27/2024]
Abstract
We investigated the changes in internal flexibility of amyloid-β1-40 (Aβ) fibrils grown in the presence of rat synaptic plasma vesicles. The fibrils are produced using a modified seeded growth protocol, in which the Aβ concentration is progressively increased at the expense of the decreased lipid to protein ratio. The morphologies of each generation are carefully assessed at several fibrils' growth time points using transmission electron microscopy. The side-chain dynamics in the fibrils is investigated using deuterium solid-state NMR measurements, with techniques spanning line shapes analysis and several NMR relaxation rates measurements. The dynamics is probed in the site-specific fashion in the hydrophobic C-terminal domain and the disordered N-terminal domain. An overall strong rigidifying effect is observed in comparison with the wild-type fibrils generated in the absence of the membranes. In particular, the overall large-scale fluctuations of the N-terminal domain are significantly reduced, and the activation energies of rotameric inter-conversion in methyl-bearing side-chains of the core (L17, L34, M35, V36), as well as the ring-flipping motions of F19 are increased, indicating a restricted core environment. Membrane-induced flexibility changes in Aβ aggregates can be important for the re-alignment of protein aggregates within the membrane, which in turn would act as a disruption pathway of the bilayers' integrity.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Bailey Frazier
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York, USA, 13902
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO, USA, 80204
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3
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Vugmeyster L, Rodgers A, Ostrovsky D, James McKnight C, Fu R. Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 352:107493. [PMID: 37271094 PMCID: PMC10330767 DOI: 10.1016/j.jmr.2023.107493] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
We demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO 80204, USA
| | - C James McKnight
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, United States
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL 32310, USA
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4
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Borcik C, Eason IR, Vanderloop B, Wylie BJ. 2H, 13C-Cholesterol for Dynamics and Structural Studies of Biological Membranes. ACS OMEGA 2022; 7:17151-17160. [PMID: 35647452 PMCID: PMC9134247 DOI: 10.1021/acsomega.2c00796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/08/2022] [Indexed: 05/19/2023]
Abstract
We present a cost-effective means of 2H and 13C enrichment of cholesterol. This method exploits the metabolism of 2H,13C-acetate into acetyl-CoA, the first substrate in the mevalonate pathway. We show that growing the cholesterol producing strain RH6827 of Saccharomyces cerevisiae in 2H,13C-acetate-enriched minimal media produces a skip-labeled pattern of deuteration. We characterize this cholesterol labeling pattern by mass spectrometry and solid-state nuclear magnetic resonance spectroscopy. It is confirmed that most 2H nuclei retain their original 2H-13C bonds from acetate throughout the biosynthetic pathway. We then quantify the changes in 13C chemical shifts brought by deuteration and the impact upon 13C-13C spin diffusion. Finally, using adiabatic rotor echo short pulse irradiation cross-polarization (RESPIRATIONCP), we acquire the 2H-13C correlation spectra to site specifically quantify cholesterol dynamics in two model membranes as a function of temperature. These measurements show that cholesterol acyl chains at physiological temperatures in mixtures of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), sphingomyelin, and cholesterol are more dynamic than cholesterol in POPC. However, this overall change in motion is not uniform across the cholesterol molecule. This result establishes that this cholesterol labeling pattern will have great utility in reporting on cholesterol dynamics and orientation in a variety of environments and with different membrane bilayer components, as well as monitoring the mevalonate pathway product interactions within the bilayer. Finally, the flexibility and universality of acetate labeling will allow this technique to be widely applied to a large range of lipids and other natural products.
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5
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Bada Juarez JF, Judge PJ, Adam S, Axford D, Vinals J, Birch J, Kwan TOC, Hoi KK, Yen HY, Vial A, Milhiet PE, Robinson CV, Schapiro I, Moraes I, Watts A. Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization. Nat Commun 2021; 12:629. [PMID: 33504778 PMCID: PMC7840839 DOI: 10.1038/s41467-020-20596-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
Many transmembrane receptors have a desensitized state, in which they are unable to respond to external stimuli. The family of microbial rhodopsin proteins includes one such group of receptors, whose inactive or dark-adapted (DA) state is established in the prolonged absence of light. Here, we present high-resolution crystal structures of the ground (light-adapted) and DA states of Archaerhodopsin-3 (AR3), solved to 1.1 Å and 1.3 Å resolution respectively. We observe significant differences between the two states in the dynamics of water molecules that are coupled via H-bonds to the retinal Schiff Base. Supporting QM/MM calculations reveal how the DA state permits a thermodynamic equilibrium between retinal isomers to be established, and how this same change is prevented in the ground state in the absence of light. We suggest that the different arrangement of internal water networks in AR3 is responsible for the faster photocycle kinetics compared to homologs.
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Affiliation(s)
- Juan F Bada Juarez
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter J Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Javier Vinals
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - James Birch
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Tristan O C Kwan
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
- National Physical Laboratory, Hampton Road, Teddington, London, TW11 0LW, UK
| | - Kin Kuan Hoi
- Chemistry Research Laboratory, Oxford University, Mansfield Road, Oxford, OX1 3TA, UK
| | - Hsin-Yung Yen
- OMass Therapeutics, The Schrodinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Anthony Vial
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - Pierre-Emmanuel Milhiet
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - Carol V Robinson
- Chemistry Research Laboratory, Oxford University, Mansfield Road, Oxford, OX1 3TA, UK
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
- National Physical Laboratory, Hampton Road, Teddington, London, TW11 0LW, UK.
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK.
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6
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Roy PP, Kato Y, Abe-Yoshizumi R, Pieri E, Ferré N, Kandori H, Buckup T. Mapping the ultrafast vibrational dynamics of all-trans and 13-cis retinal isomerization in Anabaena Sensory Rhodopsin. Phys Chem Chem Phys 2018; 20:30159-30173. [PMID: 30484447 DOI: 10.1039/c8cp05469j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Discrepancies in the isomerization dynamics and quantum yields of the trans and cis retinal protonated Schiff base is a well-known issue in the context of retinal photochemistry. Anabaena Sensory Rhodopsin (ASR) is a microbial retinal protein that comprises a retinal chromophore in two ground state (GS) conformations: all-trans, 15-anti (AT) and 13-cis, 15-syn (13C). In this study, we applied impulsive vibrational spectroscopic techniques (DFWM, pump-DFWM and pump-IVS) to ASR to shed more light on how the structural changes take place in the excited state within the same protein environment. Our findings point to distinct features in the ground state structural conformations as well as to drastically different evolutions in the excited state manifold. The ground state vibrational spectra show stronger Raman activity of the C14-H out-of-plane wag (at about 805 cm-1) for the 13C isomer than that for the AT isomer, which hints at a pre-distortion of 13C in the ground state. Evolution of the Raman frequency after interaction with the actinic pulse shows a blue-shift for the C[double bond, length as m-dash]C stretching and CH3 rocking mode for both isomers. For AT, however, the blue-shift is not instantaneous as observed for the 13C isomer, rather it takes more than 200 fs to reach the maximum frequency shift. This frequency blue-shift is rationalized by a decrease in the effective conjugation length during the isomerization reaction, which further confirms a slower formation of the twisted state for the AT isomer and corroborates the presence of a barrier in the excited state trajectory previously predicted by quantum chemical calculations.
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Affiliation(s)
- Partha Pratim Roy
- Physikalisch-Chemisches Institut, Ruprecht-Karls Universität Heidelberg, D-69210, Heidelberg, Germany.
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7
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Navidi M, Yadav S, Struts AV, Brown MF, Nesnas N. Synthesis of 9-CD 3-9- cis-Retinal Cofactor of Isorhodopsin. Tetrahedron Lett 2018; 59:4521-4524. [PMID: 30692701 DOI: 10.1016/j.tetlet.2018.11.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We report the synthesis of 9-CD3-9-cis-retinal via a six-step procedure from β-ionone. The steps involve an initial deuteration of the methyl ketone of β-ionone followed by two consecutive Horner-Wadsworth-Emmons (HWE) coupling reactions and their corresponding DIBAL reductions. A final oxidation of the allylic alcohol of the retinol leads to the target compound. This deuterium labeled retinoid is an important cofactor for studying protein-retinoid interactions in isorhodopsin.
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Affiliation(s)
- Mozhgan Navidi
- Department of Biomedical & Chemical Engineering & Sciences, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Shreya Yadav
- Department of Biomedical & Chemical Engineering & Sciences, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Andrey V Struts
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - Nasri Nesnas
- Department of Biomedical & Chemical Engineering & Sciences, Florida Institute of Technology, Melbourne, Florida 32901, USA
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8
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Vugmeyster L, Ostrovsky D. Basic experiments in 2H static NMR for the characterization of protein side-chain dynamics. Methods 2018; 148:136-145. [PMID: 29705208 PMCID: PMC6133770 DOI: 10.1016/j.ymeth.2018.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/02/2018] [Accepted: 04/24/2018] [Indexed: 12/23/2022] Open
Abstract
The focus of this review is the basic methodology for applications of static deuteron NMR for studies of dynamics in the side chains of proteins. We review experimental approaches for the measurements of static line shapes and relaxation rates as well as signal enhancement strategies using the multiple echo acquisition scheme. Further, we describe computational strategies for modeling jump and diffusive motions underlying experimental data. Applications are chosen from studies of amyloid fibrils comprising the amyloid-β protein.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO 80204, USA
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9
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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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10
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Vugmeyster L, Ostrovsky D. Static solid-state 2H NMR methods in studies of protein side-chain dynamics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 101:1-17. [PMID: 28844219 PMCID: PMC5576518 DOI: 10.1016/j.pnmrs.2017.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 05/27/2023]
Abstract
In this review, we discuss the experimental static deuteron NMR techniques and computational approaches most useful for the investigation of side-chain dynamics in protein systems. Focus is placed on the interpretation of line shape and relaxation data within the framework of motional modeling. We consider both jump and diffusion models and apply them to uncover glassy behaviors, conformational exchange and dynamical transitions in proteins. Applications are chosen from globular and membrane proteins, amyloid fibrils, peptide adsorbed on surfaces and proteins specific to connective tissues.
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11
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Buda F, Keijer T, Ganapathy S, de Grip WJ. A Quantum-mechanical Study of the Binding Pocket of Proteorhodopsin: Absorption and Vibrational Spectra Modulated by Analogue Chromophores. Photochem Photobiol 2017; 93:1399-1406. [DOI: 10.1111/php.12800] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/22/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Francesco Buda
- Leiden University; Leiden Institute of Chemistry; Leiden The Netherlands
| | - Tom Keijer
- Leiden University; Leiden Institute of Chemistry; Leiden The Netherlands
| | - Srividya Ganapathy
- Leiden University; Leiden Institute of Chemistry; Leiden The Netherlands
| | - Willem J. de Grip
- Leiden University; Leiden Institute of Chemistry; Leiden The Netherlands
- Radboud University Medical Center; Radboud Institute for Molecular Life Sciences; Nijmegen The Netherlands
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12
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Applications of NMR to membrane proteins. Arch Biochem Biophys 2017; 628:92-101. [PMID: 28529197 DOI: 10.1016/j.abb.2017.05.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 01/14/2023]
Abstract
Membrane proteins present a challenge for structural biology. In this article, we review some of the recent developments that advance the application of NMR to membrane proteins, with emphasis on structural studies in detergent-free, lipid bilayer samples that resemble the native environment. NMR spectroscopy is not only ideally suited for structure determination of membrane proteins in hydrated lipid bilayer membranes, but also highly complementary to the other principal techniques based on X-ray and electron diffraction. Recent advances in NMR instrumentation, spectroscopic methods, computational methods, and sample preparations are driving exciting new efforts in membrane protein structural biology.
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13
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Meirovitch E, Liang Z, Freed JH. Protein Dynamics in the Solid State from (2)H NMR Line Shape Analysis. II. MOMD Applied to C-D and C-CD3 Probes. J Phys Chem B 2015; 119:14022-32. [PMID: 26402431 PMCID: PMC4676681 DOI: 10.1021/acs.jpcb.5b07434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Deuterium
line shape analysis from mobile C–D and C–CD3 groups has emerged as a particularly useful tool for studying
dynamics in the solid state. The theoretical models devised so far
consist typically of sets of independent dynamic modes. Each such
mode is simple and usually case-specific. In this scenario, model
improvement entails adding yet another mode (thereby changing the
overall model), comparison of different cases is difficult, and ambiguity
is unavoidable. We recently developed the microscopic order macroscopic
disorder (MOMD) approach as a single-mode alternative. In MOMD, the
local spatial restrictions are expressed by an anisotropic potential,
the local motion by a diffusion tensor, and the local molecular geometry
by relative (magnetic and model-related) tensor orientations, all
of adjustable symmetry. This approach provides a consistent method
of analysis, thus resolving the issues above. In this study, we apply
MOMD to PS-adsorbed LKα14 peptide and dimethylammonium tetraphenylborate
(C–CD3 and N–CD3 dynamics, respectively),
as well as HhaI methyltransferase target DNA and
phase III of benzene-6-hexanoate (C–D dynamics). The success
with fitting these four disparate cases, as well as the two cases
in the previous report, demonstrates the generality of this MOMD-based
approach. In this study, C–D and C–CD3 are
both found to execute axial diffusion (rates R⊥ and R∥) in the
presence of a rhombic potential given by the L =
2 spherical harmonics (coefficients c02 and c22). R⊥ (R∥) is in the 102–103 (104–105) s–1 range, and c02 and c22 are on the
order of 2–3 kBT. Specific parameter values are determined for each mobile site.
The diffusion and quadrupolar tensors are tilted at either 120°
(consistent with trans–gauche isomerization) or nearly 110.5° (consistent with methyl exchange).
Future prospects include extension of the MOMD formalism to include
MAS, and application to 15N and 13C nuclei.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States
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14
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Meirovitch E, Liang Z, Freed JH. Protein dynamics in the solid state from 2H NMR line shape analysis: a consistent perspective. J Phys Chem B 2015; 119:2857-68. [PMID: 25594631 DOI: 10.1021/jp511386b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Deuterium line shape analysis of CD3 groups has emerged as a particularly useful tool for studying microsecond-millisecond protein motions in the solid state. The models devised so far consist of several independently conceived simple jump-type motions. They are comprised of physical quantities encoded in their simplest form; improvements are only possible by adding yet another simple motion, thereby changing the model. The various treatments developed are case-specific; hence comparison among the different systems is not possible. Here we develop a new methodology for (2)H NMR line shape analysis free of these limitations. It is based on the microscopic-order-macroscopic-disorder (MOMD) approach. In MOMD motions are described by diffusion tensors, spatial restrictions by potentials/ordering tensors, and geometric features by relative tensor orientations. Jump-type motions are recovered in the limit of large orientational potentials. Model improvement is accomplished by monitoring the magnitude, symmetry, and orientation of the various tensors. The generality of MOMD makes possible comparison among different scenarios. CD3 line shapes from the Chicken Villin Headpiece Subdomain and the Streptomyces Subtilisin Inhibitor are used as experimental examples. All of these spectra are reproduced by using rhombic local potentials constrained for simplicity to be given by the L = 2 spherical harmonics, and by axial diffusion tensors. Potential strength and rhombicity are found to be ca. 2-3 k(B)T. The diffusion tensor is tilted at 120° from the C-CD3 axis. The perpendicular (parallel) correlation times for local motion are 0.1-1.0 ms (3.3-30 μs). Activation energies in the 1.1-8.0 kcal/mol range are estimated. Future prospects include extension to the (2)H relaxation limit, application to the (15)N and (13)C NMR nuclei, and accounting for collective motions and anisotropic media.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
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15
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Cheminal A, Léonard J, Kim SY, Jung KH, Kandori H, Haacke S. 100 fs photo-isomerization with vibrational coherences but low quantum yield in Anabaena Sensory Rhodopsin. Phys Chem Chem Phys 2015; 17:25429-39. [DOI: 10.1039/c5cp04353k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Counter-intuitive photochemistry: in Anabaena Sensory Rhodopsin, the retinal 13-cis isomer isomerizes much faster than all-trans ASR, but with a 3-times lower quantum yield.
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Affiliation(s)
- Alexandre Cheminal
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg – CNRS
- 67034 Strasbourg
- France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg – CNRS
- 67034 Strasbourg
- France
| | - So-Young Kim
- Department of Life Science and Institute of Biological Interfaces
- Sogang University
- Mapo-Gu
- South Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces
- Sogang University
- Mapo-Gu
- South Korea
| | - Hideki Kandori
- Department of Frontier Materials
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Stefan Haacke
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg – CNRS
- 67034 Strasbourg
- France
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16
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Yu X, Lorigan GA. Secondary structure, backbone dynamics, and structural topology of phospholamban and its phosphorylated and Arg9Cys-mutated forms in phospholipid bilayers utilizing 13C and 15N solid-state NMR spectroscopy. J Phys Chem B 2014; 118:2124-33. [PMID: 24511878 PMCID: PMC3983341 DOI: 10.1021/jp500316s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Phospholamban (PLB) is a membrane protein that regulates heart muscle relaxation rates via interactions with the sarcoplasmic reticulum Ca(2+) ATPase (SERCA). When PLB is phosphorylated or Arg9Cys (R9C) is mutated, inhibition of SERCA is relieved. (13)C and (15)N solid-state NMR spectroscopy is utilized to investigate conformational changes of PLB upon phosphorylation and R9C mutation. (13)C═O NMR spectra of the cytoplasmic domain reveal two α-helical structural components with population changes upon phosphorylation and R9C mutation. The appearance of an unstructured component is observed on domain Ib. (15)N NMR spectra indicate an increase in backbone dynamics of the cytoplasmic domain. Wild-type PLB (WT-PLB), Ser16-phosphorylated PLB (P-PLB), and R9C-mutated PLB (R9C-PLB) all have a very dynamic domain Ib, and the transmembrane domain has an immobile component. (15)N NMR spectra indicate that the cytoplasmic domain of R9C-PLB adopts an orientation similar to P-PLB and shifts away from the membrane surface. Domain Ib (Leu28) of P-PLB and R9C-PLB loses the alignment. The R9C-PLB adopts a conformation similar to P-PLB with a population shift to a more extended and disordered state. The NMR data suggest the more extended and disordered forms of PLB may relate to inhibition relief.
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Affiliation(s)
- Xueting Yu
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
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17
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Huster D. Solid-state NMR spectroscopy to study protein-lipid interactions. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:1146-60. [PMID: 24333800 DOI: 10.1016/j.bbalip.2013.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/04/2013] [Indexed: 12/22/2022]
Abstract
The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next-neighbor boundary lipids. Therefore, a mesoscopic approach to membrane lipid-protein interactions in terms of elastic membrane deformations has been developed. Solid-state NMR has greatly contributed to the understanding of lipid-protein interactions and the modern view of biological membranes. Methods that detect the influence of proteins on the membrane as well as direct lipid-protein interactions have been developed and are reviewed here. Examples for solid-state NMR studies on the interaction of Ras proteins, the antimicrobial peptide protegrin-1, the G protein-coupled receptor rhodopsin, and the K(+) channel KcsA are discussed. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany.
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18
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Yu X, Lorigan GA. Probing the interaction of Arg9Cys mutated phospholamban with phospholipid bilayers by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2444-9. [PMID: 23850636 DOI: 10.1016/j.bbamem.2013.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 06/10/2013] [Accepted: 07/01/2013] [Indexed: 01/05/2023]
Abstract
Phospholamban (PLB) is a 52 amino acid integral membrane protein that interacts with the sarcoplasmic reticulum Ca(2+) ATPase (SERCA) and helps to regulate Ca(2+) flow. PLB inhibits SERCA impairing Ca(2+) translocation. The inhibition can be relieved upon phosphorylation of PLB. The Arg9 to Cys (R9C) mutation is a loss of function mutation with reduced inhibitory potency. The effect R9C PLB has on the membrane surface and the hydrophobic region dynamics was investigated by (31)P and (2)H solid-state NMR spectroscopy in multilamellar vesicles (MLVs). The (31)P NMR spectra indicate that, like the phosphorylated PLB (P-PLB), the mutated R9C-PLB protein has significantly less interaction with the lipid bilayer headgroup when compared to wild-type PLB (WT-PLB). Similar to P-PLB, R9C-PLB slightly decreases (31)P T1 values in the lipid headgroup region. (2)H SCD order parameters of (2)H nuclei along the lipid acyl chain decrease less dramatically for R9C-PLB and P-PLB when compared to WT-PLB. The results suggest that R9C-PLB interacts less with the membrane surface and hydrophobic region than WT-PLB. Detachment of the cytoplasmic domain of R9C-PLB from the membrane surface could be related to its loss of function.
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Affiliation(s)
- Xueting Yu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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Wand A, Gdor I, Zhu J, Sheves M, Ruhman S. Shedding New Light on Retinal Protein Photochemistry. Annu Rev Phys Chem 2013; 64:437-58. [DOI: 10.1146/annurev-physchem-040412-110148] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amir Wand
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Itay Gdor
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Jingyi Zhu
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Mordechai Sheves
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sanford Ruhman
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
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20
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Simón-Vázquez R, Domínguez M, Lórenz-Fonfría VA, Alvarez S, Bourdelande JL, de Lera AR, Padrós E, Perálvarez-Marín A. Probing a polar cluster in the retinal binding pocket of bacteriorhodopsin by a chemical design approach. PLoS One 2012; 7:e42447. [PMID: 22879987 PMCID: PMC3411786 DOI: 10.1371/journal.pone.0042447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 07/06/2012] [Indexed: 11/24/2022] Open
Abstract
Bacteriorhodopsin has a polar cluster of amino acids surrounding the retinal molecule, which is responsible for light harvesting to fuel proton pumping. From our previous studies, we have shown that threonine 90 is the pivotal amino acid in this polar cluster, both functionally and structurally. In an attempt to perform a phenotype rescue, we have chemically designed a retinal analogue molecule to compensate the drastic effects of the T90A mutation in bacteriorhodopsin. This analogue substitutes the methyl group at position C13 of the retinal hydrocarbon chain by and ethyl group (20-methyl retinal). We have analyzed the effect of reconstituting the wild-type and the T90A mutant apoproteins with all-trans-retinal and its 20-methyl derivative (hereafter, 13-ethyl retinal). Biophysical characterization indicates that recovering the steric interaction between the residue 90 and retinal, eases the accommodation of the chromophore, however it is not enough for a complete phenotype rescue. The characterization of these chemically engineered chromoproteins provides further insight into the role of the hydrogen bond network and the steric interactions involving the retinal binding pocket in bacteriorhodopsin and other microbial sensory rhodopsins.
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Affiliation(s)
- Rosana Simón-Vázquez
- Departament de Bioquímica i de Biologia Molecular and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
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21
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Kruk D, Mielczarek A, Korpala A, Kozlowski A, Earle KA, Moscicki J. Sensitivity of 2H NMR spectroscopy to motional models: proteins and highly viscous liquids as examples. J Chem Phys 2012; 136:244509. [PMID: 22755589 DOI: 10.1063/1.4730034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In order to study to what extent mechanisms of molecular motion can be unambiguously revealed by (2)H NMR spectroscopy, (2)H spectra for proteins (chicken villin protein headpiece HP36, selectively methyl-deuterated at leucine-69, C(δ) D(3)) and binary systems of high viscosity (benzene-d(6) in tricresyl phosphate) have been carefully analyzed as illustrative examples (the spectra are taken from the literature). In the first case, a model of restricted diffusion mediated by jumps between rotameric orientations has been tested against jump- and free diffusion models which describe rotational motion combined with jump dynamics. It has been found that the set of (2)H spectra of methyl-deuterated at leucine-69 chicken villin protein headpiece HP36 can be consistently explained by different motional models as well as by a gaussian distribution of correlation times assuming isotropic rotation (simple brownian diffusion model). The last finding shows that when the possible distribution of correlation times is not very broad one might not be able to distinguish between heterogeneous and homogenous (but more complex) dynamics by analyzing (2)H lineshapes. For benzene-d(6) in tricresyl phosphate, the dynamics is heterogeneous and it has been demonstrated that a gaussian distribution of correlation times reproduces well the experimental lineshapes, while for a Cole-Davidson distribution the agreement is somewhat worse. For inquires into the sensitivity of quadrupolar NMR spectral analysis (by "quadrupolar NMR spectroscopy we understand NMR spectroscopy of nuclei possessing quadrupole moment), the recently presented theoretical approach [Kruk et al., J. Chem. Phys. 135, 224511 (2011)] has been used as it allows simulating quadrupolar spectra for arbitrary motional conditions by employing the stochastic Liouville equation.
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Affiliation(s)
- D Kruk
- University of Warmia and Mazury Olsztyn, Faculty of Mathematics and Computer Science, Sloneczna 54, PL-10710 Olsztyn, Poland.
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22
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Wand A, Friedman N, Sheves M, Ruhman S. Ultrafast Photochemistry of Light-Adapted and Dark-Adapted Bacteriorhodopsin: Effects of the Initial Retinal Configuration. J Phys Chem B 2012; 116:10444-52. [DOI: 10.1021/jp2125284] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amir Wand
- Institute of Chemistry and the
Farkash Center for Light-Induced Processes, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat
Ram, Jerusalem 91904, Israel
| | - Noga Friedman
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mordechai Sheves
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sanford Ruhman
- Institute of Chemistry and the
Farkash Center for Light-Induced Processes, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat
Ram, Jerusalem 91904, Israel
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23
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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24
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Wand A, Rozin R, Eliash T, Jung KH, Sheves M, Ruhman S. Asymmetric Toggling of a Natural Photoswitch: Ultrafast Spectroscopy of Anabaena Sensory Rhodopsin. J Am Chem Soc 2011; 133:20922-32. [DOI: 10.1021/ja208371g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amir Wand
- Institute of Chemistry and Farkash Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Rinat Rozin
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Eliash
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, South Korea
| | - Mordechai Sheves
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sanford Ruhman
- Institute of Chemistry and Farkash Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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25
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Judge PJ, Watts A. Recent contributions from solid-state NMR to the understanding of membrane protein structure and function. Curr Opin Chem Biol 2011; 15:690-5. [DOI: 10.1016/j.cbpa.2011.07.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/29/2011] [Accepted: 07/29/2011] [Indexed: 12/29/2022]
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26
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Grossfield A. Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1868-78. [DOI: 10.1016/j.bbamem.2011.03.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 02/23/2011] [Accepted: 03/21/2011] [Indexed: 01/28/2023]
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27
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Vugmeyster L, Ostrovsky D, Moses M, Ford JJ, Lipton AS, Hoatson GL, Vold RL. Comparative dynamics of leucine methyl groups in FMOC-leucine and in a protein hydrophobic core probed by solid-state deuteron nuclear magnetic resonance over 7-324 K temperature range. J Phys Chem B 2010; 114:15799-807. [PMID: 21077644 DOI: 10.1021/jp1082467] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantitative dynamics of methyl groups in 9-fluorenylmethyloxycarbonyl-leucine (FMOC-leu) have been analyzed and compared with earlier studies of methyl dynamics in chicken villin headpiece subdomain protein (HP36) labeled at L69, a key hydrophobic core position. A combination of deuteron solid-state nuclear magnetic resonance experiments over the temperature range of 7-324 K and computational modeling indicated that while the two compounds show the same modes of motions, there are marked differences in the best-fit parameters of these motions. One of the main results is that the crossover observed in the dynamics of the methyl groups in the HP36 sample at 170 K is absent in FMOC-leu. A second crossover at around 95-88 K is present in both samples. The differences in the behavior of the two compounds suggest that some of the features of methyl dynamics reflect the complexity of the protein hydrophobic core and are not determined solely by local interactions.
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28
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Renault M, Cukkemane A, Baldus M. Festkörper-NMR-Spektroskopie an komplexen Biomolekülen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002823] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Renault M, Cukkemane A, Baldus M. Solid-State NMR Spectroscopy on Complex Biomolecules. Angew Chem Int Ed Engl 2010; 49:8346-57. [DOI: 10.1002/anie.201002823] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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30
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Ieronimo M, Afonin S, Koch K, Berditsch M, Wadhwani P, Ulrich AS. 19F NMR Analysis of the Antimicrobial Peptide PGLa Bound to Native Cell Membranes from Bacterial Protoplasts and Human Erythrocytes. J Am Chem Soc 2010; 132:8822-4. [DOI: 10.1021/ja101608z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Ieronimo
- Institute of Organic Chemistry and DFG-Center for Functional Nanostructures, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany, and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P.O. Box 3640,76021 Karlsruhe, Germany
| | - Sergii Afonin
- Institute of Organic Chemistry and DFG-Center for Functional Nanostructures, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany, and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P.O. Box 3640,76021 Karlsruhe, Germany
| | - Katja Koch
- Institute of Organic Chemistry and DFG-Center for Functional Nanostructures, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany, and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P.O. Box 3640,76021 Karlsruhe, Germany
| | - Marina Berditsch
- Institute of Organic Chemistry and DFG-Center for Functional Nanostructures, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany, and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P.O. Box 3640,76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute of Organic Chemistry and DFG-Center for Functional Nanostructures, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany, and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P.O. Box 3640,76021 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute of Organic Chemistry and DFG-Center for Functional Nanostructures, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany, and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P.O. Box 3640,76021 Karlsruhe, Germany
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31
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Schmidt P, Berger C, Scheidt HA, Berndt S, Bunge A, Beck-Sickinger AG, Huster D. A reconstitution protocol for the in vitro folded human G protein-coupled Y2 receptor into lipid environment. Biophys Chem 2010; 150:29-36. [PMID: 20421142 DOI: 10.1016/j.bpc.2010.02.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 02/10/2010] [Indexed: 10/19/2022]
Abstract
Although highly resolved crystal structures of G protein-coupled receptors have become available within the last decade, the need for studying these molecules in their natural membrane environment, where the molecules are rather dynamic, has been widely appreciated. Solid-state NMR spectroscopy is an excellent method to study structure and dynamics of membrane proteins in their native lipid environment. We developed a reconstitution protocol for the uniformly (15)N labeled Y(2) receptor into a bicelle-like lipid structure with high yields suitable for NMR studies. Milligram quantities of target protein were expressed in Escherichia coli using an optimized fermentation process in defined medium yielding in over 10mg/L medium of purified Y(2) receptor solubilized in SDS micelles. The structural integrity of the receptor molecules was strongly increased through refolding and subsequent reconstitution into phospholipid membranes. Specific ligand binding to the integrated receptor was determined using radioligand affinity assay. Further, by NMR measurement a dispersion of the (15)N signals comparable to native rhodopsin was shown. The efficiency of the reconstitution could also be inferred from the fact that reasonable (13)C NMR spectra at natural abundance could be acquired.
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Affiliation(s)
- Peter Schmidt
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
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32
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Tikhonova IG, Costanzi S. Unraveling the structure and function of G protein-coupled receptors through NMR spectroscopy. Curr Pharm Des 2010; 15:4003-16. [PMID: 20028318 DOI: 10.2174/138161209789824803] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
G protein-coupled receptors (GPCRs) are a large superfamily of signaling proteins expressed on the plasma membrane. They are involved in a wide range of physiological processes and, therefore, are exploited as drug targets in a multitude of therapeutic areas. In this extent, knowledge of structural and functional properties of GPCRs may greatly facilitate rational design of modulator compounds. Solution and solid-state nuclear magnetic resonance (NMR) spectroscopy represents a powerful method to gather atomistic insights into protein structure and dynamics. In spite of the difficulties inherent the solution of the structure of membrane proteins through NMR, these methods have been successfully applied, sometimes in combination with molecular modeling, to the determination of the structure of GPCR fragments, the mapping of receptor-ligand interactions, and the study of the conformational changes associated with the activation of the receptors. In this review, we provide a summary of the NMR contributions to the study of the structure and function of GPCRs, also in light of the published crystal structures.
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Affiliation(s)
- Irina G Tikhonova
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
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Vugmeyster L, Ostrovsky D, Ford JJ, Burton SD, Lipton AS, Hoatson GL, Vold RL. Probing the dynamics of a protein hydrophobic core by deuteron solid-state nuclear magnetic resonance spectroscopy. J Am Chem Soc 2009; 131:13651-8. [PMID: 19772361 DOI: 10.1021/ja902977u] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the goal of investigating dynamical features of hydrophobic cores of proteins over a wide range of temperatures, the chicken villin headpiece subdomain protein (HP36) was labeled at a "single" site corresponding to any one of the two C(delta)D(3) groups of leucine-69, which is located in a key position of the core. The main techniques employed are deuteron NMR quadrupolar echo line shape analysis, and T(1Z) (Zeeman) and T(1Q) (quadrupolar order) relaxation experiments performed at 11.7 and 17.6 T over the temperature range of 112 to 298 K. The experimental data are compared with computer simulations. The deuteron line shapes give an excellent fit to a three-mode motional model that consists of (a) fast three-site rotational jumps about the pseudo C(3) methyl spinning axis, (b) slower reorientation of the spinning axis, described by diffusion along a restricted arc, and (c) large angle jumps between traces of rotameric conformers. Relaxation behavior is described by a phenomenological distribution of activation energies for three-site hops at high temperatures that collapses to a single, distinctly smaller value for lower temperatures.
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Brown MF, Salgado GFJ, Struts AV. Retinal dynamics during light activation of rhodopsin revealed by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:177-93. [PMID: 19716801 DOI: 10.1016/j.bbamem.2009.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/25/2009] [Accepted: 08/12/2009] [Indexed: 11/28/2022]
Abstract
Rhodopsin is a canonical member of class A of the G protein-coupled receptors (GPCRs) that are implicated in many of the drug interventions in humans and are of great pharmaceutical interest. The molecular mechanism of rhodopsin activation remains unknown as atomistic structural information for the active metarhodopsin II state is currently lacking. Solid-state (2)H NMR constitutes a powerful approach to study atomic-level dynamics of membrane proteins. In the present application, we describe how information is obtained about interactions of the retinal cofactor with rhodopsin that change with light activation of the photoreceptor. The retinal methyl groups play an important role in rhodopsin function by directing conformational changes upon transition into the active state. Site-specific (2)H labels have been introduced into the methyl groups of retinal and solid-state (2)H NMR methods applied to obtain order parameters and correlation times that quantify the mobility of the cofactor in the inactive dark state, as well as the cryotrapped metarhodopsin I and metarhodopsin II states. Analysis of the angular-dependent (2)H NMR line shapes for selectively deuterated methyl groups of rhodopsin in aligned membranes enables determination of the average ligand conformation within the binding pocket. The relaxation data suggest that the beta-ionone ring is not expelled from its hydrophobic pocket in the transition from the pre-activated metarhodopsin I to the active metarhodopsin II state. Rather, the major structural changes of the retinal cofactor occur already at the metarhodopsin I state in the activation process. The metarhodopsin I to metarhodopsin II transition involves mainly conformational changes of the protein within the membrane lipid bilayer rather than the ligand. The dynamics of the retinylidene methyl groups upon isomerization are explained by an activation mechanism involving cooperative rearrangements of extracellular loop E2 together with transmembrane helices H5 and H6. These activating movements are triggered by steric clashes of the isomerized all-trans retinal with the beta4 strand of the E2 loop and the side chains of Glu(122) and Trp(265) within the binding pocket. The solid-state (2)H NMR data are discussed with regard to the pathway of the energy flow in the receptor activation mechanism.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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Brown MF, Martínez-Mayorga K, Nakanishi K, Salgado GFJ, Struts AV. Retinal conformation and dynamics in activation of rhodopsin illuminated by solid-state H NMR spectroscopy. Photochem Photobiol 2009; 85:442-53. [PMID: 19267870 DOI: 10.1111/j.1751-1097.2008.00510.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Solid-state NMR spectroscopy gives a powerful avenue for investigating G protein-coupled receptors and other integral membrane proteins in a native-like environment. This article reviews the use of solid-state (2)H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site-specific (2)H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability (2)H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three-fold (C(3)) axes with an order parameter for the off-axial motion of SC(3) approximately 0.9. For the dark state, the (2)H NMR structure of 11-cis-retinal manifests torsional twisting of both the polyene chain and the beta-ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11-cis to trans isomerization. In addition, (2)H NMR has been applied to study the retinylidene dynamics in the dark and light-activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the beta-ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the beta-ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid-state (2)H NMR thus provides information about the flow of energy that triggers changes in hydrogen-bonding networks and helix movements in the activation mechanism of the photoreceptor.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, AZ, USA.
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Gansmüller A, Concistrè M, McLean N, Johannessen OG, Marín-Montesinos I, Bovee-Geurts PHM, Verdegem P, Lugtenburg J, Brown RCD, Degrip WJ, Levitt MH. Towards an interpretation of 13C chemical shifts in bathorhodopsin, a functional intermediate of a G-protein coupled receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1350-7. [PMID: 19265671 DOI: 10.1016/j.bbamem.2009.02.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/13/2009] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
Abstract
Photoisomerization of the membrane-bound light receptor protein rhodopsin leads to an energy-rich photostate called bathorhodopsin, which may be trapped at temperatures of 120 K or lower. We recently studied bathorhodopsin by low-temperature solid-state NMR, using in situ illumination of the sample in a purpose-built NMR probe. In this way we acquired (13)C chemical shifts along the retinylidene chain of the chromophore. Here we compare these results with the chemical shifts of the dark state chromophore in rhodopsin, as well as with the chemical shifts of retinylidene model compounds in solution. An earlier solid-state NMR study of bathorhodopsin found only small changes in the (13)C chemical shifts upon isomerization, suggesting only minor perturbations of the electronic structure in the isomerized retinylidene chain. This is at variance with our recent measurements which show much larger perturbations of the (13)C chemical shifts. Here we present a tentative interpretation of our NMR results involving an increased charge delocalization inside the polyene chain of the bathorhodopsin chromophore. Our results suggest that the bathochromic shift of bathorhodopsin is due to modified electrostatic interactions between the chromophore and the binding pocket, whereas both electrostatic interactions and torsional strain are involved in the energy storage mechanism of bathorhodopsin.
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Affiliation(s)
- Axel Gansmüller
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, England, UK
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Matsuoka S, Inoue M. Application of REDOR NMR in natural product chemistry. Chem Commun (Camb) 2009:5664-75. [DOI: 10.1039/b910230b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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