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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: 28] [Impact Index Per Article: 14.0] [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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2
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Jodaitis L, van Oene T, Martens C. Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins. Int J Mol Sci 2021; 22:7267. [PMID: 34298884 PMCID: PMC8306737 DOI: 10.3390/ijms22147267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid-protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid-protein interactions in the mechanism of membrane proteins.
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Affiliation(s)
| | | | - Chloé Martens
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (L.J.); (T.v.O.)
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3
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Jirasko V, Lends A, Lakomek N, Fogeron M, Weber ME, Malär AA, Penzel S, Bartenschlager R, Meier BH, Böckmann A. Dimer Organization of Membrane‐Associated NS5A of Hepatitis C Virus as Determined by Highly Sensitive
1
H‐Detected Solid‐State NMR. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Alons Lends
- Physical Chemistry ETH Zurich 8093 Zurich Switzerland
| | | | - Marie‐Laure Fogeron
- Molecular Microbiology and Structural Biochemistry Labex Ecofect UMR 5086 CNRS Université de Lyon 1 7 passage du Vercors 69367 Lyon France
| | | | | | | | - Ralf Bartenschlager
- Department of Infectious Diseases Molecular Virology Heidelberg University Im Neuenheimer Feld 345 69120 Heidelberg Germany
- German Centre for Infection Research (DZIF) Heidelberg partner site Heidelberg Germany
| | - Beat H. Meier
- Physical Chemistry ETH Zurich 8093 Zurich Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry Labex Ecofect UMR 5086 CNRS Université de Lyon 1 7 passage du Vercors 69367 Lyon France
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4
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Jirasko V, Lends A, Lakomek N, Fogeron M, Weber ME, Malär AA, Penzel S, Bartenschlager R, Meier BH, Böckmann A. Dimer Organization of Membrane-Associated NS5A of Hepatitis C Virus as Determined by Highly Sensitive 1 H-Detected Solid-State NMR. Angew Chem Int Ed Engl 2021; 60:5339-5347. [PMID: 33205864 PMCID: PMC7986703 DOI: 10.1002/anie.202013296] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/17/2020] [Indexed: 12/17/2022]
Abstract
The Hepatitis C virus nonstructural protein 5A (NS5A) is a membrane-associated protein involved in multiple steps of the viral life cycle. Direct-acting antivirals (DAAs) targeting NS5A are a cornerstone of antiviral therapy, but the mode-of-action of these drugs is poorly understood. This is due to the lack of information on the membrane-bound NS5A structure. Herein, we present the structural model of an NS5A AH-linker-D1 protein reconstituted as proteoliposomes. We use highly sensitive proton-detected solid-state NMR methods suitable to study samples generated through synthetic biology approaches. Spectra analyses disclose that both the AH membrane anchor and the linker are highly flexible. Paramagnetic relaxation enhancements (PRE) reveal that the dimer organization in lipids requires a new type of NS5A self-interaction not reflected in previous crystal structures. In conclusion, we provide the first characterization of NS5A AH-linker-D1 in a lipidic environment shedding light onto the mode-of-action of clinically used NS5A inhibitors.
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Affiliation(s)
| | - Alons Lends
- Physical ChemistryETH Zurich8093ZurichSwitzerland
| | | | - Marie‐Laure Fogeron
- Molecular Microbiology and Structural BiochemistryLabex EcofectUMR 5086 CNRSUniversité de Lyon 17 passage du Vercors69367LyonFrance
| | | | | | | | - Ralf Bartenschlager
- Department of Infectious DiseasesMolecular VirologyHeidelberg UniversityIm Neuenheimer Feld 34569120HeidelbergGermany
- German Centre for Infection Research (DZIF)Heidelberg partner siteHeidelbergGermany
| | | | - Anja Böckmann
- Molecular Microbiology and Structural BiochemistryLabex EcofectUMR 5086 CNRSUniversité de Lyon 17 passage du Vercors69367LyonFrance
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5
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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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6
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Li J, Guo X, Li M, Xiao Y, Bao C. [Research progress in the mechanism of protein factors in regulating bone remodeling]. ZHONGGUO XIU FU CHONG JIAN WAI KE ZA ZHI = ZHONGGUO XIUFU CHONGJIAN WAIKE ZAZHI = CHINESE JOURNAL OF REPARATIVE AND RECONSTRUCTIVE SURGERY 2019; 33:115-123. [PMID: 30644271 DOI: 10.7507/1002-1892.201808059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Objective To review the role and mechanism of protein factors in bone remodeling, and provides theoretical basis for further elucidating the pathogenesis and clinical treatment of bone-related diseases. Methods The relevant research results at home and abroad in recent years were extensively consulted, analyzed, and summarized. Results Bone remodeling is an important physiological process to maintain bone homeostasis. Protein, as an important stimulator in bone remodeling, regulates the balance between bone resorption and bone formation. Conclusion At present, the research on the mechanism of protein in bone remodeling is insufficient. Therefore, it is necessary to further study the specific time, process, and interaction network of protein in bone remodeling, and to confirm its mechanism in bone remodeling, so as to reveal and treat the pathogenesis of bone-related diseases.
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Affiliation(s)
- Ju Li
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu Sichuan, 610041, P.R.China;National Clinical Research Center of Oral Diseases, Sichuan University, Chengdu Sichuan, 610041, P.R.China
| | - Xiaodong Guo
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu Sichuan, 610041, P.R.China;National Clinical Research Center of Oral Diseases, Sichuan University, Chengdu Sichuan, 610041, P.R.China
| | - Mingzheng Li
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu Sichuan, 610041, P.R.China;National Clinical Research Center of Oral Diseases, Sichuan University, Chengdu Sichuan, 610041, P.R.China;Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu Sichuan, 610041, P.R.China
| | - Yu Xiao
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu Sichuan, 610041, P.R.China;National Clinical Research Center of Oral Diseases, Sichuan University, Chengdu Sichuan, 610041,
| | - Chongyun Bao
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu Sichuan, 610041, P.R.China;Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu Sichuan, 610041,
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7
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Formation of the β-barrel assembly machinery complex in lipid bilayers as seen by solid-state NMR. Nat Commun 2018; 9:4135. [PMID: 30297837 PMCID: PMC6175958 DOI: 10.1038/s41467-018-06466-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/04/2018] [Indexed: 11/27/2022] Open
Abstract
The β-barrel assembly machinery (BAM) is a pentameric complex (BamA–E), which catalyzes the essential process of β-barrel protein insertion into the outer membrane of E. coli. Thus far, a detailed understanding of the insertion mechanism has been elusive but recent results suggest that local protein motion, in addition to the surrounding membrane environment, may be of critical relevance. We have devised a high-sensitivity solid-state NMR approach to directly probe protein motion and the structural changes associated with BAM complex assembly in lipid bilayers. Our results reveal how essential BamA domains, such as the interface formed by the polypeptide transport associated domains P4 and P5 become stabilized after complex formation and suggest that BamA β-barrel opening and P5 reorientation is directly related to complex formation in membranes. Both the lateral gate, as well as P5, exhibit local dynamics, a property that could play an integral role in substrate recognition and insertion. The β-barrel assembly machinery (BAM) catalyzes β-barrel protein insertion into the outer membrane of E.coli. Here authors employ high-sensitivity solid-state NMR to reveal how the lipid environment and formation of the BamA-BamCDE complex affect BamA structure and dynamics with regards to the lateral gate and the β-barrel associated domains.
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8
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van der Cruijsen EAW, Prokofyev AV, Pongs O, Baldus M. Probing Conformational Changes during the Gating Cycle of a Potassium Channel in Lipid Bilayers. Biophys J 2017; 112:99-108. [PMID: 28076820 DOI: 10.1016/j.bpj.2016.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/08/2016] [Accepted: 12/01/2016] [Indexed: 01/10/2023] Open
Abstract
Ion conduction across the cellular membrane requires the simultaneous opening of activation and inactivation gates of the K+ channel pore. The bacterial KcsA channel has served as a powerful system for dissecting the structural changes that are related to four major functional states associated with K+ gating. Yet, the direct observation of the full gating cycle of KcsA has remained structurally elusive, and crystal structures mimicking these gating events require mutations in or stabilization of functionally relevant channel segments. Here, we found that changes in lipid composition strongly increased the KcsA open probability. This enabled us to probe all four major gating states in native-like membranes by combining electrophysiological and solid-state NMR experiments. In contrast to previous crystallographic views, we found that the selectivity filter and turret region, coupled to the surrounding bilayer, were actively involved in channel gating. The increase in overall steady-state open probability was accompanied by a reduction in activation-gate opening, underscoring the important role of the surrounding lipid bilayer in the delicate conformational coupling of the inactivation and activation gates.
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Affiliation(s)
- Elwin A W van der Cruijsen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Alexander V Prokofyev
- Department of Physiology, Institute of Cellular Neurophysiology, University of the Saarland, Homburg, Germany
| | - Olaf Pongs
- Department of Physiology, Institute of Cellular Neurophysiology, University of the Saarland, Homburg, Germany.
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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9
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Quantum chemical approaches to [NiFe] hydrogenase. Essays Biochem 2017; 61:293-303. [PMID: 28487405 DOI: 10.1042/ebc20160079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 11/17/2022]
Abstract
The mechanism by which [NiFe] hydrogenase catalyses the oxidation of molecular hydrogen is a significant yet challenging topic in bioinorganic chemistry. With far-reaching applications in renewable energy and carbon mitigation, significant effort has been invested in the study of these complexes. In particular, computational approaches offer a unique perspective on how this enzyme functions at an electronic and atomistic level. In this article, we discuss state-of-the art quantum chemical methods and how they have helped deepen our comprehension of [NiFe] hydrogenase. We outline the key strategies that can be used to compute the (i) geometry, (ii) electronic structure, (iii) thermodynamics and (iv) kinetic properties associated with the enzymatic activity of [NiFe] hydrogenase and other bioinorganic complexes.
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10
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Spiess HW. 50th Anniversary Perspective: The Importance of NMR Spectroscopy to Macromolecular Science. Macromolecules 2017. [DOI: 10.1021/acs.macromol.6b02736] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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11
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Quinn CM, Polenova T. Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. Q Rev Biophys 2017; 50:e1. [PMID: 28093096 PMCID: PMC5483179 DOI: 10.1017/s0033583516000159] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.
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Affiliation(s)
- Caitlin M. Quinn
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
| | - Tatyana Polenova
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
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12
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Ravera E, Martelli T, Geiger Y, Fragai M, Goobes G, Luchinat C. Biosilica and bioinspired silica studied by solid-state NMR. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
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14
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Smith AN, Long JR. Dynamic Nuclear Polarization as an Enabling Technology for Solid State Nuclear Magnetic Resonance Spectroscopy. Anal Chem 2016; 88:122-32. [PMID: 26594903 PMCID: PMC5704910 DOI: 10.1021/acs.analchem.5b04376] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Adam N Smith
- Department of Chemistry, University of Florida , 214 Leigh Hall, Gainesville, Florida 32611-7200, United States
| | - Joanna R Long
- Department of Biochemistry and Molecular Biology, University of Florida , P. O. Box 100245, Gainesville, Florida 32610-0245, United States
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15
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Hansen MR, Graf R, Spiess HW. Interplay of Structure and Dynamics in Functional Macromolecular and Supramolecular Systems As Revealed by Magnetic Resonance Spectroscopy. Chem Rev 2015; 116:1272-308. [DOI: 10.1021/acs.chemrev.5b00258] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Michael Ryan Hansen
- Max Planck Institute for Polymer Research, P.O. Box 3148, 55021 Mainz, Germany
| | - Robert Graf
- Max Planck Institute for Polymer Research, P.O. Box 3148, 55021 Mainz, Germany
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16
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Ding Y, Fujimoto LM, Yao Y, Marassi FM. Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation. JOURNAL OF BIOMOLECULAR NMR 2015; 61:275-86. [PMID: 25578899 PMCID: PMC4398618 DOI: 10.1007/s10858-014-9893-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/20/2014] [Indexed: 05/22/2023]
Abstract
Solid-state NMR studies of sedimented soluble proteins has been developed recently as an attractive approach for overcoming the size limitations of solution NMR spectroscopy while bypassing the need for sample crystallization or precipitation (Bertini et al. Proc Natl Acad Sci USA 108(26):10396-10399, 2011). Inspired by the potential benefits of this method, we have investigated the ability to sediment lipid bilayer nanodiscs reconstituted with a membrane protein. In this study, we show that nanodiscs containing the outer membrane protein Ail from Yersinia pestis can be sedimented for solid-state NMR structural studies, without the need for precipitation or lyophilization. Optimized preparations of Ail in phospholipid nanodiscs support both the structure and the fibronectin binding activity of the protein. The same sample can be used for solution NMR, solid-state NMR and activity assays, facilitating structure-activity correlation experiments across a wide range of timescales.
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Affiliation(s)
- Yi Ding
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
| | - L. Miya Fujimoto
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
| | - Yong Yao
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
| | - Francesca M. Marassi
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA. [Tel: 858-795-5282; Mail: ]
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17
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Ravera E, Schubeis T, Martelli T, Fragai M, Parigi G, Luchinat C. NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:60-70. [PMID: 25797005 DOI: 10.1016/j.jmr.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/06/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Tobias Schubeis
- Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tommaso Martelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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18
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Baker LA, Baldus M. Characterization of membrane protein function by solid-state NMR spectroscopy. Curr Opin Struct Biol 2014; 27:48-55. [DOI: 10.1016/j.sbi.2014.03.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/19/2014] [Accepted: 03/25/2014] [Indexed: 12/17/2022]
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Abstract
Membrane proteins have always presented technical challenges for structural studies because of their requirement for a lipid environment. Multiple approaches exist including X-ray crystallography and electron microscopy that can give significant insights into their structure and function. However, nuclear magnetic resonance (NMR) is unique in that it offers the possibility of determining the structures of unmodified membrane proteins in their native environment of phospholipid bilayers under physiological conditions. Furthermore, NMR enables the characterization of the structure and dynamics of backbone and side chain sites of the proteins alone and in complexes with both small molecules and other biopolymers. The learning curve has been steep for the field as most initial studies were performed under non-native environments using modified proteins until ultimately progress in both techniques and instrumentation led to the possibility of examining unmodified membrane proteins in phospholipid bilayers under physiological conditions. This review aims to provide an overview of the development and application of NMR to membrane proteins. It highlights some of the most significant structural milestones that have been reached by NMR spectroscopy of membrane proteins, especially those accomplished with the proteins in phospholipid bilayer environments where they function.
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20
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Loquet A, Habenstein B, Chevelkov V, Vasa SK, Giller K, Becker S, Lange A. Atomic Structure and Handedness of the Building Block of a Biological Assembly. J Am Chem Soc 2013; 135:19135-8. [DOI: 10.1021/ja411362q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Antoine Loquet
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Birgit Habenstein
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Veniamin Chevelkov
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Suresh Kumar Vasa
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Karin Giller
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Adam Lange
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
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21
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Ferella L, Luchinat C, Ravera E, Rosato A. SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR. JOURNAL OF BIOMOLECULAR NMR 2013; 57:319-26. [PMID: 24243317 DOI: 10.1007/s10858-013-9795-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 11/11/2013] [Indexed: 05/09/2023]
Abstract
We have proposed solid state NMR (SSNMR) of sedimented solutes as a novel approach to sample preparation for biomolecular SSNMR without crystallization or other sample manipulations. The biomolecules are confined by high gravity--obtained by centrifugal forces either directly in a SSNMR rotor or in a ultracentrifugal device--into a hydrated non-crystalline solid suitable for SSNMR investigations. When gravity is removed, the sample reverts to solution and can be treated as any solution NMR sample. We here describe a simple web tool to calculate the relevant parameters for the success of the experiment.
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Affiliation(s)
- Lucio Ferella
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
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Bhaumik A, Luchinat C, Parigi G, Ravera E, Rinaldelli M. NMR crystallography on paramagnetic systems: solved and open issues. CrystEngComm 2013. [DOI: 10.1039/c3ce41485j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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