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Mori S, Shionyu M, Shimamoto K, Nomura K. Bacterial Glycolipid Acting on Protein Transport Across Membranes. Chembiochem 2024; 25:e202300808. [PMID: 38400776 DOI: 10.1002/cbic.202300808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/11/2024] [Accepted: 02/22/2024] [Indexed: 02/26/2024]
Abstract
The process of protein transport across membranes involves a variety of factors and has been extensively investigated. Traditionally, proteinaceous translocons and chaperones have been recognized as crucial factors in this process. However, recent studies have highlighted the significant roles played by lipids and a glycolipid present in biological membranes in membrane protein transport. Membrane lipids can influence transport efficiency by altering the physicochemical properties of membranes. Notably, our studies have revealed that diacylglycerol (DAG) attenuates mobility in the membrane core region, leading to a dramatic suppression of membrane protein integration. Conversely, a glycolipid in Escherichia coli inner membranes, named membrane protein integrase (MPIase), enhances integration not only through the alteration of membrane properties but also via direct interactions with membrane proteins. This review explores the mechanisms of membrane protein integration mediated by membrane lipids, specifically DAG, and MPIase. Our results, along with the employed physicochemical analysis methods such as fluorescence measurements, nuclear magnetic resonance, surface plasmon resonance, and docking simulation, are presented to elucidate these mechanisms.
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Affiliation(s)
- Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
| | - Masafumi Shionyu
- Department of Frontier Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
- Department of Chemistry Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
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2
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Length matters: Functional flip of the short TatA transmembrane helix. Biophys J 2022:S0006-3495(22)03926-1. [PMID: 36523158 DOI: 10.1016/j.bpj.2022.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The twin arginine translocase (Tat) exports folded proteins across bacterial membranes. The putative pore-forming or membrane-weakening component (TatAd in B. subtilis) is anchored to the lipid bilayer via an unusually short transmembrane α-helix (TMH), with less than 16 residues. Its tilt angle in different membranes was analyzed under hydrophobic mismatch conditions, using synchrotron radiation circular dichroism and solid-state NMR. Positive mismatch (introduced either by reconstitution in short-chain lipids or by extending the hydrophobic TMH length) increased the helix tilt of the TMH as expected. Negative mismatch (introduced either by reconstitution in long-chain lipids or by shortening the TMH), on the other hand, led to protein aggregation. These data suggest that the TMH of TatA is just about long enough for stable membrane insertion. At the same time, its short length is a crucial factor for successful translocation, as demonstrated here in native membrane vesicles using an in vitro translocation assay. Furthermore, when reconstituted in model membranes with negative spontaneous curvature, the TMH was found to be aligned parallel to the membrane surface. This intrinsic ability of TatA to flip out of the membrane core thus seems to play a key role in its membrane-destabilizing effect during Tat-dependent translocation.
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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Calcium and hydroxyapatite binding site of human vitronectin provides insights to abnormal deposit formation. Proc Natl Acad Sci U S A 2020; 117:18504-18510. [PMID: 32699145 DOI: 10.1073/pnas.2007699117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human blood protein vitronectin (Vn) is a major component of the abnormal deposits associated with age-related macular degeneration, Alzheimer's disease, and many other age-related disorders. Its accumulation with lipids and hydroxyapatite (HAP) has been demonstrated, but the precise mechanism for deposit formation remains unknown. Using a combination of solution and solid-state NMR experiments, cosedimentation assays, differential scanning fluorimetry (DSF), and binding energy calculations, we demonstrate that Vn is capable of binding both soluble ionic calcium and crystalline HAP, with high affinity and chemical specificity. Calcium ions bind preferentially at an external site, at the top of the hemopexin-like (HX) domain, with a group of four Asp carboxylate groups. The same external site is also implicated in HAP binding. Moreover, Vn acquires thermal stability upon association with either calcium ions or crystalline HAP. The data point to a mechanism whereby Vn plays an active role in orchestrating calcified deposit formation. They provide a platform for understanding the pathogenesis of macular degeneration and other related degenerative disorders, and the normal functions of Vn, especially those related to bone resorption.
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Naito A, Matsumori N, Ramamoorthy A. Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy. Biochim Biophys Acta Gen Subj 2018; 1862:307-323. [PMID: 28599848 PMCID: PMC6384124 DOI: 10.1016/j.bbagen.2017.06.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 05/28/2017] [Accepted: 06/02/2017] [Indexed: 12/12/2022]
Abstract
A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 310-helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Akira Naito
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan.
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109-1055, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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Evaluation of diacylphospholipids as boundary lipids for bacteriorhodopsin from structural and functional aspects. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2106-2115. [DOI: 10.1016/j.bbamem.2016.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/08/2016] [Accepted: 06/10/2016] [Indexed: 11/18/2022]
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7
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Ardenkjaer-Larsen JH, Boebinger GS, Comment A, Duckett S, Edison AS, Engelke F, Griesinger C, Griffin RG, Hilty C, Maeda H, Parigi G, Prisner T, Ravera E, van Bentum J, Vega S, Webb A, Luchinat C, Schwalbe H, Frydman L. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:9162-85. [PMID: 26136394 PMCID: PMC4943876 DOI: 10.1002/anie.201410653] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 01/26/2015] [Indexed: 11/07/2022]
Abstract
In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi-author interdisciplinary Review presents a state-of-the-art description of the primary approaches that were considered. Topics discussed included the future of ultrahigh-field NMR systems, emerging NMR detection technologies, new approaches to nuclear hyperpolarization, and progress in sample preparation. All of these are orthogonal efforts, whose gains could multiply and thereby enhance the sensitivity of solid- and liquid-state experiments. While substantial advances have been made in all these areas, numerous challenges remain in the quest of endowing NMR spectroscopy with the sensitivity that has characterized forms of spectroscopies based on electrical or optical measurements. These challenges, and the ways by which scientists and engineers are striving to solve them, are also addressed.
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Affiliation(s)
- Jan-Henrik Ardenkjaer-Larsen
- GE Healthcare, Broendby, Denmark; Department of Electrical Engineering, Technical University of Denmark, Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre (Denmark)
| | - Gregory S Boebinger
- U.S. National High Magnetic Field Lab, Florida State University, Tallahassee, FL 32310 (USA)
| | - Arnaud Comment
- Institute of Physics of Biological Systems, Ecole Polytechnique Fédérale de Lausanne, Lausanne (Switzerland)
| | - Simon Duckett
- Department of Chemistry, University of York, Heslington, York, YO10 5DD (UK)
| | - Arthur S Edison
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610 (USA)
| | | | | | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Lab, MIT, Cambridge, MA 02139-4703 (USA)
| | - Christian Hilty
- Department of Chemistry, Texas A&M University, College Station (USA)
| | - Hidaeki Maeda
- Riken Center for Life Science Technologies, Yokohama, Kanagawa (Japan)
| | - Giacomo Parigi
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy)
| | - Thomas Prisner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Enrico Ravera
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy)
| | | | - Shimon Vega
- Chemical Physics Department, Weizmann Institute of Science, Rehovot (Israel)
| | - Andrew Webb
- Department of Radiology, C. J. Gorter Center for High Field MRI, Leiden University Medical Center (The Netherlands)
| | - Claudio Luchinat
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy).
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany).
| | - Lucio Frydman
- Chemical Physics Department, Weizmann Institute of Science, Rehovot (Israel).
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8
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Hansen SK, Bertelsen K, Paaske B, Nielsen NC, Vosegaard T. Solid-state NMR methods for oriented membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:48-85. [PMID: 26282196 DOI: 10.1016/j.pnmrs.2015.05.001] [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: 02/06/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Oriented-sample solid-state NMR represents one of few experimental methods capable of characterising the membrane-bound conformation of proteins in the cell membrane. Since the technique was developed 25 years ago, the technique has been applied to study the structure of helix bundle membrane proteins and antimicrobial peptides, characterise protein-lipid interactions, and derive information on dynamics of the membrane anchoring of membrane proteins. We will review the major developments in various aspects of oriented-sample solid-state NMR, including sample-preparation methods, pulse sequences, theory required to interpret the experiments, perspectives for and guidelines to new experiments, and a number of representative applications.
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Affiliation(s)
- Sara K Hansen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Berit Paaske
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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9
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Ardenkjaer-Larsen JH, Boebinger GS, Comment A, Duckett S, Edison AS, Engelke F, Griesinger C, Griffin RG, Hilty C, Maeda H, Parigi G, Prisner T, Ravera E, van Bentum J, Vega S, Webb A, Luchinat C, Schwalbe H, Frydman L. Neue Ansätze zur Empfindlichkeitssteigerung in der biomolekularen NMR-Spektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410653] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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Schuster B, Sleytr UB. Biomimetic interfaces based on S-layer proteins, lipid membranes and functional biomolecules. J R Soc Interface 2014; 11:20140232. [PMID: 24812051 PMCID: PMC4032536 DOI: 10.1098/rsif.2014.0232] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/15/2014] [Indexed: 12/20/2022] Open
Abstract
Designing and utilization of biomimetic membrane systems generated by bottom-up processes is a rapidly growing scientific and engineering field. Elucidation of the supramolecular construction principle of archaeal cell envelopes composed of S-layer stabilized lipid membranes led to new strategies for generating highly stable functional lipid membranes at meso- and macroscopic scale. In this review, we provide a state-of-the-art survey of how S-layer proteins, lipids and polymers may be used as basic building blocks for the assembly of S-layer-supported lipid membranes. These biomimetic membrane systems are distinguished by a nanopatterned fluidity, enhanced stability and longevity and, thus, provide a dedicated reconstitution matrix for membrane-active peptides and transmembrane proteins. Exciting areas in the (lab-on-a-) biochip technology are combining composite S-layer membrane systems involving specific membrane functions with the silicon world. Thus, it might become possible to create artificial noses or tongues, where many receptor proteins have to be exposed and read out simultaneously. Moreover, S-layer-coated liposomes and emulsomes copying virus envelopes constitute promising nanoformulations for the production of novel targeting, delivery, encapsulation and imaging systems.
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Affiliation(s)
- Bernhard Schuster
- Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Institute for Synthetic Bioarchitectures, Muthgasse 11, 1190 Vienna, Austria
| | - Uwe B. Sleytr
- Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Institute for Biophysics, Muthgasse 11, 1190 Vienna, Austria
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11
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Marvin DA, Symmons MF, Straus SK. Structure and assembly of filamentous bacteriophages. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:80-122. [PMID: 24582831 DOI: 10.1016/j.pbiomolbio.2014.02.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/09/2014] [Indexed: 12/24/2022]
Abstract
Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of "minor" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.
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Affiliation(s)
- D A Marvin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - M F Symmons
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - S K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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Crublet E, Kerfah R, Mas G, Noirclerc-Savoye M, Lantez V, Vernet T, Boisbouvier J. A cost-effective protocol for the parallel production of libraries of 13CH3-specifically labeled mutants for NMR studies of high molecular weight proteins. Methods Mol Biol 2014; 1091:229-244. [PMID: 24203337 DOI: 10.1007/978-1-62703-691-7_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
There is increasing interest in applying NMR spectroscopy to the study of large protein assemblies. Development of methyl-specific labeling protocols combined with improved NMR spectroscopy enable nowadays studies of proteins complexes up to 1 MDa. For such large complexes, the major interest lies in obtaining structural, dynamic and interaction information in solution, which requires sequence-specific resonance assignment of NMR signals. While such analysis is quite standard for small proteins, it remains one of the major bottlenecks when the size of the protein increases. Here, we describe implementation and latest improvements of SeSAM, a fast and user-friendly approach for assignment of methyl resonances in large proteins using mutagenesis. We have improved culture medium to boost the production of methyl-specifically labeled proteins, allowing us to perform small-scale parallel production and purification of a library of (13)CH3-specifically labeled mutants. This optimized protocol is illustrated by assignment of Alanine, Isoleucine, and Valine methyl groups of the homododecameric aminopeptidase PhTET2. We estimated that this improved method allows assignment of ca. 100 methyl cross-peaks in 2 weeks, including 4 days of NMR time and less than 2 k€ of isotopic materials.
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Affiliation(s)
- Elodie Crublet
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA, Grenoble, France
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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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14
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Gopinath T, Mote KR, Veglia G. Sensitivity and resolution enhancement of oriented solid-state NMR: application to membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 75:50-68. [PMID: 24160761 PMCID: PMC3850070 DOI: 10.1016/j.pnmrs.2013.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/16/2013] [Indexed: 05/19/2023]
Abstract
Oriented solid-state NMR (O-ssNMR) spectroscopy is a major technique for the high-resolution analysis of the structure and topology of transmembrane proteins in native-like environments. Unlike magic angle spinning (MAS) techniques, O-ssNMR spectroscopy requires membrane protein preparations that are uniformly oriented (mechanically or magnetically) so that anisotropic NMR parameters, such as dipolar and chemical shift interactions, can be measured to determine structure and orientation of membrane proteins in lipid bilayers. Traditional sample preparations involving mechanically aligned lipids often result in short relaxation times which broaden the (15)N resonances and encumber the manipulation of nuclear spin coherences. The introduction of lipid bicelles as membrane mimicking systems has changed this scenario, and the more favorable relaxation properties of membrane protein (15)N and (13)C resonances make it possible to develop new, more elaborate pulse sequences for higher spectral resolution and sensitivity. Here, we describe our recent progress in the optimization of O-ssNMR pulse sequences. We explain the theory behind these experiments, demonstrate their application to small and medium size proteins, and describe the technical details for setting up these new experiments on the new generation of NMR spectrometers.
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Affiliation(s)
- T. Gopinath
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Kaustubh R. Mote
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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15
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Ding Y, Yao Y, Marassi FM. Membrane protein structure determination in membrana. Acc Chem Res 2013; 46:2182-90. [PMID: 24041243 DOI: 10.1021/ar400041a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The two principal components of biological membranes, the lipid bilayer and the proteins integrated within it, have coevolved for specific functions that mediate the interactions of cells with their environment. Molecular structures can provide very significant insights about protein function. In the case of membrane proteins, the physical and chemical properties of lipids and proteins are highly interdependent; therefore structure determination should include the membrane environment. Considering the membrane alongside the protein eliminates the possibility that crystal contacts or detergent molecules could distort protein structure, dynamics, and function and enables ligand binding studies to be performed in a natural setting. Solid-state NMR spectroscopy is compatible with three-dimensional structure determination of membrane proteins in phospholipid bilayer membranes under physiological conditions and has played an important role in elucidating the physical and chemical properties of biological membranes, providing key information about the structure and dynamics of the phospholipid components. Recently, developments in the recombinant expression of membrane proteins, sample preparation, pulse sequences for high-resolution spectroscopy, radio frequency probes, high-field magnets, and computational methods have enabled a number of membrane protein structures to be determined in lipid bilayer membranes. In this Account, we illustrate solid-state NMR methods with examples from two bacterial outer membrane proteins (OmpX and Ail) that form integral membrane β-barrels. The ability to measure orientation-dependent frequencies in the solid-state NMR spectra of membrane-embedded proteins provides the foundation for a powerful approach to structure determination based primarily on orientation restraints. Orientation restraints are particularly useful for NMR structural studies of membrane proteins because they provide information about both three-dimensional structure and the orientation of the protein within the membrane. When combined with dihedral angle restraints derived from analysis of isotropic chemical shifts, molecular fragment replacement, and de novo structure prediction, orientation restraints can yield high-quality three-dimensional structures with few or no distance restraints. Using complementary solid-state NMR methods based on oriented sample (OS) and magic angle spinning (MAS) approaches, one can resolve and assign multiple peaks through the use of (15)N/(13)C labeled samples and measure precise restraints to determine structures.
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Affiliation(s)
- Yi Ding
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yong Yao
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Francesca M. Marassi
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
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Gansmüller A, Simorre JP, Hediger S. Windowed R-PDLF recoupling: a flexible and reliable tool to characterize molecular dynamics. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 234:154-64. [PMID: 23880256 DOI: 10.1016/j.jmr.2013.06.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 05/14/2023]
Abstract
This work focuses on the improvement of the R-PDLF heteronuclear recoupling scheme, a method that allows quantification of molecular dynamics up to the microsecond timescale in heterogeneous materials. We show how the stability of the sequence towards rf-imperfections, one of the main sources of error of this technique, can be improved by the insertion of windows without irradiation into the basic elements of the symmetry-based recoupling sequence. The impact of this modification on the overall performance of the sequence in terms of scaling factor and homonuclear decoupling efficiency is evaluated. This study indicates the experimental conditions for which precise and reliable measurement of dipolar couplings can be obtained using the popular R18(1)(7) recoupling sequence, as well as alternative symmetry-based R sequences suited for fast MAS conditions. An analytical expression for the recoupled dipolar modulation has been derived that applies to a whole class of sequences with similar recoupling properties as R18(1)(7). This analytical expression provides an efficient and precise way to extract dipolar couplings from the experimental dipolar modulation curves. We hereby provide helpful tools and information for tailoring R-PDLF recoupling schemes to specific sample properties and hardware capabilities. This approach is particularly well suited for the study of materials with strong and heterogeneous molecular dynamics where a precise measurement of dipolar couplings is crucial.
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Affiliation(s)
- Axel Gansmüller
- Institut de Biologie Structurale, UMR5075 (CEA/CNRS/UJF), 38027 Grenoble, France.
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17
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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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18
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Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
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19
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Lange S, Linden AH, Akbey U, Franks WT, Loening NM, van Rossum BJ, Oschkinat H. The effect of biradical concentration on the performance of DNP-MAS-NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 216:209-12. [PMID: 22285634 DOI: 10.1016/j.jmr.2012.01.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/23/2011] [Accepted: 01/01/2012] [Indexed: 05/21/2023]
Abstract
With the technique of dynamic nuclear polarization (DNP) signal intensity in solid-state MAS-NMR experiments can be enhanced by 2-3 orders of magnitude. DNP relies on the transfer of electron spin polarization from unpaired electrons to nuclear spins. For this reason, stable organic biradicals such as TOTAPOL are commonly added to samples used in DNP experiments. We investigated the effects of biradical concentration on the relaxation, enhancement, and intensity of NMR signals, employing a series of samples with various TOTAPOL concentrations and uniformly (13)C, (15)N labeled proline. A considerable decrease of the NMR relaxation times (T(1), T(2)(∗), and T(1)(ρ)) is observed with increasing amounts of biradical due to paramagnetic relaxation enhancement (PRE). For nuclei in close proximity to the radical, decreasing T(1)(ρ) reduces cross-polarization efficiency and decreases in T(2)(∗) broaden the signal. Additionally, paramagnetic shifts of (1)H signals can cause further line broadening by impairing decoupling. On average, the combination of these paramagnetic effects (PE; relaxation enhancement, paramagnetic shifts) quenches NMR-signals from nuclei closer than 10Å to the biradical centers. On the other hand, shorter T(1) times allow the repetition rate of the experiment to be increased, which can partially compensate for intensity loss. Therefore, it is desirable to optimize the radical concentration to prevent additional line broadening and to maximize the signal-to-noise observed per unit time for the signals of interest.
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Affiliation(s)
- Sascha Lange
- FMP, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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20
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Bertini I, Engelke F, Luchinat C, Parigi G, Ravera E, Rosa C, Turano P. NMR properties of sedimented solutes. Phys Chem Chem Phys 2012; 14:439-47. [DOI: 10.1039/c1cp22978h] [Citation(s) in RCA: 43] [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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21
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Park TJ, Kim JS, Ahn HC, Kim Y. Solution and solid-state NMR structural studies of antimicrobial peptides LPcin-I and LPcin-II. Biophys J 2011; 101:1193-201. [PMID: 21889457 DOI: 10.1016/j.bpj.2011.06.067] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 06/07/2011] [Accepted: 06/23/2011] [Indexed: 11/26/2022] Open
Abstract
Lactophoricin (LPcin-I) is an antimicrobial, amphiphatic, cationic peptide with 23-amino acid residues isolated from bovine milk. Its analogous peptide, LPcin-II, lacks six N-terminal amino acids compared to LPcin-I. Interestingly, LPcin-II does not display any antimicrobial activity, whereas LPcin-I inhibits the growth of both Gram-negative and Gram-positive bacteria without exhibiting any hemolytic activity. Uniformly (15)N-labeled LPcin peptides were prepared by the recombinant expression of fusion proteins in Escherichia coli, and their properties were characterized by electrospray ionization mass spectrometry, circular dichroism spectroscopy, and antimicrobial activity tests. To understand the structure-activity relationship of these two peptides, they were studied in model membrane environments by a combination of solution and solid-state NMR spectroscopy. We determined the tertiary structure of LPcin-I and LPcin-II in the presence of dodecylphosphorylcholine micelles by solution NMR spectroscopy. Magnetically aligned unflipped bicelle samples were used to investigate the structure and topology of LPcin-I and LPcin-II by solid-state NMR spectroscopy.
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Affiliation(s)
- Tae-Joon Park
- Department of Chemistry and Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yong-In, Korea
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22
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Nieh MP, Dolinar P, Kučerka N, Kline SR, Debeer-Schmitt LM, Littrell KC, Katsaras J. Formation of kinetically trapped nanoscopic unilamellar vesicles from metastable nanodiscs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:14308-14316. [PMID: 21951150 DOI: 10.1021/la2023314] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Zwitterionic long-chain lipids (e.g., dimyristoyl phosphatidylcholine, DMPC) spontaneously form onion-like, thermodynamically stable structures in aqueous solutions (commonly known as multilamellar vesicles, or MLVs). It has also been reported that the addition of zwitterionic short-chain (i.e., dihexanoyl phosphatidylcholine, DHPC) and charged long-chain (i.e., dimyristoyl phosphatidylglycerol, DMPG) lipids to zwitterionic long-chain lipid solutions results in the formation of unilamellar vesicles (ULVs). Here, we report a kinetic study on lipid mixtures composed of DMPC, DHPC, and DMPG. Two membrane charge densities (i.e., [DMPG]/[DMPC] = 0.01 and 0.001) and two solution salinities (i.e., [NaCl] = 0 and 0.2 M) are investigated. Upon dilution of the high-concentration samples at 50 °C, thermodynamically stable MLVs are formed, in the case of both weakly charged and high salinity solution mixtures, implying that the electrostatic interactions between bilayers are insufficient to cause MLVs to unbind. Importantly, in the case of these samples small angle neutron scattering (SANS) data show that, initially, nanodiscs (also known as bicelles) or bilayered ribbons form at low temperatures (i.e., 10 °C), but transform into uniform size, nanoscopic ULVs after incubation at 10 °C for 20 h, indicating that the nanodisc is a metastable structure. The instability of nanodiscs may be attributed to low membrane rigidity due to a reduced charge density and high salinity. Moreover, the uniform-sized ULVs persist even after being heated to 50 °C, where thermodynamically stable MLVs are observed. This result clearly demonstrates that these ULVs are kinetically trapped, and that the mechanical properties (e.g., bending rigidity) of 10 °C nanodiscs favor the formation of nanoscopic ULVs over that of MLVs. From a practical point of view, this method of forming uniform-sized ULVs may lend itself to their mass production, thus making them economically feasible for medical applications that depend on monodisperse lipid-based systems for therapeutic and diagnostic purposes.
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Affiliation(s)
- Mu-Ping Nieh
- Department of Chemical, Materials & Biomolecular Engineering, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, USA.
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23
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Mananga ES, Charpentier T. Introduction of the Floquet-Magnus expansion in solid-state nuclear magnetic resonance spectroscopy. J Chem Phys 2011; 135:044109. [DOI: 10.1063/1.3610943] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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24
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Abstract
Relatively large proteins in solution, spun in NMR rotors for solid samples at typical ultracentrifugation speeds, sediment at the rotor wall. The sedimented proteins provide high-quality solid-state-like NMR spectra suitable for structural investigation. The proteins fully revert to the native solution state when spinning is stopped, allowing one to study them in both conditions. Transiently sedimented proteins can be considered a novel phase as far as NMR is concerned. NMR of transiently sedimented molecules under fast magic angle spinning has the advantage of overcoming protein size limitations of solution NMR without the need of sample crystallization/precipitation required by solid-state NMR.
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25
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Xu J, Smith PES, Soong R, Ramamoorthy A. A proton spin diffusion based solid-state NMR approach for structural studies on aligned samples. J Phys Chem B 2011; 115:4863-71. [PMID: 21466219 PMCID: PMC3085961 DOI: 10.1021/jp201501q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Rapidly expanding research on nonsoluble and noncrystalline chemical and biological materials necessitates sophisticated techniques to image these materials at atomic-level resolution. Although their study poses a formidable challenge, solid-state NMR is a powerful tool that has demonstrated application to the investigation of their molecular architecture and functioning. In particular, 2D separated-local-field (SLF) spectroscopy is increasingly applied to obtain high-resolution molecular images of these materials. However, despite the common use of SLF experiments in the structural studies of a variety of aligned molecules, the lack of a resonance assignment approach has been a major disadvantage. As a result, solid-state NMR studies have mostly been limited to aligned systems that are labeled with an isotope at a single site. Here, we demonstrate an approach for resonance assignment through a controlled reintroduction of proton spin diffusion in the 2D proton-evolved-local-field (PELF) pulse sequence. Experimental results and simulations suggest that the use of spin diffusion also enables the measurement of long-range heteronuclear dipolar couplings that can be used as additional constraints in the structural and dynamical studies of aligned molecules. The new method is used to determine the de novo atomic-level resolution structure of a liquid crystalline material, N-(4-methoxybenzylidene)-4-butylaniline, and its use on magnetically aligned bicelles is also demonstrated. We expect this technique to also be valuable in the structural studies of functional molecules like columnar liquid crystals and other biomaterials.
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Affiliation(s)
- Jiadi Xu
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055
| | - Pieter E. S. Smith
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055
| | - Ronald Soong
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055
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26
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Park SH, Das BB, De Angelis AA, Scrima M, Opella SJ. Mechanically, magnetically, and "rotationally aligned" membrane proteins in phospholipid bilayers give equivalent angular constraints for NMR structure determination. J Phys Chem B 2011; 114:13995-4003. [PMID: 20961141 DOI: 10.1021/jp106043w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The native environment for membrane proteins is the highly asymmetric phospholipid bilayer, and this has a large effect on both their structure and dynamics. Reproducing this environment in samples suitable for spectroscopic and diffraction experiments is a key issue, and flexibility in sample preparation is essential to accommodate the diverse size, shape, and other physical properties of membrane proteins. In most cases, to ensure that the biological activities are maintained, this means reconstituting the proteins in fully hydrated planar phospholipid bilayers. The asymmetric character of protein-containing bilayers means that it is possible to prepare either oriented or unoriented (powder) samples. Here we demonstrate the equivalence of mechanical, magnetic, and what we refer to as "rotational alignment" of membrane proteins in phospholipid bilayer samples for solid-state NMR spectroscopy. The trans-membrane domain of virus protein "u" (Vpu) from human immunodeficiency virus (HIV-1) and the full-length membrane-bound form of fd bacteriophage coat protein in phospholipid bilayers are used as examples. The equivalence of structural constraints from oriented and unoriented (powder) samples of membrane proteins is based on two concepts: (1) their alignment is defined by the direction of the bilayer normal relative to the magnetic field and (2) they undergo rapid rotational diffusion about the same bilayer normal in liquid crystalline membranes. The measurement of angular constraints relative to a common external axis system defined by the bilayer normal for all sites in the protein is an essential element of oriented sample (OS) solid-state NMR.
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Affiliation(s)
- Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0307, USA
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27
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Tiburu EK, Tyukhtenko S, Zhou H, Janero DR, Struppe J, Makriyannis A. Human cannabinoid 1 GPCR C-terminal domain interacts with bilayer phospholipids to modulate the structure of its membrane environment. AAPS JOURNAL 2011; 13:92-8. [PMID: 21234731 DOI: 10.1208/s12248-010-9244-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 11/21/2010] [Indexed: 02/08/2023]
Abstract
G protein-coupled receptors (GPCRs) play critical physiological and therapeutic roles. The human cannabinoid 1 GPCR (hCB1) is a prime pharmacotherapeutic target for addiction and cardiometabolic disease. Our prior biophysical studies on the structural biology of a synthetic peptide representing the functionally significant hCB1 transmembrane helix 7 (TMH7) and its cytoplasmic extension, helix 8 (H8), [hCB1(TMH7/H8)] demonstrated that the helices are oriented virtually perpendicular to each other in membrane-mimetic environments. We identified several hCB1(TMH7/H8) structure-function determinants, including multiple electrostatic amino-acid interactions and a proline kink involving the highly conserved NPXXY motif. In phospholipid bicelles, TMH7 structure, orientation, and topology relative to H8 are dynamically modulated by the surrounding membrane phospholipid bilayer. These data provide a contextual basis for the present solid-state NMR study to investigate whether intermolecular interactions between hCB1(TMH7/H8) and its phospholipid environment may affect membrane-bilayer structure. For this purpose, we measured (1)H-(13)C heteronuclear dipolar couplings for the choline, glycerol, and acyl-chain regions of dimyristoylphosphocholine in a magnetically aligned hCB1(TMH7/H8) bicelle sample. The results identify discrete regional interactions between hCB1(TMH7/H8) and membrane lipid molecules that increase phospholipid motion and decrease phospholipid order, indicating that the peptide's partial traversal of the bilayer alters membrane structure. These data offer new insight into hCB1(TMH7/H8) properties and support the concept that the membrane bilayer itself may serve as a mechanochemical mediator of hCB1/GPCR signal transduction. Since interaction with its membrane environment has been implicated in hCB1 function and its modulation by small-molecule therapeutics, our work should help inform hCB1 pharmacology and the design of hCB1-targeted drugs.
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Affiliation(s)
- Elvis K Tiburu
- Center for Drug Discovery and Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 116 Mugar Hall, Boston, Massachusetts 02115-5000, United States of America
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28
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Jayanthi S, Sinha N, Ramanathan KV. 2₄-SEMA as a sensitive and offset compensated SLF sequence. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 207:206-212. [PMID: 20880731 DOI: 10.1016/j.jmr.2010.08.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 08/23/2010] [Accepted: 08/31/2010] [Indexed: 05/29/2023]
Abstract
Separated Local Field (SLF) spectroscopy is a powerful tool for the determination of structure and dynamics of oriented systems such as membrane proteins oriented in lipid bilayers and liquid crystals. Of many SLF techniques available, Polarization Inversion Spin Exchange at Magic Angle (PISEMA) has found wide application due to its many favorable characteristics. However the pulse sequence suffers from its sensitivity to proton resonance frequency offset. Recently we have proposed a new sequence named 2(4)-SEMA (J. Chem. Phys. 132 (2010) 134301) that overcomes this problem of PISEMA. The present work demonstrates the advantage of 2(4)-SEMA as a highly sensitive SLF technique even for very large proton offset. 2(4)-SEMA has been designed for obtaining reliable dipolar couplings by switching the magic-angle spin-lock for protons over four quadrants as against the use of only two quadrants in PISEMA. It is observed that for on-resonance condition, 2(4)-SEMA gives rise to signal intensity comparable to or slightly higher than that from PISEMA. But under off-resonance conditions, intensities from 2(4)-SEMA are several fold higher than those from PISEMA. Comparison with another offset compensated pulse sequence, SAMPI4, also indicates a better intensity profile for 2(4)-SEMA. Experiments carried out on a single crystal of (15)N labeled N-acetyl-dl-valine and simulations have been used to study the relative performance of the pulse sequences considered.
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Affiliation(s)
- S Jayanthi
- Department of Physics, Indian Institute of Science, Bangalore 560 012, India
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29
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Walther TH, Grage SL, Roth N, Ulrich AS. Membrane Alignment of the Pore-Forming Component TatAd of the Twin-Arginine Translocase from Bacillus subtilis Resolved by Solid-State NMR Spectroscopy. J Am Chem Soc 2010; 132:15945-56. [DOI: 10.1021/ja106963s] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Torsten H. Walther
- DFG-Center for Functional Nanostructures (CFN), Institute of Biological Interfaces (IBG-2), and Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Stephan L. Grage
- DFG-Center for Functional Nanostructures (CFN), Institute of Biological Interfaces (IBG-2), and Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Nadine Roth
- DFG-Center for Functional Nanostructures (CFN), Institute of Biological Interfaces (IBG-2), and Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Anne S. Ulrich
- DFG-Center for Functional Nanostructures (CFN), Institute of Biological Interfaces (IBG-2), and Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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30
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Früh V, IJzerman AP, Siegal G. How to catch a membrane protein in action: a review of functional membrane protein immobilization strategies and their applications. Chem Rev 2010; 111:640-56. [PMID: 20831158 DOI: 10.1021/cr900088s] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Virginie Früh
- Division of Medicinal Chemistry, Leiden Amsterdam Center for Drug Research, Leiden University, The Netherlands
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31
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Abstract
Nuclear magnetic resonance studies of membrane proteins yield valuable insights into their structure and topology. For example, the tilt angle and rotation of the helices in an ion channel can be determined by solid-state NMR spectroscopy in aligned lipid bilayers. Details about the structure of the protein in aligned phospholipids environments are immediately apparent from inspection of the SAMMY spectrum and the data can be further used for the determination of atomic resolution three-dimensional structures. SAR by NMR is a technique that is well suited for the field of membrane transporter proteins. The experiments on protein/phospholipid samples provide a unique insight into the interaction of drugs and the functional proteins.The advances required to transform solid-state NMR from a spectroscopic technique to a generally applicable method for determining molecular structures included multiple-pulse sequences, double-resonance methods, and separated local field spectroscopy. It also required improvements in instrumentation, especially the use of high-field magnets and efficient probes capable of high-power radio-frequency irradiations at high frequencies. The pace of development is accelerating and the local field is being utilized in an increasing number of ways in spectroscopic investigations of molecular structure and dynamics. Applications to many helical membrane proteins are underway and promise to add to our understanding of membrane proteins in health and disease.
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32
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33
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Gopinath T, Verardi R, Traaseth NJ, Veglia G. Sensitivity enhancement of separated local field experiments: application to membrane proteins. J Phys Chem B 2010; 114:5089-95. [PMID: 20349983 PMCID: PMC2861489 DOI: 10.1021/jp909778a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Separated local field (SLF) experiments have been used for almost three decades to obtain structural information in solid-state NMR. These experiments resolve chemical shift anisotropy (CSA) from dipole-dipole interactions (dipolar couplings, DC) in isolated spin systems. Both CSA and DC data can be converted into orientational constraints to elucidate the secondary structure and topology of membrane proteins in oriented lipid bilayers. Here, we propose a new suite of sensitivity enhanced SLF pulse sequences to measure CSA and DC for aligned membrane proteins and liquid crystalline molecules that will decrease the time needed for data acquisition. We demonstrate the efficacy of these new sensitivity enhanced experiments using both a single crystal of N-acetyl leucine and a single pass membrane protein sarcolipin reconstituted in aligned lipid bicelles. These results lay the groundwork for the routine application of this methodology for studying the structure and topology of membrane proteins.
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Affiliation(s)
- T. Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455
| | - Raffaello Verardi
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455
| | - Nathaniel J. Traaseth
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455
- Department of Chemistry and University of Minnesota, Minneapolis, MN 55455
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34
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Bahar I, Lezon TR, Bakan A, Shrivastava IH. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 2010; 110:1463-97. [PMID: 19785456 PMCID: PMC2836427 DOI: 10.1021/cr900095e] [Citation(s) in RCA: 377] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ivet Bahar
- Department of Computational Biology, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA.
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35
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Agrawal P, Kiihne S, Hollander J, Hofmann M, Langosch D, de Groot H. A solid-state NMR study of changes in lipid phase induced by membrane-fusogenic LV-peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:202-9. [DOI: 10.1016/j.bbamem.2009.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Revised: 10/15/2009] [Accepted: 10/25/2009] [Indexed: 10/20/2022]
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36
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Naito A. Structure elucidation of membrane-associated peptides and proteins in oriented bilayers by solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2009; 36:67-76. [PMID: 19647984 DOI: 10.1016/j.ssnmr.2009.06.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Revised: 06/16/2009] [Accepted: 06/22/2009] [Indexed: 05/28/2023]
Abstract
Solid-state NMR using magnetically oriented bilayer systems provides useful information on the structure and orientation of peptides and proteins bound to lipid bilayers. The ordering of the lipid bilayer along the magnetic field can be achieved in two ways. First, lipid can be macroscopically oriented by pressing lipid-water dispersion between flat glass plates, which is called a mechanically aligned system. Second, lipid molecules themselves can be aligned spontaneously in the magnetic field because of their diamagnetic anisotropy by forming bicelles or magnetically oriented vesicle systems. Structure and orientation of the membrane-associated peptides and proteins can be achieved by analyzing structural constraints obtained from anisotropic chemical shift interactions such as chemical shift oscillation or nuclear dipolar interactions such as dipolar wave and a combination of them such as PISA wheel. Detailed structure elucidation of various kinds of membrane peptides and proteins in such oriented bilayers is presented.
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Affiliation(s)
- Akira Naito
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Japan.
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37
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Franzmann M, Otzen D, Wimmer R. Quantitative Use of Paramagnetic Relaxation Enhancements for Determining Orientations and Insertion Depths of Peptides in Micelles. Chembiochem 2009; 10:2339-47. [DOI: 10.1002/cbic.200900347] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Diller A, Loudet C, Aussenac F, Raffard G, Fournier S, Laguerre M, Grélard A, Opella SJ, Marassi FM, Dufourc EJ. Bicelles: A natural 'molecular goniometer' for structural, dynamical and topological studies of molecules in membranes. Biochimie 2009; 91:744-51. [PMID: 19248817 PMCID: PMC2899883 DOI: 10.1016/j.biochi.2009.02.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 02/13/2009] [Indexed: 10/21/2022]
Abstract
Major biological processes occur at the biological membrane. One of the great challenges is to understand the function of chemical or biological molecules inside the membrane; as well of those involved in membrane trafficking. This requires obtaining a complete picture of the in situ structure and dynamics as well as the topology and orientation of these molecules in the membrane lipid bilayer. These led to the creation of several innovative models of biological membranes in order to investigate the structure and dynamics of amphiphilic molecules, as well as integral membrane proteins having single or multiple transmembrane segments. Because the determination of the structure, dynamics and topology of molecules in membranes requires a macroscopic alignment of the system, a new membrane model called 'bicelles' that represents a crossover between lipid vesicles and classical micelles has become very popular due to its property of spontaneous self-orientation in magnetic fields. In addition, crucial factors involved in mimicking natural membranes, such as sample hydration, pH and salinity limits, are easy to control in bicelle systems. Bicelles are composed of mixtures of long chain (14-18 carbons) and short chain phospholipids (6-8 carbons) hydrated up to 98% with buffers and may adopt various morphologies depending on lipid composition, temperature and hydration. We have been developing bicelle systems under the form of nano-discs made of lipids with saturated or biphenyl-containing fatty acyl chains. Depending on the lipid nature, these membranous nano-discs may be macroscopically oriented with their normal perpendicular or parallel to the magnetic field, providing a natural 'molecular goniometer' for structural and topological studies, especially in the field of NMR. Bicelles can also be spun at the magic angle and lead to the 3D structural determination of molecules in membranes.
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Affiliation(s)
- Anna Diller
- CBMN UMR 5248, CNRS, Université Bordeaux, ENITAB, IECB, 2, rue Robert Escarpit, 33607 Pessac, France
| | - Cécile Loudet
- The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | - Gérard Raffard
- RMSB UMR 5536, CNRS, Université Bordeaux, Bordeaux, France
| | - Sylvie Fournier
- CBMN UMR 5248, CNRS, Université Bordeaux, ENITAB, IECB, 2, rue Robert Escarpit, 33607 Pessac, France
| | - Michel Laguerre
- CBMN UMR 5248, CNRS, Université Bordeaux, ENITAB, IECB, 2, rue Robert Escarpit, 33607 Pessac, France
| | - Axelle Grélard
- CBMN UMR 5248, CNRS, Université Bordeaux, ENITAB, IECB, 2, rue Robert Escarpit, 33607 Pessac, France
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
| | | | - Erick J. Dufourc
- CBMN UMR 5248, CNRS, Université Bordeaux, ENITAB, IECB, 2, rue Robert Escarpit, 33607 Pessac, France
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39
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Lee DK, Kwon BS, Ramamoorthy A. Freezing point depression of water in phospholipid membranes: a solid-state NMR study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:13598-13604. [PMID: 18991419 PMCID: PMC2649677 DOI: 10.1021/la8023698] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Lipid-water interaction plays an important role in the properties of lipid bilayers, cryoprotectants, and membrane-associated peptides and proteins. The temperature at which water bound to lipid bilayers freezes is lower than that of free water. Here, we report a solid-state NMR investigation on the freezing point depression of water in phospholipid bilayers in the presence and absence of cholesterol. Deuterium NMR spectra at different temperatures ranging from -75 to + 10 degrees C were obtained from fully (2)H2O-hydrated POPC (1-palmitoyl-2-oleoylphosphatidylcholine) multilamellar vesicles (MLVs), prepared with and without cholesterol, to determine the freezing temperature of water and the effect of cholesterol on the freezing temperature of water in POPC bilayers. Our 2H NMR experiments reveal the motional behavior of unfrozen water molecules in POPC bilayers even at temperatures significantly below 0 degrees C and show that the presence of cholesterol further lowered the freezing temperature of water in POPC bilayers. These results suggest that in the presence of cholesterol the fluidity and dynamics of lipid bilayers can be retained even at very low temperatures as exist in the liquid crystalline phase of the lipid. Therefore, bilayer samples prepared with a cryoprotectant like cholesterol should enable the performance of multidimensional solid-state NMR experiments to investigate the structure, dynamics, and topology of membrane proteins at a very low temperature with enhanced sample stability and possibly a better sensitivity. Phosphorus-31 NMR data suggest that lipid bilayers can be aligned at low temperatures, while 15N NMR experiments demonstrate that such aligned samples can be used to enhance the signal-to-noise ratio of is 15N chemical shift spectra of a 37-residue human antimicrobial peptide, LL-37.
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Affiliation(s)
- Dong-Kuk Lee
- Department of Fine Chemistry, Seoul National University of Technology, Seoul 139-743, Korea.
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40
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Ramamoorthy A, Lee DK, Santos JS, Henzler-Wildman KA. Nitrogen-14 Solid-State NMR Spectroscopy of Aligned Phospholipid Bilayers to Probe Peptide−Lipid Interaction and Oligomerization of Membrane Associated Peptides. J Am Chem Soc 2008; 130:11023-9. [DOI: 10.1021/ja802210u] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Dong-Kuk Lee
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Jose S. Santos
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
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41
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Das BB, Ajithkumar TG, Ramanathan KV. Improved pulse schemes for separated local field spectroscopy for static and spinning samples. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2008; 33:57-63. [PMID: 18406111 DOI: 10.1016/j.ssnmr.2008.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 02/06/2008] [Accepted: 02/27/2008] [Indexed: 05/26/2023]
Abstract
An improved pulse sequence for SLF experiments based on the magic sandwich (MS) scheme for homo-nuclear dipolar decoupling is proposed. The sequence incorporates a double MS, both on I and S spins and has been named as EXE-MS2. The proposed scheme which has a scaling factor of 1 is observed to be free from low intensity artifacts and provides better line-widths particularly for S spins labeled at multiple sites. The pulse sequence which has been applied on static oriented samples incorporates the EXE scheme where direct polarization of the S spin in the B(0) field is utilized in the place of polarization inversion and is observed to perform well without any loss of sensitivity while ensuring considerable reduction in rf power input into the sample. The EXE scheme has also been tested for solid samples under MAS.
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Affiliation(s)
- Bibhuti B Das
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
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42
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Mehta MA, Eddy MT, McNeill SA, Mills FD, Long JR. Determination of Peptide Backbone Torsion Angles Using Double-Quantum Dipolar Recoupling Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:2202-12. [DOI: 10.1021/ja074244w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Manish A. Mehta
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Matthew T. Eddy
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Seth A. McNeill
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Frank D. Mills
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Joanna R. Long
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
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43
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Franzin CM, Teriete P, Marassi FM. Membrane orientation of the Na,K-ATPase regulatory membrane protein CHIF determined by solid-state NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S192-S197. [PMID: 18098352 PMCID: PMC2920893 DOI: 10.1002/mrc.2144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Corticosteroid hormone-induced factor (CHIF) is a major regulatory subunit of the Na,K-ATPase, and a member of an evolutionarily conserved family of membrane proteins that regulate the function of the enzyme complex in a tissue-specific and physiological-state-specific manner. Here we present the structure of CHIF oriented in the membrane, determined by solid-state NMR orientation-dependent restraints. Because CHIF adopts a similar structure in lipid micelles and bilayers, it is possible to assign the solid-state NMR spectrum measured for (15)N-labeled CHIF in oriented bilayers from the structure determined in micelles, to obtain the global orientation of the protein in the membrane.
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Affiliation(s)
| | | | - Francesca M. Marassi
- Correspondence to: Francesca M. Marassi, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla CA 92037, CA, USA.
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44
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A high resolution structure of the putative hinge region in M2 channel-lining segments of the nicotinic acetylcholine receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2961-70. [DOI: 10.1016/j.bbamem.2007.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 10/12/2007] [Accepted: 10/15/2007] [Indexed: 02/07/2023]
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45
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McNeill SA, Gor'kov PL, Struppe J, Brey WW, Long JR. Optimizing ssNMR experiments for dilute proteins in heterogeneous mixtures at high magnetic fields. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S209-20. [PMID: 18157844 DOI: 10.1002/mrc.2146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Solid-state NMR spectroscopy at high magnetic fields is proving to be an effective technique in structural biology, particularly for proteins which are not amenable to traditional X-ray and solution NMR approaches. Several parameters can be selected to provide optimal sensitivity, improve sample stability, and ensure biological relevance for ssNMR measurements on protein samples. These include selection of sample conditions, NMR probe design, and design of pulse experiments. Here, we demonstrate and evaluate several engineering and experimental approaches for pursuing measurements on dilute proteins in heterogeneous mixtures.
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Affiliation(s)
- Seth A McNeill
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
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46
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Wu Y, Shih SCC, Goto NK. Probing the structure of the Ff bacteriophage major coat protein transmembrane helix dimer by solution NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3206-15. [PMID: 17915191 DOI: 10.1016/j.bbamem.2007.08.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2007] [Revised: 08/08/2007] [Accepted: 08/09/2007] [Indexed: 01/04/2023]
Abstract
The transmembrane (TM) segment of the major coat protein from Ff bacteriophage has been extensively studied as an example of dimerization in detergent and lipid bilayer systems. However, almost all the information regarding this interaction has been gained through mutagenesis studies, with little direct structural information being available. To this end solution NMR has the potential to provide new insights into structure of the dimer. In order to evaluate the utility of this approach we have studied a selectively 15N-labeled peptide containing the TM segment of MCP (MCPTM) by solution NMR. This peptide was found to give rise to detergent concentration-dependent spectra that were assigned to monomeric and dimeric forms. The standard free energy of this interaction in SDS was estimated from these spectra and found to be consistent with weak but specific dimerization. In addition, similar spectra could be obtained in beta-octyl glucoside with intermolecular paramagnetic relaxation experiments demonstrating a parallel arrangement of TM helices in the dimer. In both detergents backbone chemical shift differences between monomeric and dimeric forms of MCPTM showed that the largest changes occur around its GXXXG motif. The resulting structural model is consistent with observations made for MCP mutants previously characterized in biological membranes, opening the door to detailed structural characterization of this form of MCP. These results also have general implications for the study of weakly interacting TM segments by solution NMR since the use of similar sample conditions should allow structural data to be accessed for oligomeric states from a wide range systems that undergo biologically relevant but weak associations in the membrane.
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Affiliation(s)
- Yanqiu Wu
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, ON, K1N 6N5 Canada
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47
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Mahalakshmi R, Franzin CM, Choi J, Marassi FM. NMR structural studies of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3216-24. [PMID: 17916325 DOI: 10.1016/j.bbamem.2007.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/01/2007] [Accepted: 08/02/2007] [Indexed: 10/22/2022]
Abstract
The beta-barrels found in the outer membranes of prokaryotic and eukaryotic organisms constitute an important functional class of proteins. Here we present solid-state NMR spectra of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. We show that OmpX is folded in both glass-supported oriented lipid bilayers and in lipid bicelles that can be magnetically oriented with the membrane plane parallel or perpendicular to the direction of the magnetic field. The presence of resolved peaks in these spectra demonstrates that OmpX undergoes rotational diffusion around an axis perpendicular to the membrane surface. A tightly hydrogen-bonded domain of OmpX resists exchange with D2O for days and is assigned to the transmembrane beta-barrel, while peaks at isotropic resonance frequencies that disappear rapidly in D2O are assigned to the extracellular and periplasmic loops. The two-dimensional 1H/15N separated local field spectra of OmpX have several resolved peaks, and agree well with the spectra calculated from the crystal structure of OmpX rotated with the barrel axis nearly parallel (5 degrees tilt) to the direction of the magnetic field. The data indicate that it will be possible to obtain site-specific resonance assignments and to determine the structure, tilt, and rotation of OmpX in membranes using the solid-state NMR methods that are currently being applied to alpha-helical membrane proteins.
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48
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Inbaraj JJ, Cardon TB, Laryukhin M, Grosser SM, Lorigan GA. Determining the topology of integral membrane peptides using EPR spectroscopy. J Am Chem Soc 2007; 128:9549-54. [PMID: 16848493 PMCID: PMC2533427 DOI: 10.1021/ja0622204] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper reports on the development of a new structural biology technique for determining the membrane topology of an integral membrane protein inserted into magnetically aligned phospholipid bilayers (bicelles) using EPR spectroscopy. The nitroxide spin probe, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC), was attached to the pore-lining transmembrane domain (M2delta) of the nicotinic acetylcholine receptor (AChR) and incorporated into a bicelle. The corresponding EPR spectra revealed hyperfine splittings that were highly dependent on the macroscopic orientation of the bicelles with respect to the static magnetic field. The helical tilt of the peptide can be easily calculated using the hyperfine splittings gleaned from the orientational dependent EPR spectra. A helical tilt of 14 degrees was calculated for the M2delta peptide with respect to the bilayer normal of the membrane, which agrees well with previous 15N solid-state NMR studies. The helical tilt of the peptide was verified by simulating the corresponding EPR spectra using the standardized MOMD approach. This new method is advantageous because: (1) bicelle samples are easy to prepare, (2) the helical tilt can be directly calculated from the orientational-dependent hyperfine splitting in the EPR spectra, and (3) EPR spectroscopy is approximately 1000-fold more sensitive than 15N solid-state NMR spectroscopy; thus, the helical tilt of an integral membrane peptide can be determined with only 100 microg of peptide. The helical tilt can be determined more accurately by placing TOAC spin labels at several positions with this technique.
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Affiliation(s)
- Johnson J Inbaraj
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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49
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Franzin CM, Teriete P, Marassi FM. Structural similarity of a membrane protein in micelles and membranes. J Am Chem Soc 2007; 129:8078-9. [PMID: 17567018 PMCID: PMC2518691 DOI: 10.1021/ja0728371] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The anisotropic spin interactions measured for membrane proteins in weakly oriented micelles and in oriented lipid bilayers provide independent and potentially complementary high-resolution restraints for structure determination. Here we show that the membrane protein CHIF adopts a similar structure in lipid micelles and bilayers, allowing the restraints from micelle and bilayer samples to be combined in a complementary fashion to enhance the structural information. Back-calculation and assignment of the NMR spectrum of CHIF in oriented lipid bilayers, from the structure determined in micelles, provides additional restraints for structure determination as well as the global orientation of the protein in the membrane. The combined use of solution and solid-state NMR restraints also affords cross-validation for the structural analysis.
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Affiliation(s)
- Carla M. Franzin
- Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla CA 92037,
| | - Peter Teriete
- Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla CA 92037,
| | - Francesca M. Marassi
- Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla CA 92037,
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50
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Franzin CM, Gong XM, Thai K, Yu J, Marassi FM. NMR of membrane proteins in micelles and bilayers: the FXYD family proteins. Methods 2007; 41:398-408. [PMID: 17367712 PMCID: PMC2920895 DOI: 10.1016/j.ymeth.2006.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Revised: 08/10/2006] [Accepted: 08/15/2006] [Indexed: 11/25/2022] Open
Abstract
Determining the atomic resolution structures of membrane proteins is of particular interest in contemporary structural biology. Helical membrane proteins constitute one-third of the expressed proteins encoded in a genome, many drugs have membrane-bound proteins as their receptors, and mutations in membrane proteins result in human diseases. Although integral membrane proteins provide daunting technical challenges for all methods of protein structure determination, nuclear magnetic resonance (NMR) spectroscopy can be an extremely versatile and powerful method for determining their structures and characterizing their dynamics, in lipid environments that closely mimic the cell membranes. Once milligram amounts of isotopically labeled protein are expressed and purified, micelle samples can be prepared for solution NMR analysis, and lipid bilayer samples can be prepared for solid-state NMR analysis. The two approaches are complementary and can provide detailed structural and dynamic information. This paper describes the steps for membrane protein structure determination using solution and solid-state NMR. The methods for protein expression and purification, sample preparation and NMR experiments are described and illustrated with examples from the FXYD proteins, a family of regulatory subunits of the Na,K-ATPase.
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