1
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Chaudhary BP, Struppe J, Moktan H, Zoetewey D, Zhou DH, Mohanty S. Reconstitution and resonance assignments of yeast OST subunit Ost4 and its critical mutant Ost4V23D in liposomes by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2024; 78:109-117. [PMID: 38421550 DOI: 10.1007/s10858-024-00437-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
N-linked glycosylation is an essential and highly conserved co- and post-translational protein modification in all domains of life. In humans, genetic defects in N-linked glycosylation pathways result in metabolic diseases collectively called Congenital Disorders of Glycosylation. In this modification reaction, a mannose rich oligosaccharide is transferred from a lipid-linked donor substrate to a specific asparagine side-chain within the -N-X-T/S- sequence (where X ≠ Proline) of the nascent protein. Oligosaccharyltransferase (OST), a multi-subunit membrane embedded enzyme catalyzes this glycosylation reaction in eukaryotes. In yeast, Ost4 is the smallest of nine subunits and bridges the interaction of the catalytic subunit, Stt3, with Ost3 (or its homolog, Ost6). Mutations of any C-terminal hydrophobic residues in Ost4 to a charged residue destabilizes the enzyme and negatively impacts its function. Specifically, the V23D mutation results in a temperature-sensitive phenotype in yeast. Here, we report the reconstitution of both purified recombinant Ost4 and Ost4V23D each in a POPC/POPE lipid bilayer and their resonance assignments using heteronuclear 2D and 3D solid-state NMR with magic-angle spinning. The chemical shifts of Ost4 changed significantly upon the V23D mutation, suggesting a dramatic change in its chemical environment.
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Affiliation(s)
- Bharat P Chaudhary
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA
| | | | - Hem Moktan
- Department of Physics, Oklahoma State University, Stillwater, OK, 74078, USA
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David Zoetewey
- Department of Chemistry, Physics and Astronomy, Georgia College and State University, Milledgeville, GA, 31061, USA
| | - Donghua H Zhou
- Department of Physics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Smita Mohanty
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
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2
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Osborn Popp TM, Matchett BT, Green RG, Chhabra I, Mumudi S, Bernstein AD, Perodeau JR, Nieuwkoop AJ. 3D-Printable centrifugal devices for biomolecular solid state NMR rotors. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 354:107524. [PMID: 37481918 PMCID: PMC10528322 DOI: 10.1016/j.jmr.2023.107524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
The advent of magic angle spinning (MAS) rates exceeding 100 kHz has facilitated the acquisition of 1H-detected solid-state NMR spectra of biomolecules with high resolution. However, challenges can arise when preparing rotors for these experiments, due to the physical properties of biomolecular solid samples and the small dimensions of the rotors. In this study, we have designed 3D-printable centrifugal devices that facilitate efficient and consistent packing of crystalline protein slurries or viscous phospholipids into 0.7 mm rotors. We demonstrate the efficacy of these packing devices using 1H-detected solid state NMR at 105 kHz. In addition to devices for 0.7 mm rotors, we have also developed devices for other frequently employed rotor sizes and styles. We have made all our designs openly accessible, and we encourage their usage and ongoing development as a shared effort within the solid state NMR community.
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Affiliation(s)
- Thomas M Osborn Popp
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States.
| | - Brandon T Matchett
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Rashawn G Green
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Insha Chhabra
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Smriti Mumudi
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Ashley D Bernstein
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Jacqueline R Perodeau
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States.
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3
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Tzortzini E, Kolocouris A. Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the A 2A Adenosine Receptor. Biomolecules 2023; 13:957. [PMID: 37371538 DOI: 10.3390/biom13060957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipid membrane bilayers with cholesterol representing 34% of the total lipid content in mammalian plasma membranes. Membrane lipids interact with GPCRs structures and modulate their function and drug-stimulated signaling through conformational selection. It has been shown that anionic phospholipids form strong interactions between positively charged residues in the G protein and the TM5-TM6-TM 7 cytoplasmic interface of class A GPCRs stabilizing the signaling GPCR-G complex. Cholesterol with a high content in plasma membranes can be identified in more specific sites in the transmembrane region of GPCRs, such as the Cholesterol Consensus Motif (CCM) and Cholesterol Recognition Amino Acid Consensus (CRAC) motifs and other receptor dependent and receptor state dependent sites. Experimental biophysical methods, atomistic (AA) MD simulations and coarse-grained (CG) molecular dynamics simulations have been applied to investigate these interactions. We emphasized here the impact of phosphatidyl inositol-4,5-bisphosphate (PtdIns(4,5)P2 or PIP2), a minor phospholipid component and of cholesterol on the function-related conformational equilibria of the human A2A adenosine receptor (A2AR), a representative receptor in class A GPCR. Several GPCRs of class A interacted with PIP2 and cholesterol and in many cases the mechanism of the modulation of their function remains unknown. This review provides a helpful comprehensive overview for biophysics that enter the field of GPCRs-lipid systems.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
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4
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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5
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Wright AK, Paulino J, Cross TA. Emulating Membrane Protein Environments─How Much Lipid Is Required for a Native Structure: Influenza S31N M2. J Am Chem Soc 2022; 144:2137-2148. [PMID: 35089701 DOI: 10.1021/jacs.1c10174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This report investigates the homotetrameric membrane protein structure of the S31N M2 protein from Influenza A virus in the presence of a high molar ratio of lipid. The structured regions of this protein include a single transmembrane helix and an amphipathic helix. Two structures of the S31N M2 conductance domain from Influenza A virus have been deposited in the Protein Data Bank (PDB). These structures present different symmetries about the channel main axis. We present new magic angle spinning and oriented sample solid-state NMR spectroscopic data for S31N M2 in liquid crystalline lipid bilayers using protein tetramer:lipid molar ratios ranging from 1:120 to 1:240. The data is consistent with an essentially 4-fold-symmetric structure very similar to the M2 WT structure that also has a single conformation for the four monomers, except at the His37 and Trp41 functional sites when characterized in samples with a high molar ratio of lipid. While detergent solubilization is well recognized today as a nonideal environment for small membrane proteins, here we discuss the influence of a high lipid to protein ratio for samples of the S31N M2 protein to stabilize an essentially 4-fold-symmetric conformation of the M2 membrane protein. While it is generally accepted that the chemical and physical properties of the native environment of membrane proteins needs to be reproduced judiciously to achieve the native protein structure, here we show that not only the character of the emulated membrane environment is important but also the abundance of the environment is important for achieving the native structure. This is a critical finding as a membrane protein spectroscopist's goal is always to generate a sample with the highest possible protein sensitivity while obtaining spectra of the native-like structure.
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Affiliation(s)
- Anna K Wright
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Joana Paulino
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Timothy A Cross
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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6
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Weber DK, Reddy UV, Wang S, Larsen EK, Gopinath T, Gustavsson MB, Cornea RL, Thomas DD, De Simone A, Veglia G. Structural basis for allosteric control of the SERCA-Phospholamban membrane complex by Ca 2+ and phosphorylation. eLife 2021; 10:66226. [PMID: 33978571 PMCID: PMC8184213 DOI: 10.7554/elife.66226] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/10/2021] [Indexed: 01/26/2023] Open
Abstract
Phospholamban (PLN) is a mini-membrane protein that directly controls the cardiac Ca2+-transport response to β-adrenergic stimulation, thus modulating cardiac output during the fight-or-flight response. In the sarcoplasmic reticulum membrane, PLN binds to the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA), keeping this enzyme's function within a narrow physiological window. PLN phosphorylation by cAMP-dependent protein kinase A or increase in Ca2+ concentration reverses the inhibitory effects through an unknown mechanism. Using oriented-sample solid-state NMR spectroscopy and replica-averaged NMR-restrained structural refinement, we reveal that phosphorylation of PLN's cytoplasmic regulatory domain signals the disruption of several inhibitory contacts at the transmembrane binding interface of the SERCA-PLN complex that are propagated to the enzyme's active site, augmenting Ca2+ transport. Our findings address long-standing questions about SERCA regulation, epitomizing a signal transduction mechanism operated by posttranslationally modified bitopic membrane proteins.
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Affiliation(s)
- Daniel K Weber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - U Venkateswara Reddy
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Songlin Wang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Erik K Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, United States
| | - Tata Gopinath
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Martin B Gustavsson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom.,Department of Pharmacy, University of Naples 'Federico II', Naples, Italy
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States.,Department of Chemistry, University of Minnesota, Minneapolis, United States
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7
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Gopinath T, Weber D, Wang S, Larsen E, Veglia G. Solid-State NMR of Membrane Proteins in Lipid Bilayers: To Spin or Not To Spin? Acc Chem Res 2021; 54:1430-1439. [PMID: 33655754 DOI: 10.1021/acs.accounts.0c00670] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Membrane proteins mediate a plethora of cellular functions and represent important targets for drug development. Unlike soluble proteins, membrane proteins require native-like environments to fold correctly and be active. Therefore, modern structural biology techniques have aimed to determine the structure and dynamics of these membrane proteins at physiological temperature and in liquid crystalline lipid bilayers. With the flourishing of new NMR methodologies and improvements in sample preparations, magic angle spinning (MAS) and oriented sample solid-state NMR (OS-ssNMR) spectroscopy of membrane proteins is experiencing a new renaissance. Born as antagonistic approaches, these techniques nowadays offer complementary information on the structural topology and dynamics of membrane proteins reconstituted in lipid membranes. By spinning biosolid samples at the magic angle (θ = 54.7°), MAS NMR experiments remove the intrinsic anisotropy of the NMR interactions, increasing spectral resolution. Internuclear spin interactions (spin exchange) are reintroduced by RF pulses, providing distances and torsion angles to determine secondary, tertiary, and quaternary structures of membrane proteins. OS-ssNMR, on the other hand, directly detects anisotropic NMR parameters such as dipolar couplings (DC) and anisotropic chemical shifts (CS), providing orientational constraints to determine the architecture (i.e., topology) of membrane proteins relative to the lipid membrane. Defining the orientation of membrane proteins and their interactions with lipid membranes is of paramount importance since lipid-protein interactions can shape membrane protein conformations and ultimately define their functional states.In this Account, we report selected studies from our group integrating MAS and OS-ssNMR techniques to give a comprehensive view of the biological processes occurring at cellular membranes. We focus on the main experiments for both techniques, with an emphasis on new implementation to increase both sensitivity and spectral resolution. We also describe how the structural constraints derived from both isotropic and anisotropic NMR parameters are integrated into dynamic structural modeling using replica-averaged orientational-restrained molecular dynamics simulations (RAOR-MD). We showcase small membrane proteins that are involved in Ca2+ transport and regulate cardiac and skeletal muscle contractility: phospholamban (PLN, 6 kDa), sarcolipin (SLN, 4 kDa), and DWORF (4 kDa). We summarize our results for the structures of these polypeptides free and in complex with the sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA, 110 kDa). Additionally, we illustrate the progress toward the determination of the structural topology of a six transmembrane protein associated with succinate and acetate transport (SatP, hexamer 120 kDa). From these examples, the integrated MAS and OS-ssNMR approach, in combination with modern computational methods, emerges as a way to overcome the challenges posed by studying large membrane protein systems.
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8
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Narasimhan S, Pinto C, Lucini Paioni A, van der Zwan J, Folkers GE, Baldus M. Characterizing proteins in a native bacterial environment using solid-state NMR spectroscopy. Nat Protoc 2021; 16:893-918. [PMID: 33442051 DOI: 10.1038/s41596-020-00439-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/09/2020] [Indexed: 01/29/2023]
Abstract
For a long time, solid-state nuclear magnetic resonance (ssNMR) has been employed to study complex biomolecular systems at the detailed chemical, structural, or dynamic level. Recent progress in high-resolution and high-sensitivity ssNMR, in combination with innovative sample preparation and labeling schemes, offers novel opportunities to study proteins in their native setting irrespective of the molecular tumbling rate. This protocol describes biochemical preparation schemes to obtain cellular samples of both soluble as well as insoluble or membrane-associated proteins in bacteria. To this end, the protocol is suitable for studying a protein of interest in both whole cells and in cell envelope or isolated membrane preparations. In the first stage of the procedure, an appropriate strain of Escherichia coli (DE3) is transformed with a plasmid of interest harboring the protein of interest under the control of an inducible T7 promoter. Next, the cells are adapted to grow in minimal (M9) medium. Before the growth enters stationary phase, protein expression is induced, and shortly thereafter, the native E. coli RNA polymerase is inhibited using rifampicin for targeted labeling of the protein of interest. The cells are harvested after expression and prepared for ssNMR rotor filling. In addition to conventional 13C/15N-detected ssNMR, we also outline how these preparations can be readily subjected to multidimensional ssNMR experiments using dynamic nuclear polarization (DNP) or proton (1H) detection schemes. We estimate that the entire preparative procedure until NMR experiments can be started takes 3-5 days.
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Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Cecilia Pinto
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
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9
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Wang S, Gopinath T, Veglia G. Improving the quality of oriented membrane protein spectra using heat-compensated separated local field experiments. JOURNAL OF BIOMOLECULAR NMR 2019; 73:617-624. [PMID: 31463642 PMCID: PMC6861693 DOI: 10.1007/s10858-019-00273-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/21/2019] [Indexed: 05/03/2023]
Abstract
Oriented sample solid-state NMR (OS-ssNMR) spectroscopy is a powerful technique to determine the topology of membrane proteins in oriented lipid bilayers. Separated local field (SLF) experiments are central to this technique as they provide first-order orientational restraints, i.e., dipolar couplings and anisotropic chemical shifts. Despite the use of low-E (or E-free) probes, the heat generated during the execution of 2D and 3D SLF pulse sequences causes sizeable line-shape distortions. Here, we propose a new heat-compensated SE-SAMPI4 (hcSE-SAMPI4) pulse sequence that holds the temperature constant for the duration of the experiment. This modification of the SE-SAMPI4 results in sharper and more intense resonances without line-shape distortions. The spectral improvements are even more apparent when paramagnetic relaxation agents are used to speed up data collection. We tested the hcSE-SAMPI4 pulse sequence on a single-span membrane protein, sarcolipin (SLN), reconstituted in magnetically aligned lipid bicelles. In addition to eliminating peak distortions, the hcSE-SAMPI4 experiment increased the average signal-to-noise ratio by 20% with respect to the original SE-SAMPI4.
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Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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10
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Conrard L, Tyteca D. Regulation of Membrane Calcium Transport Proteins by the Surrounding Lipid Environment. Biomolecules 2019; 9:E513. [PMID: 31547139 PMCID: PMC6843150 DOI: 10.3390/biom9100513] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Abstract
Calcium ions (Ca2+) are major messengers in cell signaling, impacting nearly every aspect of cellular life. Those signals are generated within a wide spatial and temporal range through a large variety of Ca2+ channels, pumps, and exchangers. More and more evidences suggest that Ca2+ exchanges are regulated by their surrounding lipid environment. In this review, we point out the technical challenges that are currently being overcome and those that still need to be defeated to analyze the Ca2+ transport protein-lipid interactions. We then provide evidences for the modulation of Ca2+ transport proteins by lipids, including cholesterol, acidic phospholipids, sphingolipids, and their metabolites. We also integrate documented mechanisms involved in the regulation of Ca2+ transport proteins by the lipid environment. Those include: (i) Direct interaction inside the protein with non-annular lipids; (ii) close interaction with the first shell of annular lipids; (iii) regulation of membrane biophysical properties (e.g., membrane lipid packing, thickness, and curvature) directly around the protein through annular lipids; and (iv) gathering and downstream signaling of several proteins inside lipid domains. We finally discuss recent reports supporting the related alteration of Ca2+ and lipids in different pathophysiological events and the possibility to target lipids in Ca2+-related diseases.
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Affiliation(s)
- Louise Conrard
- CELL Unit, de Duve Institute and Université catholique de Louvain, UCL B1.75.05, avenue Hippocrate, 75, B-1200 Brussels, Belgium
| | - Donatienne Tyteca
- CELL Unit, de Duve Institute and Université catholique de Louvain, UCL B1.75.05, avenue Hippocrate, 75, B-1200 Brussels, Belgium.
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11
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Lacabanne D, Fogeron ML, Wiegand T, Cadalbert R, Meier BH, Böckmann A. Protein sample preparation for solid-state NMR investigations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 110:20-33. [PMID: 30803692 DOI: 10.1016/j.pnmrs.2019.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 06/09/2023]
Abstract
Preparation of a protein sample for solid-state NMR is in many aspects similar to solution-state NMR approaches, mainly with respect to the need for stable isotope labeling. But the possibility of using solid-state NMR to investigate membrane proteins in (native) lipids adds the important requirement of adapted membrane-reconstitution schemes. Also, dynamic nuclear polarization and paramagnetic NMR in solids need specific schemes using metal ions and radicals. Sample sedimentation has enabled structural investigations of objects inaccessible to other structural techniques, but rotor filling using sedimentation has become increasingly complex with smaller and smaller rotors, as needed for higher and higher magic-angle spinning (MAS) frequencies. Furthermore, solid-state NMR can investigate very large proteins and their complexes without the concomitant increase in line widths, motivating the use of selective labeling and unlabeling strategies, as well as segmental labeling, to decongest spectra. The possibility of investigating sub-milligram amounts of protein today using advanced fast MAS techniques enables alternative protein synthesis schemes such as cell-free expression. Here we review these specific aspects of solid-state NMR sample preparation.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France; Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - 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, 69367 Lyon, France.
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12
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Moradi S, Nowroozi A, Shahlaei M. Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study. RSC Adv 2019; 9:4644-4658. [PMID: 35520151 PMCID: PMC9060685 DOI: 10.1039/c8ra08441f] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/12/2019] [Accepted: 01/16/2019] [Indexed: 12/20/2022] Open
Abstract
This review gives an overview about the some of the most important possible analyzes, technical challenges, and existing protocols that can be performed on the biological membrane by the molecular dynamics simulation.
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Affiliation(s)
- Sajad Moradi
- Nano Drug Delivery Research Center
- Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Amin Nowroozi
- Pharmaceutical Sciences Research Center
- Faculty of Pharmacy
- Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Mohsen Shahlaei
- Medical Biology Research Center
- Kermanshah University of Medical Sciences
- Kermanshah
- Iran
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13
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Pfeil MP, Pyne ALB, Losasso V, Ravi J, Lamarre B, Faruqui N, Alkassem H, Hammond K, Judge PJ, Winn M, Martyna GJ, Crain J, Watts A, Hoogenboom BW, Ryadnov MG. Tuneable poration: host defense peptides as sequence probes for antimicrobial mechanisms. Sci Rep 2018; 8:14926. [PMID: 30297841 PMCID: PMC6175903 DOI: 10.1038/s41598-018-33289-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 09/26/2018] [Indexed: 02/02/2023] Open
Abstract
The spread of antimicrobial resistance stimulates discovery strategies that place emphasis on mechanisms circumventing the drawbacks of traditional antibiotics and on agents that hit multiple targets. Host defense peptides (HDPs) are promising candidates in this regard. Here we demonstrate that a given HDP sequence intrinsically encodes for tuneable mechanisms of membrane disruption. Using an archetypal HDP (cecropin B) we show that subtle structural alterations convert antimicrobial mechanisms from native carpet-like scenarios to poration and non-porating membrane exfoliation. Such distinct mechanisms, studied using low- and high-resolution spectroscopy, nanoscale imaging and molecular dynamics simulations, all maintain strong antimicrobial effects, albeit with diminished activity against pathogens resistant to HDPs. The strategy offers an effective search paradigm for the sequence probing of discrete antimicrobial mechanisms within a single HDP.
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Affiliation(s)
- Marc-Philipp Pfeil
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Alice L B Pyne
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
| | - Valeria Losasso
- STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, UK
| | - Jascindra Ravi
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Baptiste Lamarre
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Nilofar Faruqui
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Hasan Alkassem
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, UK
| | - Katharine Hammond
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
| | - Peter J Judge
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Martyn Winn
- STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, UK
| | | | - Jason Crain
- IBM Research, Yorktown Heights, NY, 10598, USA
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
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14
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Impact of membrane curvature on amyloid aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1741-1764. [PMID: 29709613 DOI: 10.1016/j.bbamem.2018.04.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 12/11/2022]
Abstract
The misfolding, amyloid aggregation, and fibril formation of intrinsically disordered proteins/peptides (or amyloid proteins) have been shown to cause a number of disorders. The underlying mechanisms of amyloid fibrillation and structural properties of amyloidogenic precursors, intermediates, and amyloid fibrils have been elucidated in detail; however, in-depth examinations on physiologically relevant contributing factors that induce amyloidogenesis and lead to cell death remain challenging. A large number of studies have attempted to characterize the roles of biomembranes on protein aggregation and membrane-mediated cell death by designing various membrane components, such as gangliosides, cholesterol, and other lipid compositions, and by using various membrane mimetics, including liposomes, bicelles, and different types of lipid-nanodiscs. We herein review the dynamic effects of membrane curvature on amyloid generation and the inhibition of amyloidogenic proteins and peptides, and also discuss how amyloid formation affects membrane curvature and integrity, which are key for understanding relationships with cell death. Small unilamellar vesicles with high curvature and large unilamellar vesicles with low curvature have been demonstrated to exhibit different capabilities to induce the nucleation, amyloid formation, and inhibition of amyloid-β peptides and α-synuclein. Polymorphic amyloidogenesis in small unilamellar vesicles was revealed and may be viewed as one of the generic properties of interprotein interaction-dominated amyloid formation. Several mechanical models and phase diagrams are comprehensively shown to better explain experimental findings. The negative membrane curvature-mediated mechanisms responsible for the toxicity of pancreatic β cells by the amyloid aggregation of human islet amyloid polypeptide (IAPP) and binding of the precursors of the semen-derived enhancer of viral infection (SEVI) are also described. The curvature-dependent binding modes of several types of islet amyloid polypeptides with high-resolution NMR structures are also discussed.
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15
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Schubeis T, Le Marchand T, Andreas LB, Pintacuda G. 1H magic-angle spinning NMR evolves as a powerful new tool for membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 287:140-152. [PMID: 29413327 DOI: 10.1016/j.jmr.2017.11.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 06/08/2023]
Abstract
Building on a decade of continuous advances of the community, the recent development of very fast (60 kHz and above) magic-angle spinning (MAS) probes has revolutionised the field of solid-state NMR. This new spinning regime reduces the 1H-1H dipolar couplings, so that direct detection of the larger magnetic moment available from 1H is now possible at high resolution, not only in deuterated molecules but also in fully-protonated substrates. Such capabilities allow rapid "fingerprinting" of samples with a ten-fold reduction of the required sample amounts with respect to conventional approaches, and permit extensive, robust and expeditious assignment of small-to-medium sized proteins (up to ca. 300 residues), and the determination of inter-nuclear proximities, relative orientations of secondary structural elements, protein-cofactor interactions, local and global dynamics. Fast MAS and 1H detection techniques have nowadays been shown to be applicable to membrane-bound systems. This paper reviews the strategies underlying this recent leap forward in sensitivity and resolution, describing its potential for the detailed characterization of membrane proteins.
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Affiliation(s)
- Tobias Schubeis
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Loren B Andreas
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France.
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16
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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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17
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Ravula T, Hardin NZ, Ramadugu SK, Cox SJ, Ramamoorthy A. Formation of pH-Resistant Monodispersed Polymer-Lipid Nanodiscs. Angew Chem Int Ed Engl 2018; 57:1342-1345. [PMID: 29232017 DOI: 10.1002/anie.201712017] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Indexed: 12/24/2022]
Abstract
Polymer lipid nanodiscs are an invaluable system for structural and functional studies of membrane proteins in their near-native environment. Despite the recent advances in the development and usage of polymer lipid nanodisc systems, lack of control over size and poor tolerance to pH and divalent metal ions are major limitations for further applications. A facile modification of a low-molecular-weight styrene maleic acid copolymer is demonstrated to form monodispersed lipid bilayer nanodiscs that show ultra-stability towards divalent metal ion concentration over a pH range of 2.5 to 10. The macro-nanodiscs (>20 nm diameter) show magnetic alignment properties that can be exploited for high-resolution structural studies of membrane proteins and amyloid proteins using solid-state NMR techniques. The new polymer, SMA-QA, nanodisc is a robust membrane mimetic tool that offers significant advantages over currently reported nanodisc systems.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Nathaniel Z Hardin
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Sudheer Kumar Ramadugu
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Sarah J Cox
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
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18
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Ravula T, Hardin NZ, Ramadugu SK, Cox SJ, Ramamoorthy A. Formation of pH-Resistant Monodispersed Polymer-Lipid Nanodiscs. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Thirupathi Ravula
- Biophysics Program and Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
| | - Nathaniel Z. Hardin
- Biophysics Program and Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
| | - Sudheer Kumar Ramadugu
- Biophysics Program and Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
| | - Sarah J. Cox
- Biophysics Program and Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
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19
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Chandra B, Maity BK, Das A, Maiti S. Fluorescence quenching by lipid encased nanoparticles shows that amyloid-β has a preferred orientation in the membrane. Chem Commun (Camb) 2018; 54:7750-7753. [DOI: 10.1039/c8cc02108b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Short range plasmonic fields around a nanoparticle can modulate fluorescence or Raman processes.
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Affiliation(s)
| | | | - Anirban Das
- Tata Institute of Fundamental Research
- Homi Bhabha Road
- Mumbai
- India
| | - Sudipta Maiti
- Tata Institute of Fundamental Research
- Homi Bhabha Road
- Mumbai
- India
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20
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Wang S, Gopinath T, Veglia G. Application of paramagnetic relaxation enhancements to accelerate the acquisition of 2D and 3D solid-state NMR spectra of oriented membrane proteins. Methods 2017; 138-139:54-61. [PMID: 29274874 DOI: 10.1016/j.ymeth.2017.12.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 12/21/2022] Open
Abstract
Oriented sample solid-state NMR (OS-ssNMR) spectroscopy is uniquely suited to determine membrane protein topology at the atomic resolution in liquid crystalline bilayers under physiological temperature. However, the inherent low sensitivity of this technique has hindered the throughput of multidimensional experiments necessary for resonance assignments and structure determination. In this work, we show that doping membrane protein bicelle preparations with paramagnetic ion chelated lipids and exploiting paramagnetic relaxation effects it is possible to accelerate the acquisition of both 2D and 3D multidimensional experiments with significant saving in time. We demonstrate the efficacy of this method for a small membrane protein, sarcolipin, reconstituted in DMPC/POPC/DHPC oriented bicelles. In particular, using Cu2+-DMPE-DTPA as a dopant, we observed a decrease of 1H T1 of sarcolipin by 2/3, allowing us to reduce the recycle delay up to 3 times. We anticipate that these new developments will enable the routine acquisition of multidimensional OS-ssNMR experiments.
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Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, 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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21
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Yasuhara K, Arakida J, Ravula T, Ramadugu SK, Sahoo B, Kikuchi JI, Ramamoorthy A. Spontaneous Lipid Nanodisc Fomation by Amphiphilic Polymethacrylate Copolymers. J Am Chem Soc 2017; 139:18657-18663. [PMID: 29171274 DOI: 10.1021/jacs.7b10591] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is a growing interest in the use of lipid bilayer nanodiscs for various biochemical and biomedical applications. Among the different types of nanodiscs, the unique features of synthetic polymer-based nanodiscs have attracted additional interest. A styrene-maleic acid (SMA) copolymer demonstrated to form lipid nanodiscs has been used for structural biology related studies on membrane proteins. However, the application of SMA polymer based lipid nanodiscs is limited because of the strong absorption of the aromatic group interfering with various experimental measurements. Thus, there is considerable interest in the development of other molecular frameworks for the formation of polymer-based lipid nanodiscs. In this study, we report the first synthesis and characterization of a library of polymethacrylate random copolymers as alternatives to SMA polymer. In addition, we experimentally demonstrate the ability of these polymers to form lipid bilayer nanodiscs through the fragmentation of lipid vesicles by means of light scattering, electron microscopy, differential scanning calorimetry, and solution and solid-state NMR experiments. We further demonstrate a unique application of the newly developed polymer for kinetics and structural characterization of the aggregation of human islet amyloid polypeptide (also known as amylin) within the lipid bilayer of the polymer nanodiscs using thioflavin-T-based fluorescence and circular dichroism experiments. Our results demonstrate that the reported new styrene-free polymers can be used in high-throughput biophysical experiments. Therefore, we expect that the new polymer nanodiscs will be valuable in the structural studies of amyloid proteins and membrane proteins by various biophysical techniques.
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Affiliation(s)
- Kazuma Yasuhara
- Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama-cho, Ikoma, Nara 6300192, Japan
| | - Jin Arakida
- Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama-cho, Ikoma, Nara 6300192, Japan
| | - Thirupathi Ravula
- Biophysics Program and Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109-1055, United States
| | - Sudheer Kumar Ramadugu
- Biophysics Program and Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109-1055, United States
| | - Bikash Sahoo
- Biophysics Program and Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109-1055, United States
| | - Jun-Ichi Kikuchi
- Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama-cho, Ikoma, Nara 6300192, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109-1055, United States
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22
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Molugu TR, Lee S, Brown MF. Concepts and Methods of Solid-State NMR Spectroscopy Applied to Biomembranes. Chem Rev 2017; 117:12087-12132. [PMID: 28906107 DOI: 10.1021/acs.chemrev.6b00619] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Concepts of solid-state NMR spectroscopy and applications to fluid membranes are reviewed in this paper. Membrane lipids with 2H-labeled acyl chains or polar head groups are studied using 2H NMR to yield knowledge of their atomistic structures in relation to equilibrium properties. This review demonstrates the principles and applications of solid-state NMR by unifying dipolar and quadrupolar interactions and highlights the unique features offered by solid-state 2H NMR with experimental illustrations. For randomly oriented multilamellar lipids or aligned membranes, solid-state 2H NMR enables direct measurement of residual quadrupolar couplings (RQCs) due to individual C-2H-labeled segments. The distribution of RQC values gives nearly complete profiles of the segmental order parameters SCD(i) as a function of acyl segment position (i). Alternatively, one can measure residual dipolar couplings (RDCs) for natural abundance lipid samples to obtain segmental SCH order parameters. A theoretical mean-torque model provides acyl-packing profiles representing the cumulative chain extension along the normal to the aqueous interface. Equilibrium structural properties of fluid bilayers and various thermodynamic quantities can then be calculated, which describe the interactions with cholesterol, detergents, peptides, and integral membrane proteins and formation of lipid rafts. One can also obtain direct information for membrane-bound peptides or proteins by measuring RDCs using magic-angle spinning (MAS) in combination with dipolar recoupling methods. Solid-state NMR methods have been extensively applied to characterize model membranes and membrane-bound peptides and proteins, giving unique information on their conformations, orientations, and interactions in the natural liquid-crystalline state.
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Affiliation(s)
- Trivikram R Molugu
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Soohyun Lee
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Michael F Brown
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
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23
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Yamamoto K, Caporini MA, Im SC, Waskell L, Ramamoorthy A. Transmembrane Interactions of Full-length Mammalian Bitopic Cytochrome-P450-Cytochrome-b 5 Complex in Lipid Bilayers Revealed by Sensitivity-Enhanced Dynamic Nuclear Polarization Solid-state NMR Spectroscopy. Sci Rep 2017; 7:4116. [PMID: 28646173 PMCID: PMC5482851 DOI: 10.1038/s41598-017-04219-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/11/2017] [Indexed: 01/12/2023] Open
Abstract
The dynamic protein-protein and protein-ligand interactions of integral bitopic membrane proteins with a single membrane-spanning helix play a plethora of vital roles in the cellular processes associated with human health and diseases, including signaling and enzymatic catalysis. While an increasing number of high-resolution structural studies of membrane proteins have successfully manifested an in-depth understanding of their biological functions, intact membrane-bound bitopic protein-protein complexes pose tremendous challenges for structural studies by crystallography or solution NMR spectroscopy. Therefore, there is a growing interest in developing approaches to investigate the functional interactions of bitopic membrane proteins embedded in lipid bilayers at atomic-level. Here we demonstrate the feasibility of dynamic nuclear polarization (DNP) magic-angle-spinning NMR techniques, along with a judiciously designed stable isotope labeling scheme, to measure atomistic-resolution transmembrane-transmembrane interactions of full-length mammalian ~72-kDa cytochrome P450-cytochrome b5 complex in lipid bilayers. Additionally, the DNP sensitivity-enhanced two-dimensional 13C/13C chemical shift correlations via proton driven spin diffusion provided distance constraints to characterize protein-lipid interactions and revealed the transmembrane topology of cytochrome b5. The results reported in this study would pave ways for high-resolution structural and topological investigations of membrane-bound full-length bitopic protein complexes under physiological conditions.
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Affiliation(s)
- Kazutoshi Yamamoto
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Marc A Caporini
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, 01821, USA
| | - Sang-Choul Im
- Department of Anesthesiology, VA Medical Center, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Lucy Waskell
- Department of Anesthesiology, VA Medical Center, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA.
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24
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Overcoming bottlenecks in the membrane protein structural biology pipeline. Biochem Soc Trans 2017; 44:838-44. [PMID: 27284049 DOI: 10.1042/bst20160049] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Indexed: 02/07/2023]
Abstract
Membrane proteins account for a third of the eukaryotic proteome, but are greatly under-represented in the Protein Data Bank. Unfortunately, recent technological advances in X-ray crystallography and EM cannot account for the poor solubility and stability of membrane protein samples. A limitation of conventional detergent-based methods is that detergent molecules destabilize membrane proteins, leading to their aggregation. The use of orthologues, mutants and fusion tags has helped improve protein stability, but at the expense of not working with the sequence of interest. Novel detergents such as glucose neopentyl glycol (GNG), maltose neopentyl glycol (MNG) and calixarene-based detergents can improve protein stability without compromising their solubilizing properties. Styrene maleic acid lipid particles (SMALPs) focus on retaining the native lipid bilayer of a membrane protein during purification and biophysical analysis. Overcoming bottlenecks in the membrane protein structural biology pipeline, primarily by maintaining protein stability, will facilitate the elucidation of many more membrane protein structures in the near future.
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25
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Niroomand H, Mukherjee D, Khomami B. Tuning the photoexcitation response of cyanobacterial Photosystem I via reconstitution into Proteoliposomes. Sci Rep 2017; 7:2492. [PMID: 28559589 PMCID: PMC5449388 DOI: 10.1038/s41598-017-02746-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/19/2017] [Indexed: 12/25/2022] Open
Abstract
The role of natural thylakoid membrane housing of Photosystem I (PSI), the transmembrane photosynthetic protein, in its robust photoactivated charge separation with near unity quantum efficiency is not fundamentally understood. To this end, incorporation of suitable protein scaffolds for PSI incorporation is of great scientific and device manufacturing interest. Areas of interest include solid state bioelectronics, and photoelectrochemical devices that require bio-abio interfaces that do not compromise the photoactivity and photostability of PSI. Therefore, the surfactant-induced membrane solubilization of a negatively charged phospholipid (DPhPG) with the motivation of creating biomimetic reconstructs of PSI reconstitution in DPhPG liposomes is studied. Specifically, a simple yet elegant method for incorporation of PSI trimeric complexes into DPhPG bilayer membranes that mimic the natural thylakoid membrane housing of PSI is introduced. The efficacy of this method is demonstrated via absorption and fluorescence spectroscopy measurements as well as direct visualization using atomic force microscopy. This study provides direct evidence that PSI confinements in synthetic lipid scaffolds can be used for tuning the photoexcitation characteristics of PSI. Hence, it paves the way for development of fundamental understanding of microenvironment alterations on photochemical response of light activated membrane proteins.
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Affiliation(s)
- Hanieh Niroomand
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA.,Department of Chemical and Biomolecular Engineering, Knoxville, USA
| | - Dibyendu Mukherjee
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA. .,Department of Chemical and Biomolecular Engineering, Knoxville, USA. .,Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, USA.
| | - Bamin Khomami
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA. .,Department of Chemical and Biomolecular Engineering, Knoxville, USA. .,Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, USA.
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26
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Mandal A, Boatz JC, Wheeler TB, van der Wel PCA. On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR. JOURNAL OF BIOMOLECULAR NMR 2017; 67:165-178. [PMID: 28229262 PMCID: PMC5445385 DOI: 10.1007/s10858-017-0089-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/19/2017] [Indexed: 05/07/2023]
Abstract
A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation.
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Affiliation(s)
- Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Jennifer C Boatz
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Travis B Wheeler
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
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Lacabanne D, Kunert B, Gardiennet C, Meier BH, Bo Ckmann A. Sample Preparation for Membrane Protein Structural Studies by Solid-State NMR. Methods Mol Biol 2017; 1635:345-358. [PMID: 28755379 DOI: 10.1007/978-1-4939-7151-0_19] [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] [Indexed: 01/13/2023]
Abstract
Conformational studies of membrane proteins remain a challenge in the field of structural biology, and in particular the investigation of the proteins in a native-like lipid environment. Solid-state NMR presents a valuable opportunity for this, and we present here three critical steps in the solid-state NMR sample preparation, i.e., membrane reconstitution of the protein in native lipids, rotor filling, and sample quality assessment, at the example of the Bacillus subtilis ATP-binding cassette transporter BmrA.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS - Université de Lyon, 7 Passage du Vercors, 69367, Lyon, France
| | - Britta Kunert
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS - Université de Lyon, 7 Passage du Vercors, 69367, Lyon, France
| | - Carole Gardiennet
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS - Université de Lyon, 7 Passage du Vercors, 69367, Lyon, France.,CRM2, UMR 7036, CNRS, Université de Lorraine, 54506, Vandoeuvre-lès-Nancy, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Anja Bo Ckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS - Université de Lyon, 7 Passage du Vercors, 69367, Lyon, France.
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28
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Senicourt L, Duma L, Papadopoulos V, Lacapere JJ. Solid-State NMR of Membrane Protein Reconstituted in Proteoliposomes, the Case of TSPO. Methods Mol Biol 2017; 1635:329-344. [PMID: 28755378 DOI: 10.1007/978-1-4939-7151-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural studies of membrane proteins (MP) in a native or native-like environment remain a challenge. X-ray crystallography of three-dimensional crystals of MP in lipids and cryo-electron microscopy of two-dimensional crystals also in lipids have given atomic structures of several MP. Recent developments of solid-state NMR (ssNMR) provided structural data of MP in lipids and should give access to the dynamic behavior of MP's in a native-like environment. Preparation of samples for ssNMR is not trivial with overexpressed proteins since purified recombinant MP have to be reincorporated in proteoliposomes and concentrated in the small volume of the rotor used for ssNMR studies. We present here the protocol that we have used to study the recombinant mouse TSPO1, an integral membrane protein of 20 kDa mostly found in the outer membrane of mitochondria and overexpressed in E. coli bacteria.
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Affiliation(s)
- Lucile Senicourt
- Sorbonne Universités-UPMC University of Paris 06, Département de Chimie, École Normale Supérieure-PSL Research University, CNRS UMR 7203 LBM, 4 Place Jussieu, 75005, Paris Cedex 05, France
| | - Luminita Duma
- CNRS Enzyme and Cell Engineering Laboratory, Sorbonne Universités, Université de Technologie de Compiègne, Rue Roger Couttolenc, CS 60319, 60203, Compiègne Cedex, France
| | - Vassilios Papadopoulos
- The Research Institute of the McGill, University Health Center, Montreal, QC, Canada, H4A 3J1.,Department of Medicine, McGill University, Montreal, QC, Canada, H4A 3J1
| | - Jean-Jacques Lacapere
- Sorbonne Universités-UPMC University of Paris 06, Département de Chimie, École Normale Supérieure-PSL Research University, CNRS UMR 7203 LBM, 4 Place Jussieu, 75005, Paris Cedex 05, France.
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29
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Pandey A, Shin K, Patterson RE, Liu XQ, Rainey JK. Current strategies for protein production and purification enabling membrane protein structural biology. Biochem Cell Biol 2016; 94:507-527. [PMID: 27010607 PMCID: PMC5752365 DOI: 10.1139/bcb-2015-0143] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).
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Affiliation(s)
- Aditya Pandey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyungsoo Shin
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Robin E. Patterson
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Xiang-Qin Liu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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Hisao GS, Harland MA, Brown RA, Berthold DA, Wilson TE, Rienstra CM. An efficient method and device for transfer of semisolid materials into solid-state NMR spectroscopy rotors. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 265:172-6. [PMID: 26905816 PMCID: PMC4818695 DOI: 10.1016/j.jmr.2016.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 01/17/2016] [Indexed: 05/23/2023]
Abstract
The study of mass-limited biological samples by magic angle spinning (MAS) solid-state NMR spectroscopy critically relies upon the high-yield transfer of material from a biological preparation into the MAS rotor. This issue is particularly important for maintaining biological activity and hydration of semi-solid samples such as membrane proteins in lipid bilayers, pharmaceutical formulations, microcrystalline proteins and protein fibrils. Here we present protocols and designs for rotor-packing devices specifically suited for packing hydrated samples into Pencil-style 1.6 mm, 3.2 mm standard, and 3.2 mm limited speed MAS rotors. The devices are modular and therefore readily adaptable to other rotor and/or ultracentrifugation tube geometries.
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Affiliation(s)
- Grant S Hisao
- University of Illinois at Urbana-Champaign, Department of Chemistry, 600 South Mathews Avenue, Urbana, IL 61801, USA.
| | - Michael A Harland
- University of Illinois at Urbana-Champaign, School of Chemical Sciences Machine Shop, 505 South Matthews Ave., Urbana, IL 61801, USA.
| | - Robert A Brown
- University of Illinois at Urbana-Champaign, School of Chemical Sciences Machine Shop, 505 South Matthews Ave., Urbana, IL 61801, USA
| | - Deborah A Berthold
- University of Illinois at Urbana-Champaign, Department of Chemistry, 600 South Mathews Avenue, Urbana, IL 61801, USA.
| | - Thomas E Wilson
- University of Illinois at Urbana-Champaign, School of Chemical Sciences Machine Shop, 505 South Matthews Ave., Urbana, IL 61801, USA.
| | - Chad M Rienstra
- University of Illinois at Urbana-Champaign, Department of Chemistry, 600 South Mathews Avenue, Urbana, IL 61801, USA; University of Illinois at Urbana-Champaign, Department of Biochemistry, Center for Biophysics and Quantitative Biology, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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31
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Accurate Determination of Conformational Transitions in Oligomeric Membrane Proteins. Sci Rep 2016; 6:23063. [PMID: 26975211 PMCID: PMC4791661 DOI: 10.1038/srep23063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/25/2016] [Indexed: 12/27/2022] Open
Abstract
The structural dynamics governing collective motions in oligomeric membrane proteins play key roles in vital biomolecular processes at cellular membranes. In this study, we present a structural refinement approach that combines solid-state NMR experiments and molecular simulations to accurately describe concerted conformational transitions identifying the overall structural, dynamical, and topological states of oligomeric membrane proteins. The accuracy of the structural ensembles generated with this method is shown to reach the statistical error limit, and is further demonstrated by correctly reproducing orthogonal NMR data. We demonstrate the accuracy of this approach by characterising the pentameric state of phospholamban, a key player in the regulation of calcium uptake in the sarcoplasmic reticulum, and by probing its dynamical activation upon phosphorylation. Our results underline the importance of using an ensemble approach to characterise the conformational transitions that are often responsible for the biological function of oligomeric membrane protein states.
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32
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Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2390-2400. [PMID: 26946244 DOI: 10.1016/j.bbamem.2016.02.037] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/25/2016] [Accepted: 02/28/2016] [Indexed: 11/22/2022]
Abstract
Lipid molecules are able to selectively interact with specific sites on integral membrane proteins, and modulate their structure and function. Identification and characterization of these sites are of importance for our understanding of the molecular basis of membrane protein function and stability, and may facilitate the design of lipid-like drug molecules. Molecular dynamics simulations provide a powerful tool for the identification of these sites, complementing advances in membrane protein structural biology and biophysics. We describe recent notable biomolecular simulation studies which have identified lipid interaction sites on a range of different membrane proteins. The sites identified in these simulation studies agree well with those identified by complementary experimental techniques. This demonstrates the power of the molecular dynamics approach in the prediction and characterization of lipid interaction sites on integral membrane proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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33
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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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34
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Leftin A, Molugu TR, Job C, Beyer K, Brown MF. Area per lipid and cholesterol interactions in membranes from separated local-field (13)C NMR spectroscopy. Biophys J 2015; 107:2274-86. [PMID: 25418296 DOI: 10.1016/j.bpj.2014.07.044] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 06/24/2014] [Accepted: 07/15/2014] [Indexed: 10/24/2022] Open
Abstract
Investigations of lipid membranes using NMR spectroscopy generally require isotopic labeling, often precluding structural studies of complex lipid systems. Solid-state (13)C magic-angle spinning NMR spectroscopy at natural isotopic abundance gives site-specific structural information that can aid in the characterization of complex biomembranes. Using the separated local-field experiment DROSS, we resolved (13)C-(1)H residual dipolar couplings that were interpreted with a statistical mean-torque model. Liquid-disordered and liquid-ordered phases were characterized according to membrane thickness and average cross-sectional area per lipid. Knowledge of such structural parameters is vital for molecular dynamics simulations, and provides information about the balance of forces in membrane lipid bilayers. Experiments were conducted with both phosphatidylcholine (dimyristoylphosphatidylcholine (DMPC) and palmitoyloleoylphosphatidylcholine (POPC)) and egg-yolk sphingomyelin (EYSM) lipids, and allowed us to extract segmental order parameters from the (13)C-(1)H residual dipolar couplings. Order parameters were used to calculate membrane structural quantities, including the area per lipid and bilayer thickness. Relative to POPC, EYSM is more ordered in the ld phase and experiences less structural perturbation upon adding 50% cholesterol to form the lo phase. The loss of configurational entropy is smaller for EYSM than for POPC, thus favoring its interaction with cholesterol in raftlike lipid systems. Our studies show that solid-state (13)C NMR spectroscopy is applicable to investigations of complex lipids and makes it possible to obtain structural parameters for biomembrane systems where isotope labeling may be prohibitive.
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Affiliation(s)
- Avigdor Leftin
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Trivikram R Molugu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Constantin Job
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Klaus Beyer
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona; Department of Physics, University of Arizona, Tucson, Arizona.
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35
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Nomura T, Cox CD, Bavi N, Sokabe M, Martinac B. Unidirectional incorporation of a bacterial mechanosensitive channel into liposomal membranes. FASEB J 2015; 29:4334-45. [PMID: 26116700 DOI: 10.1096/fj.15-275198] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/22/2015] [Indexed: 11/11/2022]
Abstract
The bacterial mechanosensitive channel of small conductance (MscS) plays a crucial role in the protection of bacterial cells against hypo-osmotic shock. The functional characteristics of MscS have been extensively studied using liposomal reconstitution. This is a widely used experimental paradigm and is particularly important for mechanosensitive channels as channel activity can be probed free from cytoskeletal influence. A perpetual issue encountered using this paradigm is unknown channel orientation. Here we examine the orientation of MscS in liposomes formed using 2 ion channel reconstitution methods employing the powerful combination of patch clamp electrophysiology, confocal microscopy, and continuum mechanics simulation. Using the previously determined electrophysiological and pharmacological properties of MscS, we were able to determine that in liposomes, independent of lipid composition, MscS adopts the same orientation seen in native membranes. These results strongly support the idea that these specific methods result in uniform incorporation of membrane ion channels and caution against making assumptions about mechanosensitive channel orientation using the stimulus type alone.
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Affiliation(s)
- Takeshi Nomura
- *Molecular Cardiology and Biophysics Division/Mechanosensory Biophysics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia; Department of Physical Therapy, Faculty of Rehabilitation, Graduate School of Health Sciences, Kyushu Nutrition Welfare University, Kitakyushu, Japan; St. Vincent's Clinical School, The University of New South Wales, Sydney, New South Wales, Australia; and Mechanobiology Laboratory, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Charles D Cox
- *Molecular Cardiology and Biophysics Division/Mechanosensory Biophysics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia; Department of Physical Therapy, Faculty of Rehabilitation, Graduate School of Health Sciences, Kyushu Nutrition Welfare University, Kitakyushu, Japan; St. Vincent's Clinical School, The University of New South Wales, Sydney, New South Wales, Australia; and Mechanobiology Laboratory, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Navid Bavi
- *Molecular Cardiology and Biophysics Division/Mechanosensory Biophysics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia; Department of Physical Therapy, Faculty of Rehabilitation, Graduate School of Health Sciences, Kyushu Nutrition Welfare University, Kitakyushu, Japan; St. Vincent's Clinical School, The University of New South Wales, Sydney, New South Wales, Australia; and Mechanobiology Laboratory, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Sokabe
- *Molecular Cardiology and Biophysics Division/Mechanosensory Biophysics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia; Department of Physical Therapy, Faculty of Rehabilitation, Graduate School of Health Sciences, Kyushu Nutrition Welfare University, Kitakyushu, Japan; St. Vincent's Clinical School, The University of New South Wales, Sydney, New South Wales, Australia; and Mechanobiology Laboratory, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Boris Martinac
- *Molecular Cardiology and Biophysics Division/Mechanosensory Biophysics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia; Department of Physical Therapy, Faculty of Rehabilitation, Graduate School of Health Sciences, Kyushu Nutrition Welfare University, Kitakyushu, Japan; St. Vincent's Clinical School, The University of New South Wales, Sydney, New South Wales, Australia; and Mechanobiology Laboratory, Nagoya University Graduate School of Medicine, Nagoya, Japan
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36
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Gopinath T, Mote KR, Veglia G. Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples. JOURNAL OF BIOMOLECULAR NMR 2015; 62:53-61. [PMID: 25749871 PMCID: PMC4981477 DOI: 10.1007/s10858-015-9916-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/03/2015] [Indexed: 05/20/2023]
Abstract
We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments.
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Affiliation(s)
| | | | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
- Department of Chemistry and University of Minnesota, Minneapolis, MN 55455
- Corresponding Author. Gianluigi Veglia, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, Phone: (612) 625-0758, Fax: (612) 625-2163,
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37
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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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38
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De Simone A, Mote KR, Veglia G. Structural dynamics and conformational equilibria of SERCA regulatory proteins in membranes by solid-state NMR restrained simulations. Biophys J 2015; 106:2566-76. [PMID: 24940774 DOI: 10.1016/j.bpj.2014.03.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 03/14/2014] [Accepted: 03/19/2014] [Indexed: 01/08/2023] Open
Abstract
Solid-state NMR spectroscopy is emerging as a powerful approach to determine structure, topology, and conformational dynamics of membrane proteins at the atomic level. Conformational dynamics are often inferred and quantified from the motional averaging of the NMR parameters. However, the nature of these motions is difficult to envision based only on spectroscopic data. Here, we utilized restrained molecular dynamics simulations to probe the structural dynamics, topology and conformational transitions of regulatory membrane proteins of the calcium ATPase SERCA, namely sarcolipin and phospholamban, in explicit lipid bilayers. Specifically, we employed oriented solid-state NMR data, such as dipolar couplings and chemical shift anisotropy measured in lipid bicelles, to refine the conformational ensemble of these proteins in lipid membranes. The samplings accurately reproduced the orientations of transmembrane helices and showed a significant degree of convergence with all of the NMR parameters. Unlike the unrestrained simulations, the resulting sarcolipin structures are in agreement with distances and angles for hydrogen bonds in ideal helices. In the case of phospholamban, the restrained ensemble sampled the conformational interconversion between T (helical) and R (unfolded) states for the cytoplasmic region that could not be observed using standard structural refinements with the same experimental data set. This study underscores the importance of implementing NMR data in molecular dynamics protocols to better describe the conformational landscapes of membrane proteins embedded in realistic lipid membranes.
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Affiliation(s)
- Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Kaustubh R Mote
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota; Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota.
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39
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Yamamoto K, Pearcy P, Lee DK, Yu C, Im SC, Waskell L, Ramamoorthy A. Temperature-resistant bicelles for structural studies by solid-state NMR spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:1496-1504. [PMID: 25565453 DOI: 10.1021/la5043876] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Three-dimensional structure determination of membrane proteins is important to fully understand their biological functions. However, obtaining a high-resolution structure has been a major challenge mainly due to the difficulties in retaining the native folding and function of membrane proteins outside of the cellular membrane environment. These challenges are acute if the protein contains a large soluble domain, as it needs bulk water unlike the transmembrane domains of an integral membrane protein. For structural studies on such proteins either by nuclear magnetic resonance (NMR) spectroscopy or X-ray crystallography, bicelles have been demonstrated to be superior to conventional micelles, yet their temperature restrictions attributed to their thermal instabilities are a major disadvantage. Here, we report an approach to overcome this drawback through searching for an optimum combination of bicellar compositions. We demonstrate that bicelles composed of 1,2-didecanoyl-sn-glycero-3-phosphocholine (DDPC) and 1,2-diheptanoyl-sn-glycero-3-phosphocholin (DHepPC), without utilizing additional stabilizing chemicals, are quite stable and are resistant to temperature variations. These temperature-resistant bicelles have a robust bicellar phase and magnetic alignment over a broad range of temperatures, between -15 and 80 °C, retain the native structure of a membrane protein, and increase the sensitivity of solid-state NMR experiments performed at low temperatures. Advantages of two-dimensional separated-local field (SLF) solid-state NMR experiments at a low temperature are demonstrated on magnetically aligned bicelles containing an electron carrier membrane protein, cytochrome b5. Morphological information on different DDPC-based bicellar compositions, varying q ratio/size, and hydration levels obtained from (31)P NMR experiments in this study is also beneficial for a variety of biophysical and spectroscopic techniques, including solution NMR and magic-angle-spinning (MAS) NMR for a wide range of temperatures.
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Affiliation(s)
- Kazutoshi Yamamoto
- Department of Chemistry and Biophysics, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109-1055, United States
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Abstract
In this chapter we describe the use of solid state nuclear magnetic spectroscopy to study the structure of lyotropic phases and lipid model membranes and show its ability to probe, site specifically, at a sub-Ångstrom resolution. Here, we demonstrate the immense versatility of the technique and its ability to provide information on the different liquid crystalline phases present. A multinuclear for example (31)P, (1)H, and (13)C approach is able to elucidate both the structure and dynamics over a wide variety of timescales. This coupled with a non-perturbing label (2)H is able to provide information such as the order parameters for a wide variety of different liquid phases.
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Affiliation(s)
- Arwen I I Tyler
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK,
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41
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Judge PJ, Taylor GF, Dannatt HRW, Watts A. Solid-state nuclear magnetic resonance spectroscopy for membrane protein structure determination. Methods Mol Biol 2015; 1261:331-47. [PMID: 25502207 DOI: 10.1007/978-1-4939-2230-7_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR (ssNMR) is a versatile technique that can provide high-resolution (sub-angstrom) structural data for integral membrane proteins embedded in native and model membrane environments. The methodologies for a priori structure determination have for the most part been developed using samples with crystalline and fibrous morphologies. However, the techniques are now being applied to large, polytopic membrane proteins including receptors, ion channels, and porins. ssNMR data may be used to annotate and refine existing structures in regions of the protein not fully resolved by crystallography (including ligand-binding sites and mobile solvent accessible loop regions). This review describes the spectroscopic experiments and data analysis methods (including assignment) used to generate high-resolution structural data for membrane proteins. We also consider the range of sample morphologies that are appropriate for study by this method.
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Affiliation(s)
- Peter J Judge
- Biomembrane Structure Unit, Biochemistry Department, South Parks Road, Oxford, OX1 3QU, UK
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42
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Structure of CrgA, a cell division structural and regulatory protein from Mycobacterium tuberculosis, in lipid bilayers. Proc Natl Acad Sci U S A 2014; 112:E119-26. [PMID: 25548160 DOI: 10.1073/pnas.1415908112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The 93-residue transmembrane protein CrgA in Mycobacterium tuberculosis is a central component of the divisome, a large macromolecular machine responsible for cell division. Through interactions with multiple other components including FtsZ, FtsQ, FtsI (PBPB), PBPA, and CwsA, CrgA facilitates the recruitment of the proteins essential for peptidoglycan synthesis to the divisome and stabilizes the divisome. CrgA is predicted to have two transmembrane helices. Here, the structure of CrgA was determined in a liquid-crystalline lipid bilayer environment by solid-state NMR spectroscopy. Oriented-sample data yielded orientational restraints, whereas magic-angle spinning data yielded interhelical distance restraints. These data define a complete structure for the transmembrane domain and provide rich information on the conformational ensembles of the partially disordered N-terminal region and interhelical loop. The structure of the transmembrane domain was refined using restrained molecular dynamics simulations in an all-atom representation of the same lipid bilayer environment as in the NMR samples. The two transmembrane helices form a left-handed packing arrangement with a crossing angle of 24° at the conserved Gly39 residue. This helix pair exposes other conserved glycine and alanine residues to the fatty acyl environment, which are potential sites for binding CrgA's partners such as CwsA and FtsQ. This approach combining oriented-sample and magic-angle spinning NMR spectroscopy in native-like lipid bilayers with restrained molecular dynamics simulations represents a powerful tool for structural characterization of not only isolated membrane proteins, but their complexes, such as those that form macromolecular machines.
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43
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Murray DT, Li C, Gao FP, Qin H, Cross TA. Membrane protein structural validation by oriented sample solid-state NMR: diacylglycerol kinase. Biophys J 2014; 106:1559-69. [PMID: 24739155 DOI: 10.1016/j.bpj.2014.02.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/29/2014] [Accepted: 02/12/2014] [Indexed: 12/28/2022] Open
Abstract
The validation of protein structures through functional assays has been the norm for many years. Functional assays perform this validation for water-soluble proteins very well, but they need to be performed in the same environment as that used for the structural analysis. This is difficult for membrane proteins that are often structurally characterized in detergent environments, although functional assays for these proteins are most frequently performed in lipid bilayers. Because the structure of membrane proteins is known to be sensitive to the membrane mimetic environment, such functional assays are appropriate for validating the protein construct, but not the membrane protein structure. Here, we compare oriented sample solid-state NMR spectral data of diacylglycerol kinase previously published with predictions of such data from recent structures of this protein. A solution NMR structure of diacylglycerol kinase has been obtained in detergent micelles and three crystal structures have been obtained in a monoolein cubic phase. All of the structures are trimeric with each monomer having three transmembrane and one amphipathic helices. However, the solution NMR structure shows typical perturbations induced by a micelle environment that is reflected in the predicted solid-state NMR resonances from the structural coordinates. The crystal structures show few such perturbations, especially for the wild-type structure and especially for the monomers that do not have significant crystal contacts. For these monomers the predicted and observed data are nearly identical. The thermostabilized constructs do show more perturbations, especially the A41C mutation that introduces a hydrophilic residue into what would be the middle of the lipid bilayer inducing additional hydrogen bonding between trimers. These results demonstrate a general technique for validating membrane protein structures with minimal data obtained from membrane proteins in liquid crystalline lipid bilayers by oriented sample solid-state NMR.
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Affiliation(s)
- Dylan T Murray
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Molecular and Atomic Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, PR China
| | - F Philip Gao
- Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas
| | - Huajun Qin
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida
| | - Timothy A Cross
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida.
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Influence of the lipid membrane environment on structure and activity of the outer membrane protein Ail from Yersinia pestis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:712-20. [PMID: 25433311 DOI: 10.1016/j.bbamem.2014.11.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 10/24/2014] [Accepted: 11/19/2014] [Indexed: 11/20/2022]
Abstract
The surrounding environment has significant consequences for the structural and functional properties of membrane proteins. While native structure and function can be reconstituted in lipid bilayer membranes, the detergents used for protein solubilization are not always compatible with biological activity and, hence, not always appropriate for direct detection of ligand binding by NMR spectroscopy. Here we describe how the sample environment affects the activity of the outer membrane protein Ail (attachment invasion locus) from Yersinia pestis. Although Ail adopts the correct β-barrel fold in micelles, the high detergent concentrations required for NMR structural studies are not compatible with the ligand binding functionality of the protein. We also describe preparations of Ail embedded in phospholipid bilayer nanodiscs, optimized for NMR studies and ligand binding activity assays. Ail in nanodiscs is capable of binding its human ligand fibronectin and also yields high quality NMR spectra that reflect the proper fold. Binding activity assays, developed to be performed directly with the NMR samples, show that ligand binding involves the extracellular loops of Ail. The data show that even when detergent micelles support the protein fold, detergents can interfere with activity in subtle ways.
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45
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Wang S, Ladizhansky V. Recent advances in magic angle spinning solid state NMR of membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 82:1-26. [PMID: 25444696 DOI: 10.1016/j.pnmrs.2014.07.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 07/16/2014] [Accepted: 07/20/2014] [Indexed: 05/14/2023]
Abstract
Membrane proteins mediate many critical functions in cells. Determining their three-dimensional structures in the native lipid environment has been one of the main objectives in structural biology. There are two major NMR methodologies that allow this objective to be accomplished. Oriented sample NMR, which can be applied to membrane proteins that are uniformly aligned in the magnetic field, has been successful in determining the backbone structures of a handful of membrane proteins. Owing to methodological and technological developments, Magic Angle Spinning (MAS) solid-state NMR (ssNMR) spectroscopy has emerged as another major technique for the complete characterization of the structure and dynamics of membrane proteins. First developed on peptides and small microcrystalline proteins, MAS ssNMR has recently been successfully applied to large membrane proteins. In this review we describe recent progress in MAS ssNMR methodologies, which are now available for studies of membrane protein structure determination, and outline a few examples, which highlight the broad capability of ssNMR spectroscopy.
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Affiliation(s)
- Shenlin Wang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada; Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
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46
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Stoilova-McPhie S, Grushin K, Dalm D, Miller J. Lipid nanotechnologies for structural studies of membrane-associated proteins. Proteins 2014; 82:2902-9. [PMID: 24957666 PMCID: PMC5292012 DOI: 10.1002/prot.24631] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 06/04/2014] [Accepted: 06/08/2014] [Indexed: 11/09/2022]
Abstract
We present a methodology of lipid nanotubes (LNT) and nanodisks technologies optimized in our laboratory for structural studies of membrane-associated proteins at close to physiological conditions. The application of these lipid nanotechnologies for structure determination by cryo-electron microscopy (cryo-EM) is fundamental for understanding and modulating their function. The LNTs in our studies are single bilayer galactosylceramide based nanotubes of ∼20 nm inner diameter and a few microns in length, that self-assemble in aqueous solutions. The lipid nanodisks (NDs) are self-assembled discoid lipid bilayers of ∼10 nm diameter, which are stabilized in aqueous solutions by a belt of amphipathic helical scaffold proteins. By combining LNT and ND technologies, we can examine structurally how the membrane curvature and lipid composition modulates the function of the membrane-associated proteins. As proof of principle, we have engineered these lipid nanotechnologies to mimic the activated platelet's phosphtaidylserine rich membrane and have successfully assembled functional membrane-bound coagulation factor VIII in vitro for structure determination by cryo-EM. The macromolecular organization of the proteins bound to ND and LNT are further defined by fitting the known atomic structures within the calculated three-dimensional maps. The combination of LNT and ND technologies offers a means to control the design and assembly of a wide range of functional membrane-associated proteins and complexes for structural studies by cryo-EM. The presented results confirm the suitability of the developed methodology for studying the functional structure of membrane-associated proteins, such as the coagulation factors, at a close to physiological environment.
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Affiliation(s)
- Svetla Stoilova-McPhie
- Department of Neuroscience and Cell Biology, The University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555
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47
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Kunert B, Gardiennet C, Lacabanne D, Calles-Garcia D, Falson P, Jault JM, Meier BH, Penin F, Böckmann A. Efficient and stable reconstitution of the ABC transporter BmrA for solid-state NMR studies. Front Mol Biosci 2014; 1:5. [PMID: 25988146 PMCID: PMC4428385 DOI: 10.3389/fmolb.2014.00005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/26/2014] [Indexed: 01/20/2023] Open
Abstract
We present solid-state NMR sample preparation and first 2D spectra of the Bacillus subtilis ATP-binding cassette (ABC) transporter BmrA, a membrane protein involved in multidrug resistance. The homodimeric 130-kDa protein is a challenge for structural characterization due to its membrane-bound nature, size, inherent flexibility and insolubility. We show that reconstitution of this protein in lipids from Bacillus subtilis at a lipid-protein ratio of 0.5 w/w allows for optimal protein insertion in lipid membranes with respect to two central NMR requirements, high signal-to-noise in the spectra and sample stability over a time period of months. The obtained spectra point to a well-folded protein and a highly homogenous preparation, as witnessed by the narrow resonance lines and the signal dispersion typical for the expected secondary structure distribution of BmrA. This opens the way for studies of the different conformational states of the transporter in the export cycle, as well as on interactions with substrates, via chemical-shift fingerprints and sequential resonance assignments.
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Affiliation(s)
- Britta Kunert
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Carole Gardiennet
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Denis Lacabanne
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Daniel Calles-Garcia
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Pierre Falson
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Jean-Michel Jault
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | | | - François Penin
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Anja Böckmann
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
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48
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Murray D, Griffin J, Cross TA. Detergent optimized membrane protein reconstitution in liposomes for solid state NMR. Biochemistry 2014; 53:2454-63. [PMID: 24665863 PMCID: PMC4004220 DOI: 10.1021/bi500144h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 03/24/2014] [Indexed: 12/18/2022]
Abstract
For small helical membrane proteins, their structures are highly sensitive to their environment, and solid state NMR is a structural technique that can characterize these membrane proteins in native-like lipid bilayers and proteoliposomes. To date, a systematic method by which to evaluate the effect of the solubilizing detergent on proteoliposome preparations for solid state NMR of membrane proteins has not been presented in the literature. A set of experiments are presented aimed at determining the conditions most amenable to dialysis mediated reconstitution sample preparation. A membrane protein from M. tuberculosis is used to illustrate the method. The results show that a detergent that stabilizes the most protein is not always ideal and sometimes cannot be removed by dialysis. By focusing on the lipid and protein binding properties of the detergent, proteoliposome preparations can be readily produced, which provide double the signal-to-noise ratios for both the oriented sample and magic angle spinning solid state NMR. The method will allow more membrane protein drug targets to be structurally characterized in lipid bilayer environments.
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Affiliation(s)
- Dylan
T. Murray
- Institute
for Molecular Biophysics, Florida State
University, 91 Chieftan
Way, Tallahassee, Florida 32306, United States
- The
National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - James Griffin
- The
National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
- Department
of Chemistry and Biochemistry, Florida State
University, 95 Chieftan
Way, Tallahassee, Florida 32306, United States
| | - Timothy A. Cross
- Institute
for Molecular Biophysics, Florida State
University, 91 Chieftan
Way, Tallahassee, Florida 32306, United States
- The
National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
- Department
of Chemistry and Biochemistry, Florida State
University, 95 Chieftan
Way, Tallahassee, Florida 32306, United States
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49
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Murray DT, Hung I, Cross TA. Assignment of oriented sample NMR resonances from a three transmembrane helix protein. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 240:34-44. [PMID: 24509383 PMCID: PMC3980497 DOI: 10.1016/j.jmr.2013.12.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/21/2013] [Accepted: 12/28/2013] [Indexed: 06/03/2023]
Abstract
Oriented sample solid state NMR techniques have been routinely employed to determine the structures of membrane proteins with one or two transmembrane helices. For larger proteins the technique has been limited by spectral resolution and lack of assignment strategies. Here, a strategy for resonance assignment is devised and applied to a three transmembrane helix protein. Sequence specific assignments for all labeled transmembrane amino acid sites are obtained, which provide a set of orientational restraints and helix orientations in the bilayer. Our experiments expand the utility of solid state NMR in membrane protein structure characterization to three transmembrane helix proteins and represent a straightforward strategy for routinely characterizing multiple transmembrane helix protein structures.
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Affiliation(s)
- D T Murray
- Institute for Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - I Hung
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - T A Cross
- Institute for Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
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50
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Cross TA, Ekanayake V, Paulino J, Wright A. Solid state NMR: The essential technology for helical membrane protein structural characterization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 239:100-9. [PMID: 24412099 PMCID: PMC3957465 DOI: 10.1016/j.jmr.2013.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 05/21/2023]
Abstract
NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.
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Affiliation(s)
- Timothy A Cross
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
| | - Vindana Ekanayake
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Joana Paulino
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Anna Wright
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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