1
|
Söldner B, Grohe K, Neidig P, Auch J, Blach S, Klein A, Vasa SK, Schäfer LV, Linser R. Integrated Assessment of the Structure and Dynamics of Solid Proteins. J Phys Chem Lett 2023; 14:1725-1731. [PMID: 36757335 DOI: 10.1021/acs.jpclett.2c03398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Understanding macromolecular function, interactions, and stability hinges on detailed assessment of conformational ensembles. For solid proteins, accurate elucidation of the spatial aspects of dynamics at physiological temperatures is limited by the qualitative character or low abundance of solid-state nuclear magnetic resonance internuclear distance information. Here, we demonstrate access to abundant proton-proton internuclear distances for integrated structural biology and chemistry with unprecedented accuracy. Apart from highest-resolution single-state structures, the exact distances enable molecular dynamics (MD) ensemble simulations orchestrated by a dense network of experimental interproton distance boundaries gathered in the context of their physical lattices. This direct embedding of experimental ensemble distances into MD will provide access to representative, atomic-level spatial details of conformational dynamics in supramolecular assemblies, crystalline and lipid-embedded proteins, and beyond.
Collapse
Affiliation(s)
- Benedikt Söldner
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Kristof Grohe
- Bruker BioSpin GmbH, Rudolf-Plank-Straße 23, 76275 Ettlingen, Germany
| | - Peter Neidig
- Bruker BioSpin GmbH, Rudolf-Plank-Straße 23, 76275 Ettlingen, Germany
| | - Jelena Auch
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Sebastian Blach
- Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Alexander Klein
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| |
Collapse
|
2
|
Reddy UV, Weber DK, Wang S, Larsen EK, Gopinath T, De Simone A, Robia S, Veglia G. A kink in DWORF helical structure controls the activation of the sarcoplasmic reticulum Ca 2+-ATPase. Structure 2022; 30:360-370.e6. [PMID: 34875216 PMCID: PMC8897251 DOI: 10.1016/j.str.2021.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/14/2021] [Accepted: 11/11/2021] [Indexed: 12/31/2022]
Abstract
SERCA is a P-type ATPase embedded in the sarcoplasmic reticulum and plays a central role in muscle relaxation. SERCA's function is regulated by single-pass membrane proteins called regulins. Unlike other regulins, dwarf open reading frame (DWORF) expressed in cardiac muscle has a unique activating effect. Here, we determine the structure and topology of DWORF in lipid bilayers using a combination of oriented sample solid-state NMR spectroscopy and replica-averaged orientationally restrained molecular dynamics. We found that DWORF's structural topology consists of a dynamic N-terminal domain, an amphipathic juxtamembrane helix that crosses the lipid groups at an angle of 64°, and a transmembrane C-terminal helix with an angle of 32°. A kink induced by Pro15, unique to DWORF, separates the two helical domains. A single Pro15Ala mutant significantly decreases the kink and eliminates DWORF's activating effect on SERCA. Overall, our findings directly link DWORF's structural topology to its activating effect on SERCA.
Collapse
Affiliation(s)
- U. Venkateswara Reddy
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel K. Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Erik K. Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tata Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK,Department of Pharmacy, University of Naples “Federico II”, Naples, 80131, Italy
| | - Seth Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN 55455, USA; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
3
|
Wang S, Gopinath T, Larsen EK, Weber DK, Walker C, Uddigiri VR, Mote KR, Sahoo SK, Periasamy M, Veglia G. Structural basis for sarcolipin's regulation of muscle thermogenesis by the sarcoplasmic reticulum Ca 2+-ATPase. SCIENCE ADVANCES 2021; 7:eabi7154. [PMID: 34826239 PMCID: PMC8626070 DOI: 10.1126/sciadv.abi7154] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/06/2021] [Indexed: 06/10/2023]
Abstract
The sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA) plays a central role in muscle contractility and nonshivering thermogenesis. SERCA is regulated by sarcolipin (SLN), a single-pass membrane protein that uncouples Ca2+ transport from ATP hydrolysis, promoting futile enzymatic cycles and heat generation. The molecular determinants for regulating heat release by the SERCA/SLN complex are unclear. Using thermocalorimetry, chemical cross-linking, and solid-state NMR spectroscopy in oriented phospholipid bicelles, we show that SERCA’s functional uncoupling and heat release rate are dictated by specific SERCA/SLN intramembrane interactions, with the carboxyl-terminal residues anchoring SLN to the SR membrane in an inhibitory topology. Systematic deletion of the carboxyl terminus does not prevent the SERCA/SLN complex formation but reduces uncoupling in a graded manner. These studies emphasize the critical role of lipids in defining the active topology of SLN and modulating the heat release rate by the SERCA/SLN complex, with implications in fat metabolism and basal metabolic rate.
Collapse
Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tata Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Erik K. Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel K. Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Venkateswara Reddy Uddigiri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kaustubh R. Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500046, India
| | - Sanjaya K. Sahoo
- Department of Physiology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Muthu Periasamy
- Department of Physiology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Department of Internal Medicine, College of Medicine, University of Central Florida, Orlando, FL 32827, 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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Weber DK, Veglia G. A theoretical assessment of structure determination of multi-span membrane proteins by oriented sample solid-state NMR spectroscopy. Aust J Chem 2020; 73:246-251. [PMID: 33162560 DOI: 10.1071/ch19307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Oriented sample solid state NMR (OS-ssNMR) spectroscopy allows direct determination of the structure and topology of membrane proteins reconstituted into aligned lipid bilayers. While OS-ssNMR theoretically has no upper size limit, its application to multi-span membrane proteins has not been established since most studies have been restricted to single or dual span proteins and peptides. Here, we present a critical assessment of the application of this method to multi-span membrane proteins. We used molecular dynamics simulations to back-calculate [15N-1H] separated local field (SLF) spectra from a G protein-coupled receptor (GPCR) and show that fully resolved spectra can be obtained theoretically for a multi-span membrane protein with currently achievable resonance linewidths.
Collapse
Affiliation(s)
- Daniel K Weber
- 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
| |
Collapse
|
7
|
Aguayo-Ortiz R, Fernández-de Gortari E, Espinoza-Fonseca LM. Conserved Luminal C-Terminal Domain Dynamically Controls Interdomain Communication in Sarcolipin. J Chem Inf Model 2020; 60:3985-3991. [PMID: 32668157 DOI: 10.1021/acs.jcim.0c00418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sarcolipin (SLN) mediates Ca2+ transport and metabolism in muscle by regulating the activity of the Ca2+ pump SERCA. SLN has a conserved luminal C-terminal domain that contributes to its functional divergence among homologous SERCA regulators, but the precise mechanistic role of this domain remains poorly understood. We used all-atom molecular dynamics (MD) simulations of SLN totaling 77.5 μs to show that the N- (NT) and C-terminal (CT) domains function in concert. Analysis of the MD simulations showed that serial deletions of the SLN C-terminus do not affect the stability of the peptide nor induce dissociation of SLN from the membrane but promote a gradual decrease in both the tilt angle of the transmembrane helix and the local thickness of the lipid bilayer. Mutual information analysis showed that the NT and CT domains communicate with each other in SLN and that interdomain communication is partially or completely abolished upon deletion of the conserved segment Tyr29-Tyr31 as well as by serial deletions beyond this domain. Phosphorylation of SLN at residue Thr5 also induces changes in the communication between the CT and NT domains, which thus provides additional evidence for interdomain communication within SLN. We found that interdomain communication is independent of the force field used and lipid composition, which thus demonstrates that communication between the NT and CT domains is an intrinsic functional feature of SLN. We propose the novel hypothesis that the conserved C-terminus is an essential element required for dynamic control of SLN regulatory function.
Collapse
Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Eli Fernández-de Gortari
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
8
|
Salnikov ES, Aussenac F, Abel S, Purea A, Tordo P, Ouari O, Bechinger B. Dynamic Nuclear Polarization / solid-state NMR of membranes. Thermal effects and sample geometry. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 100:70-76. [PMID: 30995597 DOI: 10.1016/j.ssnmr.2019.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Whereas specially designed dinitroxide biradicals, reconstitution protocols, oriented sample geometries and NMR probes have helped to much increase the DNP enhancement factors of membrane samples they still lag considerably behind those obtained from glasses made of protein solutions. Here we show that not only the MAS rotor material but also the distribution of the membrane samples within the NMR rotor have a pronounced effect on the DNP enhancement. These observations are rationalized with the cooling efficiency and the internal properties of the sample, monitored by their T1 relaxation, microwave ON versus OFF signal intensities and DNP effect. The data are suggestive that for membranes the speed of cooling has a pronounced effect on the membrane properties and concomitantly the distribution of biradicals within the sample.
Collapse
Affiliation(s)
| | | | - Sebastian Abel
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | | | - Paul Tordo
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | - Olivier Ouari
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | - Burkhard Bechinger
- Institute of Chemistry, University of Strasbourg / CNRS, UMR7177, 67070, Strasbourg, France.
| |
Collapse
|
9
|
Salnikov ES, Abel S, Karthikeyan G, Karoui H, Aussenac F, Tordo P, Bechinger B, Ouari O. Dynamic Nuclear Polarization/Solid-State NMR Spectroscopy of Membrane Polypeptides: Free-Radical Optimization for Matrix-Free Lipid Bilayer Samples. Chemphyschem 2017; 18:2103-2113. [PMID: 28574169 DOI: 10.1002/cphc.201700389] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/24/2017] [Indexed: 01/07/2023]
Abstract
Dynamic nuclear polarization (DNP) boosts the sensitivity of NMR spectroscopy by orders of magnitude and makes investigations previously out of scope possible. For magic-angle-spinning (MAS) solid-state NMR spectroscopy studies, the samples are typically mixed with biradicals dissolved in a glass-forming solvent and are investigated at cryotemperatures. Herein, we present new biradical polarizing agents developed for matrix-free samples such as supported lipid bilayers, which are systems widely used for the investigation of membrane polypeptides of high biomedical importance. A series of 11 biradicals with different structures, geometries, and physicochemical properties were comprehensively tested for DNP performance in lipid bilayers, some of them developed specifically for DNP investigations of membranes. The membrane-anchored biradicals PyPol-C16, AMUPOL-cholesterol, and bTurea-C16 were found to exhibit improved g-tensor alignment, inter-radical distance, and dispersion. Consequently, these biradicals show the highest signal enhancement factors so far obtained for matrix-free membranes or other matrix-free samples and may potentially shorten NMR acquisition times by three orders of magnitude. Furthermore, the optimal biradical-to-lipid ratio, sample deuteration, and membrane lipid composition were determined under static and MAS conditions. To rationalize biradical performance better, DNP enhancement was measured by using the 13 C and 15 N signals of lipids and a peptide as a function of the biradical concentration, DNP build-up time, resonance line width, quenching effect, microwave power, and MAS frequency.
Collapse
Affiliation(s)
- Evgeniy S Salnikov
- Institut de chimie, UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Sébastien Abel
- Aix Marseille Univ, CNRS, ICR UMR 7273, 13013, Marseille, France
| | | | - Hakim Karoui
- Aix Marseille Univ, CNRS, ICR UMR 7273, 13013, Marseille, France
| | - Fabien Aussenac
- Bruker Biospin, 34, rue de l'industrie, 67166, Wissembourg, France
| | - Paul Tordo
- Aix Marseille Univ, CNRS, ICR UMR 7273, 13013, Marseille, France
| | - Burkhard Bechinger
- Institut de chimie, UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, ICR UMR 7273, 13013, Marseille, France
| |
Collapse
|
10
|
Tzitzoglaki C, Wright A, Freudenberger K, Hoffmann A, Tietjen I, Stylianakis I, Kolarov F, Fedida D, Schmidtke M, Gauglitz G, Cross TA, Kolocouris A. Binding and Proton Blockage by Amantadine Variants of the Influenza M2WT and M2S31N Explained. J Med Chem 2017; 60:1716-1733. [DOI: 10.1021/acs.jmedchem.6b01115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Christina Tzitzoglaki
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| | - Anna Wright
- Institute
of Molecular Biophysics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
| | - Kathrin Freudenberger
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Anja Hoffmann
- Department
of Virology and Antiviral Therapy, Jena University Hospital, Hans Knoell Strasse 2, D-07745 Jena, Germany
| | - Ian Tietjen
- Department
of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ioannis Stylianakis
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| | - Felix Kolarov
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - David Fedida
- Department
of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michaela Schmidtke
- Department
of Virology and Antiviral Therapy, Jena University Hospital, Hans Knoell Strasse 2, D-07745 Jena, Germany
| | - Günter Gauglitz
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Timothy A. Cross
- Institute
of Molecular Biophysics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
- Department
of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Antonios Kolocouris
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| |
Collapse
|
11
|
Structural Ensembles of Membrane-bound α-Synuclein Reveal the Molecular Determinants of Synaptic Vesicle Affinity. Sci Rep 2016; 6:27125. [PMID: 27273030 PMCID: PMC4897633 DOI: 10.1038/srep27125] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/05/2016] [Indexed: 01/05/2023] Open
Abstract
A detailed characterisation of the molecular determinants of membrane binding by α-synuclein (αS), a 140-residue protein whose aggregation is associated with Parkinson's disease, is of fundamental significance to clarify the manner in which the balance between functional and dysfunctional processes are regulated for this protein. Despite its biological relevance, the structural nature of the membrane-bound state αS remains elusive, in part because of the intrinsically dynamic nature of the protein and also because of the difficulties in studying this state in a physiologically relevant environment. In the present study we have used solid-state NMR and restrained MD simulations to refine structure and topology of the N-terminal region of αS bound to the surface of synaptic-like membranes. This region has fundamental importance in the binding mechanism of αS as it acts as to anchor the protein to lipid bilayers. The results enabled the identification of the key elements for the biological properties of αS in its membrane-bound state.
Collapse
|
12
|
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.
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
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.
Collapse
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,
| |
Collapse
|
15
|
Opella SJ. Solid-state NMR and membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:129-37. [PMID: 25681966 PMCID: PMC4372479 DOI: 10.1016/j.jmr.2014.11.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/17/2014] [Accepted: 11/30/2014] [Indexed: 05/15/2023]
Abstract
The native environment for a membrane protein is a phospholipid bilayer. Because the protein is immobilized on NMR timescales by the interactions within a bilayer membrane, solid-state NMR methods are essential to obtain high-resolution spectra. Approaches have been developed for both unoriented and oriented samples, however, they all rest on the foundation of the most fundamental aspects of solid-state NMR, and the chemical shift and homo- and hetero-nuclear dipole-dipole interactions. Solid-state NMR has advanced sufficiently to enable the structures of membrane proteins to be determined under near-native conditions in phospholipid bilayers.
Collapse
Affiliation(s)
- Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
16
|
Romo TD, Grossfield A. How fast is your camera? Timescales for molecular motion and their role in restraining molecular dynamics. Biophys J 2015; 106:2549-51. [PMID: 24940771 DOI: 10.1016/j.bpj.2014.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/02/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022] Open
Affiliation(s)
- Tod D Romo
- Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Alan Grossfield
- Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
| |
Collapse
|