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Schwarze B, Korn A, Höfling C, Zeitschel U, Krueger M, Roßner S, Huster D. Peptide backbone modifications of amyloid β (1-40) impact fibrillation behavior and neuronal toxicity. Sci Rep 2021; 11:23767. [PMID: 34887476 PMCID: PMC8660793 DOI: 10.1038/s41598-021-03091-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022] Open
Abstract
Fibril formation of amyloid β (Aβ) peptides is one of the key molecular events connected to Alzheimer's disease. The pathway of formation and mechanism of action of Aβ aggregates in biological systems is still object of very active research. To this end, systematic modifications of the Phe19-Leu34 hydrophobic contact, which has been reported in almost all structural studies of Aβ40 fibrils, helps understanding Aβ folding pathways and the underlying free energy landscape of the amyloid formation process. In our approach, a series of Aβ40 peptide variants with two types of backbone modifications, namely incorporation of (i) a methylene or an ethylene spacer group and (ii) a N-methylation at the amide functional group, of the amino acids at positions 19 or 34 was applied. These mutations are expected to challenge the inter-β-strand side chain contacts as well as intermolecular backbone β-sheet hydrogen bridges. Using a multitude of biophysical methods, it is shown that these backbone modifications lead, in most of the cases, to alterations in the fibril formation kinetics, a higher local structural heterogeneity, and a somewhat modified fibril morphology without generally impairing the fibril formation capacity of the peptides. The toxicological profile found for the variants depend on the type and extent of the modification.
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Affiliation(s)
- Benedikt Schwarze
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Alexander Korn
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Corinna Höfling
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Ulrike Zeitschel
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Martin Krueger
- Institute of Anatomy, Leipzig University, Liebigstr. 13, 04103, Leipzig, Germany
| | - Steffen Roßner
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany.
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2
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Korn A, Höfling C, Zeitschel U, Krueger M, Roßner S, Huster D. Incorporation of the Nonproteinogenic Amino Acid β-Methylamino-alanine Affects Amyloid β Fibril Properties and Toxicity. ACS Chem Neurosci 2020; 11:1038-1047. [PMID: 32141731 DOI: 10.1021/acschemneuro.9b00660] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The nonproteinogenic amino acid β-methylamino alarelevant example for environmental hazards are nonnine (BMAA) is a neurotoxin and represents a potential risk factor for neurodegenerative diseases. Despite intense research over the last years, the pathological mechanism of BMAA is still unclear. One of the main open questions is whether BMAA can be misincorporated into proteins, especially as a substitute for serine, and whether this has structural and functional consequences for the afflicted proteins leading to early onset neurodegeneration. In this study, we hypothesize that BMAA was indeed incorporated into Aβ40 molecules and study the structural and dynamical consequences of such misincorporation along with the effect such mutated Aβ40 peptides have on neuronal cells. We used the synthetic β-amyloid peptide (Aβ40), a known key player in the development of Alzheimer's disease, to incorporate BMAA substitutions at three different positions in the peptide sequence: Ser8BMAA at the peptide's N-terminus, Phe19BMAA in the hydrophobic core region, and S26BMAA in the flexible turn region of Aβ40 fibrils. We performed a set of biophysical experiments including fluorescence, circular dichroism, solid-state NMR spectroscopy, transmission electron microscopy, and X-ray diffraction to investigate structural and functional aspects of the mutated peptides compared to wildtype Aβ40. All variants showed high structural tolerance to BMAA misincorporation. In contrast, the cellular response and neuronal survival were affected in a mutation site-specific manner. As a consequence, we can state from the physicochemical point of view that, if BMAA was misincorporated into proteins, it could indeed represent a risk factor that could potentially play a role in neurodegeneration. Further research addressing the role of BMAA, especially its protein-associated form, should be performed to obtain a better understanding of neurodegenerative diseases and to develop new therapeutic strategies.
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Affiliation(s)
- Alexander Korn
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Corinna Höfling
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, D-04103 Leipzig, Germany
| | - Ulrike Zeitschel
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, D-04103 Leipzig, Germany
| | - Martin Krueger
- Institute of Anatomy, Leipzig University, Liebigstr 13, D-04103 Leipzig, Germany
| | - Steffen Roßner
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, D-04103 Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, D-04107 Leipzig, Germany
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3
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Matlahov I, van der Wel PCA. Hidden motions and motion-induced invisibility: Dynamics-based spectral editing in solid-state NMR. Methods 2018; 148:123-135. [PMID: 29702226 DOI: 10.1016/j.ymeth.2018.04.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022] Open
Abstract
Solid-state nuclear magnetic resonance (ssNMR) spectroscopy enables the structural characterization of a diverse array of biological assemblies that include amyloid fibrils, non-amyloid aggregates, membrane-associated proteins and viral capsids. Such biological samples feature functionally relevant molecular dynamics, which often affect different parts of the sample in different ways. Solid-state NMR experiments' sensitivity to dynamics represents a double-edged sword. On the one hand, it offers a chance to measure dynamics in great detail. On the other hand, certain types of motion lead to signal loss and experimental inefficiencies that at first glance interfere with the application of ssNMR to overly dynamic proteins. Dynamics-based spectral editing (DYSE) ssNMR methods leverage motion-dependent signal losses to simplify spectra and enable the study of sub-structures with particular motional properties.
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Affiliation(s)
- Irina Matlahov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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4
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Williams JK, Schmidt-Rohr K, Hong M. Aromatic spectral editing techniques for magic-angle-spinning solid-state NMR spectroscopy of uniformly (13)C-labeled proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 72:118-26. [PMID: 26440131 PMCID: PMC4674322 DOI: 10.1016/j.ssnmr.2015.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/08/2015] [Accepted: 09/11/2015] [Indexed: 05/15/2023]
Abstract
The four aromatic amino acids in proteins, namely histidine, phenylalanine, tyrosine, and tryptophan, have strongly overlapping (13)C chemical shift ranges between 100 and 160ppm, and have so far been largely neglected in solid-state NMR determination of protein structures. Yet aromatic residues play important roles in biology through π-π and cation-π interactions. To better resolve and assign aromatic residues' (13)C signals in magic-angle-spinning (MAS) solid-state NMR spectra, we introduce two spectral editing techniques. The first method uses gated (1)H decoupling in a proton-driven spin-diffusion (PDSD) experiment to remove all protonated (13)C signals and retain only non-protonated carbon signals in the aromatic region of the (13)C spectra. The second technique uses chemical shift filters and (1)H-(13)C dipolar dephasing to selectively detect the Cα, Cβ and CO cross peaks of aromatic residues while suppressing the signals of all aliphatic residues. We demonstrate these two techniques on amino acids, a model peptide, and the microcrystalline protein GB1, and show that they significantly simplify the 2D NMR spectra and both reveal and permit the ready assignment of the aromatic residues' signals.
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Affiliation(s)
- Jonathan K Williams
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Klaus Schmidt-Rohr
- Department of Chemistry, Brandeis University, Waltham, MA 02453, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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5
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Huster D, Madhu PK. Simplifying solid-state NMR spectra for biophysical studies on membrane proteins: selective targeting of sites and interactions. Biophys J 2014; 106:2083-4. [PMID: 24853736 PMCID: PMC4052239 DOI: 10.1016/j.bpj.2014.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 12/14/2022] Open
Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany; Tata Institute of Fundamental Research, Department of Chemical Sciences, Colaba, Mumbai, India.
| | - Perunthiruthy K Madhu
- Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany; Tata Institute of Fundamental Research, Department of Chemical Sciences, Colaba, Mumbai, India; Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Narsingi, Hyderabad, India
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6
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Mou Y, Tsai TWT, Chan JCC. Constant time tensor correlation experiments by non-gamma-encoded recoupling pulse sequences. J Chem Phys 2012; 137:164201. [PMID: 23126702 DOI: 10.1063/1.4757957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Constant-time tensor correlation under magic-angle spinning conditions is an important technique in solid-state nuclear magnetic resonance spectroscopy for the measurements of backbone or side-chain torsion angles of polypeptides and proteins. We introduce a general method for the design of constant-time tensor correlation experiments under magic-angle spinning. Our method requires that the amplitude of the average Hamiltonian must depend on all the three Euler angles bringing the principal axis system to the rotor-fixed frame, which is commonly referred to as non-gamma encoding. We abbreviate this novel approach as COrrelation of Non-Gamma-Encoded Experiment (CONGEE), which exploits the orientation-dependence of non-gamma-encoded sequences with respect to the magic-angle rotation axis. By manipulating the relative orientation of the average Hamiltonians created by two non-gamma-encoded sequences, one can obtain a modulation of the detected signal, from which the structural information can be extracted when the tensor orientations relative to the molecular frame are known. CONGEE has a prominent feature that the number of rf pulses and the total pulse sequence duration can be maintained to be constant so that for torsion angle determination the effects of systematic errors owing to the experimental imperfections and/or T(2) effects could be minimized. As a proof of concept, we illustrate the utility of CONGEE in the correlation between the C' chemical shift tensor and the C(α)-H(α) dipolar tensor for the backbone psi angle determination. In addition to a detailed theoretical analysis, numerical simulations and experiments measured for [U-(13)C, (15)N]-L-alanine and N-acetyl-[U-(13)C, (15)N]-D,L-valine are used to validate our approach at a spinning frequency of 20 kHz.
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Affiliation(s)
- Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, Taiwan
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7
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Scheidt HA, Sickert A, Meier T, Castellucci N, Tomasini C, Huster D. The interaction of lipid modified pseudopeptides with lipid membranes. Org Biomol Chem 2011; 9:6998-7006. [DOI: 10.1039/c1ob05652b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Zhang Y, Doherty T, Li J, Lu W, Barinka C, Lubkowski J, Hong M. Resonance assignment and three-dimensional structure determination of a human alpha-defensin, HNP-1, by solid-state NMR. J Mol Biol 2010; 397:408-22. [PMID: 20097206 DOI: 10.1016/j.jmb.2010.01.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 12/28/2009] [Accepted: 01/14/2010] [Indexed: 11/26/2022]
Abstract
Human alpha-defensins [human neutrophil peptides (HNPs)] are immune defense mini-proteins that act by disrupting microbial cell membranes. Elucidating the three-dimensional (3D) structures of HNPs in lipid membranes is important for understanding their mechanisms of action. Using solid-state NMR (SSNMR), we have determined the 3D structure of HNP-1 in a microcrystalline state outside the lipid membrane, which provides benchmarks for structure determination and comparison with the membrane-bound state. From a suite of two-dimensional and 3D magic-angle spinning experiments, (13)C and (15)N chemical shifts that yielded torsion angle constraints were obtained, while inter-residue distances were obtained to restrain the 3D fold. Together, these constraints led to the first high-resolution SSNMR structure of a human defensin. The SSNMR structure has close similarity to the crystal structures of the HNP family, with the exception of the loop region between the first and second beta-strands. The difference, which is partially validated by direct torsion angle measurements of selected loop residues, suggests possible conformational variation and flexibility of this segment of the protein, which may regulate HNP interaction with the phospholipid membrane of microbial cells.
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Affiliation(s)
- Yuan Zhang
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
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Coelho C, Rocha J, Madhu PK, Mafra L. Practical aspects of Lee-Goldburg based CRAMPS techniques for high-resolution 1H NMR spectroscopy in solids: implementation and applications. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 194:264-282. [PMID: 18703365 DOI: 10.1016/j.jmr.2008.07.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 07/15/2008] [Accepted: 07/18/2008] [Indexed: 05/26/2023]
Abstract
Elucidating the local environment of the hydrogen atoms is an important problem in materials science. Because (1)H spectra in solid-state nuclear magnetic resonance (NMR) suffer from low resolution due to homogeneous broadening, even under magic-angle spinning (MAS), information of chemical interest may only be obtained using certain high-resolution (1)H MAS techniques. (1)H Lee-Goldburg (LG) CRAMPS (Combined Rotation And Multiple-Pulse Spectroscopy) methods are particularly well suited for studying inorganic-organic hybrid materials, rich in (1)H nuclei. However, setting up CRAMPS experiments is time-consuming and not entirely trivial, facts that have discouraged their widespread use by materials scientists. To change this status quo, here we describe and discuss some important aspects of the experimental implementation of CRAMPS techniques based on LG decoupling schemes, such as FSLG (Frequency Switched), and windowed and windowless PMLG (Phase Modulated). In particular, we discuss the influence on the quality of the (1)H NMR spectra of the different parameters at play, for example LG (Lee-Goldburg) pulses, radio-frequency (rf) phase, frequency switching, and pulse imperfections, using glycine and adamantane as model compounds. The efficiency and robustness of the different LG-decoupling schemes is then illustrated on the following materials: organo-phosphorus ligand, N-(phosphonomethyl)iminodiacetic acid [H(4)pmida] [I], and inorganic-organic hybrid materials (C(4)H(12)N(2))[Ge(2)(pmida)(2)OH(2)] x 4H(2)O [II] and (C(2)H(5)NH(3))[Ti(H(1.5)PO(4))(PO(4))](2) x H(2)O [III].
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Affiliation(s)
- Cristina Coelho
- Department of Chemistry, CICECO, University of Aveiro, Aveiro, Portugal
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10
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Tang M, Waring AJ, Hong M. Arginine dynamics in a membrane-bound cationic beta-hairpin peptide from solid-state NMR. Chembiochem 2008; 9:1487-92. [PMID: 18442147 DOI: 10.1002/cbic.200800005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The site-specific motion of Arg residues in a membrane-bound disulfide-linked antimicrobial peptide, protegrin-1 (PG-1), was investigated by using magic-angle-spinning solid-state NMR spectroscopy to better understand the membrane insertion and lipid interaction of this cationic membrane-disruptive peptide. The C-H and N-H dipolar couplings and 13C chemical shift anisotropies were measured in the anionic POPE/POPG membrane, and were found to be reduced from the rigid-limit values by varying extents; this indicates the presence of segmental motion. An Arg residue at the beta-turn region of the peptide showed much weaker spin interactions, which indicates larger amplitudes of motion than an Arg residue in the beta-strand region of the peptide. This is consistent with the exposure of the beta turn to the membrane surface and the immersion of the beta strand in the hydrophobic middle of the membrane, and supports the previously proposed oligomerization of the peptide into beta barrels in the anionic membrane. The 13C T2 and 1H T(1rho) relaxation times indicate that the beta-turn backbone undergoes large-amplitude intermediate-timescale motion in the fluid phase of the membrane; this causes significant line broadening and loss of spectral intensity. This study illustrates the strong correlation between the dynamics and structure of membrane proteins, and the capability of solid-state NMR spectroscopy to provide detailed information on site-specific dynamics in complex membrane-protein assemblies.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
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11
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Cady SD, Hong M. Amantadine-induced conformational and dynamical changes of the influenza M2 transmembrane proton channel. Proc Natl Acad Sci U S A 2008; 105:1483-8. [PMID: 18230730 PMCID: PMC2234170 DOI: 10.1073/pnas.0711500105] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Indexed: 11/18/2022] Open
Abstract
The M2 protein of influenza A virus forms a transmembrane proton channel important for viral infection and replication. Amantadine blocks this channel, thus inhibiting viral replication. Elucidating the high-resolution structure of the M2 protein and its change upon amantadine binding is crucial for designing antiviral drugs to combat the growing resistance of influenza A viruses against amantadine. We used magic-angle-spinning solid-state NMR to determine the conformation and dynamics of the transmembrane domain of the protein M2TMP in the apo- and amantadine-bound states in lipid bilayers. (13)C chemical shifts and torsion angles of the protein in 1,2-dilauroyl-sn-glycero-3-phosphatidylcholine (DLPC) bilayers indicate that M2TMP is alpha-helical in both states, but the average conformation differs subtly, especially at the G34-I35 linkage and V27 side chain. In the liquid-crystalline membrane, the complexed M2TMP shows dramatically narrower lines than the apo peptide. Analysis of the homogeneous and inhomogeneous line widths indicates that the apo-M2TMP undergoes significant microsecond-time scale motion, and amantadine binding alters the motional rates, causing line-narrowing. Amantadine also reduces the conformational heterogeneity of specific residues, including the G34/I35 pair and several side chains. Finally, amantadine causes the helical segment N-terminal to G34 to increase its tilt angle by 3 degrees , and the G34-I35 torsion angles cause a kink of 5 degrees in the amantadine-bound helix. These data indicate that amantadine affects the M2 proton channel mainly by changing the distribution and exchange rates among multiple low-energy conformations and only subtly alters the average conformation and orientation. Amantadine-resistant mutations thus may arise from binding-incompetent changes in the conformational equilibrium.
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Affiliation(s)
- Sarah D. Cady
- Department of Chemistry, Iowa State University, Ames, IA 50011
| | - Mei Hong
- Department of Chemistry, Iowa State University, Ames, IA 50011
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12
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Doherty T, Waring AJ, Hong M. Dynamic Structure of Disulfide-Removed Linear Analogs of Tachyplesin-I in the Lipid Bilayer from Solid-State NMR. Biochemistry 2007; 47:1105-16. [DOI: 10.1021/bi701390t] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tim Doherty
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, and Department of Medicine, University of California at Los Angeles, Los Angeles, California 90095
| | - Alan J. Waring
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, and Department of Medicine, University of California at Los Angeles, Los Angeles, California 90095
| | - Mei Hong
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, and Department of Medicine, University of California at Los Angeles, Los Angeles, California 90095
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Varga K, Tian L, McDermott AE. Solid-state NMR study and assignments of the KcsA potassium ion channel of S. lividans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1604-13. [PMID: 17974509 DOI: 10.1016/j.bbapap.2007.08.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 08/15/2007] [Accepted: 08/29/2007] [Indexed: 10/22/2022]
Abstract
The extraordinary efficiency and selectivity of potassium channels have made them ideal systems for biophysical and functional studies of ion conduction. We carried out solid-state NMR studies of the selectivity filter region of the protein. Partial site-specific assignments of the NMR signals were obtained based on high field multidimensional solid-state NMR spectra of uniformly (13)C, (15)N enriched KcsA potassium channel from Streptomyces lividans. Both backbone and sidechain atoms were assigned for residues V76-D80 and P83-L90, in and near the selectivity filter region of the protein; this region exhibits good dispersion and useful chemical shift fingerprints. This study will enable structure, dynamic and mechanistic studies of ion conduction by NMR.
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Affiliation(s)
- Krisztina Varga
- Department of Chemistry, Columbia University, 3000 Broadway MC 3113, New York, NY 10027, USA
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14
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Cady SD, Goodman C, Tatko CD, DeGrado WF, Hong M. Determining the orientation of uniaxially rotating membrane proteins using unoriented samples: a 2H, 13C, AND 15N solid-state NMR investigation of the dynamics and orientation of a transmembrane helical bundle. J Am Chem Soc 2007; 129:5719-29. [PMID: 17417850 DOI: 10.1021/ja070305e] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Membrane protein orientation has traditionally been determined by NMR using mechanically or magnetically aligned samples. Here we show a new NMR approach that abolishes the need for preparing macroscopically aligned membranes. When the protein undergoes fast uniaxial rotation around the bilayer normal, the 0 degrees -frequency of the motionally averaged powder spectrum is identical to the frequency of the aligned protein whose alignment axis is along the magnetic field. Thus, one can use unoriented membranes to determine the orientation of the protein relative to the bilayer normal. We demonstrate this approach on the M2 transmembrane peptide (M2TMP) of influenza A virus, which is known to assemble into a proton-conducting tetrameric helical bundle. The fast uniaxial rotational diffusion of the M2TMP helical bundle around the membrane normal is characterized via 2H quadrupolar couplings, C-H and N-H dipolar couplings, 13C chemical shift anisotropies, and 1H T1rho relaxation times. We then show that 15N chemical shift anisotropy and N-H dipolar coupling measured on these powder samples can be analyzed to yield precise tilt angles and rotation angles of the helices. The data show that the tilt angle of the M2TMP helices depends on the membrane thickness to reduce the hydrophobic mismatch. Moreover, the orientation of a longer M2 peptide containing both the transmembrane domain and cytoplasmic residues is similar to the orientation of the transmembrane domain alone, suggesting that the transmembrane domain regulates the orientation of this protein and that structural information obtained from M2TMP may be extrapolated to the longer peptide. This powder-NMR approach for orientation determination is generally applicable and can be extended to larger membrane proteins.
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Affiliation(s)
- Sarah D Cady
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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15
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Hong M. Solid-state NMR studies of the structure, dynamics, and assembly of beta-sheet membrane peptides and alpha-helical membrane proteins with antibiotic activities. Acc Chem Res 2006; 39:176-83. [PMID: 16548506 DOI: 10.1021/ar040037e] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
beta-Sheet antimicrobial peptides and alpha-helical channel-forming colicins are bactericidal molecules that target the lipid membranes of sensitive cells. Understanding the mechanisms of action of these proteins requires knowledge of their three-dimensional structure in the lipid bilayer. Solid-state NMR has been used to determine the conformation, orientation, depth of insertion, oligomerization, mobility, and lipid interaction of these membrane peptides and proteins. We review the NMR methods developed and applied to study the structure and dynamics of these antibiotic membrane proteins. These studies shed light on how these peptides disrupt lipid membranes and provide fundamental insights into the folding of beta-sheet and alpha-helical membrane proteins.
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Affiliation(s)
- Mei Hong
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
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16
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van Beek JD, Meier BH. A DOQSY approach for the elucidation of torsion angle distributions in biopolymers: application to silk. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 178:106-20. [PMID: 16243550 DOI: 10.1016/j.jmr.2005.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 09/04/2005] [Accepted: 09/07/2005] [Indexed: 05/05/2023]
Abstract
Silk from the wild silkworm Samia cynthia ricini with a molecular mass of about 300kDa consists of alternating repeats of nano-crystalline poly-(Ala) and non-crystalline glycine-rich domains. The backbone torsion angles between pairs of these two amino acids is determined by DOQSY solid-state NMR spectroscopy: the alanine-rich domains are predominantly in a beta-sheet conformation, whereas the glycine-rich domains are found to be partially in an extended beta-sheet conformation and partially in an approximately 3(1)-helical conformation. In the cast film from liquid silk significantly different secondary structures were found: the alanine-rich domains are alpha-helical conformation, whereas the results for glycine-labelled sample are explained by a random-coil state. A detailed error analysis of the technique is presented.
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17
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Sinha N, Hong M. X–1H rotational-echo double-resonance NMR for torsion angle determination of peptides. Chem Phys Lett 2003. [DOI: 10.1016/j.cplett.2003.09.088] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Abstract
This chapter discusses recent progress in the investigation and use of (13)C, (15)N, and (19)F nuclear magnetic resonance (NMR) chemical shifts and chemical shift tensors in proteins and model systems primarily using quantum chemical (ab initio Hartree-Fock and density functional theory) techniques. Correlations between spectra and structure are made and the techniques applied to other spectroscopic and electrostatic properties as well, including hydrogen bonding, ligand binding to heme proteins, J-couplings, electric field gradients, and atoms-in-molecules theory, together with a brief review of the use of NMR chemical shifts in drug design.
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Affiliation(s)
- Eric Oldfield
- Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
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Hong M, Yao X, Jakes K, Huster D. Investigation of Molecular Motions by Lee-Goldburg Cross-Polarization NMR Spectroscopy. J Phys Chem B 2002. [DOI: 10.1021/jp0156064] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mei Hong
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, and Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Xiaolan Yao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, and Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Karen Jakes
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, and Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Daniel Huster
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, and Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
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Lipid-peptide interaction investigated by NMR. CURRENT TOPICS IN MEMBRANES 2002. [DOI: 10.1016/s1063-5823(02)52008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Structural insight into the interaction of amyloid-β peptide with biological membranes by solid state NMR. FOCUS ON STRUCTURAL BIOLOGY 2001. [DOI: 10.1007/978-94-017-2579-8_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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