1
|
Gardon L, Becker N, Gremer L, Heise H. Structural Impact of N-terminal Pyroglutamate in an Amyloid-β(3-42) Fibril Probed by Solid-State NMR Spectroscopy. Chemistry 2024; 30:e202303007. [PMID: 38100216 DOI: 10.1002/chem.202303007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Indexed: 12/31/2023]
Abstract
Extracellular amyloid-β (Aβ) plaques, primarily formed by Aβ(1-40) and Aβ(1-42) fibrils, are a hallmark of Alzheimer's disease. The Aβ peptide can undergo a high variety of different post-translational modifications including formation of a pyroglutamate (pGlu, pE) at N-terminal Glu3 or Glu11 of truncated Aβ(3-x) or Aβ(11-x), respectively. Here we studied structural similarities and differences between pEAβ(3-42) and LS-shaped Aβ(1-42) fibrils grown under identical conditions (pH 2) using solid-state NMR spectroscopy. We show that the central region of pEAβ(3-42) fibrils including the turn region around V24 is almost identical to Aβ(1-42) showing similar β-strands also at the N-terminus. The missing N-terminal residues D1-A2 along with pE3 formation in pEAβ(3-42) preclude a salt bridge between K28-D1' as in Aβ(1-42) fibrils. G37 and G38 act as highly sensitive internal sensors for the modified N-terminus, which remains rigid over ~five pH units.
Collapse
Affiliation(s)
- Luis Gardon
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
| | - Nina Becker
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
| | - Lothar Gremer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
| | - Henrike Heise
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
| |
Collapse
|
2
|
Xiang S, Pinto C, Baldus M. Divide and Conquer: A Tailored Solid‐state NMR Approach to Study Large Membrane Protein Complexes. Angew Chem Int Ed Engl 2022; 61:e202203319. [PMID: 35712982 PMCID: PMC9540533 DOI: 10.1002/anie.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Indexed: 11/18/2022]
Abstract
Membrane proteins are known to exert many essential biological functions by forming complexes in cell membranes. An example refers to the β‐barrel assembly machinery (BAM), a 200 kDa pentameric complex containing BAM proteins A–E that catalyzes the essential process of protein insertion into the outer membrane of gram‐negative bacteria. While progress has been made in capturing three‐dimensional structural snapshots of the BAM complex, the role of the lipoprotein BamC in the complex assembly in functional lipid bilayers has remained unclear. We have devised a component‐selective preparation scheme to directly study BamC as part of the entire BAM complex in lipid bilayers. Combination with proton‐detected solid‐state NMR methods allowed us to probe the structure, dynamics, and supramolecular topology of full‐length BamC embedded in the entire complex in lipid bilayers. Our approach may help decipher how individual proteins contribute to the dynamic formation and functioning of membrane protein complexes in membranes.
Collapse
Affiliation(s)
- ShengQi Xiang
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
- MOE Key Lab for Cellular Dynamics School of Life Sciences University of Science and Technology of China 96 Jinzhai Road Hefei 230026 Anhui China
| | - Cecilia Pinto
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
- Current address: Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Van der Maasweg 9 2629 H. Z. Delft The Netherlands
| | - Marc Baldus
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| |
Collapse
|
3
|
Xiang S, Pinto C, Baldus M. Divide and Conquer: A Tailored Solid‐state NMR Approach to Study Large Membrane Protein Complexes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- ShengQi Xiang
- University of Science and Technology of China, Anhui, MOE Key lab for Cellular Dynamics CHINA
| | - Cecilia Pinto
- Delft University of Technology: Technische Universiteit Delft Department of Bionanoscience NETHERLANDS
| | - Marc Baldus
- Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 Utrecht NETHERLANDS
| |
Collapse
|
4
|
Dufourc EJ. Bicelles and nanodiscs for biophysical chemistry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183478. [PMID: 32971065 DOI: 10.1016/j.bbamem.2020.183478] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/14/2023]
Abstract
Membrane nanoobjects are very important tools to study biomembrane properties. Two types are described herein: Bicelles and Nanodiscs. Bicelles are obtained by thorough water mixing of long chain and short chain lipids and may take the form of membranous discs of 10-50 nm. Temperature-composition-hydration diagrams have been established for Phosphatidylcholines and show limited domains of existence. Bicelles can be doped with charged lipids, surfactants or with cholesterol and offer a wide variety of membranous platforms for structural biology. Internal dynamics as measured by solid-state NMR is very similar to that of liposomes in their fluid phase. Because of the magnetic susceptibility anisotropy of the lipid chains, discs may be aligned along or perpendicular to the magnetic field. They may serve as weak orienting media to provide distance information in determining the 3D structure of soluble proteins. In different conditions they show strong orienting properties which may be used to study the 3D structure, topology and dynamics of membrane proteins. Lipid Bicelles with biphenyl chains or doped with lanthanides show long lasting remnant orientation after removing the magnetic field due to smectic-like properties. An alternative to pure lipid Bicelles is provided by nanodiscs where the half torus composed by short chain lipids is replaced by proteins. This renders the nano-objects less fragile as they can be used to stabilize membrane protein assemblies to be studied by electron microscopy. Internal dynamics is again similar to liposomes except that the phase transition is abolished, possibly due to lateral constrain imposed by the toroidal proteins limiting the disc size. Advantages and drawbacks of both nanoplatforms are discussed.
Collapse
Affiliation(s)
- Erick J Dufourc
- Institute of Chemistry and Biology of membranes and Nanoobjects, UMR5248, CNRS, University of Bordeaux, Bordeaux Polytechnic Institute, Allée Geoffroy Saint Hilaire, 33600 Pessac, France.
| |
Collapse
|
5
|
Marin-Montesinos I, Goyard D, Gillon E, Renaudet O, Imberty A, Hediger S, De Paëpe G. Selective high-resolution DNP-enhanced NMR of biomolecular binding sites. Chem Sci 2019; 10:3366-3374. [PMID: 30996925 PMCID: PMC6429603 DOI: 10.1039/c8sc05696j] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/01/2019] [Indexed: 01/01/2023] Open
Abstract
Locating binding sites in biomolecular assemblies and solving their structures are of the utmost importance to unravel functional aspects of the system and provide experimental data that can be used for structure-based drug design. This often still remains a challenge, both in terms of selectivity and sensitivity for X-ray crystallography, cryo-electron microscopy and NMR. In this work, we introduce a novel method called Selective Dynamic Nuclear Polarization (Sel-DNP) that allows selective highlighting and identification of residues present in the binding site. This powerful site-directed approach relies on the use of localized paramagnetic relaxation enhancement induced by a ligand-functionalized paramagnetic construct combined with difference spectroscopy to recover high-resolution and high-sensitivity information from binding sites. The identification of residues involved in the binding is performed using spectral fingerprints obtained from a set of high-resolution multidimensional spectra with varying selectivities. The methodology is demonstrated on the galactophilic lectin LecA, for which we report well-resolved DNP-enhanced spectra with linewidths between 0.5 and 1 ppm, which enable the de novo assignment of the binding interface residues, without using previous knowledge of the binding site location. Since this approach produces clean and resolved difference spectra containing a limited number of residues, resonance assignment can be performed without any limitation with respect to the size of the biomolecular system and only requires the production of one protein sample (e.g. 13C,15N-labeled protein).
Collapse
Affiliation(s)
| | - David Goyard
- Univ. Grenoble Alpes , CNRS , DCM , Grenoble , France
| | - Emilie Gillon
- Univ. Grenoble Alpes , CNRS , CERMAV , Grenoble , France
| | | | - Anne Imberty
- Univ. Grenoble Alpes , CNRS , CERMAV , Grenoble , France
| | - Sabine Hediger
- Univ. Grenoble Alpes , CEA , CNRS , INAC-MEM , Grenoble , France . ;
| | - Gaël De Paëpe
- Univ. Grenoble Alpes , CEA , CNRS , INAC-MEM , Grenoble , France . ;
| |
Collapse
|
6
|
Sumowski CV, Hanni M, Schweizer S, Ochsenfeld C. Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides. J Chem Theory Comput 2015; 10:122-33. [PMID: 26579896 DOI: 10.1021/ct400713t] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.
Collapse
Affiliation(s)
- Chris Vanessa Sumowski
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Matti Hanni
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Sabine Schweizer
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| |
Collapse
|
7
|
Brown LS, Ladizhansky V. Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy. Protein Sci 2015; 24:1333-46. [PMID: 25973959 DOI: 10.1002/pro.2700] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 12/21/2022]
Abstract
Membrane proteins play many critical roles in cells, mediating flow of material and information across cell membranes. They have evolved to perform these functions in the environment of a cell membrane, whose physicochemical properties are often different from those of common cell membrane mimetics used for structure determination. As a result, membrane proteins are difficult to study by traditional methods of structural biology, and they are significantly underrepresented in the protein structure databank. Solid-state Nuclear Magnetic Resonance (SSNMR) has long been considered as an attractive alternative because it allows for studies of membrane proteins in both native-like membranes composed of synthetic lipids and in cell membranes. Over the past decade, SSNMR has been rapidly developing into a major structural method, and a growing number of membrane protein structures obtained by this technique highlights its potential. Here we discuss membrane protein sample requirements, review recent progress in SSNMR methodologies, and describe recent advances in characterizing membrane proteins in the environment of a cellular membrane.
Collapse
Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| |
Collapse
|
8
|
Ward ME, Brown LS, Ladizhansky V. Advanced solid-state NMR techniques for characterization of membrane protein structure and dynamics: application to Anabaena Sensory Rhodopsin. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:119-128. [PMID: 25637099 DOI: 10.1016/j.jmr.2014.11.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
Studies of the structure, dynamics, and function of membrane proteins (MPs) have long been considered one of the main applications of solid-state NMR (SSNMR). Advances in instrumentation, and the plethora of new SSNMR methodologies developed over the past decade have resulted in a number of high-resolution structures and structural models of both bitopic and polytopic α-helical MPs. The necessity to retain lipids in the sample, the high proportion of one type of secondary structure, differential dynamics, and the possibility of local disorder in the loop regions all create challenges for structure determination. In this Perspective article we describe our recent efforts directed at determining the structure and functional dynamics of Anabaena Sensory Rhodopsin, a heptahelical transmembrane (7TM) protein. We review some of the established and emerging methods which can be utilized for SSNMR-based structure determination, with a particular focus on those used for ASR, a bacterial protein which shares its 7TM architecture with G-protein coupled receptors.
Collapse
Affiliation(s)
- Meaghan E Ward
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
|
11
|
Nakanishi K, Crouch R. Application of Artificial Pigments to Structure Determination and Study of Photoinduced Transformations of Retinal Proteins. Isr J Chem 2013. [DOI: 10.1002/ijch.199500030] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
12
|
Li J, van der Wel PCA. Spinning-rate encoded chemical shift correlations from rotational resonance solid-state NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 230:117-24. [PMID: 23475055 PMCID: PMC3635064 DOI: 10.1016/j.jmr.2013.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/22/2013] [Accepted: 02/04/2013] [Indexed: 05/23/2023]
Abstract
Structural measurements in magic-angle-spinning (MAS) solid-state NMR rely heavily on (13)C-(13)C distance measurements. Broadbanded recoupling methods are used to generate many cross-peaks, but have complex polarization transfer mechanisms that limit the precision of distance constraints and can suffer from weak intensities for distant peaks due to relaxation, the broad distribution of polarization, as well as dipolar truncation. Frequency-selective methods that feature narrow-banded recoupling can reduce these effects. Indeed, rotational resonance (R(2)) experiments have found application in many different biological systems, where they have afforded improved precision and accuracy. Unfortunately, a highly selective transfer mechanism also leads to few cross-peaks in the resulting spectra, which complicates the extraction of multiple constraints. R(2)-width (R(2)W) measurements that scan a range of MAS rates to probe the R(2) matching conditions of one or more sites can improve precision, and also permit multiple simultaneous distance measurements. However, multidimensional R(2)W can be very time-consuming. Here, we present an approach that facilitates the acquisition of 2D-like spectra based on a series of 1D R(2)W experiments, by taking advantage of the chemical shift information encoded in the MAS rates where matching occurs. This yields a more time-efficient experiment with many of the benefits of more conventional multidimensional R(2)W measurements. The obtained spectra reveal long-distance (13)C-(13)C cross-peaks resulting from R(2)-mediated polarization transfer. This experiment also enables the efficient setup and targeted implementation of traditional R(2) or R(2)W experiments. Analogous applications may extend to other variable-MAS and frequency-selective solid-state NMR experiments.
Collapse
Affiliation(s)
- Jun Li
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, Pennsylvania 15260, USA
| | - Patrick C. A. van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, Pennsylvania 15260, USA
| |
Collapse
|
13
|
Jawla S, Ni QZ, Barnes A, Guss W, Daviso E, Herzfeld J, Griffin R, Temkin R. Continuously Tunable 250 GHz Gyrotron with a Double Disk Window for DNP-NMR Spectroscopy. JOURNAL OF INFRARED, MILLIMETER AND TERAHERTZ WAVES 2013; 34:42-52. [PMID: 23539422 PMCID: PMC3607393 DOI: 10.1007/s10762-012-9947-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In this paper, we describe the design and experimental results from the rebuild of a 250 GHz gyrotron used for Dynamic Nuclear Polarization enhanced Nuclear Magnetic Resonance spectroscopy on a 380 MHz spectrometer. Tuning bandwidth of approximately 2 GHz is easily achieved at a fixed magnetic field of 9.24 T and a beam current of 95 mA producing an average output power of >10 W over the entire tuning band. This tube incorporates a double disk output sapphire window in order to maximize the transmission at 250.58 GHz. DNP Signal enhancement of >125 is achieved on a 13C-Urea sample using this gyrotron.
Collapse
Affiliation(s)
- Sudheer Jawla
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA-02139, USA
| | - Qing Zhe Ni
- Francis Bitter Magnet Lab and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA-02139, USA
| | - Alexander Barnes
- Francis Bitter Magnet Lab and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA-02139, USA
| | - William Guss
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA-02139, USA
| | - Eugenio Daviso
- Francis Bitter Magnet Lab and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA-02139, USA
- Department of Chemistry, Brandies University, Waltham, MA-02454, USA
| | - Judith Herzfeld
- Department of Chemistry, Brandies University, Waltham, MA-02454, USA
| | - Robert Griffin
- Francis Bitter Magnet Lab and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA-02139, USA
| | - Richard Temkin
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA-02139, USA
| |
Collapse
|
14
|
De Paëpe G. Dipolar Recoupling in Magic Angle Spinning Solid-State Nuclear Magnetic Resonance. Annu Rev Phys Chem 2012; 63:661-84. [DOI: 10.1146/annurev-physchem-032511-143726] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gaël De Paëpe
- Service de Chimie Inorganique et Biologique, UMR-E 3 CEA/UJF-Grenoble 1, Institut Nanosciences et Cryogénie, F-38054 Grenoble, France;
| |
Collapse
|
15
|
Carlomagno T. NMR in natural products: understanding conformation, configuration and receptor interactions. Nat Prod Rep 2012; 29:536-54. [PMID: 22456471 DOI: 10.1039/c2np00098a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of natural products in complex with macromolecular receptors.
Collapse
Affiliation(s)
- Teresa Carlomagno
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg
| |
Collapse
|
16
|
Lange S, Linden AH, Akbey U, Franks WT, Loening NM, van Rossum BJ, Oschkinat H. The effect of biradical concentration on the performance of DNP-MAS-NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 216:209-12. [PMID: 22285634 DOI: 10.1016/j.jmr.2012.01.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/23/2011] [Accepted: 01/01/2012] [Indexed: 05/21/2023]
Abstract
With the technique of dynamic nuclear polarization (DNP) signal intensity in solid-state MAS-NMR experiments can be enhanced by 2-3 orders of magnitude. DNP relies on the transfer of electron spin polarization from unpaired electrons to nuclear spins. For this reason, stable organic biradicals such as TOTAPOL are commonly added to samples used in DNP experiments. We investigated the effects of biradical concentration on the relaxation, enhancement, and intensity of NMR signals, employing a series of samples with various TOTAPOL concentrations and uniformly (13)C, (15)N labeled proline. A considerable decrease of the NMR relaxation times (T(1), T(2)(∗), and T(1)(ρ)) is observed with increasing amounts of biradical due to paramagnetic relaxation enhancement (PRE). For nuclei in close proximity to the radical, decreasing T(1)(ρ) reduces cross-polarization efficiency and decreases in T(2)(∗) broaden the signal. Additionally, paramagnetic shifts of (1)H signals can cause further line broadening by impairing decoupling. On average, the combination of these paramagnetic effects (PE; relaxation enhancement, paramagnetic shifts) quenches NMR-signals from nuclei closer than 10Å to the biradical centers. On the other hand, shorter T(1) times allow the repetition rate of the experiment to be increased, which can partially compensate for intensity loss. Therefore, it is desirable to optimize the radical concentration to prevent additional line broadening and to maximize the signal-to-noise observed per unit time for the signals of interest.
Collapse
Affiliation(s)
- Sascha Lange
- FMP, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | | | | | | | | | | | | |
Collapse
|
17
|
De Paëpe G, Lewandowski JR, Loquet A, Eddy M, Megy S, Böckmann A, Griffin RG. Heteronuclear proton assisted recoupling. J Chem Phys 2011; 134:095101. [PMID: 21384999 DOI: 10.1063/1.3541251] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe a theoretical framework for understanding the heteronuclear version of the third spin assisted recoupling polarization transfer mechanism and demonstrate its potential for detecting long-distance intramolecular and intermolecular (15)N-(13)C contacts in biomolecular systems. The pulse sequence, proton assisted insensitive nuclei cross polarization (PAIN-CP) relies on a cross term between (1)H-(15)N and (1)H-(13)C dipolar couplings to mediate zero- and∕or double-quantum (15)N-(13)C recoupling. In particular, using average Hamiltonian theory we derive effective Hamiltonians for PAIN-CP and show that the transfer is mediated by trilinear terms of the form N(±)C(∓)H(z) (ZQ) or N(±)C(±)H(z) (DQ) depending on the rf field strengths employed. We use analytical and numerical simulations to explain the structure of the PAIN-CP optimization maps and to delineate the appropriate matching conditions. We also detail the dependence of the PAIN-CP polarization transfer with respect to local molecular geometry and explain the observed reduction in dipolar truncation. In addition, we demonstrate the utility of PAIN-CP in structural studies with (15)N-(13)C spectra of two uniformly (13)C,(15)N labeled model microcrystalline proteins-GB1, a 56 amino acid peptide, and Crh, a 85 amino acid domain swapped dimer (MW=2×10.4 kDa). The spectra acquired at high magic angle spinning frequencies (ω(r)∕2π>20 kHz) and magnetic fields (ω(0H)∕2π=700-900 MHz) using moderate rf fields, yield multiple long-distance intramonomer and intermonomer (15)N-(13)C contacts. We use these distance restraints, in combination with the available x-ray structure as a homology model, to perform a calculation of the monomer subunit of the Crh protein.
Collapse
Affiliation(s)
- Gaël De Paëpe
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | | | | | | | | | | | | |
Collapse
|
18
|
Nanni EA, Barnes AB, Matsuki Y, Woskov PP, Corzilius B, Griffin RG, Temkin RJ. Microwave field distribution in a magic angle spinning dynamic nuclear polarization NMR probe. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 210:16-23. [PMID: 21382733 PMCID: PMC3081422 DOI: 10.1016/j.jmr.2011.02.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 02/01/2011] [Accepted: 02/01/2011] [Indexed: 05/05/2023]
Abstract
We present a calculation of the microwave field distribution in a magic angle spinning (MAS) probe utilized in dynamic nuclear polarization (DNP) experiments. The microwave magnetic field (B(1S)) profile was obtained from simulations performed with the High Frequency Structure Simulator (HFSS) software suite, using a model that includes the launching antenna, the outer Kel-F stator housing coated with Ag, the RF coil, and the 4mm diameter sapphire rotor containing the sample. The predicted average B(1S) field is 13μT/W(1/2), where S denotes the electron spin. For a routinely achievable input power of 5W the corresponding value is γ(S)B(1S)=0.84MHz. The calculations provide insights into the coupling of the microwave power to the sample, including reflections from the RF coil and diffraction of the power transmitted through the coil. The variation of enhancement with rotor wall thickness was also successfully simulated. A second, simplified calculation was performed using a single pass model based on Gaussian beam propagation and Fresnel diffraction. This model provided additional physical insight and was in good agreement with the full HFSS simulation. These calculations indicate approaches to increasing the coupling of the microwave power to the sample, including the use of a converging lens and fine adjustment of the spacing of the windings of the RF coil. The present results should prove useful in optimizing the coupling of microwave power to the sample in future DNP experiments. Finally, the results of the simulation were used to predict the cross effect DNP enhancement (ϵ) vs. ω(1S)/(2π) for a sample of (13)C-urea dissolved in a 60:40 glycerol/water mixture containing the polarizing agent TOTAPOL; very good agreement was obtained between theory and experiment.
Collapse
Affiliation(s)
- Emilio A Nanni
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | | | | | | | | | | | | |
Collapse
|
19
|
Vogt F, Aurentz D, Mueller K. Determination of internuclear distances from solid-state nuclear magnetic resonance: Dipolar transforms and regularization methods. Mol Phys 2011. [DOI: 10.1080/00268979809483225] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- F.G. Vogt
- a Department of Chemistry , The Pennsylvania State University , 152 Davey Laboratory, University Park , PA , USA
| | - D.J. Aurentz
- a Department of Chemistry , The Pennsylvania State University , 152 Davey Laboratory, University Park , PA , USA
| | - K.T. Mueller
- a Department of Chemistry , The Pennsylvania State University , 152 Davey Laboratory, University Park , PA , USA
| |
Collapse
|
20
|
Boender G, Vega S, De Groot HM. A physical interpretation of the Floquet description of magic angle spinning nuclear magnetic resonance spectroscopy. Mol Phys 2011. [DOI: 10.1080/00268979809483226] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- G.J. Boender
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , Leiden , RA , The Netherlands
- b Department of Chemical Physics , Weizmann Institute of Science , Rehovot , Israel
| | - S. Vega
- b Department of Chemical Physics , Weizmann Institute of Science , Rehovot , Israel
| | - H.J. M. De Groot
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , Leiden , RA , The Netherlands
| |
Collapse
|
21
|
|
22
|
Groesbeek M, Rood GA, Lugtenburg J. Synthesis of (12,13-13C2)retinal and (13,1413C2)retinal: A strategy to prepare multiple-13C-labeled conjugated systems. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19921110307] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
23
|
Groesbeek M, Kirillova YG, Boeff R, Lugtenburg J. Synthesis of six novel retinals and their interaction with bacterioopsin. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19941130107] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
24
|
Jansen F, Kwestro M, Schmitt D, Lugtenburg J. Synthesis and characterization of all-E (12,12′-13C2)-, (13,13′-13C2)-, (14,14′-13C2)-, (15,15′-13C2)- and (20,20′-13C2)astaxanthin. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19941131205] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
25
|
Ogrel A, Vasilenko IA, Lugtenburg J, Raap J. Enzymatic synthesis of specifically 2
H-labelled L-glutamic acids and 2
H-, 15
N-, 13
C-labelled L-glutamines on a preparative scale. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19941130706] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
26
|
Spijker-Assink MB, Robijn GW, Ippel JH, Lugtenburg J, Groen BH, van Dam K. (1R)- and (1S)-5-demethyl-8,16-methanobacteriorhodopsin and its properties. The synthesis and spectroscopy of 5-demethyl-8,16-methanoretinal in optically active and isotopic forms. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19921110104] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
27
|
Groesbeek M, van Galen AJJ, Ippel JH, Berden JA, Lugtenburg J. Three bacteriorhodopsins with ring-didemethylated 6-s
-locked chromophores and their properties. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19931120401] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
28
|
Ippel J, Spijker-Assink M, Groesbeek M, van der Steen R, Altona C, Lugtenburg J. Conformational analysis of all-E
-retinal, all-E
-8,16-methanoretinal, (1S
)-all-E
-8,16-methano-18-norretinal, and all-E
-17,18-dinor-8,16-methanoretinal by means of NMR spectroscopy and molecular dynamics. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19941130205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
29
|
Bahar I, Lezon TR, Bakan A, Shrivastava IH. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 2010; 110:1463-97. [PMID: 19785456 PMCID: PMC2836427 DOI: 10.1021/cr900095e] [Citation(s) in RCA: 377] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ivet Bahar
- Department of Computational Biology, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA.
| | | | | | | |
Collapse
|
30
|
Is the lifetime of light-stimulated cGMP phosphodiesterase regulated by recoverin through its regulation of rhodopsin phosphorylation? Behav Brain Sci 2010. [DOI: 10.1017/s0140525x00039522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
31
|
|
32
|
|
33
|
|
34
|
|
35
|
|
36
|
|
37
|
Ladizhansky V. Homonuclear dipolar recoupling techniques for structure determination in uniformly 13C-labeled proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2009; 36:119-128. [PMID: 19729285 DOI: 10.1016/j.ssnmr.2009.07.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 07/21/2009] [Indexed: 05/28/2023]
Abstract
In solid-state NMR magic angle spinning is often used to remove line broadening associated with anisotropic interactions, such as chemical shift anisotropy and dipolar couplings. Dipolar recoupling refers to sequences of pulses designed to reintroduce dipolar interactions that are otherwise averaged by magic angle spinning. One of the key applications of homonuclear (and heteronuclear) dipolar recoupling is for the purpose of protein structure determination. Recoupling experiments, originally designed for applications in spin-pair labeled samples, have been revised in recent years for applications in samples with extensive or uniform incorporation of isotopic labels. In these samples multiple internuclear distances can in principle be probed simultaneously, but the dipolar truncation effects (i.e. attenuation of the effects of weak couplings by strong ones) circumvent such measurements. In this article we review some of the recent developments in homonuclear recoupling methods that allow overcoming this problem.
Collapse
Affiliation(s)
- Vladimir Ladizhansky
- Department of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada.
| |
Collapse
|
38
|
Patching SG, Edwards R, Middleton DA. Structural analysis of uniformly (13)C-labelled solids from selective angle measurements at rotational resonance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 199:242-246. [PMID: 19487142 DOI: 10.1016/j.jmr.2009.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 04/24/2009] [Accepted: 05/04/2009] [Indexed: 05/27/2023]
Abstract
We demonstrate that individual H-C-C-H torsional angles in uniformly labelled organic solids can be estimated by selective excitation of (13)C double-quantum coherences under magic-angle spinning at rotational resonance. By adapting a straightforward one-dimensional experiment described earlier [T. Karlsson, M. Eden, H. Luhman, M.H. Levitt, J. Magn. Reson. 145 (2000) 95-107], a double-quantum filtered spectrum selective for Calpha and Cbeta of uniformly labelled L-[(13)C,(15)N]valine is obtained with 25% efficiency. The evolution of Calpha-Cbeta double-quantum coherence under the influence of the dipolar fields of bonded protons is monitored to provide a value of the Halpha-Calpha-Cbeta-Hbeta torsional angle that is consistent with the crystal structure. In addition, double-quantum filtration selective for C6 and C1' of uniformly labelled [(13)C,(15)N]uridine is achieved with 12% efficiency for a (13)C-(13)C distance of 2.5A, yielding a reliable estimate of the C6-H and C1'-H projection angle defining the relative orientations of the nucleoside pyrimidine and ribose rings. This procedure will be useful, in favourable cases, for structural analysis of fully labelled small molecules such as receptor ligands that are not readily synthesised with labels placed selectively at structurally diagnostic sites.
Collapse
Affiliation(s)
- Simon G Patching
- Astbury Centre for Structural Molecular Biology and Institute of Membrane and Systems Biology, University of Leeds, Leeds, United Kingdom
| | | | | |
Collapse
|
39
|
McDermott A. Structure and dynamics of membrane proteins by magic angle spinning solid-state NMR. Annu Rev Biophys 2009; 38:385-403. [PMID: 19245337 DOI: 10.1146/annurev.biophys.050708.133719] [Citation(s) in RCA: 288] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins remain difficult to study by traditional methods. Magic angle spinning solid-state NMR (MAS SSNMR) methods present an important approach for studying membrane proteins of moderate size. Emerging MAS SSNMR methods are based on extensive assignments of the nuclei as a basis for structure determination and characterization of function. These methods have already been used to characterize fibrils and globular proteins and are being increasingly used to study membrane proteins embedded in lipids. This review highlights recent applications to intrinsic membrane proteins and summarizes recent technical advances that will enable these methods to be utilized for more complex membrane protein systems in the near future.
Collapse
Affiliation(s)
- Ann McDermott
- Department of Chemistry, Columbia University, New York, NY 10027, USA.
| |
Collapse
|
40
|
Lewandowski JR, De Paëpe G, Eddy MT, Struppe J, Maas W, Griffin RG. Proton assisted recoupling at high spinning frequencies. J Phys Chem B 2009; 113:9062-9. [PMID: 19489532 PMCID: PMC2738631 DOI: 10.1021/jp810280t] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate the successful application of (13)C-(13)C proton assisted recoupling (PAR) on [U-(13)C,(15)N] N-f-MLF-OH and [U-(13)C,(15)N] protein GB1 at high magic angle spinning (MAS) frequencies (omega(r)/2pi = 65 kHz). Specifically, by combining PAR mixing with low power heteronuclear decoupling (omega(1H)/2pi approximately 16 kHz) and high spinning frequencies, we obtain high resolution 2D spectra displaying long-range (13)C-(13)C contacts from which distance estimates can be extracted. These experiments therefore demonstrate the possibility of performing high resolution structural studies in the limit of high spinning frequency and low power (1)H decoupling, a regime which optimizes the resolution of protein samples and preserves their integrity.
Collapse
Affiliation(s)
- Józef R. Lewandowski
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Gaël De Paëpe
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Matthew T. Eddy
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jochem Struppe
- Bruker BioSpin Corporation, Billerica, Massachusetts 01821
| | - Werner Maas
- Bruker BioSpin Corporation, Billerica, Massachusetts 01821
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| |
Collapse
|
41
|
Bayro MJ, Huber M, Ramachandran R, Davenport TC, Meier BH, Ernst M, Griffin RG. Dipolar truncation in magic-angle spinning NMR recoupling experiments. J Chem Phys 2009; 130:114506. [PMID: 19317544 DOI: 10.1063/1.3089370] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Quantitative solid-state NMR distance measurements in strongly coupled spin systems are often complicated due to the simultaneous presence of multiple noncommuting spin interactions. In the case of zeroth-order homonuclear dipolar recoupling experiments, the recoupled dipolar interaction between distant spins is attenuated by the presence of stronger couplings to nearby spins, an effect known as dipolar truncation. In this article, we quantitatively investigate the effect of dipolar truncation on the polarization-transfer efficiency of various homonuclear recoupling experiments with analytical theory, numerical simulations, and experiments. In particular, using selectively (13)C-labeled tripeptides, we compare the extent of dipolar truncation in model three-spin systems encountered in protein samples produced with uniform and alternating labeling. Our observations indicate that while the extent of dipolar truncation decreases in the absence of directly bonded nuclei, two-bond dipolar couplings can generate significant dipolar truncation of small, long-range couplings. Therefore, while alternating labeling alleviates the effects of dipolar truncation, and thus facilitates the application of recoupling experiments to large spin systems, it does not represent a complete solution to this outstanding problem.
Collapse
Affiliation(s)
- Marvin J Bayro
- Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | | | | | |
Collapse
|
42
|
Lewandowski JR, De Paëpe G, Eddy MT, Griffin RG. (15)N-(15)N proton assisted recoupling in magic angle spinning NMR. J Am Chem Soc 2009; 131:5769-76. [PMID: 19334788 PMCID: PMC2754755 DOI: 10.1021/ja806578y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a new magic angle spinning (MAS) NMR experiment for obtaining (15)N-(15)N correlation spectra. The approach yields direct information about the secondary and tertiary structure of proteins, including identification of alpha-helical stretches and interstrand connectivity in antiparallel beta-sheets, which are of major interest for structural studies of membrane proteins and amyloid fibrils. The method, (15)N-(15)N proton assisted recoupling (PAR), relies on a second-order mechanism, third spin assisted recoupling (TSAR), used previously in the context of (15)N-(13)C and (13)C-(13)C polarization transfer schemes. In comparison to (15)N-(15)N proton-driven spin diffusion experiments, the PAR technique accelerates polarization transfer between (15)N's by a factor of approximately 10(2)-10(3) and is furthermore applicable over the entire range of currently available MAS frequencies (10-70 kHz).
Collapse
Affiliation(s)
- Józef R Lewandowski
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | |
Collapse
|
43
|
Shi L, Ahmed MA, Zhang W, Whited G, Brown LS, Ladizhansky V. Three-Dimensional Solid-State NMR Study of a Seven-Helical Integral Membrane Proton Pump—Structural Insights. J Mol Biol 2009; 386:1078-93. [DOI: 10.1016/j.jmb.2009.01.011] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
44
|
Renault M, Saurel O, Czaplicki J, Demange P, Gervais V, Löhr F, Réat V, Piotto M, Milon A. Solution State NMR Structure and Dynamics of KpOmpA, a 210 Residue Transmembrane Domain Possessing a High Potential for Immunological Applications. J Mol Biol 2009; 385:117-30. [DOI: 10.1016/j.jmb.2008.10.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 09/16/2008] [Accepted: 10/04/2008] [Indexed: 10/21/2022]
|
45
|
De Paëpe G, Lewandowski JR, Loquet A, Böckmann A, Griffin RG. Proton assisted recoupling and protein structure determination. J Chem Phys 2008; 129:245101. [PMID: 19123534 PMCID: PMC2755343 DOI: 10.1063/1.3036928] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 11/03/2008] [Indexed: 11/14/2022] Open
Abstract
We introduce a homonuclear version of third spin assisted recoupling, a second-order mechanism that can be used for polarization transfer between (13)C or (15)N spins in magic angle spinning (MAS) NMR experiments, particularly at high spinning frequencies employed in contemporary high field MAS experiments. The resulting sequence, which we refer to as proton assisted recoupling (PAR), relies on a cross-term between (1)H-(13)C (or (1)H-(15)N) couplings to mediate zero quantum (13)C-(13)C (or (15)N-(15)N recoupling). In particular, using average Hamiltonian theory we derive an effective Hamiltonian for PAR and show that the transfer is mediated by trilinear terms of the form C(1) (+/-)C(2) (-/+)H(Z) for (13)C-(13)C recoupling experiments (or N(1) (+/-)N(2) (-/+)H(Z) for (15)N-(15)N). We use analytical and numerical simulations to explain the structure of the PAR optimization maps and to delineate the PAR matching conditions. We also detail the PAR polarization transfer dependence with respect to the local molecular geometry and explain the observed reduction in dipolar truncation. Finally, we demonstrate the utility of PAR in structural studies of proteins with (13)C-(13)C spectra of uniformly (13)C, (15)N labeled microcrystalline Crh, a 85 amino acid model protein that forms a domain swapped dimer (MW=2 x 10.4 kDa). The spectra, which were acquired at high MAS frequencies (omega(r)2pi>20 kHz) and magnetic fields (750-900 MHz (1)H frequencies) using moderate rf fields, exhibit numerous cross peaks corresponding to long (up to 6-7 A) (13)C-(13)C distances which are particularly useful in protein structure determination. Using results from PAR spectra we calculate the structure of the Crh protein.
Collapse
Affiliation(s)
- Gaël De Paëpe
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | |
Collapse
|
46
|
Lopez JJ, Kaiser C, Shastri S, Glaubitz C. Double quantum filtering homonuclear MAS NMR correlation spectra: a tool for membrane protein studies. JOURNAL OF BIOMOLECULAR NMR 2008; 41:97-104. [PMID: 18506579 DOI: 10.1007/s10858-008-9245-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Revised: 04/24/2008] [Accepted: 04/27/2008] [Indexed: 05/26/2023]
Abstract
13C homonuclear correlation spectra based on proton driven spin diffusion (PDSD) are becoming increasingly important for obtaining distance constraints from multiply labeled biomolecules by MAS NMR. One particular challenging situation arises when such constraints are to be obtained from spectra with a large natural abundance signal background which causes detrimental diagonal peak intensities. They obscure cross peaks, and furthermore impede the calculation of a buildup rates matrix which may be used to derive distance constraints, as carried out in "NMR crystallography". Here, we combine double quantum (DQ) filtering with 13C-13C dipolar assisted rotational resonance (DARR) experiments to yield correlation spectra free of natural abundance contributions. Two experimental schemes, using DQ filtering prior to evolution (DOPE), and after mixing (DOAM), have been evaluated. Diagonal peak intensities along the spectrum diagonal are removed completely, and crosspeaks close to the diagonal are easily identifiable. For DOAM spectra with negligible mixing times, it is possible to carry out 'assignment walks' which simplify peak identification substantially. The method is demonstrated on 13C-cys labeled proteorhodopsin, a 27 kDa membrane protein. The magnetization transfer characteristics were studied using buildup curves obtained on uniformly 13C labelled crystalline tripeptide MLF. Our data show that DQ filtered DARR experiments pave the way for obtaining through space constraints for structural studies on ligands, bound to membrane receptors, or on small fragments within large proteins.
Collapse
Affiliation(s)
- Jakob J Lopez
- Institute for Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | | | | | | |
Collapse
|
47
|
De Paëpe G, Lewandowski JR, Griffin RG. Spin dynamics in the modulation frame: Application to homonuclear recoupling in magic angle spinning solid-state NMR. J Chem Phys 2008; 128:124503. [DOI: 10.1063/1.2834732] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
48
|
Peng X, Libich D, Janik R, Harauz G, Ladizhansky V. Dipolar Chemical Shift Correlation Spectroscopy for Homonuclear Carbon Distance Measurements in Proteins in the Solid State: Application to Structure Determination and Refinement. J Am Chem Soc 2007; 130:359-69. [DOI: 10.1021/ja076658v] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaohu Peng
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - David Libich
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - Rafal Janik
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - George Harauz
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| |
Collapse
|
49
|
Brown MF, Heyn MP, Job C, Kim S, Moltke S, Nakanishi K, Nevzorov AA, Struts AV, Salgado GFJ, Wallat I. Solid-state 2H NMR spectroscopy of retinal proteins in aligned membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1768:2979-3000. [PMID: 18021739 PMCID: PMC5233718 DOI: 10.1016/j.bbamem.2007.10.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 10/10/2007] [Accepted: 10/10/2007] [Indexed: 11/21/2022]
Abstract
Solid-state 2H NMR spectroscopy gives a powerful avenue to investigating the structures of ligands and cofactors bound to integral membrane proteins. For bacteriorhodopsin (bR) and rhodopsin, retinal was site-specifically labeled by deuteration of the methyl groups followed by regeneration of the apoprotein. 2H NMR studies of aligned membrane samples were conducted under conditions where rotational and translational diffusion of the protein were absent on the NMR time scale. The theoretical lineshape treatment involved a static axial distribution of rotating C-C2H3 groups about the local membrane frame, together with the static axial distribution of the local normal relative to the average normal. Simulation of solid-state 2H NMR lineshapes gave both the methyl group orientations and the alignment disorder (mosaic spread) of the membrane stack. The methyl bond orientations provided the angular restraints for structural analysis. In the case of bR the retinal chromophore is nearly planar in the dark- and all-trans light-adapted states, as well upon isomerization to 13-cis in the M state. The C13-methyl group at the "business end" of the chromophore changes its orientation to the membrane upon photon absorption, moving towards W182 and thus driving the proton pump in energy conservation. Moreover, rhodopsin was studied as a prototype for G protein-coupled receptors (GPCRs) implicated in many biological responses in humans. In contrast to bR, the retinal chromophore of rhodopsin has an 11-cis conformation and is highly twisted in the dark state. Three sites of interaction affect the torsional deformation of retinal, viz. the protonated Schiff base with its carboxylate counterion; the C9-methyl group of the polyene; and the beta-ionone ring within its hydrophobic pocket. For rhodopsin, the strain energy and dynamics of retinal as established by 2H NMR are implicated in substituent control of activation. Retinal is locked in a conformation that is twisted in the direction of the photoisomerization, which explains the dark stability of rhodopsin and allows for ultra-fast isomerization upon absorption of a photon. Torsional strain is relaxed in the meta I state that precedes subsequent receptor activation. Comparison of the two retinal proteins using solid-state 2H NMR is thus illuminating in terms of their different biological functions.
Collapse
Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Janik R, Peng X, Ladizhansky V. (13)C-(13)C distance measurements in U-(13)C, (15)N-labeled peptides using rotational resonance width experiment with a homogeneously broadened matching condition. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 188:129-40. [PMID: 17644014 DOI: 10.1016/j.jmr.2007.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Revised: 06/06/2007] [Accepted: 06/06/2007] [Indexed: 05/16/2023]
Abstract
In this publication, we introduce a version of the rotational resonance width experiment with a homogeneously broadened matching condition. The increase in the bandwidth is achieved by the reduction of the proton decoupling power during mixing, which results in the reduction of zero-quantum relaxation, and broadens the rotational resonance condition. We show that one can achieve recoupling of the carbonyl-aliphatic side chain dipolar interactions band selectively, while avoiding the recoupling of strongly interacting C'-Calpha and C'-Cbeta spin pairs. The attenuation of the multi-spin effects in the presence of short zero-quantum relaxation enables a two-spin approximation to be employed for the analysis of the experimental data. The systematic error introduced by this approximation is estimated by comparing the results with a three-spin simulation. The experiment is demonstrated in [U-(13)C,(15)N]N-acetyl-L-Val-L-Leu dipeptide, where 11 distances, ranging from 2.5 to 6 A, were measured.
Collapse
Affiliation(s)
- Rafal Janik
- Department of Physics and Biophysics, Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
| | | | | |
Collapse
|