201
|
|
202
|
Loquet A, Laage S, Gardiennet C, Elena B, Emsley L, Böckmann A, Lesage A. Methyl Proton Contacts Obtained Using Heteronuclear Through-Bond Transfers in Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:10625-32. [DOI: 10.1021/ja801464g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antoine Loquet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Ségolène Laage
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Bénédicte Elena
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Lyndon Emsley
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Anne Lesage
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| |
Collapse
|
203
|
Affiliation(s)
- Cecil Dybowski*
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Shi Bai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| |
Collapse
|
204
|
Zhou DH, Rienstra CM. High-performance solvent suppression for proton detected solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 192:167-72. [PMID: 18276175 PMCID: PMC2443633 DOI: 10.1016/j.jmr.2008.01.012] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 01/23/2008] [Accepted: 01/29/2008] [Indexed: 05/05/2023]
Abstract
High-sensitivity proton detected experiments in solid-state NMR have been recently demonstrated in proton diluted proteins as well as fully protonated samples under fast magic-angle spinning. One key element for performing successful proton detection is effective solvent suppression achieved by pulsed field gradients (PFG) and/or saturation pulses. Here we report a high-performance solvent suppression method that attenuates multiple solvent signals simultaneously by more than a factor of 10,000, achieved by an optimized combination of homospoil gradients and supercycled saturation pulses. This method, which we call Multiple Intense Solvent Suppression Intended for Sensitive Spectroscopic Investigation of Protonated Proteins, Instantly (MISSISSIPPI), can be applied without a PFG probe. It opens up new opportunities for two-dimensional heteronuclear correlation spectroscopy of hydrated proteins at natural abundance as well as high-sensitivity and multi-dimensional experimental investigation of protein-solvent interactions.
Collapse
Affiliation(s)
- Donghua H. Zhou
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana,IL61801,USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana,IL61801,USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana,IL61801,USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana,IL61801,USA
- *Corresponding author. Tel: 217-244-4655, Fax: 217-244-3186, e-mail address:
| |
Collapse
|
205
|
Shi L, Peng X, Ahmed MAM, Edwards D, Brown LS, Ladizhansky V. Resolution enhancement by homonuclear J-decoupling: application to three-dimensional solid-state magic angle spinning NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2008; 41:9-15. [PMID: 18404253 DOI: 10.1007/s10858-008-9233-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 03/17/2008] [Accepted: 03/20/2008] [Indexed: 05/26/2023]
Abstract
We describe a simple protocol to achieve homonuclear J-decoupling in the indirect dimensions of multidimensional experiments, and to enhance spectral resolution of the backbone Calpha carbons in the 3D NCACX experiment. In the proposed protocol, the refocusing of the Calpha-CO homonuclear J-couplings is achieved by applying an off-resonance selective pi pulse to the CO spectral region in the middle of Calpha chemical shift evolution. As is commonly used in solution NMR, a compensatory echo period is used to refocus the unwanted chemical shift evolution of Calpha spins, which takes place during the off-resonance selective pulse. The experiments were carried out on the beta1 immunoglobulin binding domain of protein G (GB1). In GB1, such implementation results in significantly reduced line widths, and leads to an overall sensitivity enhancement.
Collapse
Affiliation(s)
- Lichi Shi
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | | | | | | | | | | |
Collapse
|
206
|
Blanc F, Basset JM, Copéret C, Sinha A, Tonzetich ZJ, Schrock RR, Solans-Monfort X, Clot E, Eisenstein O, Lesage A, Emsley L. Dynamics of Silica-Supported Catalysts Determined by Combining Solid-State NMR Spectroscopy and DFT Calculations. J Am Chem Soc 2008; 130:5886-900. [DOI: 10.1021/ja077749v] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frédéric Blanc
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Jean-Marie Basset
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Christophe Copéret
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Amritanshu Sinha
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Zachary J. Tonzetich
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Richard R. Schrock
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Xavier Solans-Monfort
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Eric Clot
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Odile Eisenstein
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Anne Lesage
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Lyndon Emsley
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| |
Collapse
|
207
|
Yang J, Tasayco ML, Polenova T. Magic Angle Spinning NMR Experiments for Structural Studies of Differentially Enriched Protein Interfaces and Protein Assemblies. J Am Chem Soc 2008; 130:5798-807. [DOI: 10.1021/ja711304e] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, and Department of Chemistry, The City College of New York, Convent Avenue at 138th Street, New York, New York 10031
| | - Maria Luisa Tasayco
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, and Department of Chemistry, The City College of New York, Convent Avenue at 138th Street, New York, New York 10031
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, and Department of Chemistry, The City College of New York, Convent Avenue at 138th Street, New York, New York 10031
| |
Collapse
|
208
|
Helmus JJ, Nadaud PS, Höfer N, Jaroniec CP. Determination of methyl 13C-15N dipolar couplings in peptides and proteins by three-dimensional and four-dimensional magic-angle spinning solid-state NMR spectroscopy. J Chem Phys 2008; 128:052314. [PMID: 18266431 DOI: 10.1063/1.2817638] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We describe three- and four-dimensional semiconstant-time transferred echo double resonance (SCT-TEDOR) magic-angle spinning solid-state nuclear magnetic resonance (NMR) experiments for the simultaneous measurement of multiple long-range (15)N-(13)C(methyl) dipolar couplings in uniformly (13)C, (15)N-enriched peptides and proteins with high resolution and sensitivity. The methods take advantage of (13)C spin topologies characteristic of the side-chain methyl groups in amino acids alanine, isoleucine, leucine, methionine, threonine, and valine to encode up to three distinct frequencies ((15)N-(13)C(methyl) dipolar coupling, (15)N chemical shift, and (13)C(methyl) chemical shift) within a single SCT evolution period of initial duration approximately 1(1)J(CC) (where (1)J(CC) approximately 35 Hz, is the one-bond (13)C(methyl)-(13)C J-coupling) while concurrently suppressing the modulation of NMR coherences due to (13)C-(13)C and (15)N-(13)C J-couplings and transverse relaxation. The SCT-TEDOR schemes offer several important advantages over previous methods of this type. First, significant (approximately twofold to threefold) gains in experimental sensitivity can be realized for weak (15)N-(13)C(methyl) dipolar couplings (corresponding to structurally interesting, approximately 3.5 A or longer, distances) and typical (13)C(methyl) transverse relaxation rates. Second, the entire SCT evolution period can be used for (13)C(methyl) and/or (15)N frequency encoding, leading to increased spectral resolution with minimal additional coherence decay. Third, the experiments are inherently "methyl selective," which results in simplified NMR spectra and obviates the use of frequency-selective pulses or other spectral filtering techniques. Finally, the (15)N-(13)C cross-peak buildup trajectories are purely dipolar in nature (i.e., not influenced by J-couplings or relaxation), which enables the straightforward extraction of (15)N-(13)C(methyl) distances using an analytical model. The SCT-TEDOR experiments are demonstrated on a uniformly (13)C, (15)N-labeled peptide, N-acetyl-valine, and a 56 amino acid protein, B1 immunoglobulin-binding domain of protein G (GB1), where the measured (15)N-(13)C(methyl) dipolar couplings provide site-specific information about side-chain dihedral angles and the packing of protein molecules in the crystal lattice.
Collapse
Affiliation(s)
- Jonathan J Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | | | | |
Collapse
|
209
|
Wylie BJ, Rienstra CM. Multidimensional solid state NMR of anisotropic interactions in peptides and proteins. J Chem Phys 2008; 128:052207. [PMID: 18266412 DOI: 10.1063/1.2834735] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Accurate determinations of chemical shift anisotropy (CSA) tensors are valuable for NMR of biological systems. In this review we describe recent developments in CSA measurement techniques and applications, particularly in the context of peptides and proteins. These techniques include goniometeric measurements of single crystals, slow magic-angle spinning studies of powder samples, and CSA recoupling under moderate to fast MAS. Experimental CSA data can be analyzed by comparison with ab initio calculations for structure determination and refinement. This approach has particularly high potential for aliphatic (13)C analysis, especially Calpha tensors which are directly related to structure. Carbonyl and (15)N CSA tensors demonstrate a more complex dependence upon hydrogen bonding and electrostatics, in addition to conformational dependence. The improved understanding of these tensors and the ability to measure them quantitatively provide additional opportunities for structure determination, as well as insights into dynamics.
Collapse
Affiliation(s)
- Benjamin J Wylie
- Department of Chemistry, Department of Biochemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | | |
Collapse
|
210
|
Bayro MJ, Ramachandran R, Caporini MA, Eddy MT, Griffin RG. Radio frequency-driven recoupling at high magic-angle spinning frequencies: homonuclear recoupling sans heteronuclear decoupling. J Chem Phys 2008; 128:052321. [PMID: 18266438 DOI: 10.1063/1.2834736] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe solid-state NMR homonuclear recoupling experiments at high magic-angle spinning (MAS) frequencies using the radio frequency-driven recoupling (RFDR) scheme. The effect of heteronuclear decoupling interference during RFDR recoupling at high spinning frequencies is investigated experimentally and via numerical simulations, resulting in the identification of optimal decoupling conditions. The effects of MAS frequency, RF field amplitude, bandwidth, and chemical shift offsets are examined. Most significantly, it is shown that broadband homonuclear correlation spectra can be efficiently obtained using RFDR without decoupling during the mixing period in fully protonated samples, thus considerably reducing the rf power requirements for acquisition of (13)C-(13)C correlation spectra. The utility of RFDR sans decoupling is demonstrated with broadband correlation spectra of a peptide and a model protein at high MAS frequencies and high magnetic field.
Collapse
Affiliation(s)
- Marvin J Bayro
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | |
Collapse
|
211
|
Qiang W, Bodner ML, Weliky DP. Solid-state NMR spectroscopy of human immunodeficiency virus fusion peptides associated with host-cell-like membranes: 2D correlation spectra and distance measurements support a fully extended conformation and models for specific antiparallel strand registries. J Am Chem Soc 2008; 130:5459-71. [PMID: 18370385 DOI: 10.1021/ja077302m] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human immunodeficiency virus (HIV) is "enveloped" by a membrane, and infection of a host cell begins with fusion between viral and target cell membranes. Fusion is catalyzed by the HIV gp41 protein which contains a functionally critical approximately 20-residue apolar "fusion peptide" (HFP) that associates with target cell membranes. In this study, chemically synthesized HFPs were associated with host-cell-like membranes and had "scatter-uniform" labeling (SUL), that is, only one residue of each amino acid type was U-(13)C, (15)N labeled. For the first sixteen HFP residues, an unambiguous (13)C chemical shift assignment was derived from 2D (13)C/(13)C correlation spectra with short mixing times, and the shifts were consistent with continuous beta-strand conformation. (13)C-(13)C contacts between residues on adjacent strands were derived from correlation spectra with long mixing times and suggested close proximity of the following residues: Ala-6/Gly-10, Ala-6/Phe-11, and Ile-4/Gly-13. Specific antiparallel beta-strand registries were further tested using a set of HFPs that were (13)CO-labeled at Ala-14 and (15)N-labeled at either Val-2, Gly-3, Ile-4, or Gly-5. The solid-state NMR data were fit with 50-60% population of antiparallel HFP with either Ala-14/Gly-3 or Ala-14/Ile-4 registries and 40-50% population of structures not specified by the NMR experiments. The first two registries correlated with intermolecular hydrogen bonding of 15-16 apolar N-terminal residues and this hydrogen-bonding pattern would be consistent with a predominant location of these residues in the hydrophobic membrane interior. To our knowledge, these results provide the first residue-specific structural models for membrane-associated HFP in its beta-strand conformation.
Collapse
Affiliation(s)
- Wei Qiang
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | | | | |
Collapse
|
212
|
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
|
213
|
Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR. Proc Natl Acad Sci U S A 2008; 105:4621-6. [PMID: 18344321 DOI: 10.1073/pnas.0712393105] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of approximately 1 A, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 +/- 0.13 A (1.52 +/- 0.12 A for all heavy atoms), which improved to 0.49 +/- 0.05 A (1.19 +/- 0.07 A) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 +/- 0.06 A bbRMSD (1.06 +/- 0.07 A); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 +/- 0.09 A; 1.29 +/- 0.07 A) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.
Collapse
|
214
|
Chevelkov V, Diehl A, Reif B. Measurement of N15-T1 relaxation rates in a perdeuterated protein by magic angle spinning solid-state nuclear magnetic resonance spectroscopy. J Chem Phys 2008; 128:052316. [DOI: 10.1063/1.2819311] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
215
|
Bodner ML, Gabrys CM, Struppe JO, Weliky DP. C13–C13 and N15–C13 correlation spectroscopy of membrane-associated and uniformly labeled human immunodeficiency virus and influenza fusion peptides: Amino acid-type assignments and evidence for multiple conformations. J Chem Phys 2008; 128:052319. [DOI: 10.1063/1.2829984] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
216
|
Li Y, Berthold DA, Gennis RB, Rienstra CM. Chemical shift assignment of the transmembrane helices of DsbB, a 20-kDa integral membrane enzyme, by 3D magic-angle spinning NMR spectroscopy. Protein Sci 2008; 17:199-204. [PMID: 18227427 PMCID: PMC2222720 DOI: 10.1110/ps.073225008] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 11/06/2007] [Accepted: 11/10/2007] [Indexed: 10/22/2022]
Abstract
The Escherichia coli inner membrane enzyme DsbB catalyzes disulfide bond formation in periplasmic proteins, by transferring electrons to ubiquinone from DsbA, which in turn directly oxidizes cysteines in substrate proteins. We have previously shown that DsbB can be prepared in a state that gives highly resolved magic-angle spinning (MAS) NMR spectra. Here we report sequential 13C and 15N chemical shift assignments for the majority of the residues in the transmembrane helices, achieved by three-dimensional (3D) correlation experiments on a uniformly 13C, 15N-labeled sample at 750-MHz 1H frequency. We also present a four-dimensional (4D) correlation spectrum, which confirms assignments in some highly congested regions of the 3D spectra. Overall, our results show the potential to assign larger membrane proteins using 3D and 4D correlation experiments and form the basis of further structural and dynamical studies of DsbB by MAS NMR.
Collapse
Affiliation(s)
- Ying Li
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | | | | |
Collapse
|
217
|
Huang L, McDermott AE. Partial site-specific assignment of a uniformly (13)C, (15)N enriched membrane protein, light-harvesting complex 1 (LH1), by solid state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1098-108. [PMID: 18267103 DOI: 10.1016/j.bbabio.2008.01.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 01/02/2008] [Accepted: 01/03/2008] [Indexed: 10/22/2022]
Abstract
Partial site-specific assignments are reported for the solid state NMR spectra of light-harvesting complex 1, a 160 kDa integral membrane protein. The assignments were derived from 600 MHz (15)N-(13)CO-(13)Calpha and (15)N-(13)Calpha-(13)CX correlation spectra, using uniformly (13)C, (15)N enriched hydrated material, in an intact and precipitated form. Sequential assignments were verified using characteristic (15)N-(13)Calpha-(13)Cbeta side chain chemical shifts observed in 3D experiments. Tertiary contacts found in 2D DARR spectra of the selectively (13)C enriched sample provided further confirmatory evidence for the assignments. The assignments include the region of the Histidine ligands binding the Bacteriochlorophyll chromophore. The chemical shifts of Calpha and Cbeta resonances indicated the presence of typical alpha-helical secondary structure, consistent with previous studies.
Collapse
Affiliation(s)
- Lei Huang
- Key Laboratory of Molecular Engineering of Polymers of the Ministry of Education, Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | | |
Collapse
|
218
|
Mehta MA, Eddy MT, McNeill SA, Mills FD, Long JR. Determination of Peptide Backbone Torsion Angles Using Double-Quantum Dipolar Recoupling Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:2202-12. [DOI: 10.1021/ja074244w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Manish A. Mehta
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Matthew T. Eddy
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Seth A. McNeill
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Frank D. Mills
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Joanna R. Long
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| |
Collapse
|
219
|
Zhou DH, Shea JJ, Nieuwkoop AJ, Franks WT, Wylie BJ, Mullen C, Sandoz D, Rienstra CM. Solid-state protein-structure determination with proton-detected triple-resonance 3D magic-angle-spinning NMR spectroscopy. Angew Chem Int Ed Engl 2008; 46:8380-3. [PMID: 17907259 PMCID: PMC2790053 DOI: 10.1002/anie.200702905] [Citation(s) in RCA: 196] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Donghua H. Zhou
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 (USA)
| | - John J. Shea
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana, IL 61801 (USA)
| | - Andrew J. Nieuwkoop
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana, IL 61801 (USA)
| | - W. Trent Franks
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana, IL 61801 (USA)
| | - Benjamin J. Wylie
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 (USA)
| | | | | | - Chad M. Rienstra
- Fax: (+1) 217-244-4655, E-mail: , http://www.scs.uiuc.edu/~rienstra
| |
Collapse
|
220
|
Schmidt HLF, Sperling LJ, Gao YG, Wylie BJ, Boettcher JM, Wilson SR, Rienstra CM. Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction. J Phys Chem B 2007; 111:14362-9. [PMID: 18052145 PMCID: PMC2774121 DOI: 10.1021/jp075531p] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of micro- or nanocrystalline proteins by magic-angle spinning (MAS) solid-state NMR (SSNMR) gives atomic-resolution insight into structure in cases when single crystals cannot be obtained for diffraction studies. Subtle differences in the local chemical environment around the protein, including the characteristics of the cosolvent and the buffer, determine whether a protein will form single crystals. The impact of these small changes in formulation is also evident in the SSNMR spectra; however, the changes lead only to correspondingly subtle changes in the spectra. Here, we demonstrate that several formulations of GB1 microcrystals yield very high quality SSNMR spectra, although only a subset of conditions enable growth of single crystals. We have characterized these polymorphs by X-ray powder diffraction and assigned the SSNMR spectra. Assignments of the 13C and 15N SSNMR chemical shifts confirm that the backbone structure is conserved, indicative of a common protein fold, but side chain chemical shifts are changed on the surface of the protein, in a manner dependent upon crystal packing and electrostatic interactions with salt in the mother liquor. Our results demonstrate the ability of SSNMR to reveal minor structural differences among crystal polymorphs. This ability has potential practical utility for studying the formulation chemistry of industrial and therapeutic proteins, as well as for deriving fundamental insights into the phenomenon of single-crystal growth.
Collapse
Affiliation(s)
- Heather L Frericks Schmidt
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61821, USA
| | | | | | | | | | | | | |
Collapse
|
221
|
|
222
|
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
|
223
|
Chevelkov V, Diehl A, Reif B. Quantitative measurement of differential 15N-H(alpha/beta)T2 relaxation rates in a perdeuterated protein by MAS solid-state NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S156-60. [PMID: 18157805 DOI: 10.1002/mrc.2129] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Dynamic parameters become more and more accessible in the study of uniformly isotopically enriched proteins by MAS solid-state NMR. We demonstrate that T(2)-related relaxation properties can quantitatively be determined in a sample of a perdeuterated microcrystalline protein by the measurement of (15)N,(1)H dipole, (15)N CSA cross-correlated relaxation rates. We find that the measured cross-correlated relaxation rates are independent of the MAS rotation frequency, and therefore reflect local dynamic fluctuations of the protein structure.
Collapse
|
224
|
Yang J, Paramasivam S, Marulanda D, Cataldi M, Tasayco ML, Polenova T. Magic angle spinning NMR spectroscopy of thioredoxin reassemblies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S73-S83. [PMID: 18157811 DOI: 10.1002/mrc.2092] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Differentially isotopically enriched 1-73((13)C,(15)N)/74-108((15)N) and 1-73((15)N)/74-108((13)C,(15)N) Escherichia coli thioredoxin reassemblies prepared by fragment complementation were investigated by high-resolution magic angle spinning solid-state NMR spectroscopy. Nearly complete resonance assignments, secondary and tertiary structure analysis are reported for 1-73((13)C,(15)N)/74-108((15)N) reassembled thioredoxin. Temperature dependence of the dipolar-assisted rotational resonance (DARR) spectra reveals the residues undergoing intermediate timescale motions at temperatures below - 15 degrees C. Analysis of the DARR intensity buildups as a function of mixing time in these reassemblies indicates that at long mixing times medium- and long-range cross-peaks do not experience dipolar truncation, suggesting that isotopic dilution is not required for gaining nontrivial distance restraints for structure calculations.
Collapse
Affiliation(s)
- Jun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | | | | | | | | | | |
Collapse
|
225
|
Graesser DT, Wylie BJ, Nieuwkoop AJ, Franks WT, Rienstra CM. Long-range 19F-15N distance measurements in highly-13C, 15N-enriched solid proteins with 19F-dephased REDOR shift (FRESH) spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S129-S134. [PMID: 18157807 DOI: 10.1002/mrc.2126] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We present a novel rotational-echo double resonance (REDOR) method for detection of multiple (19)F-(15)N distances in solid proteins. The method is applicable to protein samples containing a single (19)F label, in addition to high levels of (13)C and (15)N enrichment. REDOR dephasing pulses are applied on the (19)F channel during an indirect constant time chemical shift evolution period on (15)N, and polarization is then transferred to (13)C for detection, with high-power (1)H decoupling throughout the sequence. This four-channel experiment reports site-specifically on (19)F-(15)N distances, with highly accurate determinations of approximately 5 A distances and detection of correlations arising from internuclear distances of at least 8 A. We demonstrate the method on the well-characterized 56-residue model protein GB1, where the sole tryptophan residue (Trp-43) has been labeled with 5-(19)F-Trp, in a bacterial growth medium also including (13)C-glucose and (15)N ammonium chloride. In GB1, 11 distances are determined, all agreeing within 20% of the X-ray structure distances. We envision the experiment will be utilized to measure quantitative long-range distances for protein structure determination.
Collapse
Affiliation(s)
- Daniel T Graesser
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 68101, USA
| | | | | | | | | |
Collapse
|
226
|
McNeill SA, Gor'kov PL, Struppe J, Brey WW, Long JR. Optimizing ssNMR experiments for dilute proteins in heterogeneous mixtures at high magnetic fields. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S209-20. [PMID: 18157844 DOI: 10.1002/mrc.2146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Solid-state NMR spectroscopy at high magnetic fields is proving to be an effective technique in structural biology, particularly for proteins which are not amenable to traditional X-ray and solution NMR approaches. Several parameters can be selected to provide optimal sensitivity, improve sample stability, and ensure biological relevance for ssNMR measurements on protein samples. These include selection of sample conditions, NMR probe design, and design of pulse experiments. Here, we demonstrate and evaluate several engineering and experimental approaches for pursuing measurements on dilute proteins in heterogeneous mixtures.
Collapse
Affiliation(s)
- Seth A McNeill
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | | | | | | | | |
Collapse
|
227
|
Chen L, Kaiser JM, Lai J, Polenova T, Yang J, Rienstra CM, Mueller LJ. J-based 2D homonuclear and heteronuclear correlation in solid-state proteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S84-S92. [PMID: 18157839 DOI: 10.1002/mrc.2107] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Scalar-based two-dimensional heteronuclear experiments are reported for NCO and NCA chemical shift correlation in the solid state. In conjunction with homonuclear CACO correlation, these experiments form a useful set for tracing connectivities and assigning backbone resonances in solid-state proteins. The applicability of this approach is demonstrated on two proteins, the β 1 immunoglobulin binding domain of protein G at 9.4 T and reassembled thioredoxin at 14.1 T, using different decoupling conditions and MAS frequencies. These constant-time J-based correlation experiments exhibit increased resolution in the indirect dimension owing to homonuclear and heteronuclear decoupling, and because the indirect evolution and transfer periods are combined into a single constant time interval, this increased resolution is not obtained at the cost of sensitivity. These experiments are also shown to be compatible with in-phase anti-phase (IPAP) selection, giving increased resolution in the directly detected dimension.
Collapse
Affiliation(s)
- Lingling Chen
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | | | | | | | | | | | | |
Collapse
|
228
|
Dürr UH, Waskell L, Ramamoorthy A. The cytochromes P450 and b5 and their reductases—Promising targets for structural studies by advanced solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3235-59. [DOI: 10.1016/j.bbamem.2007.08.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/08/2007] [Indexed: 02/02/2023]
|
229
|
Böckmann A. High-resolution solid-state MAS NMR of proteins-Crh as an example. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S24-S31. [PMID: 18081212 DOI: 10.1002/mrc.2106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 09/04/2007] [Accepted: 09/12/2007] [Indexed: 05/25/2023]
Abstract
Solid-state NMR spectroscopy provides unique possibilities for the structural investigation of insoluble molecules at the atomic level. Recent efforts aim at solving the complete structures of biological macromolecules using high-resolution magic angle spinning NMR. Structurally homogenous samples of [(13)C,(15)N]-labeled proteins have to be used in this type of studies. Microcrystalline model proteins present valuable tools for the developments of methods towards this goal. This review discusses recent progress in the field, using the Crh protein as an illustrative example. We discuss strategies for resonance assignments and for the determination of structure and dynamics, as well as techniques for the detection of protein interaction partners and folding mechanisms by solid-state NMR methods.
Collapse
Affiliation(s)
- Anja Böckmann
- IFR 128 BioSciences Lyon-Gerland, IBCP UMR 5086 CNRS/Université de Lyon Claude Bernard, 7 passage du Vercors, 69367 Lyon, France.
| |
Collapse
|
230
|
Zhou D, Shea J, Nieuwkoop A, Franks W, Wylie B, Mullen C, Sandoz D, Rienstra C. Solid-State Protein-Structure Determination with Proton-Detected Triple-Resonance 3D Magic-Angle-Spinning NMR Spectroscopy. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702905] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
231
|
Kijac AZ, Li Y, Sligar SG, Rienstra CM. Magic-angle spinning solid-state NMR spectroscopy of nanodisc-embedded human CYP3A4. Biochemistry 2007; 46:13696-703. [PMID: 17985934 DOI: 10.1021/bi701411g] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome P450 (CYP) 3A4 contributes to the metabolism of approximately 50% of commercial drugs by oxidizing a large number of structurally diverse substrates. Like other endoplasmic reticulum-localized P450s, CYP3A4 contains a membrane-anchoring N-terminal helix and a significant number of hydrophobic domains, important for the interaction between CYP3A4 and the membrane. Although the membrane affects specificity of CYP3A4 ligand binding, the structural details of the interaction have not been revealed so far because X-ray crystallography studies are available only for the soluble domain of CYP3A4. Here we report sample preparation and initial magic-angle spinning (MAS) solid-state NMR (SSNMR) of CYP3A4 (Delta3-12) embedded in a nanoscale membrane bilayer, or Nanodisc. The growth protocol yields approximately 2.5 mg of the enzymatically active, uniformly 13C,15N-enriched CYP3A4 from 1 L of growth medium. Polyethylene glycol 3350-precipitated CYP3A4 in Nanodiscs yields spectra of high resolution and sensitivity, consistent with a folded, homogeneous protein. CYP3A4 in Nanodiscs remains enzymatically active throughout the precipitation protocol as monitored by bromocriptine binding. The 13C line widths measured from 13C-13C 2D chemical shift correlation spectra are approximately 0.5 ppm. The secondary structure distribution within several amino acid types determined from 13C chemical shifts is consistent with the ligand-free X-ray structures. These results demonstrate that MAS SSNMR can be performed on Nanodisc-embedded membrane proteins in a folded, active state. The combination of SSNMR and Nanodisc methodologies opens up new possibilities for obtaining structural information on CYP3A4 and other integral membrane proteins with full retention of functionality.
Collapse
Affiliation(s)
- Aleksandra Z Kijac
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 618001, USA
| | | | | | | |
Collapse
|
232
|
Kloepper KD, Hartman KL, Ladror DT, Rienstra CM. Solid-state NMR spectroscopy reveals that water is nonessential to the core structure of alpha-synuclein fibrils. J Phys Chem B 2007; 111:13353-6. [PMID: 17985869 DOI: 10.1021/jp077036z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein aggregation is implicated in the etiology of numerous neurodegenerative diseases. An understanding of aggregation mechanisms is enhanced by atomic-resolution structural information, of which relatively little is currently available. Lewy bodies, the pathological hallmark of Parkinson's disease, contain large quantities of fibrillar alpha-synuclein (AS). Here we present solid-state NMR spectroscopy studies of dried AS fibrils. The spectra have high resolution and sensitivity, and the site-resolved chemical shifts agree very well with those previously observed for hydrated fibrils. The conserved chemical shifts indicate that bulk water is nonessential to the fibril core structure. Moreover, the sample preparation procedure yields major improvements in spectral sensitivity, without compromising spectral resolution. This advance will greatly assist the atomic-resolution structural analysis of AS fibrils.
Collapse
Affiliation(s)
- Kathryn D Kloepper
- Department of Chemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | | | | |
Collapse
|
233
|
Wylie BJ, Sperling LJ, Rienstra CM. Isotropic chemical shifts in magic-angle spinning NMR spectra of proteins. Phys Chem Chem Phys 2007; 10:405-13. [PMID: 18174982 DOI: 10.1039/b710736f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we examine the effect of magic-angle spinning (MAS) rate upon lineshape and observed peak position for backbone carbonyl (C') peaks in NMR spectra of uniformly-(13)C,15N-labeled (U-(13)C,15N) solid proteins. 2D N-C' spectra of U-(13)C,15N microcrystalline protein GB1 were acquired at six MAS rates, and the site-resolved C' lineshapes were analyzed by numerical simulations and comparison to spectra from a sparsely labeled sample (derived from 1,3-(13)C-glycerol). Spectra of the U-(13)C,15N sample demonstrate large variations in the signal-to-noise ratio and peak positions, which are absent in spectra of the sparsely labeled sample, in which most 13C' sites do not possess a directly bonded 13CA. These effects therefore are a consequence of rotational resonance, which is a well-known phenomenon. Yet the magnitude of this effect pertaining to chemical shift assignment has not previously been examined. To quantify these effects in high-resolution protein spectra, we performed exact numerical two- and four-spin simulations of the C' lineshapes, which reproduced the experimentally observed features. Observed peak positions differ from the isotropic shift by up to 1.0 ppm, even for MAS rates relatively far (a few ppm) from rotational resonance. Although under these circumstances the correct isotropic chemical shift values may be determined through simulation, systematic errors are minimized when the MAS rate is equivalent to approximately 85 ppm for 13C. This moderate MAS condition simplifies spectral assignment and enables data sets from different labeling patterns and spinning rates to be used most efficiently for structure determination.
Collapse
Affiliation(s)
- Benjamin J Wylie
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | | | | |
Collapse
|
234
|
Kloepper KD, Zhou DH, Li Y, Winter KA, George JM, Rienstra CM. Temperature-dependent sensitivity enhancement of solid-state NMR spectra of alpha-synuclein fibrils. JOURNAL OF BIOMOLECULAR NMR 2007; 39:197-211. [PMID: 17899395 DOI: 10.1007/s10858-007-9189-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 08/09/2007] [Indexed: 05/11/2023]
Abstract
The protein alpha-synuclein (AS) is the primary fibrillar component of Lewy bodies, the pathological hallmark of Parkinson's disease. Wild-type human AS and the three mutant forms linked to Parkinson's disease (A53T, A30P, and E46K) all form fibrils through a nucleation-dependent pathway; however, the biophysical details of these fibrillation events are not yet well understood. Atomic-level structural insight is required in order to elucidate the potential role of AS fibrils in Parkinson's disease. Here we show that low temperature acquisition of magic-angle spinning NMR spectra of wild type AS fibrils-greatly enhances spectral sensitivity, enabling the detection of a substantially larger number of spin systems. At 0 +/- 3 degrees C sample temperature, cross polarization (CP) experiments yield weak signals. Lower temperature spectra (-40 +/- 3 degrees C) demonstrated several times greater signal intensity, an effect further amplified in 3D 15N-13C-13C experiments, which are required to perform backbone assignments on this sample. Thus 3D experiments enabled assignments of most amino acids in the rigid part of the fibril (approximately residues 64 to 94), as well as tentative site-specific assignments for T22, V26, A27, Y39, G41, S42, H50, V52, A53, T54, V55, V63, A107, I112, and S129. Most of these signals were not observed in 2D or 3D spectra at 0 +/- 3 degrees C. Spectra acquired at low temperatures therefore permitted more complete chemical shift assignments. Observation of the majority of residues in AS fibrils represents an important step towards solving the 3D structure.
Collapse
Affiliation(s)
- Kathryn D Kloepper
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | | | | | | | | | | |
Collapse
|
235
|
Shastri S, Vonck J, Pfleger N, Haase W, Kuehlbrandt W, Glaubitz C. Proteorhodopsin: characterisation of 2D crystals by electron microscopy and solid state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3012-9. [PMID: 17964280 DOI: 10.1016/j.bbamem.2007.10.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 09/29/2007] [Accepted: 10/02/2007] [Indexed: 11/15/2022]
Abstract
Proteorhodopsin (PR) a recent addition to retinal type 1 protein family, is a bacterial homologue of archaeal bacteriorhodopsin. It was found to high abundance in gamma-proteobacteria in the photic zone of the oceans and has been shown to act as a photoactive proton pump. It is therefore involved in the utilisation of light energy for energy production within the cell. Based on data from biodiversity screens, hundreds of variants were discovered worldwide, which are spectrally tuned to the available light at different locations in the sea. Here, we present a characterisation of 2D crystals of the green variant of proteorhodopsin by electron microscopy and solid state NMR. 2D crystal formation with hexagonal protein packing was observed under a very wide range of conditions indicating that PR might be also closely packed under native conditions. A low-resolution 2D projection map reveals a ring-shaped oligomeric assembly of PR. The protein state was analysed by 15N MAS NMR on lysine, tryptophan and methionine labelled samples. The chemical shift of the protonated Schiff base was almost identical to non-crystalline preparations. All residues could be cross-polarised in non-frozen samples. Lee-Goldberg cross-polarisation has been used to probe protein backbone mobility.
Collapse
Affiliation(s)
- Sarika Shastri
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe University, Max von Laue Str. 9, D-60438 Frankfurt am Main, Germany
| | | | | | | | | | | |
Collapse
|
236
|
Franks WT, Kloepper KD, Wylie BJ, Rienstra CM. Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins. JOURNAL OF BIOMOLECULAR NMR 2007; 39:107-31. [PMID: 17687624 DOI: 10.1007/s10858-007-9179-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 07/05/2007] [Accepted: 07/10/2007] [Indexed: 05/16/2023]
Abstract
Chemical shift assignment is the first step in all established protocols for structure determination of uniformly labeled proteins by NMR. The explosive growth in recent years of magic-angle spinning (MAS) solid-state NMR (SSNMR) applications is largely attributable to improved methods for backbone and side-chain chemical shift correlation spectroscopy. However, the techniques developed so far have been applied primarily to proteins in the size range of 5-10 kDa, despite the fact that SSNMR has no inherent molecular weight limits. Rather, the degeneracy inherent to many 2D and 3D SSNMR spectra of larger proteins has prevented complete unambiguous chemical shift assignment. Here we demonstrate the implementation of 4D backbone chemical shift correlation experiments for assignment of solid proteins. The experiments greatly reduce spectral degeneracy at a modest cost in sensitivity, which is accurately described by theory. We consider several possible implementations and investigate the CANCOCX pulse sequence in detail. This experiment involves three cross polarization steps, from H to CA[i], CA[i] to N[i], and N[i] to C'[i-1], followed by a final homonuclear mixing period. With short homonuclear mixing times (<20 ms), backbone correlations are observed with high sensitivity; with longer mixing times (>200 ms), long-range correlations are revealed. For example, a single 4D experiment with 225 ms homonuclear mixing time reveals approximately 200 uniquely resolved medium and long-range correlations in the 56-residue protein GB1. In addition to experimental demonstrations in the 56-residue protein GB1, we present a theoretical analysis of anticipated improvements in resolution for much larger proteins and compare these results in detail with the experiments, finding good agreement between experiment and theory under conditions of stable instrumental performance.
Collapse
Affiliation(s)
- W Trent Franks
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | | | | | | |
Collapse
|
237
|
Rupasinghe SG, Duan H, Frericks Schmidt HL, Berthold DA, Rienstra CM, Schuler MA. High-yield expression and purification of isotopically labeled cytochrome P450 monooxygenases for solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3061-70. [PMID: 18005930 DOI: 10.1016/j.bbamem.2007.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2007] [Revised: 09/11/2007] [Accepted: 09/13/2007] [Indexed: 10/22/2022]
Abstract
Cytochrome P450 monooxygenases (P450s), which represent the major group of drug metabolizing enzymes in humans, also catalyze important synthetic and detoxicative reactions in insects, plants and many microbes. Flexibilities in their catalytic sites and membrane associations are thought to play central roles in substrate binding and catalytic specificity. To date, Escherichia coli expression strategies for structural analysis of eukaryotic membrane-bound P450s by X-ray crystallography have necessitated full or partial removal of their N-terminal signal anchor domain and, often, replacement of residues more peripherally associated with the membrane (such as the F-G loop region). Even with these modifications, investigations of P450 structural flexibility remain challenging with multiple single crystal conditions needed to identify spatial variations between substrate-free and different substrate-bound forms. To overcome these limitations, we have developed methods for the efficient expression of 13C- and 15N-labeled P450s and analysis of their structures by magic-angle spinning solid-state NMR (SSNMR) spectroscopy. In the presence of co-expressed GroEL and GroES chaperones, full-length (53 kDa) Arabidopsis 13C,15N-labeled His4CYP98A3 is expressed at yields of 2-4 mg per liter of minimal media without the necessity of generating side chain modifications or N-terminal deletions. Precipitated His4CYP98A3 generates high quality SSNMR spectra consistent with a homogeneous, folded protein. These data highlight the potential of these methodologies to contribute to the structural analysis of membrane-bound proteins.
Collapse
Affiliation(s)
- Sanjeewa G Rupasinghe
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA
| | | | | | | | | | | |
Collapse
|
238
|
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.
Collapse
Affiliation(s)
- Krisztina Varga
- Department of Chemistry, Columbia University, 3000 Broadway MC 3113, New York, NY 10027, USA
| | | | | |
Collapse
|
239
|
Zhou DH, Shah G, Cormos M, Mullen C, Sandoz D, Rienstra CM. Proton-detected solid-state NMR spectroscopy of fully protonated proteins at 40 kHz magic-angle spinning. J Am Chem Soc 2007; 129:11791-801. [PMID: 17725352 DOI: 10.1021/ja073462m] [Citation(s) in RCA: 212] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Remarkable progress in solid-state NMR has enabled complete structure determination of uniformly labeled proteins in the size range of 5-10 kDa. Expanding these applications to larger or mass-limited systems requires further improvements in spectral sensitivity, for which inverse detection of 13C and 15N signals with 1H is one promising approach. Proton detection has previously been demonstrated to offer sensitivity benefits in the limit of sparse protonation or with approximately 30 kHz magic-angle spinning (MAS). Here we focus on experimental schemes for proteins with approximately 100% protonation. Full protonation simplifies sample preparation and permits more complete chemical shift information to be obtained from a single sample. We demonstrate experimental schemes using the fully protonated, uniformly 13C,15N-labeled protein GB1 at 40 kHz MAS rate with 1.6-mm rotors. At 500 MHz proton frequency, 1-ppm proton line widths were observed (500 +/- 150 Hz), and the sensitivity was enhanced by 3 and 4 times, respectively, versus direct 13C and 15N detection. The enhanced sensitivity enabled a family of 3D experiments for spectral assignment to be performed in a time-efficient manner with less than a micromole of protein. CANH, CONH, and NCAH 3D spectra provided sufficient resolution and sensitivity to make full backbone and partial side-chain proton assignments. At 750 MHz proton frequency and 40 kHz MAS rate, proton line widths improve further in an absolute sense (360 +/- 115 Hz). Sensitivity and resolution increase in a better than linear manner with increasing magnetic field, resulting in 14 times greater sensitivity for 1H detection relative to that of 15N detection.
Collapse
Affiliation(s)
- Donghua H Zhou
- Department of Chemistry, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | | | | | | | | |
Collapse
|
240
|
Zhong L, Bamm VV, Ahmed MAM, Harauz G, Ladizhansky V. Solid-state NMR spectroscopy of 18.5 kDa myelin basic protein reconstituted with lipid vesicles: spectroscopic characterisation and spectral assignments of solvent-exposed protein fragments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3193-205. [PMID: 17920035 DOI: 10.1016/j.bbamem.2007.08.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Revised: 08/10/2007] [Accepted: 08/10/2007] [Indexed: 10/22/2022]
Abstract
Myelin basic protein (MBP, 18.5 kDa isoform) is a peripheral membrane protein that is essential for maintaining the structural integrity of the multilamellar myelin sheath of the central nervous system. Reconstitution of the most abundant 18.5 kDa MBP isoform with lipid vesicles yields an aggregated assembly mimicking the protein's natural environment, but which is not amenable to standard solution NMR spectroscopy. On the other hand, the mobility of MBP in such a system is variable, depends on the local strength of the protein-lipid interaction, and in general is of such a time scale that the dipolar interactions are averaged out. Here, we used a combination of solution and solid-state NMR (ssNMR) approaches: J-coupling-driven polarization transfers were combined with magic angle spinning and high-power decoupling to yield high-resolution spectra of the mobile fragments of 18.5 kDa murine MBP in membrane-associated form. To partially circumvent the problem of short transverse relaxation, we implemented three-dimensional constant-time correlation experiments (NCOCX, NCACX, CONCACX, and CAN(CO)CX) that were able to provide interresidue and intraresidue backbone correlations. These experiments resulted in partial spectral assignments for mobile fragments of the protein. Additional nuclear Overhauser effect spectroscopy (NOESY)-based experiments revealed that the mobile fragments were exposed to solvent and were likely located outside the lipid bilayer, or in its hydrophilic portion. Chemical shift index analysis showed that the fragments were largely disordered under these conditions. These combined approaches are applicable to ssNMR investigations of other peripheral membrane proteins reconstituted with lipids.
Collapse
Affiliation(s)
- Ligang Zhong
- Department of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
| | | | | | | | | |
Collapse
|
241
|
Ramachandran R, Griffin RG. Description of depolarization effects in double-quantum solid state nuclear magnetic resonance experiments using multipole-multimode Floquet theory. J Chem Phys 2007; 125:44510. [PMID: 16942159 DOI: 10.1063/1.2216711] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using an analytical model based on multipole-multimode Floquet theory (MMFT), we describe the polarization loss (or depolarization) observed in double-quantum (DQ) dipolar recoupling magic angle spinning (MAS) experiments. Specifically, the factors responsible for depolarization are analyzed in terms of higher order corrections to the spin Hamiltonian in addition to the usual phenomenological decay rate constant. From the MMFT model and the effective Hamiltonians, we elucidate the rationale behind the inclusion of a phenomenological damping term in DQ recoupling experiments. As a test of this theoretical approach, the recoupling efficiency of one class of (13)C-(13)C and (13)C-(15)N resonance width dipolar recoupling experiments are investigated at different magnetic field strengths and compared with the more exact numerical simulations. In contrast to existing analytical treatments, the role of higher order corrections is clearly explained in the context of the MMFT approach leading to a better understanding of the underlying spin physics. Furthermore, the analytical model presented herein provides a general framework for describing coherent and incoherent effects in homonuclear and heteronuclear DQ MAS recoupling experiments.
Collapse
Affiliation(s)
- Ramesh Ramachandran
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | |
Collapse
|
242
|
Chen L, Kaiser JM, Polenova T, Yang J, Rienstra CM, Mueller LJ. Backbone Assignments in Solid-State Proteins Using J-Based 3D Heteronuclear Correlation Spectroscopy. J Am Chem Soc 2007; 129:10650-1. [PMID: 17691789 DOI: 10.1021/ja073498e] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lingling Chen
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | | | | | | | | | | |
Collapse
|
243
|
Matsuki Y, Akutsu H, Fujiwara T. Spectral fitting for signal assignment and structural analysis of uniformly 13C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics. JOURNAL OF BIOMOLECULAR NMR 2007; 38:325-39. [PMID: 17612797 DOI: 10.1007/s10858-007-9170-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 05/24/2007] [Indexed: 05/16/2023]
Abstract
We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional (13)C-(13)C magic-angle-spinning solid-state NMR spectra of uniformly (13)C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent chemical shift obtained with SHIFTX and the cross-peak intensities computed for recoupled dipolar interactions. This method was applied to a membrane-bound 14-residue peptide, mastoparan-X. The obtained C', C(alpha) and C(beta) chemical shifts agreed with those reported previously at the precisions of 0.2, 0.7 and 0.4 ppm, respectively. This spectral fitting program also provides backbone dihedral angles with a precision of about 50 degrees from the spectra even with resonance overlaps. The restraints on the angles were improved by applying protein database program TALOS to the obtained chemical shifts. The peptide structure provided by these restraints was consistent with the reported structure at the backbone RMSD of about 1 A.
Collapse
Affiliation(s)
- Yoh Matsuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | | | | |
Collapse
|
244
|
Chen L, Olsen RA, Elliott DW, Boettcher JM, Zhou DH, Rienstra CM, Mueller LJ. Constant-time through-bond 13C correlation spectroscopy for assigning protein resonances with solid-state NMR spectroscopy. J Am Chem Soc 2007; 128:9992-3. [PMID: 16881610 DOI: 10.1021/ja062347t] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Even as available magnetic fields for NMR continue to increase, resolution remains one of the most critical limitations in assigning and solving structures of larger biomolecules. Here we present a novel constant-time through-bond correlation spectroscopy for solids that offers superior resolution for 13C chemical shift assignments in proteins. In this experiment, the indirect evolution and transfer periods are combined into a single constant time interval, offering increased resolution while not sacrificing sensitivity. In GB1, this allows us to resolve peaks that are otherwise unresolved and to make assignments in the absence of multibond transfers.
Collapse
Affiliation(s)
- Lingling Chen
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | | | | | | | | | | | | |
Collapse
|
245
|
Nadaud PS, Helmus JJ, Jaroniec CP. 13C and 15N chemical shift assignments and secondary structure of the B3 immunoglobulin-binding domain of streptococcal protein G by magic-angle spinning solid-state NMR spectroscopy. BIOMOLECULAR NMR ASSIGNMENTS 2007; 1:117-120. [PMID: 19636843 DOI: 10.1007/s12104-007-9041-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 06/29/2007] [Indexed: 05/28/2023]
Abstract
Complete 13C and 15N assignments of the B3 IgG-binding domain of protein G (GB3) in the microcrystalline solid phase, obtained using 2D and 3D MAS NMR, are presented. The chemical shifts are used to predict the protein backbone conformation and compared with solution-state shifts.
Collapse
Affiliation(s)
- Philippe S Nadaud
- Department of Chemistry, The Ohio State University, 1035 Evans Laboratory, 100 West 18th Avenue, Columbus, OH 43210, USA
| | | | | |
Collapse
|
246
|
Nadaud PS, Helmus JJ, Höfer N, Jaroniec CP. Long-range structural restraints in spin-labeled proteins probed by solid-state nuclear magnetic resonance spectroscopy. J Am Chem Soc 2007; 129:7502-3. [PMID: 17530852 DOI: 10.1021/ja072349t] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philippe S Nadaud
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | | | | |
Collapse
|
247
|
Qiang W, Yang J, Weliky DP. Solid-state nuclear magnetic resonance measurements of HIV fusion peptide to lipid distances reveal the intimate contact of beta strand peptide with membranes and the proximity of the Ala-14-Gly-16 region with lipid headgroups. Biochemistry 2007; 46:4997-5008. [PMID: 17417873 PMCID: PMC2631438 DOI: 10.1021/bi6024808] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus (HIV) infection begins with fusion between viral and host cell membranes and is catalyzed by the HIV gp41 fusion protein. The approximately 20 N-terminal apolar residues of gp41 are called the HIV fusion peptide (HFP), interact with the host cell membrane, and play a key role in fusion. In this study, the membrane location of peptides which contained the HFP sequence (AVGIGALFLGFLGAAGSTMGARS) was probed in samples containing either only phospholipids or phospholipids and cholesterol. Four HFPs were examined which each contained 13CO labeling at three sequential residues between G5 and G16. The 13CO chemical shifts indicated that HFP had predominant beta strand conformation over the labeled residues in the samples. The internuclear distances between the HFP 13CO groups and the lipid 31P atoms were measured using solid-state nuclear magnetic resonance rotational-echo double-resonance experiments. The shortest 13CO-31P distances of 5-6 A were observed for HFP labeled between A14 and G16 and correlated with intimate association of beta strand HFP and membranes. These results were confirmed with measurements using HFPs singly labeled with 13CO at A6 or A14. To our knowledge, these data are the first measurements of distances between HIV fusion peptide nuclei and lipid P, and qualitative models of the membrane location of oligomeric beta strand HFP which are consistent with the experimental data are presented. Observation of intimate contact between beta strand HFP and membranes provides a rationale for further investigation of the relationship between structure and fusion activity for this conformation.
Collapse
Affiliation(s)
- Wei Qiang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| | - Jun Yang
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - David P. Weliky
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| |
Collapse
|
248
|
Abstract
Constant-time dipolar recoupling pulse sequences are advantageous in structural studies by solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) because they yield experimental data that are relatively insensitive to radio-frequency pulse imperfections and nuclear spin relaxation processes. A new approach to the construction of constant-time homonuclear dipolar recoupling sequences is described, based on symmetry properties of the recoupled dipole-dipole interaction Hamiltonian under cyclic displacements in time with respect to the MAS sample rotation period. A specific symmetry-based pulse sequence called PITHIRDS-CT is introduced and demonstrated experimentally. (13)C NMR data for singly-(13)C-labeled amino acid powders and amyloid fibrils indicate the effectiveness of PITHIRDS-CT in measurements of intermolecular distances in solids. (15)N-detected and (13)C-detected measurements of intramolecular (15)N-(15)N distances in peptides with alpha-helical and beta-sheet structures indicate the utility of PITHIRDS-CT in studies of molecular conformations, especially measurements of backbone psi torsion angles in peptides containing uniformly (15)N- and (13)C-labeled amino acids.
Collapse
Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
| |
Collapse
|
249
|
Wylie BJ, Sperling LJ, Frericks HL, Shah GJ, Franks WT, Rienstra CM. Chemical-Shift Anisotropy Measurements of Amide and Carbonyl Resonances in a Microcrystalline Protein with Slow Magic-Angle Spinning NMR Spectroscopy. J Am Chem Soc 2007; 129:5318-9. [PMID: 17425317 DOI: 10.1021/ja0701199] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin J Wylie
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | | | | | | | | | | |
Collapse
|
250
|
Werner K, Lehner I, Dhiman HK, Richter C, Glaubitz C, Schwalbe H, Klein-Seetharaman J, Khorana HG. Combined solid state and solution NMR studies of alpha,epsilon-15N labeled bovine rhodopsin. JOURNAL OF BIOMOLECULAR NMR 2007; 37:303-12. [PMID: 17318366 DOI: 10.1007/s10858-007-9143-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Accepted: 01/08/2007] [Indexed: 05/14/2023]
Abstract
Rhodopsin is the visual pigment of the vertebrate rod photoreceptor cell and is the only member of the G protein coupled receptor family for which a crystal structure is available. Towards the study of dynamics in rhodopsin, we report NMR-spectroscopic investigations of alpha,epsilon-15N-tryptophan labeled rhodopsin in detergent micelles and reconstituted in phospholipids. Using a combination of solid state 13C,15N-REDOR and HETCOR experiments of all possible 13C'(i-1) carbonyl/15N(i)-tryptophan isotope labeled amide pairs, and H/D exchange 1H,15N-HSQC experiments conducted in solution, we assigned chemical shifts to all five rhodopsin tryptophan backbone 15N nuclei and partially to their bound protons. 1H,15N chemical shift assignment was achieved for indole side chains of Trp35(1.30) and Trp175(4.65). 15N chemical shifts were found to be similar when comparing those obtained in the native like reconstituted lipid environment and those obtained in detergent micelles for all tryptophans except Trp175(4.65) at the membrane interface. The results suggest that the integrated solution and solid state NMR approach presented provides highly complementary information in the study of structure and dynamics of large membrane proteins like rhodopsin.
Collapse
Affiliation(s)
- Karla Werner
- Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main, Germany
| | | | | | | | | | | | | | | |
Collapse
|