1
|
Xiao H, Zhao W, Zhang Y, Kang H, Zhang Z, Yang J. Selective correlations between aliphatic 13C nuclei in protein solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 365:107730. [PMID: 38981307 DOI: 10.1016/j.jmr.2024.107730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/12/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024]
Abstract
Solid-state nuclear magnetic resonance (NMR) is a potent tool for studying the structures and dynamics of insoluble proteins. It starts with signal assignment through multi-dimensional correlation experiments, where the aliphatic 13Cα-13Cβ correlation is indispensable for identifying specific residues. However, developing efficient methods for achieving this correlation is a challenge in solid-state NMR. We present a simple band-selective zero-quantum (ZQ) recoupling method, named POST-C4161 (PC4), which enhances 13Cα-13Cβ correlations under moderate magic-angle spinning (MAS) conditions. PC4 requires minimal 13C radio-frequency (RF) field and proton decoupling, exhibits high stability against RF variations, and achieves superior efficiency. Comparative tests on various samples, including the formyl-Met-Leu-Phe (fMLF) tripeptide, microcrystalline β1 immunoglobulin binding domain of protein G (GB1), and membrane protein of mechanosensitive channel of large conductance from Methanosarcina acetivorans (MaMscL), demonstrate that PC4 selectively enhances 13Cα-13Cβ correlations by up to 50 % while suppressing unwanted correlations, as compared to the popular dipolar-assisted rotational resonance (DARR). It has addressed the long-standing need for selective 13C-13C correlation methods. We anticipate that this simple but efficient PC4 method will have immediate applications in structural biology by solid-state NMR.
Collapse
Affiliation(s)
- Hang Xiao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Weijing Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; Interdisciplinary Institute of NMR and Molecular Sciences, School of Chemistry and Chemical Engineering, The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan 430081, PR China
| | - Yan Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Huimin Kang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; Interdisciplinary Institute of NMR and Molecular Sciences, School of Chemistry and Chemical Engineering, The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan 430081, PR China.
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; Interdisciplinary Institute of NMR and Molecular Sciences, School of Chemistry and Chemical Engineering, The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan 430081, PR China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, PR China.
| |
Collapse
|
2
|
Smith BC, Silvers R. 1H, 13C, and 15N resonance assignments of the La Motif of the human La-related protein 1. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:111-118. [PMID: 38691336 DOI: 10.1007/s12104-024-10176-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Human La-related protein 1 (HsLARP1) is involved in post-transcriptional regulation of certain 5' terminal oligopyrimidine (5'TOP) mRNAs as well as other mRNAs and binds to both the 5'TOP motif and the 3'-poly(A) tail of certain mRNAs. HsLARP1 is heavily involved in cell proliferation, cell cycle defects, and cancer, where HsLARP1 is significantly upregulated in malignant cells and tissues. Like all LARPs, HsLARP1 contains a folded RNA binding domain, the La motif (LaM). Our current understanding of post-transcriptional regulation that emanates from the intricate molecular framework of HsLARP1 is currently limited to small snapshots, obfuscating our understanding of the full picture on HsLARP1 functionality in post-transcriptional events. Here, we present the nearly complete resonance assignment of the LaM of HsLARP1, providing a significant platform for future NMR spectroscopic studies.
Collapse
Affiliation(s)
- Benjamin C Smith
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA
| | - Robert Silvers
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL, 32306, USA.
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.
| |
Collapse
|
3
|
Medeiros-Silva J, Dregni AJ, Somberg NH, Duan P, Hong M. Atomic structure of the open SARS-CoV-2 E viroporin. SCIENCE ADVANCES 2023; 9:eadi9007. [PMID: 37831764 PMCID: PMC10575589 DOI: 10.1126/sciadv.adi9007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
Abstract
The envelope (E) protein of the SARS-CoV-2 virus forms cation-conducting channels in the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of infected cells. The calcium channel activity of E is associated with the inflammatory responses of COVID-19. Using solid-state NMR (ssNMR) spectroscopy, we have determined the open-state structure of E's transmembrane domain (ETM) in lipid bilayers. Compared to the closed state, open ETM has an expansive water-filled amino-terminal chamber capped by key glutamate and threonine residues, a loose phenylalanine aromatic belt in the middle, and a constricted polar carboxyl-terminal pore filled with an arginine and a threonine residue. This structure gives insights into how protons and calcium ions are selected by ETM and how they permeate across the hydrophobic gate of this viroporin.
Collapse
Affiliation(s)
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | |
Collapse
|
4
|
Smith BC, Silvers R. NMR Resonance Assignment of the LA Motif of Human LA-Related Protein 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539749. [PMID: 37214987 PMCID: PMC10197598 DOI: 10.1101/2023.05.09.539749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Human La-related protein 1 (HsLARP1) is involved in post-transcriptional regulation of certain 5' s terminal oligopyrimidine (5'TOP) mRNAs as well as other mRNAs and binds to both the 5'TOP motif and the 3'-poly(A) tail of certain mRNAs. HsLARP1 is heavily involved in cell proliferation, cell cycle defects, and cancer, where HsLARP1 is significantly upregulated in malignant cells and tissues. Like all LARPs, HsLARP1 contains a folded RNA binding domain, the La motif (LaM). Our current understanding of post-transcriptional regulation that emanates from the intricate molecular framework of HsLARP1 is currently limited to small snapshots, obfuscating our understanding of the full picture on HsLARP1 functionality in post-transcriptional events. Here, we present the nearly complete resonance assignment of the LaM of HsLARP1, providing a significant platform for future NMR spectroscopic studies.
Collapse
|
5
|
Shamir Y, Goldbourt A. Atomic-Resolution Structure of the Protein Encoded by Gene V of fd Bacteriophage in Complex with Viral ssDNA Determined by Magic-Angle Spinning Solid-State NMR. J Am Chem Soc 2022; 145:300-310. [PMID: 36542094 PMCID: PMC9837838 DOI: 10.1021/jacs.2c09957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
F-specific filamentous phages, elongated particles with circular single-stranded DNA encased in a symmetric protein capsid, undergo an intermediate step, where thousands of homodimers of a non-structural protein, gVp, bind to newly synthesized strands of DNA, preventing further DNA replication and preparing the circular genome in an elongated conformation for assembly of a new virion structure at the membrane. While the structure of the free homodimer is known, the ssDNA-bound conformation has yet to be determined. We report an atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage in the nucleoprotein complex elucidated via magic-angle spinning solid-state NMR. The model presents significant conformational changes with respect to the free form. These modifications facilitate the binding mechanism and possibly promote cooperative binding in the assembly of the gVp-ssDNA complex.
Collapse
|
6
|
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
Collapse
Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| |
Collapse
|
7
|
Lends A, Berbon M, Habenstein B, Nishiyama Y, Loquet A. Protein resonance assignment by solid-state NMR based on 1H-detected 13C double-quantum spectroscopy at fast MAS. JOURNAL OF BIOMOLECULAR NMR 2021; 75:417-427. [PMID: 34813018 DOI: 10.1007/s10858-021-00386-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Solid-state NMR spectroscopy is a powerful technique to study insoluble and non-crystalline proteins and protein complexes at atomic resolution. The development of proton (1H) detection at fast magic-angle spinning (MAS) has considerably increased the analytical capabilities of the technique, enabling the acquisition of 1H-detected fingerprint experiments in few hours. Here an approach based on double-quantum (DQ) 13C spectroscopy, detected on 1H, is proposed for fast MAS regime (> 60 kHz) to perform the sequential assignment of insoluble proteins of small size, without any specific deuteration requirement. By combining two three-dimensional 1H detected experiments correlating a 13C DQ dimension respectively to its intra-residue and sequential 15 N-1H pairs, a sequential walk through DQ (Ca + CO) resonance is obtained. The approach takes advantage of fast MAS to achieve an efficient sensitivity and the addition of a DQ dimension provides spectral features useful for the resonance assignment process.
Collapse
Affiliation(s)
- Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France.
| | - Mélanie Berbon
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Birgit Habenstein
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Yusuke Nishiyama
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa, 230-0045, Japan.
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo, 196-8558, Japan.
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France.
| |
Collapse
|
8
|
Tong Q, Tan H, Li J, Xie H, Zhao Y, Chen Y, Yang J. Extensively sparse 13C labeling to simplify solid-state NMR 13C spectra of membrane proteins. JOURNAL OF BIOMOLECULAR NMR 2021; 75:245-254. [PMID: 34148188 DOI: 10.1007/s10858-021-00372-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Solid-state Nuclear Magnetic Resonance (ssNMR) is an emerging technique to investigate the structures and dynamics of membrane proteins in an artificial or native membrane environment. However, the structural studies of proteins by ssNMR are usually prolonged or impeded by signal assignments, especially the assignments of signals for collection of distance restraints, because of serious overlapping of signals in 2D 13C-13C spectra. Sparse labeling of 13C spins is an effective approach to simplify the 13C spectra and facilitate the extractions of distance restraints. Here, we propose a new reverse labeling combination of six types of amino acid residues (Ile, Leu, Phe, Trp, Tyr and Lys), and show a clean reverse labeling effect on a model membrane protein E. coli aquaporin Z (AqpZ). We further combine this reverse labeling combination and alternate 13C-12C labeling, and demonstrate an enhanced dilution effect in 13C-13C spectra. In addition, the influences of reverse labeling on the labeling of the other types of residues are quantitatively analyzed in the two strategies (1, reverse labeling and 2, reverse labeling combining alternate 13C-12C labeling). The signal intensities of some other types of residues in 2D 13C-13C spectra are observed to be 20-50% weaker because of the unwanted reverse labeling. The extensively sparse 13C labeling proposed in this study is expected to be useful in the collection of distance restraints using 2D 13C-13C spectra of membrane proteins.
Collapse
Affiliation(s)
- Qiong Tong
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Huan Tan
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jianping Li
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Yongxiang Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Yanke Chen
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China.
| |
Collapse
|
9
|
Porat G, Lusky OS, Dayan N, Goldbourt A. Nonuniformly sampled exclusively- 13 C/ 15 N 4D solid-state NMR experiments: Assignment and characterization of IKe phage capsid. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:237-246. [PMID: 32603513 DOI: 10.1002/mrc.5072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/11/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
An important step in the process of protein research by NMR is the assignment of chemical shifts. In the coat protein of IKe bacteriophage, there are 53 residues making up a long helix resulting in relatively high spectral ambiguity. Assignment thus requires the collection of a set of three-dimensional (3D) experiments and the preparation of sparsely labeled samples. Increasing the dimensionality can facilitate fast and reliable assignment of IKe and of larger proteins. Recent progress in nonuniform sampling techniques made the application of multidimensional NMR solid-state experiments beyond 3D more practical. 4D 1 H-detected experiments have been demonstrated in high-fields and at spinning speeds of 60 kHz and higher but are not practical at spinning speeds of 10-20 kHz for fully protonated proteins. Here, we demonstrate the applicability of a nonuniformly sampled 4D 13 C/15 N-only correlation experiment performed at a moderate field of 14.1 T, which can incorporate sufficiently long acquisition periods in all dimensions. We show how a single CANCOCX experiment, supported by several 2D carbon-based correlation experiments, is utilized for the assignment of heteronuclei in the coat protein of the IKe bacteriophage. One sparsely labeled sample was used to validate sidechain assignment of several hydrophobic-residue sidechains. A comparison to solution NMR studies of isolated IKe coat proteins embedded in micelles points to key residues involved in structural rearrangement of the capsid upon assembly of the virus. The benefits of 4D to a quicker assignment are discussed, and the method may prove useful for studying proteins at relatively low fields.
Collapse
Affiliation(s)
- Gal Porat
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, 19716, USA
| | - Orr Simon Lusky
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Nir Dayan
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
- Schulich Faculty of Chemistry, Technion-Institute of Technology, Haifa, Israel
| | - Amir Goldbourt
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| |
Collapse
|
10
|
Marshall JW, de Mattos-Shipley KMJ, Ghannam IAY, Munawar A, Killen JC, Lazarus CM, Cox RJ, Willis CL, Simpson TJ. Fusarochromene, a novel tryptophan-derived metabolite from Fusarium sacchari. Org Biomol Chem 2021; 19:182-187. [PMID: 33107888 DOI: 10.1039/d0ob02031a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fusarochromene isolated from the plant pathogenic fungus, Fusarium sacchari is closely related to a group of mycotoxins including fusarochromanone previously isolated from various Fusaria spp. Despite their assumed polyketide biogenesis, incorporation studies with 13C-labelled acetate, glycerol and tryptophans show that fusarochromene is unexpectedly derived via oxidative cleavage of the aromatic amino acid tryptophan. A putative biosynthetic gene cluster has been identified.
Collapse
Affiliation(s)
- James W Marshall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Wiegand T. A solid-state NMR tool box for the investigation of ATP-fueled protein engines. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:1-32. [PMID: 32471533 DOI: 10.1016/j.pnmrs.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
Motor proteins are involved in a variety of cellular processes. Their main purpose is to convert the chemical energy released during adenosine triphosphate (ATP) hydrolysis into mechanical work. In this review, solid-state Nuclear Magnetic Resonance (NMR) approaches are discussed allowing studies of structures, conformational events and dynamic features of motor proteins during a variety of enzymatic reactions. Solid-state NMR benefits from straightforward sample preparation based on sedimentation of the proteins directly into the Magic-Angle Spinning (MAS) rotor. Protein resonance assignment is the crucial and often time-limiting step in interpreting the wealth of information encoded in the NMR spectra. Herein, potentials, challenges and limitations in resonance assignment for large motor proteins are presented, focussing on both biochemical and spectroscopic approaches. This work highlights NMR tools available to study the action of the motor domain and its coupling to functional processes, as well as to identify protein-nucleotide interactions during events such as DNA replication. Arrested protein states of reaction coordinates such as ATP hydrolysis can be trapped for NMR studies by using stable, non-hydrolysable ATP analogues that mimic the physiological relevant states as accurately as possible. Recent advances in solid-state NMR techniques ranging from Dynamic Nuclear Polarization (DNP), 31P-based heteronuclear correlation experiments, 1H-detected spectra at fast MAS frequencies >100 kHz to paramagnetic NMR are summarized and their applications to the bacterial DnaB helicase from Helicobacter pylori are discussed.
Collapse
Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
| |
Collapse
|
12
|
Kaur H, Grahl A, Hartmann JB, Hiller S. Sample Preparation and Technical Setup for NMR Spectroscopy with Integral Membrane Proteins. Methods Mol Biol 2020; 2127:373-396. [PMID: 32112334 DOI: 10.1007/978-1-0716-0373-4_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
NMR spectroscopy is a method of choice to characterize structure, function, and dynamics of integral membrane proteins at atomic resolution. Here, we describe protocols for sample preparation and characterization by NMR spectroscopy of two integral membrane proteins with different architecture, the α-helical membrane protein MsbA and the β-barrel membrane protein BamA. The protocols describe recombinant expression in E. coli, protein refolding, purification, and reconstitution in suitable membrane mimetics, as well as key setup steps for basic NMR experiments. These include experiments on protein samples in the solid state under magic angle spinning (MAS) conditions and experiments on protein samples in aqueous solution. Since MsbA and BamA are typical examples of their respective architectural classes, the protocols presented here can also serve as a reference for other integral membrane proteins.
Collapse
Affiliation(s)
- Hundeep Kaur
- Biozentrum, University of Basel, Basel, Switzerland
| | - Anne Grahl
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | |
Collapse
|
13
|
Smith AN, Märker K, Hediger S, De Paëpe G. Natural Isotopic Abundance 13C and 15N Multidimensional Solid-State NMR Enabled by Dynamic Nuclear Polarization. J Phys Chem Lett 2019; 10:4652-4662. [PMID: 31361489 DOI: 10.1021/acs.jpclett.8b03874] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Dynamic nuclear polarization (DNP) has made feasible solid-state NMR experiments that were previously thought impractical due to sensitivity limitations. One such class of experiments is the structural characterization of organic and biological samples at natural isotopic abundance (NA). Herein, we describe the many advantages of DNP-enabled ssNMR at NA, including the extraction of long-range distance constraints using dipolar recoupling pulse sequences without the deleterious effects of dipolar truncation. In addition to the theoretical underpinnings in the analysis of these types of experiments, numerous applications of DNP-enabled ssNMR at NA are discussed.
Collapse
Affiliation(s)
- Adam N Smith
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM , F-38000 Grenoble , France
| | - Katharina Märker
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM , F-38000 Grenoble , France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM , F-38000 Grenoble , France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM , F-38000 Grenoble , France
| |
Collapse
|
14
|
Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
Collapse
Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
| |
Collapse
|
15
|
RIP2 filament formation is required for NOD2 dependent NF-κB signalling. Nat Commun 2018; 9:4043. [PMID: 30279485 PMCID: PMC6168553 DOI: 10.1038/s41467-018-06451-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/06/2018] [Indexed: 11/08/2022] Open
Abstract
Activation of the innate immune pattern recognition receptor NOD2 by the bacterial muramyl-dipeptide peptidoglycan fragment triggers recruitment of the downstream adaptor kinase RIP2, eventually leading to NF-κB activation and proinflammatory cytokine production. Here we show that full-length RIP2 can form long filaments mediated by its caspase recruitment domain (CARD), in common with other innate immune adaptor proteins. We further show that the NOD2 tandem CARDs bind to one end of the RIP2 CARD filament, suggesting a mechanism for polar filament nucleation by activated NOD2. We combine X-ray crystallography, solid-state NMR and high-resolution cryo-electron microscopy to determine the atomic structure of the helical RIP2 CARD filament, which reveals the intermolecular interactions that stabilize the assembly. Using structure-guided mutagenesis, we demonstrate the importance of RIP2 polymerization for the activation of NF-κB signalling by NOD2. Our results could be of use to develop new pharmacological strategies to treat inflammatory diseases characterised by aberrant NOD2 signalling.
Collapse
|
16
|
Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
Collapse
Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
| |
Collapse
|
17
|
Wiegand T, Cadalbert R, von Schroetter C, Allain FHT, Meier BH. Segmental isotope labelling and solid-state NMR of a 12 × 59 kDa motor protein: identification of structural variability. JOURNAL OF BIOMOLECULAR NMR 2018; 71:237-245. [PMID: 29948439 DOI: 10.1007/s10858-018-0196-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/01/2018] [Indexed: 05/26/2023]
Abstract
Segmental isotope labelling enables the NMR study of an individual domain within a multidomain protein, but still in the context of the entire full-length protein. Compared to the fully labelled protein, spectral overlap can be greatly reduced. We here describe segmental labelling of the (double-) hexameric DnaB helicase from Helicobacter pylori using a ligation approach. Solid-state spectra demonstrate that the ligated protein has the same structure and structural order as the directly expressed full-length protein. We uniformly 13C/15N labeled the N-terminal domain (147 residues) of the protein, while the C-terminal domain (311 residues) remained in natural abundance. The reduced signal overlap in solid-state NMR spectra allowed to identify structural "hotspots" for which the structure of the N-terminal domain in the context of the oligomeric full-length protein differs from the one in the isolated form. They are located near the linker between the two domains, in an α-helical hairpin.
Collapse
Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | | | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
| |
Collapse
|
18
|
Lacabanne D, Meier BH, Böckmann A. Selective labeling and unlabeling strategies in protein solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2018; 71:141-150. [PMID: 29197975 DOI: 10.1007/s10858-017-0156-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/23/2017] [Indexed: 06/07/2023]
Abstract
Selective isotope labeling is central in NMR experiments and often allows to push the limits on the systems investigated. It has the advantage to supply additional resolution by diminishing the number of signals in the spectra. This is particularly interesting when dealing with the large protein systems which are currently becoming accessible to solid-state NMR studies. Isotope labeled proteins for NMR experiments are most often expressed in E. coli systems, where bacteria are grown in minimal media supplemented with 15NH4Cl and 13C-glucose as sole source of nitrogen and carbon. For amino acids selective labeling or unlabeling, specific amino acids are supplemented in the minimal medium. The aim is that they will be incorporated in the protein by the bacteria. However, E. coli amino-acid anabolism and catabolism tend to interconnect different pathways, remnant of a subway system. These connections lead to inter conversion between amino acids, called scrambling. A thorough understanding of the involved pathways is thus important to obtain the desired labeling schemes, as not all combinations of amino acids are adapted. We present here a detailed overview of amino-acid metabolism in this context. Each amino-acid pathway is described in order to define accessible combinations for 13C or 15N specific labeling or unlabeling. Using as example the ABC transporter BmrA, a membrane protein of 600 residues, we demonstrate how these strategies can be applied. Indeed, even though there is no size limit in solid-state NMR, large (membrane) proteins are still a challenge due to heavy signal overlap. To initiate resonance assignment in these large systems, we describe how selectively labeled samples can be obtained with the addition of labeled or unlabeled amino acids in the medium. The reduced spectral overlap enabled us to identify typical spectral fingerprints and to initiate sequential assignment using the more sensitive 2D DARR experiments with long mixing time showing inter-residue correlations.
Collapse
Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
| |
Collapse
|
19
|
Higman VA. Solid-state MAS NMR resonance assignment methods for proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 106-107:37-65. [PMID: 31047601 DOI: 10.1016/j.pnmrs.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 06/09/2023]
Abstract
The prerequisite to structural or functional studies of proteins by NMR is generally the assignment of resonances. Since the first assignment of proteins by solid-state MAS NMR was conducted almost two decades ago, a wide variety of different pulse sequences and methods have been proposed and continue to be developed. Traditionally, a variety of 2D and 3D 13C-detected experiments have been used for the assignment of backbone and side-chain 13C and 15N resonances. These methods have found widespread use across the field. But as the hardware has changed and higher spinning frequencies and magnetic fields are becoming available, the ability to use direct proton detection is opening up a new set of assignment methods based on triple-resonance experiments. This review describes solid-state MAS NMR assignment methods using carbon detection and proton detection at different deuteration levels. The use of different isotopic labelling schemes as an aid to assignment in difficult cases is discussed as well as the increasing number of software packages that support manual and automated resonance assignment.
Collapse
Affiliation(s)
- Victoria A Higman
- Department of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TU, UK.
| |
Collapse
|
20
|
3D structure determination of amyloid fibrils using solid-state NMR spectroscopy. Methods 2018; 138-139:26-38. [DOI: 10.1016/j.ymeth.2018.03.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 01/08/2023] Open
|
21
|
Quinn CM, Wang M, Polenova T. NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology. Methods Mol Biol 2018; 1688:1-35. [PMID: 29151202 PMCID: PMC6217836 DOI: 10.1007/978-1-4939-7386-6_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
As a result of profound gains in sensitivity and resolution afforded by ultrahigh magnetic fields, transformative applications in the fields of structural biology and materials science are being realized. The development of dual low temperature superconducting (LTS)/high-temperature superconducting (HTS) magnets has enabled the achievement of magnetic fields above 1 GHz (23.5 T), which will open doors to an unprecedented new range of applications. In this contribution, we discuss the promise of ultrahigh field magnetic resonance. We highlight several methodological developments pertinent at high-magnetic fields including measurement of 1H-1H distances and 1H chemical shift anisotropy in the solid state as well as studies of quadrupolar nuclei such as 17O. Higher magnetic fields have advanced heteronuclear detection in solution NMR, valuable for applications including metabolomics and disordered proteins, as well as expanded use of proton detection in the solid state in conjunction with ultrafast magic angle spinning. We also present several recent applications to structural studies of the AP205 bacteriophage, the M2 channel from Influenza A, and biomaterials such as human bone. Gains in sensitivity and resolution from increased field strengths will enable advanced applications of NMR spectroscopy including in vivo studies of whole cells and intact virions.
Collapse
Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA.
| |
Collapse
|
22
|
Gupta R, Polenova T. Magic angle spinning NMR spectroscopy guided atomistic characterization of structure and dynamics in HIV-1 protein assemblies. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2017.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
23
|
Kang SJ, Todokoro Y, Bak S, Suzuki T, Yoshida M, Fujiwara T, Akutsu H. Direct assignment of 13C solid-state NMR signals of TF oF 1 ATP synthase subunit c-ring in lipid membranes and its implication for the ring structure. JOURNAL OF BIOMOLECULAR NMR 2018; 70:53-65. [PMID: 29197977 DOI: 10.1007/s10858-017-0158-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
FoF1-ATP synthase catalyzes ATP hydrolysis/synthesis coupled with a transmembrane H+ translocation in membranes. The Fo c-subunit ring plays a major role in this reaction. We have developed an assignment strategy for solid-state 13C NMR (ssNMR) signals of the Fo c-subunit ring of thermophilic Bacillus PS3 (TFo c-ring, 72 residues), carrying one of the basic folds of membrane proteins. In a ssNMR spectrum of uniformly 13C-labeled sample, the signal overlap has been a major bottleneck because most amino acid residues are hydrophobic. To overcome signal overlapping, we developed a method designated as COmplementary Sequential assignment with MInimum Labeling Ensemble (COSMILE). According to this method, we generated three kinds of reverse-labeled samples to suppress signal overlapping. To assign the carbon signals sequentially, two-dimensional Cα(i+1)-C'Cα(i) correlation and dipolar assisted rotational resonance (DARR) experiments were performed under magic-angle sample spinning. On the basis of inter- and intra-residue 13C-13C chemical shift correlations, 97% of Cα, 97% of Cβ and 92% of C' signals were assigned directly from the spectra. Secondary structure analysis predicted a hairpin fold of two helices with a central loop. The effects of saturated and unsaturated phosphatidylcholines on TFo c-ring structure were examined. The DARR spectra at 15 ms mixing time are essentially similar to each other in saturated and unsaturated lipid membranes, suggesting that TFo c-rings have similar structures under the different environments. The spectrum of the sample in saturated lipid membranes showed better resolution and structural stability in the gel state. The C-terminal helix was suggested to locate in the outer layer of the c-ring.
Collapse
Affiliation(s)
- Su-Jin Kang
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
- Department of Biophysics and Chemical Biology, Seoul National University, Kwanak-Gu, Seoul, 151-742, Republic of Korea
| | - Yasuto Todokoro
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Suyeon Bak
- Department of Biophysics and Chemical Biology, Seoul National University, Kwanak-Gu, Seoul, 151-742, Republic of Korea
| | - Toshiharu Suzuki
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masasuke Yoshida
- Department of Molecular Bioscience, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, 603-8555, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Hideo Akutsu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan.
- Department of Biophysics and Chemical Biology, Seoul National University, Kwanak-Gu, Seoul, 151-742, Republic of Korea.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, 230-0045, Japan.
| |
Collapse
|
24
|
Abstract
β-barrel proteins mediate nutrient uptake in bacteria and serve vital functions in cell signaling and adhesion. For the 14-strand outer membrane protein G of Escherichia coli, opening and closing is pH-dependent. Different roles of the extracellular loops in this process were proposed, and X-ray and solution NMR studies were divergent. Here, we report the structure of outer membrane protein G investigated in bilayers of E. coli lipid extracts by magic-angle-spinning NMR. In total, 1847 inter-residue 1H–1H and 13C–13C distance restraints, 256 torsion angles, but no hydrogen bond restraints are used to calculate the structure. The length of β-strands is found to vary beyond the membrane boundary, with strands 6–8 being the longest and the extracellular loops 3 and 4 well ordered. The site of barrel closure at strands 1 and 14 is more disordered than most remaining strands, with the flexibility decreasing toward loops 3 and 4. Loop 4 presents a well-defined helix. Porins, like OmpG, are embedded in the outer membrane of bacteria and facilitate uptake and secretion of nutrients and ions. Here the authors present a protocol for solid state NMR structure determination of proteins larger than 25 kDa and use it to structurally characterize membrane embedded OmpG.
Collapse
|
25
|
Jolly MM, Jarvis JA, Carravetta M, Levitt MH, Williamson PTF. Bidirectional band-selective magnetization transfer along the protein backbone doubles the information content of solid-state NMR correlation experiments. JOURNAL OF BIOMOLECULAR NMR 2017; 69:197-205. [PMID: 29116557 PMCID: PMC5736786 DOI: 10.1007/s10858-017-0147-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 10/21/2017] [Indexed: 05/05/2023]
Abstract
Resonance assignment is the first stage towards solving the structure of a protein. This is normally achieved by the employment of separate inter and intra residue experiments. By utilising the mixed rotation and rotary recoupling (MIRROR) condition it is possible to double the information content through the efficient bidirectional transfer of magnetization from the CO to its adjacent Cα and the Cα of the subsequent amino acid. We have incorporated this into a 3D experiment, a 3D-MIRROR-NCOCA, where correlations present in the 3D spectrum permit the sequential assignment of the protein backbone from a single experiment as we have demonstrated on a microcrystalline preparation of GB3. Furthermore, the low-power requirements of the MIRROR recoupling sequence facilitate the development of a low-power 3D-NCOCA experiment. This has enabled us to realise significant reductions in acquisition times, allowing the acquisition of a single 3D-NCOCA spectrum suitable for a full backbone resonance assignment of GB3 in less than 24 h.
Collapse
Affiliation(s)
- M M Jolly
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - J A Jarvis
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - M Carravetta
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - M H Levitt
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - P T F Williamson
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| |
Collapse
|
26
|
Loquet A, Tolchard J, Berbon M, Martinez D, Habenstein B. Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy. J Vis Exp 2017:55779. [PMID: 28994783 PMCID: PMC5752270 DOI: 10.3791/55779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13C/15N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.
Collapse
Affiliation(s)
- Antoine Loquet
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux;
| | - James Tolchard
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux
| | - Melanie Berbon
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux
| | - Denis Martinez
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux
| | - Birgit Habenstein
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux;
| |
Collapse
|
27
|
Hora M, Sarkar R, Morris V, Xue K, Prade E, Harding E, Buchner J, Reif B. MAK33 antibody light chain amyloid fibrils are similar to oligomeric precursors. PLoS One 2017; 12:e0181799. [PMID: 28746363 PMCID: PMC5528828 DOI: 10.1371/journal.pone.0181799] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 07/09/2017] [Indexed: 12/25/2022] Open
Abstract
Little structural information is available so far on amyloid fibrils consisting of immunoglobulin light chains. It is not understood which features of the primary sequence of the protein result in fibril formation. We report here MAS solid-state NMR studies to identify the structured core of κ-type variable domain light chain fibrils. The core contains residues of the CDR2 and the β-strands D, E, F and G of the native immunoglobulin fold. The assigned core region of the fibril is distinct in comparison to the core identified in a previous solid-state NMR study on AL-09 by Piehl at. al, suggesting that VL fibrils can adopt different topologies. In addition, we investigated a soluble oligomeric intermediate state, previously termed the alternatively folded state (AFS), using NMR and FTIR spectroscopy. The NMR oligomer spectra display a high degree of similarity when compared to the fibril spectra, indicating a high structural similarity of the two aggregation states. Based on comparison to the native state NMR chemical shifts, we suggest that fibril formation via domain-swapping seems unlikely. Moreover, we used our results to test the quality of different amyloid prediction algorithms.
Collapse
Affiliation(s)
- Manuel Hora
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Neuherberg, Germany
| | - Riddhiman Sarkar
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Neuherberg, Germany
| | - Vanessa Morris
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Neuherberg, Germany
| | - Kai Xue
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Neuherberg, Germany
| | - Elke Prade
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
| | - Emma Harding
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
| | - Johannes Buchner
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
| | - Bernd Reif
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Neuherberg, Germany
- * E-mail:
| |
Collapse
|
28
|
Bacterial Filamentous Appendages Investigated by Solid-State NMR Spectroscopy. Methods Mol Biol 2017. [PMID: 28667627 DOI: 10.1007/978-1-4939-7033-9_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The assembly of filamentous appendages at the surface of bacteria is essential in many infection mechanisms. The extent of mechanical, dynamical, and functional properties of such appendages is very diverse, ranging from a structural scaffold of the pathogen-host cell interaction to cell motility, surface adhesion, or the export of virulence effectors. In particular, the architectures of several bacterial secretion systems have revealed the presence of filamentous architectures, known as pili, fimbriae, andneedles. At the macroscopic level, filamentous bacterial appendages appear as thin extracellular filaments of several nanometers in diameter and up to several microns in length. The structural characterization of these appendages at atomic-scale resolution represents an extremely challenging task because of their inherent noncrystallinity and very poor solubility. Here, we describe protocols based on recent advances in solid-state NMR spectroscopy to investigate the secondary structure, subunit-subunit protein interactions, symmetry parameters, and atomic architecture of bacterial filaments.
Collapse
|
29
|
Mandal A, Boatz JC, Wheeler TB, van der Wel PCA. On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR. JOURNAL OF BIOMOLECULAR NMR 2017; 67:165-178. [PMID: 28229262 PMCID: PMC5445385 DOI: 10.1007/s10858-017-0089-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/19/2017] [Indexed: 05/07/2023]
Abstract
A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation.
Collapse
Affiliation(s)
- Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Jennifer C Boatz
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Travis B Wheeler
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
| |
Collapse
|
30
|
Piehl D, Blancas-Mejía LM, Wall JS, Kennel SJ, Ramirez-Alvarado M, Rienstra CM. Immunoglobulin Light Chains Form an Extensive and Highly Ordered Fibril Involving the N- and C-Termini. ACS OMEGA 2017; 2:712-720. [PMID: 28261692 PMCID: PMC5331457 DOI: 10.1021/acsomega.6b00494] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/08/2017] [Indexed: 05/03/2023]
Abstract
Light-chain (AL)-associated amyloidosis is a systemic disorder involving the formation and deposition of immunoglobulin AL fibrils in various bodily organs. One severe instance of AL disease is exhibited by the patient-derived variable domain (VL) of the light chain AL-09, a 108 amino acid residue protein containing seven mutations relative to the corresponding germline protein, κI O18/O8 VL. Previous work has demonstrated that the thermodynamic stability of native AL-09 VL is greatly lowered by two of these mutations, Y87H and N34I, whereas a third mutation, K42Q, further increases the kinetics of fibril formation. However, detailed knowledge regarding the residues that are responsible for stabilizing the misfolded fibril structure is lacking. In this study, using solid-state NMR spectroscopy, we show that the majority of the AL-09 VL sequence is immobilized in the fibrils and that the N- and C-terminal portions of the sequence are particularly well-structured. Thus, AL-09 VL forms an extensively ordered and β-strand-rich fibril structure. Furthermore, we demonstrate that the predominant β-sheet secondary structure and rigidity observed for in vitro prepared AL-09 VL fibrils are qualitatively similar to those observed for AL fibrils extracted from postmortem human spleen tissue, suggesting that this conformation may be representative of a common feature of AL fibrils.
Collapse
Affiliation(s)
- Dennis
W. Piehl
- Department
of Biochemistry, Department of Chemistry, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Luis M. Blancas-Mejía
- Department
of Biochemistry and Molecular Biology, Mayo
Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Jonathan S. Wall
- Department of Medicine and Department of Radiology, University
of Tennessee Graduate School of Medicine, 1924 Alcoa Hwy, Knoxville, Tennessee 37920, United States
| | - Stephen J. Kennel
- Department of Medicine and Department of Radiology, University
of Tennessee Graduate School of Medicine, 1924 Alcoa Hwy, Knoxville, Tennessee 37920, United States
| | - Marina Ramirez-Alvarado
- Department
of Biochemistry and Molecular Biology, Mayo
Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
- E-mail: . Phone: (507)-284-2705 (M.R.-A.)
| | - Chad M. Rienstra
- Department
of Biochemistry, Department of Chemistry, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
- E-mail: . Phone: (217)-244-4655 (C.M.R.)
| |
Collapse
|
31
|
Quinn CM, Polenova T. Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. Q Rev Biophys 2017; 50:e1. [PMID: 28093096 PMCID: PMC5483179 DOI: 10.1017/s0033583516000159] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.
Collapse
Affiliation(s)
- Caitlin M. Quinn
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
| | - Tatyana Polenova
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
| |
Collapse
|
32
|
Nuzzio KM, Watt ED, Boettcher JM, Gajsiewicz JM, Morrissey JH, Rienstra CM. High-Resolution NMR Studies of Human Tissue Factor. PLoS One 2016; 11:e0163206. [PMID: 27657719 PMCID: PMC5033421 DOI: 10.1371/journal.pone.0163206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/06/2016] [Indexed: 11/20/2022] Open
Abstract
In normal hemostasis, the blood clotting cascade is initiated when factor VIIa (fVIIa, other clotting factors are named similarly) binds to the integral membrane protein, human tissue factor (TF). The TF/fVIIa complex in turn activates fX and fIX, eventually concluding with clot formation. Several X-ray crystal structures of the soluble extracellular domain of TF (sTF) exist; however, these structures are missing electron density in functionally relevant regions of the protein. In this context, NMR can provide complementary structural information as well as dynamic insights into enzyme activity. The resolution and sensitivity for NMR studies are greatly enhanced by the ability to prepare multiple milligrams of protein with various isotopic labeling patterns. Here, we demonstrate high-yield production of several isotopically labeled forms of recombinant sTF, allowing for high-resolution NMR studies both in the solid and solution state. We also report solution NMR spectra at sub-mM concentrations of sTF, ensuring the presence of dispersed monomer, as well as the first solid-state NMR spectra of sTF. Our improved sample preparation and precipitation conditions have enabled the acquisition of multidimensional NMR data sets for TF chemical shift assignment and provide a benchmark for TF structure elucidation.
Collapse
Affiliation(s)
- Kristin M. Nuzzio
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Eric D. Watt
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - John M. Boettcher
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Joshua M. Gajsiewicz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - James H. Morrissey
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
| |
Collapse
|
33
|
Abstract
AbstractIncreasing evidence suggests that most proteins occur and function in complexes rather than as isolated entities when embedded in cellular membranes. Nuclear magnetic resonance (NMR) provides increasing possibilities to study structure, dynamics and assembly of such systems. In our review, we discuss recent methodological progress to study membrane–protein complexes (MPCs) by NMR, starting with expression, isotope-labeling and reconstitution protocols. We review approaches to deal with spectral complexity and limited spectral spectroscopic sensitivity that are usually encountered in NMR-based studies of MPCs. We highlight NMR applications in various classes of MPCs, including G-protein-coupled receptors, ion channels and retinal proteins and extend our discussion to protein–protein complexes that span entire cellular compartments or orchestrate processes such as protein transport across or within membranes. These examples demonstrate the growing potential of NMR-based studies of MPCs to provide critical insight into the energetics of protein–ligand and protein–protein interactions that underlie essential biological functions in cellular membranes.
Collapse
|
34
|
Bayro MJ, Tycko R. Structure of the Dimerization Interface in the Mature HIV-1 Capsid Protein Lattice from Solid State NMR of Tubular Assemblies. J Am Chem Soc 2016; 138:8538-46. [PMID: 27298207 PMCID: PMC5550895 DOI: 10.1021/jacs.6b03983] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The HIV-1 capsid protein (CA) forms the capsid shell that encloses RNA within a mature HIV-1 virion. Previous studies by electron microscopy have shown that the capsid shell is primarily a triangular lattice of CA hexamers, with variable curvature that destroys the ideal symmetry of a planar lattice. The mature CA lattice depends on CA dimerization, which occurs through interactions between helix 9 segments of the C-terminal domain (CTD) of CA. Several high-resolution structures of the CTD-CTD dimerization interface have been reported, based on X-ray crystallography and multidimensional solution nuclear magnetic resonance (NMR), with significant differences in amino acid side chain conformations and helix 9-helix 9 orientations. In a structural model for tubular CA assemblies based on cryogenic electron microscopy (cryoEM) [Zhao et al. Nature, 2013, 497, 643-646], the dimerization interface is substantially disordered. The dimerization interface structure in noncrystalline CA assemblies and the extent to which this interface is structurally ordered within a curved lattice have therefore been unclear. Here we describe solid state NMR measurements on the dimerization interface in tubular CA assemblies, which contain the curved triangular lattice of a mature virion, including quantitative measurements of intermolecular and intramolecular distances using dipolar recoupling techniques, solid state NMR chemical shifts, and long-range side chain-side chain contacts. When combined with restraints on the distance and orientation between helix 9 segments from the cryoEM study, the solid state NMR data lead to a unique high-resolution structure for the dimerization interface in the noncrystalline lattice of CA tubes. These results demonstrate that CA lattice curvature is not dependent on disorder or variability in the dimerization interface. This work also demonstrates the feasibility of local structure determination within large noncrystalline assemblies formed by high-molecular-weight proteins, using modern solid state NMR methods.
Collapse
Affiliation(s)
- Marvin J. Bayro
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| |
Collapse
|
35
|
Lu JX, Bayro MJ, Tycko R. Major Variations in HIV-1 Capsid Assembly Morphologies Involve Minor Variations in Molecular Structures of Structurally Ordered Protein Segments. J Biol Chem 2016; 291:13098-112. [PMID: 27129282 DOI: 10.1074/jbc.m116.720557] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Indexed: 12/13/2022] Open
Abstract
We present the results of solid state nuclear magnetic resonance (NMR) experiments on HIV-1 capsid protein (CA) assemblies with three different morphologies, namely wild-type CA (WT-CA) tubes with 35-60 nm diameters, planar sheets formed by the Arg(18)-Leu mutant (R18L-CA), and R18L-CA spheres with 20-100 nm diameters. The experiments are intended to elucidate molecular structural variations that underlie these variations in CA assembly morphology. We find that multidimensional solid state NMR spectra of (15)N,(13)C-labeled CA assemblies are remarkably similar for the three morphologies, with only small differences in (15)N and (13)C chemical shifts, no significant differences in NMR line widths, and few differences in the number of detectable NMR cross-peaks. Thus, the pronounced differences in morphology do not involve major differences in the conformations and identities of structurally ordered protein segments. Instead, morphological variations are attributable to variations in conformational distributions within disordered segments, which do not contribute to the solid state NMR spectra. Variations in solid state NMR signals from certain amino acid side chains are also observed, suggesting differences in the intermolecular dimerization interface between curved and planar CA lattices, as well as possible differences in intramolecular helix-helix packing.
Collapse
Affiliation(s)
- Jun-Xia Lu
- From the Laboratory of Chemical Physics, NIDKK, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Marvin J Bayro
- From the Laboratory of Chemical Physics, NIDKK, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Robert Tycko
- From the Laboratory of Chemical Physics, NIDKK, National Institutes of Health, Bethesda, Maryland 20892-0520
| |
Collapse
|
36
|
Habenstein B, Loquet A. Solid-state NMR: An emerging technique in structural biology of self-assemblies. Biophys Chem 2016; 210:14-26. [DOI: 10.1016/j.bpc.2015.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022]
|
37
|
|
38
|
Colvin MT, Silvers R, Frohm B, Su Y, Linse S, Griffin RG. High resolution structural characterization of Aβ42 amyloid fibrils by magic angle spinning NMR. J Am Chem Soc 2015; 137:7509-18. [PMID: 26001057 PMCID: PMC4623963 DOI: 10.1021/jacs.5b03997] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
The presence of amyloid plaques composed
of amyloid beta (Aβ)
fibrils is a hallmark of Alzheimer’s disease (AD). The Aβ
peptide is present as several length variants with two common alloforms
consisting of 40 and 42 amino acids, denoted Aβ1–40 and Aβ1–42, respectively. While there have
been numerous reports that structurally characterize fibrils of Aβ1–40, very little is known about the structure of amyloid
fibrils of Aβ1–42, which are considered the
more toxic alloform involved in AD. We have prepared isotopically 13C/15N labeled AβM01–42 fibrils in vitro from recombinant protein and examined their 13C–13C and 13C–15N magic angle spinning (MAS) NMR spectra. In contrast to several
other studies of Aβ fibrils, we observe spectra with excellent
resolution and a single set of chemical shifts, suggesting the presence
of a single fibril morphology. We report the initial structural characterization
of AβM01–42 fibrils utilizing 13C and 15N shift assignments of 38 of the 43 residues,
including the backbone and side chains, obtained through a series
of cross-polarization based 2D and 3D 13C–13C, 13C–15N MAS NMR experiments for rigid
residues along with J-based 2D TOBSY experiments for dynamic residues.
We find that the first ∼5 residues are dynamic and most efficiently
detected in a J-based TOBSY spectrum. In contrast, residues 16–42
are easily observed in cross-polarization experiments and most likely
form the amyloid core. Calculation of ψ and φ dihedral
angles from the chemical shift assignments indicate that 4 β-strands
are present in the fibril’s secondary structure.
Collapse
Affiliation(s)
- Michael T Colvin
- †Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Robert Silvers
- †Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Birgitta Frohm
- ‡Department of Biochemistry and Structural Biology, Lund University, SE22100 Lund, Sweden
| | - Yongchao Su
- †Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sara Linse
- ‡Department of Biochemistry and Structural Biology, Lund University, SE22100 Lund, Sweden
| | - Robert G Griffin
- †Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
39
|
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
|
40
|
Eddy MT, Su Y, Silvers R, Andreas L, Clark L, Wagner G, Pintacuda G, Emsley L, Griffin RG. Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 61:299-310. [PMID: 25634301 PMCID: PMC4398622 DOI: 10.1007/s10858-015-9903-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/20/2015] [Indexed: 05/09/2023]
Abstract
The human voltage dependent anion channel 1 (VDAC) is a 32 kDa β-barrel integral membrane protein that controls the transport of ions across the outer mitochondrial membrane. Despite the determination of VDAC solution and diffraction structures, a structural basis for the mechanism of its function is not yet fully understood. Biophysical studies suggest VDAC requires a lipid bilayer to achieve full function, motivating the need for atomic resolution structural information of VDAC in a membrane environment. Here we report an essential step toward that goal: extensive assignments of backbone and side chain resonances for VDAC in DMPC lipid bilayers via magic angle spinning nuclear magnetic resonance (MAS NMR). VDAC reconstituted into DMPC lipid bilayers spontaneously forms two-dimensional lipid crystals, showing remarkable spectral resolution (0.5-0.3 ppm for (13)C line widths and <0.5 ppm (15)N line widths at 750 MHz). In addition to the benefits of working in a lipid bilayer, several distinct advantages are observed with the lipid crystalline preparation. First, the strong signals and sharp line widths facilitated extensive NMR resonance assignments for an integral membrane β-barrel protein in lipid bilayers by MAS NMR. Second, a large number of residues in loop regions were readily observed and assigned, which can be challenging in detergent-solubilized membrane proteins where loop regions are often not detected due to line broadening from conformational exchange. Third, complete backbone and side chain chemical shift assignments could be obtained for the first 25 residues, which comprise the functionally important N-terminus. The reported assignments allow us to compare predicted torsion angles for VDAC prepared in DMPC 2D lipid crystals, DMPC liposomes, and LDAO-solubilized samples to address the possible effects of the membrane mimetic environment on the conformation of the protein. Concluding, we discuss the strengths and weaknesses of the reported assignment approach and the great potential for even more complete assignment studies and de novo structure determination via (1)H detected MAS NMR.
Collapse
Affiliation(s)
- Matthew T. Eddy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yongchao Su
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert Silvers
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Loren Andreas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lindsay Clark
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Guido Pintacuda
- Centre de RMN à Tres̀ Hauts Champs, Institut des Sciences Analytiques (CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Lyndon Emsley
- Centre de RMN à Tres̀ Hauts Champs, Institut des Sciences Analytiques (CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Robert G. Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Corresponding Author:
| |
Collapse
|
41
|
Tycko R. On the problem of resonance assignments in solid state NMR of uniformly ¹⁵N,¹³C-labeled proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:166-172. [PMID: 25797013 PMCID: PMC4371143 DOI: 10.1016/j.jmr.2015.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/05/2015] [Accepted: 02/08/2015] [Indexed: 05/31/2023]
Abstract
Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated annealing (MCSA) algorithm to search for assignments from artificial three-dimensional spectra that are constructed from the reported isotropic (15)N and (13)C chemical shifts of two proteins whose structures have been determined by solution NMR methods. The results demonstrate how assignment simulations can provide new insights into factors that affect the assignment process, which can then help guide the design of experimental strategies. Specifically, simulations are performed for the catalytic domain of SrtC (147 residues, primarily β-sheet secondary structure) and the N-terminal domain of MLKL (166 residues, primarily α-helical secondary structure). Assuming unambiguous residue-type assignments and four ideal three-dimensional data sets (NCACX, NCOCX, CONCA, and CANCA), uncertainties in chemical shifts must be less than 0.4 ppm for assignments for SrtC to be unique, and less than 0.2 ppm for MLKL. Eliminating CANCA data has no significant effect, but additionally eliminating CONCA data leads to more stringent requirements for chemical shift precision. Introducing moderate ambiguities in residue-type assignments does not have a significant effect.
Collapse
Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
| |
Collapse
|
42
|
Sinnige T, Houben K, Pritisanac I, Renault M, Boelens R, Baldus M. Insight into the conformational stability of membrane-embedded BamA using a combined solution and solid-state NMR approach. JOURNAL OF BIOMOLECULAR NMR 2015; 61:321-332. [PMID: 25567766 DOI: 10.1007/s10858-014-9891-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
The β-barrel assembly machinery (BAM) is involved in folding and insertion of outer membrane proteins in Gram-negative bacteria, a process that is still poorly understood. With its 790 residues, BamA presents a challenge to current NMR methods. We utilized a "divide and conquer" approach in which we first obtained resonance assignments for BamA's periplasmic POTRA domains 4 and 5 by solution NMR. Comparison of these assignments to solid-state NMR (ssNMR) data obtained on two BamA constructs including the transmembrane domain and one or two soluble POTRA domains suggested that the fold of POTRA domain 5 critically depends on the interface with POTRA 4. Using specific labeling schemes we furthermore obtained ssNMR resonance assignments for residues in the extracellular loop 6 that is known to be crucial for BamA-mediated substrate folding and insertion. Taken together, our data provide novel insights into the conformational stability of membrane-embedded, non-crystalline BamA.
Collapse
Affiliation(s)
- Tessa Sinnige
- NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | | | | | | | | | | |
Collapse
|
43
|
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
|
44
|
Su Y, Andreas L, Griffin RG. Magic angle spinning NMR of proteins: high-frequency dynamic nuclear polarization and (1)H detection. Annu Rev Biochem 2015; 84:465-97. [PMID: 25839340 DOI: 10.1146/annurev-biochem-060614-034206] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Magic angle spinning (MAS) NMR studies of amyloid and membrane proteins and large macromolecular complexes are an important new approach to structural biology. However, the applicability of these experiments, which are based on (13)C- and (15)N-detected spectra, would be enhanced if the sensitivity were improved. Here we discuss two advances that address this problem: high-frequency dynamic nuclear polarization (DNP) and (1)H-detected MAS techniques. DNP is a sensitivity enhancement technique that transfers the high polarization of exogenous unpaired electrons to nuclear spins via microwave irradiation of electron-nuclear transitions. DNP boosts NMR signal intensities by factors of 10(2) to 10(3), thereby overcoming NMR's inherent low sensitivity. Alternatively, it permits structural investigations at the nanomolar scale. In addition, (1)H detection is feasible primarily because of the development of MAS rotors that spin at frequencies of 40 to 60 kHz or higher and the preparation of extensively (2)H-labeled proteins.
Collapse
Affiliation(s)
- Yongchao Su
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
| | | | | |
Collapse
|
45
|
Wang T, Williams JK, Schmidt-Rohr K, Hong M. Relaxation-compensated difference spin diffusion NMR for detecting 13C-13C long-range correlations in proteins and polysaccharides. JOURNAL OF BIOMOLECULAR NMR 2015; 61:97-107. [PMID: 25510834 PMCID: PMC4522165 DOI: 10.1007/s10858-014-9889-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 12/03/2014] [Indexed: 05/04/2023]
Abstract
The measurement of long-range distances remains a challenge in solid-state NMR structure determination of biological macromolecules. In 2D and 3D correlation spectra of uniformly (13)C-labeled biomolecules, inter-residue, inter-segmental, and intermolecular (13)C-(13)C cross peaks that provide important long-range distance constraints for three-dimensional structures often overlap with short-range cross peaks that only reflect the covalent structure of the molecule. It is therefore desirable to develop new approaches to obtain spectra containing only long-range cross peaks. Here we show that a relaxation-compensated modification of the commonly used 2D (1)H-driven spin diffusion (PDSD) experiment allows the clean detection of such long-range cross peaks. By adding a z-filter to keep the total z-period of the experiment constant, we compensate for (13)C T1 relaxation. As a result, the difference spectrum between a long- and a scaled short-mixing time spectrum show only long-range correlation signals. We show that one- and two-bond cross peaks equalize within a few tens of milliseconds. Within ~200 ms, the intensity equilibrates within an amino acid residue and a monosaccharide to a value that reflects the number of spins in the local network. With T1 relaxation compensation, at longer mixing times, inter-residue and inter-segmental cross peaks increase in intensity whereas intra-segmental cross-peak intensities remain unchanged relative to each other and can all be subtracted out. Without relaxation compensation, the difference 2D spectra exhibit both negative and positive intensities due to heterogeneous T1 relaxation in most biomolecules, which can cause peak cancellation. We demonstrate this relaxation-compensated difference PDSD approach on amino acids, monosaccharides, a crystalline model peptide, a membrane-bound peptide and a plant cell wall sample. The resulting difference spectra yield clean multi-bond, inter-residue and intermolecular correlation peaks, which are often difficult to resolve in the parent 2D spectra.
Collapse
Affiliation(s)
- Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Jonathan K. Williams
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Klaus Schmidt-Rohr
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| |
Collapse
|
46
|
Schubeis T, Lührs T, Ritter C. Unambiguous Assignment of Short- and Long-Range Structural Restraints by Solid-State NMR Spectroscopy with Segmental Isotope Labeling. Chembiochem 2014; 16:51-4. [DOI: 10.1002/cbic.201402446] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Indexed: 11/11/2022]
|
47
|
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
|
48
|
Kunert B, Gardiennet C, Lacabanne D, Calles-Garcia D, Falson P, Jault JM, Meier BH, Penin F, Böckmann A. Efficient and stable reconstitution of the ABC transporter BmrA for solid-state NMR studies. Front Mol Biosci 2014; 1:5. [PMID: 25988146 PMCID: PMC4428385 DOI: 10.3389/fmolb.2014.00005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/26/2014] [Indexed: 01/20/2023] Open
Abstract
We present solid-state NMR sample preparation and first 2D spectra of the Bacillus subtilis ATP-binding cassette (ABC) transporter BmrA, a membrane protein involved in multidrug resistance. The homodimeric 130-kDa protein is a challenge for structural characterization due to its membrane-bound nature, size, inherent flexibility and insolubility. We show that reconstitution of this protein in lipids from Bacillus subtilis at a lipid-protein ratio of 0.5 w/w allows for optimal protein insertion in lipid membranes with respect to two central NMR requirements, high signal-to-noise in the spectra and sample stability over a time period of months. The obtained spectra point to a well-folded protein and a highly homogenous preparation, as witnessed by the narrow resonance lines and the signal dispersion typical for the expected secondary structure distribution of BmrA. This opens the way for studies of the different conformational states of the transporter in the export cycle, as well as on interactions with substrates, via chemical-shift fingerprints and sequential resonance assignments.
Collapse
Affiliation(s)
- Britta Kunert
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Carole Gardiennet
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Denis Lacabanne
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Daniel Calles-Garcia
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Pierre Falson
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Jean-Michel Jault
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | | | - François Penin
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| | - Anja Böckmann
- Labex Ecofect, Bases Moleculaires et Structurales des Systemes Infectieux, UMR 5086 CNRS, IBCP, Université de Lyon 1Lyon, France
| |
Collapse
|
49
|
Su Y, Sarell CJ, Eddy MT, Debelouchina GT, Andreas LB, Pashley CL, Radford SE, Griffin RG. Secondary structure in the core of amyloid fibrils formed from human β₂m and its truncated variant ΔN6. J Am Chem Soc 2014; 136:6313-25. [PMID: 24679070 PMCID: PMC4017606 DOI: 10.1021/ja4126092] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
![]()
Amyloid
fibrils formed from initially soluble proteins with diverse
sequences are associated with an array of human diseases. In the human
disorder, dialysis-related amyloidosis (DRA), fibrils contain two
major constituents, full-length human β2-microglobulin
(hβ2m) and a truncation variant, ΔN6 which
lacks the N-terminal six amino acids. These fibrils are assembled
from initially natively folded proteins with an all antiparallel β-stranded
structure. Here, backbone conformations of wild-type hβ2m and ΔN6 in their amyloid forms have been determined
using a combination of dilute isotopic labeling strategies and multidimensional
magic angle spinning (MAS) NMR techniques at high magnetic fields,
providing valuable structural information at the atomic-level about
the fibril architecture. The secondary structures of both fibril types,
determined by the assignment of ∼80% of the backbone resonances
of these 100- and 94-residue proteins, respectively, reveal substantial
backbone rearrangement compared with the location of β-strands
in their native immunoglobulin folds. The identification of seven
β-strands in hβ2m fibrils indicates that approximately
70 residues are in a β-strand conformation in the fibril core.
By contrast, nine β-strands comprise the fibrils formed from
ΔN6, indicating a more extensive core. The precise location
and length of β-strands in the two fibril forms also differ.
The results indicate fibrils of ΔN6 and hβ2m have an extensive core architecture involving the majority of residues
in the polypeptide sequence. The common elements of the backbone structure
of the two proteins likely facilitates their ability to copolymerize
during amyloid fibril assembly.
Collapse
Affiliation(s)
- Yongchao Su
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology Cambridge, Massachusetts 02139, United States
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Carlsson N, Gustafsson H, Thörn C, Olsson L, Holmberg K, Åkerman B. Enzymes immobilized in mesoporous silica: a physical-chemical perspective. Adv Colloid Interface Sci 2014; 205:339-60. [PMID: 24112562 DOI: 10.1016/j.cis.2013.08.010] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 01/13/2023]
Abstract
Mesoporous materials as support for immobilized enzymes have been explored extensively during the last two decades, primarily not only for biocatalysis applications, but also for biosensing, biofuels and enzyme-controlled drug delivery. The activity of the immobilized enzymes inside the pores is often different compared to that of the free enzymes, and an important challenge is to understand how the immobilization affects the enzymes in order to design immobilization conditions that lead to optimal enzyme activity. This review summarizes methods that can be used to understand how material properties can be linked to changes in enzyme activity. Real-time monitoring of the immobilization process and techniques that demonstrate that the enzymes are located inside the pores is discussed by contrasting them to the common practice of indirectly measuring the depletion of the protein concentration or enzyme activity in the surrounding bulk phase. We propose that pore filling (pore volume fraction occupied by proteins) is the best standard for comparing the amount of immobilized enzymes at the molecular level, and present equations to calculate pore filling from the more commonly reported immobilized mass. Methods to detect changes in enzyme structure upon immobilization and to study the microenvironment inside the pores are discussed in detail. Combining the knowledge generated from these methodologies should aid in rationally designing biocatalyst based on enzymes immobilized in mesoporous materials.
Collapse
Affiliation(s)
- Nils Carlsson
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Physical Chemistry, 412 96 Gothenburg, Sweden
| | - Hanna Gustafsson
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Applied Surface Chemistry, 412 96 Gothenburg, Sweden
| | - Christian Thörn
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Industrial Biotechnology, 412 96 Gothenburg, Sweden
| | - Lisbeth Olsson
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Industrial Biotechnology, 412 96 Gothenburg, Sweden
| | - Krister Holmberg
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Applied Surface Chemistry, 412 96 Gothenburg, Sweden.
| | - Björn Åkerman
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Physical Chemistry, 412 96 Gothenburg, Sweden
| |
Collapse
|