1
|
Costello WN, Xiao Y, Mentink-Vigier F, Kragelj J, Frederick KK. DNP-assisted solid-state NMR enables detection of proteins at nanomolar concentrations in fully protonated cellular milieu. JOURNAL OF BIOMOLECULAR NMR 2024; 78:95-108. [PMID: 38520488 DOI: 10.1007/s10858-024-00436-9] [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: 11/09/2023] [Accepted: 02/09/2024] [Indexed: 03/25/2024]
Abstract
With the sensitivity enhancements conferred by dynamic nuclear polarization (DNP), magic angle spinning (MAS) solid state NMR spectroscopy experiments can attain the necessary sensitivity to detect very low concentrations of proteins. This potentially enables structural investigations of proteins at their endogenous levels in their biological contexts where their native stoichiometries with potential interactors is maintained. Yet, even with DNP, experiments are still sensitivity limited. Moreover, when an isotopically-enriched target protein is present at physiological levels, which typically range from low micromolar to nanomolar concentrations, the isotope content from the natural abundance isotopes in the cellular milieu can outnumber the isotope content of the target protein. Using isotopically enriched yeast prion protein, Sup35NM, diluted into natural abundance yeast lysates, we optimized sample composition. We found that modest cryoprotectant concentrations and fully protonated environments support efficient DNP. We experimentally validated theoretical calculations of the limit of specificity for an isotopically enriched protein in natural abundance cellular milieu. We establish that, using pulse sequences that are selective for adjacent NMR-active nuclei, proteins can be specifically detected in cellular milieu at concentrations in the hundreds of nanomolar. Finally, we find that maintaining native stoichiometries of the protein of interest to the components of the cellular environment may be important for proteins that make specific interactions with cellular constituents.
Collapse
Affiliation(s)
- Whitney N Costello
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
| | | | - Jaka Kragelj
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
- Slovenian NMR centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Kendra K Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA.
- Center for Alzheimer's and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
2
|
Beriashvili D, Zhou J, Liu Y, Folkers GE, Baldus M. Cellular Applications of DNP Solid-State NMR - State of the Art and a Look to the Future. Chemistry 2024; 30:e202400323. [PMID: 38451060 DOI: 10.1002/chem.202400323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Sensitivity enhanced dynamic nuclear polarization solid-state NMR is emerging as a powerful technique for probing the structural properties of conformationally homogenous and heterogenous biomolecular species irrespective of size at atomic resolution within their native environments. Herein we detail advancements that have made acquiring such data, specifically within the confines of intact bacterial and eukaryotic cell a reality and further discuss the type of structural information that can presently be garnered by the technique's exploitation. Subsequently, we discuss bottlenecks that have thus far curbed cellular DNP-ssNMR's broader adoption namely due a lack of sensitivity and spectral resolution. We also explore possible solutions ranging from utilization of new pulse sequences, design of better performing polarizing agents, and application of additional biochemical/ cell biological methodologies.
Collapse
Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jiaxin Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics, Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics, Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| |
Collapse
|
3
|
Fernando LD, Zhao W, Gautam I, Ankur A, Wang T. Polysaccharide assemblies in fungal and plant cell walls explored by solid-state NMR. Structure 2023; 31:1375-1385. [PMID: 37597511 PMCID: PMC10843855 DOI: 10.1016/j.str.2023.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/30/2023] [Accepted: 07/26/2023] [Indexed: 08/21/2023]
Abstract
Structural analysis of macromolecular complexes within their natural cellular environment presents a significant challenge. Recent applications of solid-state NMR (ssNMR) techniques on living fungal cells and intact plant tissues have greatly enhanced our understanding of the structure of extracellular matrices. Here, we selectively highlight the most recent progress in this field. Specifically, we discuss how ssNMR can provide detailed insights into the chemical composition and conformational structure of pectin, and the consequential impact on polysaccharide interactions and cell wall organization. We elaborate on the use of ssNMR data to uncover the arrangement of the lignin-polysaccharide interface and the macrofibrillar structure in native plant stems or during degradation processes. We also comprehend the dynamic structure of fungal cell walls under various morphotypes and stress conditions. Finally, we assess how the combination of NMR with other techniques can enhance our capacity to address unresolved structural questions concerning these complex macromolecular assemblies.
Collapse
Affiliation(s)
- Liyanage D Fernando
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Wancheng Zhao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Isha Gautam
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Ankur Ankur
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.
| |
Collapse
|
4
|
Beriashvili D, Yao R, D'Amico F, Krafčíková M, Gurinov A, Safeer A, Cai X, Mulder MPC, Liu Y, Folkers GE, Baldus M. A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity. Chem Sci 2023; 14:9892-9899. [PMID: 37736634 PMCID: PMC10510770 DOI: 10.1039/d3sc02117c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Studying the structural aspects of proteins within sub-cellular compartments is of growing interest. Dynamic nuclear polarization supported solid-state NMR (DNP-ssNMR) is uniquely suited to provide such information, but critically lacks the desired sensitivity and resolution. Here we utilize SNAPol-1, a novel biradical, to conduct DNP-ssNMR at high-magnetic fields (800 MHz/527 GHz) inside HeLa cells and isolated cell nuclei electroporated with [13C,15N] labeled ubiquitin. We report that SNAPol-1 passively diffuses and homogenously distributes within whole cells and cell nuclei providing ubiquitin spectra of high sensitivity and remarkably improved spectral resolution. For cell nuclei, physical enrichment facilitates a further 4-fold decrease in measurement time and provides an exclusive structural view of the nuclear ubiquitin pool. Taken together, these advancements enable atomic interrogation of protein conformational plasticity at atomic resolution and with sub-cellular specificity.
Collapse
Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ru Yao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Francesca D'Amico
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Michaela Krafčíková
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Andrei Gurinov
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Adil Safeer
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| |
Collapse
|
5
|
Shekar SC, Zhao W, Fernando LD, Hung I, Wang T. A 13C three-dimensional DQ-SQ-SQ correlation experiment for high-resolution analysis of complex carbohydrates using solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 336:107148. [PMID: 35121490 DOI: 10.1016/j.jmr.2022.107148] [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: 12/28/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Complex carbohydrates are the key components of the protective cell walls of microbial pathogens and the bioenergy reservoir in plants and algae. Structural characterization of these polymorphic molecules requires assistance from multidimensional 13C correlation approaches. To facilitate the analysis of carbohydrate structure using solid-state NMR, we present a three-dimensional (3D) 13C-13C-13C experiment that includes a double-quantum (DQ) dimension and is thus free of the cube's body diagonal. The enhanced resolution supports the unambiguous resonance assignment of many polysaccharides in plant and fungal cell walls using uniformly 13C-labeled cells of spruce and Aspergillus fumigatus. Long-range structural restraints were effectively obtained to revisit our understanding of the spatial organization of plant cellulose microfibrils. The method is widely applicable to the investigations of cellular carbohydrates and carbon-based biomaterials.
Collapse
Affiliation(s)
- S Chandra Shekar
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Wancheng Zhao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Liyanage D Fernando
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Ivan Hung
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA.
| |
Collapse
|
6
|
Shekar SC, Zhao W, Weldeghiorghis TK, Wang T. Effect of cross polarization radiofrequency phases on signal phase. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 117:101771. [PMID: 34973555 DOI: 10.1016/j.ssnmr.2021.101771] [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: 08/22/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Utilizing phases of radio frequency (RF) pulses to manipulate spin dynamics is routine in NMR and MRI, leading to spectacular techniques like phase cycling. In a very different area, cross polarization (CP) also has a long history as part of a vast number of solid-state NMR pulse sequences. However, a detailed study devoted to the effect of CP RF phases on NMR signal, seems not to be readily available. From first principles, we arrive at a simple dependence of NMR signal on arbitrary CP RF phases, for static and MAS conditions, accompanied by experimental verification. In the process, the CP propagator emerges as a product of RF "pulses" and a period of "free precession", conforming to coherence transfer pathway theory. The theoretical expressions may lend confidence for dealing with CP blocks with tunable phases in pulse sequences.
Collapse
Affiliation(s)
- S Chandra Shekar
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Wancheng Zhao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | | | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
| |
Collapse
|
7
|
Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
Collapse
Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| |
Collapse
|
8
|
Cai X, Lucini Paioni A, Adler A, Yao R, Zhang W, Beriashvili D, Safeer A, Gurinov A, Rockenbauer A, Song Y, Baldus M, Liu Y. Highly Efficient Trityl-Nitroxide Biradicals for Biomolecular High-Field Dynamic Nuclear Polarization. Chemistry 2021; 27:12758-12762. [PMID: 34181286 DOI: 10.1002/chem.202102253] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Indexed: 12/22/2022]
Abstract
Dynamic nuclear polarization (DNP) is a powerful method to enhance the sensitivity of solid-state magnetic nuclear resonance (ssNMR) spectroscopy. However, its biomolecular applications at high magnetic fields (preferably>14 T) have so far been limited by the intrinsically low efficiency of polarizing agents and sample preparation aspects. Herein, we report a new class of trityl-nitroxide biradicals, dubbed SNAPols that combine high DNP efficiency with greatly enhanced hydrophilicity. SNAPol-1, the best compound in the series, shows DNP enhancement factors at 18.8 T of more than 100 in small molecules and globular proteins and also exhibits strong DNP enhancements in membrane proteins and cellular preparations. By integrating optimal sensitivity and high resolution, we expect widespread applications of this new polarizing agent in high-field DNP/ssNMR spectroscopy, especially for complex biomolecules.
Collapse
Affiliation(s)
- Xinyi Cai
- The province and ministry co-sponsored collaborative innovation center for medical epigenetics Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Agnes Adler
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ru Yao
- The province and ministry co-sponsored collaborative innovation center for medical epigenetics Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Wenxiao Zhang
- The province and ministry co-sponsored collaborative innovation center for medical epigenetics Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - David Beriashvili
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Adil Safeer
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Andrei Gurinov
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry Hungarian Academy of Sciences and Department of Physics, Budapest University of Technology and Economics Budafoki ut 8, 1111, Budapest, Hungary
| | - Yuguang Song
- The province and ministry co-sponsored collaborative innovation center for medical epigenetics Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Yangping Liu
- The province and ministry co-sponsored collaborative innovation center for medical epigenetics Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| |
Collapse
|
9
|
Narasimhan S, Pinto C, Lucini Paioni A, van der Zwan J, Folkers GE, Baldus M. Characterizing proteins in a native bacterial environment using solid-state NMR spectroscopy. Nat Protoc 2021; 16:893-918. [PMID: 33442051 DOI: 10.1038/s41596-020-00439-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/09/2020] [Indexed: 01/29/2023]
Abstract
For a long time, solid-state nuclear magnetic resonance (ssNMR) has been employed to study complex biomolecular systems at the detailed chemical, structural, or dynamic level. Recent progress in high-resolution and high-sensitivity ssNMR, in combination with innovative sample preparation and labeling schemes, offers novel opportunities to study proteins in their native setting irrespective of the molecular tumbling rate. This protocol describes biochemical preparation schemes to obtain cellular samples of both soluble as well as insoluble or membrane-associated proteins in bacteria. To this end, the protocol is suitable for studying a protein of interest in both whole cells and in cell envelope or isolated membrane preparations. In the first stage of the procedure, an appropriate strain of Escherichia coli (DE3) is transformed with a plasmid of interest harboring the protein of interest under the control of an inducible T7 promoter. Next, the cells are adapted to grow in minimal (M9) medium. Before the growth enters stationary phase, protein expression is induced, and shortly thereafter, the native E. coli RNA polymerase is inhibited using rifampicin for targeted labeling of the protein of interest. The cells are harvested after expression and prepared for ssNMR rotor filling. In addition to conventional 13C/15N-detected ssNMR, we also outline how these preparations can be readily subjected to multidimensional ssNMR experiments using dynamic nuclear polarization (DNP) or proton (1H) detection schemes. We estimate that the entire preparative procedure until NMR experiments can be started takes 3-5 days.
Collapse
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Cecilia Pinto
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
| |
Collapse
|
10
|
Ehren HL, Appels FV, Houben K, Renault MA, Wösten HA, Baldus M. Characterization of the cell wall of a mushroom forming fungus at atomic resolution using solid-state NMR spectroscopy. Cell Surf 2020; 6:100046. [PMID: 33204900 PMCID: PMC7649524 DOI: 10.1016/j.tcsw.2020.100046] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 01/18/2023] Open
Abstract
Cell walls are essential in the interaction of fungi with the (a)biotic environment and are also key to hyphal morphogenesis and mechanical strength. Here, we used solid-state NMR (ssNMR) spectroscopy combined with HPLC and GC-MS to study the structural organization of the cell wall of a representative of the Basidiomycota, one of the two main phyla of fungi. Based on the data we propose a refined model for the cell wall of a basidiomycete. In this model, the rigid core is built from α- and β-(1,3)-glucan, β-(1,3)-(1,6)-glucan, highly branched and single stranded β-(1,4)-chitin as well as polymeric fucose. The mobile fraction of the cell wall is composed of β-(1,3)-glucan, β-(1,3)-(1,6)-glucan, β-(1,6)-glucan, α-linked reducing and non-reducing ends and polymeric mannose. Together, these findings provide novel insights into the structural organization of the cell wall of the model basidiomycete S. commune that was previously based on destructive chemical and enzymatic analysis.
Collapse
Affiliation(s)
- Helena Leona Ehren
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Freek V.W. Appels
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Klaartje Houben
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Marie A.M. Renault
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Han A.B. Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| |
Collapse
|
11
|
Gopinath T, Weber DK, Veglia G. Multi-receiver solid-state NMR using polarization optimized experiments (POE) at ultrafast magic angle spinning. JOURNAL OF BIOMOLECULAR NMR 2020; 74:267-285. [PMID: 32333193 PMCID: PMC7236978 DOI: 10.1007/s10858-020-00316-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/11/2020] [Indexed: 05/04/2023]
Abstract
Ultrafast magic angle spinning (MAS) technology and 1H detection have dramatically enhanced the sensitivity of solid-state NMR (ssNMR) spectroscopy of biopolymers. We previously showed that, when combined with polarization optimized experiments (POE), these advancements enable the simultaneous acquisition of multi-dimensional 1H- or 13C-detected experiments using a single receiver. Here, we propose a new sub-class within the POE family, namely HC-DUMAS, HC-MEIOSIS, and HC-MAeSTOSO, that utilize dual receiver technology for the simultaneous detection of 1H and 13C nuclei. We also expand this approach to record 1H-, 13C-, and 15N-detected homonuclear 2D spectra simultaneously using three independent receivers. The combination of POE and multi-receiver technology will further shorten the total experimental time of ssNMR experiments for biological solids.
Collapse
Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
| |
Collapse
|
12
|
Narasimhan S, Folkers GE, Baldus M. When Small becomes Too Big: Expanding the Use of In‐Cell Solid‐State NMR Spectroscopy. Chempluschem 2020; 85:760-768. [DOI: 10.1002/cplu.202000167] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/31/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
| | - Marc Baldus
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
| |
Collapse
|
13
|
Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers GE, Ovaa H, Baldus M. DNP-Supported Solid-State NMR Spectroscopy of Proteins Inside Mammalian Cells. Angew Chem Int Ed Engl 2019; 58:12969-12973. [PMID: 31233270 PMCID: PMC6772113 DOI: 10.1002/anie.201903246] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Indexed: 11/25/2022]
Abstract
Elucidating at atomic level how proteins interact and are chemically modified in cells represents a leading frontier in structural biology. We have developed a tailored solid-state NMR spectroscopic approach that allows studying protein structure inside human cells at atomic level under high-sensitivity dynamic nuclear polarization (DNP) conditions. We demonstrate the method using ubiquitin (Ub), which is critically involved in cellular functioning. Our results pave the way for structural studies of larger proteins or protein complexes inside human cells, which have remained elusive to in-cell solution-state NMR spectroscopy due to molecular size limitations.
Collapse
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
| | - Stephan Scherpe
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Marc Baldus
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
| |
Collapse
|
14
|
Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers GE, Ovaa H, Baldus M. DNP‐Supported Solid‐State NMR Spectroscopy of Proteins Inside Mammalian Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903246] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Stephan Scherpe
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| |
Collapse
|
15
|
Zhang Z, Liu H, Deng J, Tycko R, Yang J. Optimization of band-selective homonuclear dipolar recoupling in solid-state NMR by a numerical phase search. J Chem Phys 2019; 150:154201. [PMID: 31005077 DOI: 10.1063/1.5092986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Spin polarization transfers among aliphatic 13C nuclei, especially 13Cα-13Cβ transfers, permit correlations of their nuclear magnetic resonance (NMR) frequencies that are essential for signal assignments in multidimensional solid-state NMR of proteins. We derive and demonstrate a new radio-frequency (RF) excitation sequence for homonuclear dipolar recoupling that enhances spin polarization transfers among aliphatic 13C nuclei at moderate magic-angle spinning (MAS) frequencies. The phase-optimized recoupling sequence with five π pulses per MAS rotation period (denoted as PR5) is derived initially from systematic numerical simulations in which only the RF phases are varied. Subsequent theoretical analysis by average Hamiltonian theory explains the favorable properties of numerically optimized phase schemes. The high efficiency of spin polarization transfers in simulations is preserved in experiments, in part because the RF field amplitude in PR5 is only 2.5 times the MAS frequency so that relatively low 1H decoupling powers are required. Experiments on a microcrystalline sample of the β1 immunoglobulin binding domain of protein G demonstrate an average enhancement factor of 1.6 for 13Cα → 13Cβ polarization transfers, compared to the standard 13C-13C spin-diffusion method, implying a two-fold time saving in relevant 2D and 3D experiments.
Collapse
Affiliation(s)
- Zhengfeng Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Hui Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Jing Deng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Jun Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| |
Collapse
|
16
|
Lapin J, Nevzorov AA. Automated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 293:104-114. [PMID: 29920407 DOI: 10.1016/j.jmr.2018.06.004] [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: 03/15/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
An automated technique for the sequential assignment of NMR backbone resonances of oriented protein samples has been developed and tested based on 15N-15N homonuclear exchange and spin-exchanged separated local-field spectra. By treating the experimental spectral intensity as a pseudopotential, the Monte-Carlo Simulated Annealing algorithm has been employed to seek lowest-energy assignment solutions over a large sampling space where direct enumeration would be unfeasible. The determined sequential assignments have been scored based on the positions of the crosspeaks resulting from the possible orders for the main peaks. This approach is versatile in terms of the parameters that can be specified to achieve the best-fit result. At a minimum the algorithm requires a continuous segment of the main-peak chemical shifts obtained from a uniformly labeled sample and a spin-exchanged experimental spectrum represented as a 2D matrix array. With selective labeling experiments, groups of chemical shifts corresponding to specific locations in the protein backbone can be fixed, thereby decreasing the sampling space. The output from the program consists of a list of top-score main peak assignments, which can be subjected to further scoring criteria until a consensus solution is found. The algorithm has first been tested on a synthetic spectrum with randomly generated chemical shifts and dipolar couplings for the main peaks. The original assignments have been successfully recovered for as many as 100 main peaks when residue-type information was used even in the presence of substantial spectral peak overlap. The algorithm was then applied to assigning two sets of experimental spectra to recover and confirm the previously established assignments in an automated fashion. For the 20-residue transmembrane domain of Pf1 coat protein reconstituted in magnetically aligned bicelles, the original assignment by Park et al. (2010) was recovered by the automated algorithm with additional input from 5 selectively labeled amino acid spectra. The second case considered was the 46 residue Pf1 bacteriophage from Thiriot et al. (2005) and Knox et al. (2010), of which 38 residues were fit. Automated fitting resulted in several possible assignments but not exactly the original assignment. By using a post-fitting filtering procedure based on the number of missed cross peaks and Pf1 helical structure, a consensus spectroscopic assignment is proposed covering 84% of the original assignment. While the automated assignment works best in spectra with well-resolved crosspeaks, it also tolerates substantial spectral crowding to yield reasonable assignments in the cases where ambiguity and degeneracy of possible assignment solutions are inevitable.
Collapse
Affiliation(s)
- Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
| |
Collapse
|
17
|
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
|
18
|
Craft DL, Sonstrom RE, Rovnyak VG, Rovnyak D. Nonuniform sampling by quantiles. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 288:109-121. [PMID: 29453083 DOI: 10.1016/j.jmr.2018.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 01/24/2018] [Accepted: 01/24/2018] [Indexed: 06/08/2023]
Abstract
A flexible strategy for choosing samples nonuniformly from a Nyquist grid using the concept of statistical quantiles is presented for broad classes of NMR experimentation. Quantile-directed scheduling is intuitive and flexible for any weighting function, promotes reproducibility and seed independence, and is generalizable to multiple dimensions. In brief, weighting functions are divided into regions of equal probability, which define the samples to be acquired. Quantile scheduling therefore achieves close adherence to a probability distribution function, thereby minimizing gaps for any given degree of subsampling of the Nyquist grid. A characteristic of quantile scheduling is that one-dimensional, weighted NUS schedules are deterministic, however higher dimensional schedules are similar within a user-specified jittering parameter. To develop unweighted sampling, we investigated the minimum jitter needed to disrupt subharmonic tracts, and show that this criterion can be met in many cases by jittering within 25-50% of the subharmonic gap. For nD-NUS, three supplemental components to choosing samples by quantiles are proposed in this work: (i) forcing the corner samples to ensure sampling to specified maximum values in indirect evolution times, (ii) providing an option to triangular backfill sampling schedules to promote dense/uniform tracts at the beginning of signal evolution periods, and (iii) providing an option to force the edges of nD-NUS schedules to be identical to the 1D quantiles. Quantile-directed scheduling meets the diverse needs of current NUS experimentation, but can also be used for future NUS implementations such as off-grid NUS and more. A computer program implementing these principles (a.k.a. QSched) in 1D- and 2D-NUS is available under the general public license.
Collapse
Affiliation(s)
- D Levi Craft
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States
| | - Reilly E Sonstrom
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States
| | - Virginia G Rovnyak
- University of Virginia School of Nursing, Charlottesville, VA 22908, United States
| | - David Rovnyak
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States.
| |
Collapse
|
19
|
Nagashima H, Tricot G, Trébosc J, Lafon O, Amoureux JP, Pourpoint F. 3D correlation NMR spectrum between three distinct heteronuclei for the characterization of inorganic samples: Application on sodium alumino-phosphate materials. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 84:164-170. [PMID: 28351540 DOI: 10.1016/j.ssnmr.2017.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/03/2017] [Accepted: 03/13/2017] [Indexed: 06/06/2023]
Abstract
We report here an original NMR sequence allowing the acquisition of 3D correlation NMR spectra between three distinct heteronuclei, among which two are half-integer spin quadrupolar nuclei. Furthermore, as two of them exhibit close Larmor frequency, this experiment was acquired using a standard triple-resonance probe equipped with a commercial frequency splitter. This NMR technique was tested and applied to sodium alumino-phosphate compounds with 31P as the spin-1/2 nucleus and 23Na and 27Al as the close Larmor frequencies isotopes. To the best of our knowledge, such experiment with direct 31P and indirect 27Al and 23Na detection is the first example of 3D NMR experiment in solids involving three distinct heteronuclei. This sequence has first been demonstrated on a mixture of Al(PO3)3 and NaAlP2O7 crystalline phases, for which a selective observation of NaAlP2O7 is possible through the 3D map edition. This 3D correlation experiment is then applied to characterize mixing and phase segregation in a partially devitrified glass that has been proposed as a material for the sequestration of radioactive waste. The 31P-{23Na,27Al} 3D experiment conducted on the partially devitrified glass material conclusively demonstrates that the amorphous component of the material does not contain aluminum. The as-synthesized material thus presents a poor resistance against water, which is a severe limitation for its application in the radioactive waste encapsulation domain.
Collapse
Affiliation(s)
- Hiroki Nagashima
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR 8181 - UCCS - Unité de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Grégory Tricot
- Univ. Lille, CNRS, UMR 8516 - LASIR - Laboratoire de Spectrochimie Infrarouge et Raman, F-59000 Lille, France
| | - Julien Trébosc
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR 8181 - UCCS - Unité de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Olivier Lafon
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR 8181 - UCCS - Unité de Catalyse et Chimie du Solide, F-59000 Lille, France; Institut Universitaire de France, 1 rue Descartes, Paris Cedex 5 75231, France
| | - Jean-Paul Amoureux
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR 8181 - UCCS - Unité de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Frédérique Pourpoint
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR 8181 - UCCS - Unité de Catalyse et Chimie du Solide, F-59000 Lille, France.
| |
Collapse
|
20
|
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
|
21
|
Palmer MR, Suiter CL, Henry GE, Rovnyak J, Hoch JC, Polenova T, Rovnyak D. Sensitivity of nonuniform sampling NMR. J Phys Chem B 2015; 119:6502-15. [PMID: 25901905 DOI: 10.1021/jp5126415] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many information-rich multidimensional experiments in nuclear magnetic resonance spectroscopy can benefit from a signal-to-noise ratio (SNR) enhancement of up to about 2-fold if a decaying signal in an indirect dimension is sampled with nonconsecutive increments, termed nonuniform sampling (NUS). This work provides formal theoretical results and applications to resolve major questions about the scope of the NUS enhancement. First, we introduce the NUS Sensitivity Theorem in which any decreasing sampling density applied to any exponentially decaying signal always results in higher sensitivity (SNR per square root of measurement time) than uniform sampling (US). Several cases will illustrate this theorem and show that even conservative applications of NUS improve sensitivity by useful amounts. Next, we turn to a serious limitation of uniform sampling: the SNR by US decreases for extending evolution times, and thus total experimental times, beyond 1.26T2 (T2 = signal decay constant). Thus, SNR and resolution cannot be simultaneously improved by extending US beyond 1.26T2. We find that NUS can eliminate this constraint, and we introduce the matched NUS SNR Theorem: an exponential sampling density matched to the signal decay always improves the SNR with additional evolution time. Though proved for a specific case, broader classes of NUS densities also improve SNR with evolution time. Applications of these theoretical results are given for a soluble plant natural product and a solid tripeptide (u-(13)C,(15)N-MLF). These formal results clearly demonstrate the inadequacies of applying US to decaying signals in indirect nD-NMR dimensions, supporting a broader adoption of NUS.
Collapse
Affiliation(s)
- Melissa R Palmer
- †Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Christopher L Suiter
- ‡Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Geneive E Henry
- §Department of Chemistry, Susquehanna University, Selinsgrove, Pennsylvania 17837, United States
| | - James Rovnyak
- ∥Department of Mathematics, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Jeffrey C Hoch
- ⊥Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Tatyana Polenova
- ‡Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - David Rovnyak
- †Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| |
Collapse
|
22
|
G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy. Biochem J 2013; 450:443-57. [DOI: 10.1042/bj20121644] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
GPCRs (G-protein-coupled receptors) are versatile signalling molecules at the cell surface and make up the largest and most diverse family of membrane receptors in the human genome. They convert a large variety of extracellular stimuli into intracellular responses through the activation of heterotrimeric G-proteins, which make them key regulatory elements in a broad range of normal and pathological processes, and are therefore one of the most important targets for pharmaceutical drug discovery. Knowledge of a GPCR structure enables us to gain a mechanistic insight into its function and dynamics, and further aid rational drug design. Despite intensive research carried out over the last three decades, resolving the structural basis of GPCR function is still a major activity. The crystal structures obtained in the last 5 years provide the first opportunity to understand how protein structure dictates the unique functional properties of these complex signalling molecules. However, owing to the intrinsic hydrophobicity, flexibility and instability of membrane proteins, it is still a challenge to crystallize GPCRs, and, when this is possible, it is no longer in its native membrane environment and no longer without modification. Furthermore, the conformational change of the transmembrane α-helices associated with the structure activation increases the difficulty of capturing the activation state of a GPCR to a higher resolution by X-ray crystallography. On the other hand, solid-state NMR may offer a unique opportunity to study membrane protein structure, ligand binding and activation at atomic resolution in the native membrane environment, as well as described functionally significant dynamics. In the present review, we discuss some recent achievements of solid-state NMR for understanding GPCRs, the largest mammalian proteome at ~1% of the total expressed proteins. Structural information, details of determination, details of ligand conformations and the consequences of ligand binding to initiate activation can all be explored with solid-state NMR.
Collapse
|
23
|
Cukkemane A, Nand D, Gradmann S, Weingarth M, Kaupp UB, Baldus M. Solid-state NMR [13C,15N] resonance assignments of the nucleotide-binding domain of a bacterial cyclic nucleotide-gated channel. BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:225-9. [PMID: 22302441 PMCID: PMC3438399 DOI: 10.1007/s12104-012-9363-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/17/2012] [Indexed: 05/21/2023]
Abstract
Channels regulated by cyclic nucleotides are key signalling proteins in several biological pathways. The regulatory aspect is conferred by a C-terminal cyclic nucleotide-binding domain (CNBD). We report resonance assignments of the CNBD of a bacterial mlCNG channel obtained using 2D and 3D solid-state NMR under Magic-angle Spinning conditions. A secondary chemical shift analysis of the 141 residue protein suggests a three-dimensional fold seen in earlier X-ray and solution-state NMR work and points to spectroscopic polymorphism for a selected set of resonances.
Collapse
Affiliation(s)
- Abhishek Cukkemane
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Deepak Nand
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sabine Gradmann
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Markus Weingarth
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - U. Benjamin Kaupp
- Center of Advanced European Studies and Research (Caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Marc Baldus
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
24
|
Paramasivam S, Suiter CL, Hou G, Sun S, Palmer M, Hoch JC, Rovnyak D, Polenova T. Enhanced sensitivity by nonuniform sampling enables multidimensional MAS NMR spectroscopy of protein assemblies. J Phys Chem B 2012; 116:7416-27. [PMID: 22667827 DOI: 10.1021/jp3032786] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report dramatic sensitivity enhancements in multidimensional MAS NMR spectra by the use of nonuniform sampling (NUS) and introduce maximum entropy interpolation (MINT) processing that assures the linearity between the time and frequency domains of the NUS acquired data sets. A systematic analysis of sensitivity and resolution in 2D and 3D NUS spectra reveals that with NUS, at least 1.5- to 2-fold sensitivity enhancement can be attained in each indirect dimension without compromising the spectral resolution. These enhancements are similar to or higher than those attained by the newest-generation commercial cryogenic probes. We explore the benefits of this NUS/MaxEnt approach in proteins and protein assemblies using 1-73-(U-(13)C,(15)N)/74-108-(U-(15)N) Escherichia coli thioredoxin reassembly. We demonstrate that in thioredoxin reassembly, NUS permits acquisition of high-quality 3D-NCACX spectra, which are inaccessible with conventional sampling due to prohibitively long experiment times. Of critical importance, issues that hinder NUS-based SNR enhancement in 3D-NMR of liquids are mitigated in the study of solid samples in which theoretical enhancements on the order of 3-4 fold are accessible by compounding the NUS-based SNR enhancement of each indirect dimension. NUS/MINT is anticipated to be widely applicable and advantageous for multidimensional heteronuclear MAS NMR spectroscopy of proteins, protein assemblies, and other biological systems.
Collapse
Affiliation(s)
- Sivakumar Paramasivam
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Giffard M, Hediger S, Lewandowski JR, Bardet M, Simorre JP, Griffin RG, De Paëpe G. Compensated second-order recoupling: application to third spin assisted recoupling. Phys Chem Chem Phys 2012; 14:7246-55. [PMID: 22513727 PMCID: PMC4440590 DOI: 10.1039/c2cp40406k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We consider the effect of phase shifts in the context of second-order recoupling techniques in solid-state NMR. Notably we highlight conditions leading to significant improvements for the Third Spin Assisted Recoupling (TSAR) mechanism and demonstrate the benefits of resulting techniques for detecting long-distance transfer in biomolecular systems. The modified pulse sequences of PAR and PAIN-CP, Phase-Shifted Proton Assisted Recoupling (AH-PS-PAR) and Phase-Shifted Proton-Assisted Insensitive Nuclei Cross Polarization (ABH-PS-PAIN-CP), still rely on cross terms between heteronuclear dipolar couplings involving assisting protons that mediate zero-quantum polarization transfer between low-γ nuclei ((13)C-(13)C, (15)N-(15)N, (15)N-(13)C polarization transfer). Using Average Hamiltonian Theory we show that phase inversion compensates off-resonance contributions and yields improved polarization transfer as well as substantial broadening of the matching conditions. PS-TSAR greatly improves on the standard TSAR based methods because it alleviates their sensitivity to precise RF settings which significantly enhances robustness of the experiments. We demonstrate these new methods on a 19.6 kDa protein (U-[(15)N, (13)C]-YajG) at high magnetic fields (up to 900 MHz (1)H frequency) and fast sample spinning (up to 65 kHz MAS frequency).
Collapse
Affiliation(s)
- Mathilde Giffard
- Laboratoire de Chimie Inorganique et Biologique, UMR-E3 (CEA/UJF) and CNRS, CEA/DSM/INAC–38054, Grenoble, France
| | - Sabine Hediger
- Laboratoire de Chimie Inorganique et Biologique, UMR-E3 (CEA/UJF) and CNRS, CEA/DSM/INAC–38054, Grenoble, France
| | | | - Michel Bardet
- Laboratoire de Chimie Inorganique et Biologique, UMR-E3 (CEA/UJF) and CNRS, CEA/DSM/INAC–38054, Grenoble, France
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale, UMR 5075 (CEA/CNRS/UJF), 38027 Grenoble, France
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Gaël De Paëpe
- Laboratoire de Chimie Inorganique et Biologique, UMR-E3 (CEA/UJF) and CNRS, CEA/DSM/INAC–38054, Grenoble, France
| |
Collapse
|
26
|
De Paëpe G. Dipolar Recoupling in Magic Angle Spinning Solid-State Nuclear Magnetic Resonance. Annu Rev Phys Chem 2012; 63:661-84. [DOI: 10.1146/annurev-physchem-032511-143726] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gaël De Paëpe
- Service de Chimie Inorganique et Biologique, UMR-E 3 CEA/UJF-Grenoble 1, Institut Nanosciences et Cryogénie, F-38054 Grenoble, France;
| |
Collapse
|
27
|
|
28
|
Renault M, Cukkemane A, Baldus M. Festkörper-NMR-Spektroskopie an komplexen Biomolekülen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002823] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
29
|
Renault M, Cukkemane A, Baldus M. Solid-State NMR Spectroscopy on Complex Biomolecules. Angew Chem Int Ed Engl 2010; 49:8346-57. [DOI: 10.1002/anie.201002823] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
30
|
Tycko R, Hu KN. A Monte Carlo/simulated annealing algorithm for sequential resonance assignment in solid state NMR of uniformly labeled proteins with magic-angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 205:304-14. [PMID: 20547467 PMCID: PMC2902575 DOI: 10.1016/j.jmr.2010.05.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 05/19/2010] [Accepted: 05/21/2010] [Indexed: 05/05/2023]
Abstract
We describe a computational approach to sequential resonance assignment in solid state NMR studies of uniformly (15)N,(13)C-labeled proteins with magic-angle spinning. As input, the algorithm uses only the protein sequence and lists of (15)N/(13)C(alpha) crosspeaks from 2D NCACX and NCOCX spectra that include possible residue-type assignments of each crosspeak. Assignment of crosspeaks to specific residues is carried out by a Monte Carlo/simulated annealing algorithm, implemented in the program MC_ASSIGN1. The algorithm tolerates substantial ambiguity in residue-type assignments and coexistence of visible and invisible segments in the protein sequence. We use MC_ASSIGN1 and our own 2D spectra to replicate and extend the sequential assignments for uniformly-labeled HET-s(218-289) fibrils previously determined manually by Siemer et al. (J. Biomol. NMR, 34 (2006) 75-87) from a more extensive set of 2D and 3D spectra. Accurate assignments by MC_ASSIGN1 do not require data that are of exceptionally high quality. Use of MC_ASSIGN1 (and its extensions to other types of 2D and 3D data) is likely to alleviate many of the difficulties and uncertainties associated with manual resonance assignments in solid state NMR studies of uniformly labeled proteins, where spectral resolution and signal-to-noise are often sub-optimal.
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
|
31
|
Loquet A, Gardiennet C, Böckmann A. Protein 3D structure determination by high-resolution solid-state NMR. CR CHIM 2010. [DOI: 10.1016/j.crci.2010.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
32
|
Li S, Zhang Y, Hong M. 3D (13)C-(13)C-(13)C correlation NMR for de novo distance determination of solid proteins and application to a human alpha-defensin. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 202:203-10. [PMID: 19963419 PMCID: PMC2819753 DOI: 10.1016/j.jmr.2009.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 11/06/2009] [Accepted: 11/13/2009] [Indexed: 05/05/2023]
Abstract
The de novo structure of an antimicrobial protein, human alpha-defensin 1 (HNP-1), is determined by combining a 3D (13)C-(13)C-(13)C (CCC) magic-angle spinning (MAS) correlation experiment with standard resonance assignment experiments. Using a short spin diffusion mixing time to assign intra-residue cross peaks and a long mixing time to detect inter-residue correlation peaks, we show that the 3D CCC experiment not only reduces the ambiguity of resonance assignment, but more importantly yields two orders of magnitude more long-range distances without recourse to existing crystal structures. Most of these distance constraints could not be obtained in a de novo fashion from 2D correlation spectra due to significant resonance overlap. Combining the distance constraints from the 3D CCC experiment and the chemical-shift-derived torsion angles, we obtained a de novo high-resolution NMR structure of HNP-1, with a heavy-atom RMSD of 3.4A from the crystal structure of the analogous HNP-3. The average energy of the minimum-energy ensemble is less than of 40kcal/mol. Thus, the 3D CCC experiment provides a reliable means of restraining the three-dimensional structure of insoluble proteins with unknown conformations.
Collapse
Affiliation(s)
| | | | - Mei Hong
- Corresponding author: Mei Hong, Tel: 515-294-3521; Fax: 515-294-0105,
| |
Collapse
|
33
|
Vosegaard T, Nielsen NC. Defining the sampling space in multidimensional NMR experiments: what should the maximum sampling time be? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 199:146-158. [PMID: 19428277 DOI: 10.1016/j.jmr.2009.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 04/06/2009] [Accepted: 04/09/2009] [Indexed: 05/27/2023]
Abstract
Efficient sampling of signals is a key issue for multiple-dimensional NMR experiments to establish the best ratio between experiment time and spectral quality. Focussing on the most widely used sampling strategy using standard rectangular sampling and data analysis by Fourier transformation, a central question is concerned with determining the optimal maximum sampling time in the individual dimensions. The spectral resolution depends directly on this choice, as do the overall experiment times when addressing the indirect dimensions. We present a theoretical, numerical, and experimental analysis of the sampling space problem and propose approaches to efficient sampling for typical cases.
Collapse
Affiliation(s)
- Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Aarhus C, Denmark.
| | | |
Collapse
|
34
|
Aluas M, Tripon C, Griffin JM, Filip X, Ladizhansky V, Griffin RG, Brown SP, Filip C. CHHC and (1)H-(1)H magnetization exchange: analysis by experimental solid-state NMR and 11-spin density-matrix simulations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 199:173-87. [PMID: 19467890 PMCID: PMC2706310 DOI: 10.1016/j.jmr.2009.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 04/20/2009] [Indexed: 05/03/2023]
Abstract
A protocol is presented for correcting the effect of non-specific cross-polarization in CHHC solid-state MAS NMR experiments, thus allowing the recovery of the (1)H-(1)H magnetization exchange functions from the mixing-time dependent buildup of experimental CHHC peak intensity. The presented protocol also incorporates a scaling procedure to take into account the effect of multiplicity of a CH(2) or CH(3) moiety. Experimental CHHC buildup curves are presented for l-tyrosine.HCl samples where either all or only one in 10 molecules are U-(13)C labeled. Good agreement between experiment and 11-spin SPINEVOLUTION simulation (including only isotropic (1)H chemical shifts) is demonstrated for the initial buildup (t(mix)<100micros) of CHHC peak intensity corresponding to an intramolecular close (2.5A) H-H proximity. Differences in the initial CHHC buildup are observed between the one in 10 dilute and 100% samples for cases where there is a close intermolecular H-H proximity in addition to a close intramolecular H-H proximity. For the dilute sample, CHHC cross-peak intensities tended to significantly lower values for long mixing times (500micros) as compared to the 100% sample. This difference is explained as being due to the dependence of the limiting total magnetization on the ratio N(obs)/N(tot) between the number of protons that are directly attached to a (13)C nucleus and hence contribute significantly to the observed (13)C CHHC NMR signal, and the total number of (1)H spins into the system. (1)H-(1)H magnetization exchange curves extracted from CHHC spectra for the 100% l-tyrosine.HCl sample exhibit a clear sensitivity to the root sum squared dipolar coupling, with fast buildup being observed for the shortest intramolecular distances (2.5A) and slower, yet observable buildup for the longer intermolecular distances (up to 5A).
Collapse
Affiliation(s)
- Mihaela Aluas
- Physics Department, Babes-Bolyai University, 400084 Cluj, Romania
| | - Carmen Tripon
- National Institute for R&D of Isotopic and Molecular Technologies, P.O. Box 700, 400293 Cluj, Romania
| | - John M. Griffin
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Xenia Filip
- Physics Department, Babes-Bolyai University, 400084 Cluj, Romania
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
| | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Steven P. Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Claudiu Filip
- National Institute for R&D of Isotopic and Molecular Technologies, P.O. Box 700, 400293 Cluj, Romania
- Corresponding Author, Fax.: ++40 264 420042, e-mail:
| |
Collapse
|
35
|
Lewandowski JR, De Paëpe G, Eddy MT, Griffin RG. (15)N-(15)N proton assisted recoupling in magic angle spinning NMR. J Am Chem Soc 2009; 131:5769-76. [PMID: 19334788 PMCID: PMC2754755 DOI: 10.1021/ja806578y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a new magic angle spinning (MAS) NMR experiment for obtaining (15)N-(15)N correlation spectra. The approach yields direct information about the secondary and tertiary structure of proteins, including identification of alpha-helical stretches and interstrand connectivity in antiparallel beta-sheets, which are of major interest for structural studies of membrane proteins and amyloid fibrils. The method, (15)N-(15)N proton assisted recoupling (PAR), relies on a second-order mechanism, third spin assisted recoupling (TSAR), used previously in the context of (15)N-(13)C and (13)C-(13)C polarization transfer schemes. In comparison to (15)N-(15)N proton-driven spin diffusion experiments, the PAR technique accelerates polarization transfer between (15)N's by a factor of approximately 10(2)-10(3) and is furthermore applicable over the entire range of currently available MAS frequencies (10-70 kHz).
Collapse
Affiliation(s)
- Józef R Lewandowski
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | |
Collapse
|
36
|
De Paëpe G, Lewandowski JR, Loquet A, Böckmann A, Griffin RG. Proton assisted recoupling and protein structure determination. J Chem Phys 2008; 129:245101. [PMID: 19123534 PMCID: PMC2755343 DOI: 10.1063/1.3036928] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 11/03/2008] [Indexed: 11/14/2022] Open
Abstract
We introduce a homonuclear version of third spin assisted recoupling, a second-order mechanism that can be used for polarization transfer between (13)C or (15)N spins in magic angle spinning (MAS) NMR experiments, particularly at high spinning frequencies employed in contemporary high field MAS experiments. The resulting sequence, which we refer to as proton assisted recoupling (PAR), relies on a cross-term between (1)H-(13)C (or (1)H-(15)N) couplings to mediate zero quantum (13)C-(13)C (or (15)N-(15)N recoupling). In particular, using average Hamiltonian theory we derive an effective Hamiltonian for PAR and show that the transfer is mediated by trilinear terms of the form C(1) (+/-)C(2) (-/+)H(Z) for (13)C-(13)C recoupling experiments (or N(1) (+/-)N(2) (-/+)H(Z) for (15)N-(15)N). We use analytical and numerical simulations to explain the structure of the PAR optimization maps and to delineate the PAR matching conditions. We also detail the PAR polarization transfer dependence with respect to the local molecular geometry and explain the observed reduction in dipolar truncation. Finally, we demonstrate the utility of PAR in structural studies of proteins with (13)C-(13)C spectra of uniformly (13)C, (15)N labeled microcrystalline Crh, a 85 amino acid model protein that forms a domain swapped dimer (MW=2 x 10.4 kDa). The spectra, which were acquired at high MAS frequencies (omega(r)2pi>20 kHz) and magnetic fields (750-900 MHz (1)H frequencies) using moderate rf fields, exhibit numerous cross peaks corresponding to long (up to 6-7 A) (13)C-(13)C distances which are particularly useful in protein structure determination. Using results from PAR spectra we calculate the structure of the Crh protein.
Collapse
Affiliation(s)
- Gaël De Paëpe
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | |
Collapse
|
37
|
Helmus JJ, Nadaud PS, Höfer N, Jaroniec CP. Determination of methyl 13C-15N dipolar couplings in peptides and proteins by three-dimensional and four-dimensional magic-angle spinning solid-state NMR spectroscopy. J Chem Phys 2008; 128:052314. [PMID: 18266431 DOI: 10.1063/1.2817638] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We describe three- and four-dimensional semiconstant-time transferred echo double resonance (SCT-TEDOR) magic-angle spinning solid-state nuclear magnetic resonance (NMR) experiments for the simultaneous measurement of multiple long-range (15)N-(13)C(methyl) dipolar couplings in uniformly (13)C, (15)N-enriched peptides and proteins with high resolution and sensitivity. The methods take advantage of (13)C spin topologies characteristic of the side-chain methyl groups in amino acids alanine, isoleucine, leucine, methionine, threonine, and valine to encode up to three distinct frequencies ((15)N-(13)C(methyl) dipolar coupling, (15)N chemical shift, and (13)C(methyl) chemical shift) within a single SCT evolution period of initial duration approximately 1(1)J(CC) (where (1)J(CC) approximately 35 Hz, is the one-bond (13)C(methyl)-(13)C J-coupling) while concurrently suppressing the modulation of NMR coherences due to (13)C-(13)C and (15)N-(13)C J-couplings and transverse relaxation. The SCT-TEDOR schemes offer several important advantages over previous methods of this type. First, significant (approximately twofold to threefold) gains in experimental sensitivity can be realized for weak (15)N-(13)C(methyl) dipolar couplings (corresponding to structurally interesting, approximately 3.5 A or longer, distances) and typical (13)C(methyl) transverse relaxation rates. Second, the entire SCT evolution period can be used for (13)C(methyl) and/or (15)N frequency encoding, leading to increased spectral resolution with minimal additional coherence decay. Third, the experiments are inherently "methyl selective," which results in simplified NMR spectra and obviates the use of frequency-selective pulses or other spectral filtering techniques. Finally, the (15)N-(13)C cross-peak buildup trajectories are purely dipolar in nature (i.e., not influenced by J-couplings or relaxation), which enables the straightforward extraction of (15)N-(13)C(methyl) distances using an analytical model. The SCT-TEDOR experiments are demonstrated on a uniformly (13)C, (15)N-labeled peptide, N-acetyl-valine, and a 56 amino acid protein, B1 immunoglobulin-binding domain of protein G (GB1), where the measured (15)N-(13)C(methyl) dipolar couplings provide site-specific information about side-chain dihedral angles and the packing of protein molecules in the crystal lattice.
Collapse
Affiliation(s)
- Jonathan J Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | | | | |
Collapse
|
38
|
Gardiennet C, Loquet A, Etzkorn M, Heise H, Baldus M, Böckmann A. Structural constraints for the Crh protein from solid-state NMR experiments. JOURNAL OF BIOMOLECULAR NMR 2008; 40:239-50. [PMID: 18320329 PMCID: PMC2579321 DOI: 10.1007/s10858-008-9229-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Accepted: 02/06/2008] [Indexed: 05/11/2023]
Abstract
We demonstrate that short, medium and long-range constraints can be extracted from proton mediated, rare-spin detected correlation solid-state NMR experiments for the microcrystalline 10.4 x 2 kDa dimeric model protein Crh. Magnetization build-up curves from cross signals in NHHC and CHHC spectra deliver detailed information on side chain conformers and secondary structure for interactions between spin pairs. A large number of medium and long-range correlations can be observed in the spectra, and an analysis of the resolved signals reveals that the constraints cover the entire sequence, also including inter-monomer contacts between the two molecules forming the domain-swapped Crh dimer. Dynamic behavior is shown to have an impact on cross signals intensities, as indicated for mobile residues or regions by contacts predicted from the crystal structure, but absent in the spectra. Our work validates strategies involving proton distance measurements for large and complex proteins as the Crh dimer, and confirms the magnetization transfer properties previously described for small molecules in solid protein samples.
Collapse
Affiliation(s)
- Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
| | - Antoine Loquet
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
| | - Manuel Etzkorn
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Henrike Heise
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Marc Baldus
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
| |
Collapse
|
39
|
De Paëpe G, Lewandowski JR, Griffin RG. Spin dynamics in the modulation frame: Application to homonuclear recoupling in magic angle spinning solid-state NMR. J Chem Phys 2008; 128:124503. [DOI: 10.1063/1.2834732] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
40
|
Loquet A, Bardiaux B, Gardiennet C, Blanchet C, Baldus M, Nilges M, Malliavin T, Böckmann A. 3D Structure Determination of the Crh Protein from Highly Ambiguous Solid-State NMR Restraints. J Am Chem Soc 2008; 130:3579-89. [DOI: 10.1021/ja078014t] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Antoine Loquet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Benjamin Bardiaux
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christophe Blanchet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marc Baldus
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Nilges
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Thérèse Malliavin
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| |
Collapse
|
41
|
Dürr UH, Waskell L, Ramamoorthy A. The cytochromes P450 and b5 and their reductases—Promising targets for structural studies by advanced solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3235-59. [DOI: 10.1016/j.bbamem.2007.08.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/08/2007] [Indexed: 02/02/2023]
|
42
|
Böckmann A. High-resolution solid-state MAS NMR of proteins-Crh as an example. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S24-S31. [PMID: 18081212 DOI: 10.1002/mrc.2106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 09/04/2007] [Accepted: 09/12/2007] [Indexed: 05/25/2023]
Abstract
Solid-state NMR spectroscopy provides unique possibilities for the structural investigation of insoluble molecules at the atomic level. Recent efforts aim at solving the complete structures of biological macromolecules using high-resolution magic angle spinning NMR. Structurally homogenous samples of [(13)C,(15)N]-labeled proteins have to be used in this type of studies. Microcrystalline model proteins present valuable tools for the developments of methods towards this goal. This review discusses recent progress in the field, using the Crh protein as an illustrative example. We discuss strategies for resonance assignments and for the determination of structure and dynamics, as well as techniques for the detection of protein interaction partners and folding mechanisms by solid-state NMR methods.
Collapse
Affiliation(s)
- Anja Böckmann
- IFR 128 BioSciences Lyon-Gerland, IBCP UMR 5086 CNRS/Université de Lyon Claude Bernard, 7 passage du Vercors, 69367 Lyon, France.
| |
Collapse
|
43
|
Baldus M. Magnetic resonance in the solid state: applications to protein folding, amyloid fibrils and membrane proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36 Suppl 1:S37-48. [PMID: 17541576 DOI: 10.1007/s00249-007-0174-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2007] [Accepted: 05/08/2007] [Indexed: 11/25/2022]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) represents a spectroscopic method to study non-crystalline molecules at atomic resolution. Advancements in spectroscopy and biochemistry provide increasing possibilities to study structure and dynamics of complex biomolecular systems by ssNMR. Here, methodological aspects and applications in the context of protein folding and aggregation are discussed. In addition, studies involving membrane proteins are considered.
Collapse
Affiliation(s)
- Marc Baldus
- Solid-state NMR, Max-Planck-Institut für Biophysikalische Chemie, 37077 Göttingen, Germany.
| |
Collapse
|
44
|
Sinha N, Grant CV, Park SH, Brown JM, Opella SJ. Triple resonance experiments for aligned sample solid-state NMR of (13)C and (15)N labeled proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 186:51-64. [PMID: 17293139 PMCID: PMC3760591 DOI: 10.1016/j.jmr.2007.01.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 01/11/2007] [Accepted: 01/21/2007] [Indexed: 05/11/2023]
Abstract
Initial steps in the development of a suite of triple-resonance (1)H/(13)C/(15)N solid-state NMR experiments applicable to aligned samples of (13)C and (15)N labeled proteins are described. The experiments take advantage of the opportunities for (13)C detection without the need for homonuclear (13)C/(13)C decoupling presented by samples with two different patterns of isotopic labeling. In one type of sample, the proteins are approximately 20% randomly labeled with (13)C in all backbone and side chain carbon sites and approximately 100% uniformly (15)N labeled in all nitrogen sites; in the second type of sample, the peptides and proteins are (13)C labeled at only the alpha-carbon and (15)N labeled at the amide nitrogen of a few residues. The requirement for homonuclear (13)C/(13)C decoupling while detecting (13)C signals is avoided in the first case because of the low probability of any two (13)C nuclei being bonded to each other; in the second case, the labeled (13)C(alpha) sites are separated by at least three bonds in the polypeptide chain. The experiments enable the measurement of the (13)C chemical shift and (1)H-(13)C and (15)N-(13)C heteronuclear dipolar coupling frequencies associated with the (13)C(alpha) and (13)C' backbone sites, which provide orientation constraints complementary to those derived from the (15)N labeled amide backbone sites. (13)C/(13)C spin-exchange experiments identify proximate carbon sites. The ability to measure (13)C-(15)N dipolar coupling frequencies and correlate (13)C and (15)N resonances provides a mechanism for making backbone resonance assignments. Three-dimensional combinations of these experiments ensure that the resolution, assignment, and measurement of orientationally dependent frequencies can be extended to larger proteins. Moreover, measurements of the (13)C chemical shift and (1)H-(13)C heteronuclear dipolar coupling frequencies for nearly all side chain sites enable the complete three-dimensional structures of proteins to be determined with this approach.
Collapse
Affiliation(s)
- Neeraj Sinha
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307 La Jolla, CA 92093-0307, USA
| | - Christopher V. Grant
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307 La Jolla, CA 92093-0307, USA
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307 La Jolla, CA 92093-0307, USA
| | | | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307 La Jolla, CA 92093-0307, USA
| |
Collapse
|
45
|
Nevzorov AA, Park SH, Opella SJ. Three-dimensional experiment for solid-state NMR of aligned protein samples in high field magnets. JOURNAL OF BIOMOLECULAR NMR 2007; 37:113-6. [PMID: 17216304 DOI: 10.1007/s10858-006-9121-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 10/27/2006] [Indexed: 05/13/2023]
Abstract
A pulse sequence that yields three-dimensional (1)H chemical shift/(1)H-(15)N heteronuclear dipolar coupling/(15)N chemical shift solid-state NMR spectra is demonstrated on a uniformly (15)N labeled membrane protein in magnetically aligned phospholipid bilayers. Based on SAMPI4, the pulse sequence yields high resolution in all three dimensions at a (1)H resonance frequency of 900 MHz with the relatively low rf field strength (33 kHz) available for a lossy aqueous sample with a commercial spectrometer and probe. The (1)H chemical shift frequency dimension is shown to select among amide resonances, which will be useful in studies of larger polytopic membrane proteins where the resonances overlap in two-dimensional spectra. Moreover, the (1)H chemical shift, which can be measured from these spectra, provides an additional orientationally dependent frequency as input for structure calculations.
Collapse
Affiliation(s)
- Alexander A Nevzorov
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307, USA
| | | | | |
Collapse
|
46
|
Schubert M, Manolikas T, Rogowski M, Meier BH. Solid-state NMR spectroscopy of 10% 13C labeled ubiquitin: spectral simplification and stereospecific assignment of isopropyl groups. JOURNAL OF BIOMOLECULAR NMR 2006; 35:167-73. [PMID: 16858625 DOI: 10.1007/s10858-006-9025-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Accepted: 04/18/2006] [Indexed: 05/10/2023]
Abstract
We describe the simplification of 13C-13C correlation spectra obtained from a microcrystalline protein sample expressed on a growth medium of 10% fully 13C labeled glucose diluted in 90% natural abundance glucose as compared to a fully labeled sample. Such a labeling scheme facilitates the backbone and side-chain resonance assignment of Phe, Tyr, His, Asp, Asn, Ile, Lys and Pro and yields an unambiguous stereospecific assignment of the valine Cgamma1, Cgamma2 13C resonances and of Leucine Cdelta2.
Collapse
Affiliation(s)
- Mario Schubert
- ETH Zurich, Physical Chemistry, 8093, Zurich, Switzerland
| | | | | | | |
Collapse
|
47
|
Zhou DH, Kloepper KD, Winter KA, Rienstra CM. Band-selective 13C homonuclear 3D spectroscopy for solid proteins at high field with rotor-synchronized soft pulses. JOURNAL OF BIOMOLECULAR NMR 2006; 34:245-57. [PMID: 16645815 DOI: 10.1007/s10858-006-0026-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 02/20/2006] [Indexed: 05/08/2023]
Abstract
We demonstrate improved 3D 13C-13C-13C chemical shift correlation experiments for solid proteins, utilizing band-selective coherence transfer, scalar decoupling and homonuclear zero-quantum polarization transfer. Judicious use of selective pulses and a z-filter period suppress artifacts with a two-step phase cycle, allowing higher digital resolution in a fixed measurement time. The novel correlation of C(ali)-C(ali)-CX (C(ali) for aliphatic carbons, CX for any carbon) reduces measurement time by an order of magnitude without sacrificing digital resolution. The experiment retains intensity from side-chain carbon resonances whose chemical shift dispersion is critical to minimize spectral degeneracy for large proteins with a predominance of secondary structure, such as beta-sheet rich fibrillar proteins and alpha-helical membrane proteins. We demonstrate the experiment for the beta1 immunoglobulin binding domain of protein G (GB1) and fibrils of the A30P mutant of alpha-synuclein, which is implicated in Parkinson's disease. Selective pulses of duration comparable the rotor period give optimal performance, but must be synchronized with the spinning in non-trivial ways to minimize chemical shift anisotropy recoupling effects. Soft pulses with a small bandwidth-duration product are best for exciting the approximately 70 ppm bandwidth required for aliphatic-only dimensions.
Collapse
Affiliation(s)
- Donghua H Zhou
- Department of Chemistry, Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA
| | | | | | | |
Collapse
|
48
|
|
49
|
Seidel K, Etzkorn M, Heise H, Becker S, Baldus M. High-Resolution Solid-State NMR Studies on Uniformly [13C,15N]-Labeled Ubiquitin. Chembiochem 2005; 6:1638-47. [PMID: 16094694 DOI: 10.1002/cbic.200500085] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Understanding of the effects of intermolecular interactions, molecular dynamics, and sample preparation on high-resolution magic-angle spinning NMR data is currently limited. Using the example of a uniformly [13C,15N]-labeled sample of ubiquitin, we discuss solid-state NMR methods tailored to the construction of 3D molecular structure and study the influence of solid-phase protein preparation on solid-state NMR spectra. A comparative analysis of 13C', 13Calpha, and 13Cbeta resonance frequencies suggests that 13C chemical-shift variations are most likely to occur in protein regions that exhibit an enhanced degree of molecular mobility. Our results can be refined by additional solid-state NMR techniques and serve as a reference for ongoing efforts to characterize the structure and dynamics of (membrane) proteins, protein complexes, and other biomolecules by high-resolution solid-state NMR.
Collapse
Affiliation(s)
- Karsten Seidel
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | | | | | | | | |
Collapse
|
50
|
Luca S, Heise H, Lange A, Baldus M. Investigation of Ligand-Receptor Systems by High-Resolution Solid-State NMR: Recent Progress and Perspectives. Arch Pharm (Weinheim) 2005; 338:217-28. [PMID: 15938000 DOI: 10.1002/ardp.200400991] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Solid-state Nuclear Magnetic Resonance (NMR) provides a general method to study molecular structure and dynamics in a non-crystalline and insoluble environment. We discuss the latest methodological progress to construct 3D molecular structures from solid-state NMR data obtained under magic-angle-spinning conditions. As shown for the neurotensin/NTS-1 system, these methods can be readily applied to the investigation of ligand-binding to G-protein coupled receptors.
Collapse
Affiliation(s)
- Sorin Luca
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | |
Collapse
|