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Miloslavina YA, Thomas B, Reus M, Gupta KBSS, Oostergetel GT, Andreas LB, Holzwarth AR, de Groot HJM. Contrasting packing modes for tubular assemblies in chlorosomes. PHOTOSYNTHESIS RESEARCH 2024; 161:105-115. [PMID: 38538911 PMCID: PMC11269348 DOI: 10.1007/s11120-024-01089-3] [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: 10/14/2023] [Accepted: 02/27/2024] [Indexed: 07/25/2024]
Abstract
The largest light-harvesting antenna in nature, the chlorosome, is a heterogeneous helical BChl self-assembly that has evolved in green bacteria to harvest light for performing photosynthesis in low-light environments. Guided by NMR chemical shifts and distance constraints for Chlorobaculum tepidum wild-type chlorosomes, the two contrasting packing modes for syn-anti parallel stacks of BChl c to form polar 2D arrays, with dipole moments adding up, are explored. Layered assemblies were optimized using local orbital density functional and plane wave pseudopotential methods. The packing mode with the lowest energy contains syn-anti and anti-syn H-bonding between stacks. It can accommodate R and S epimers, and side chain variability. For this packing, a match with the available EM data on the subunit axial repeat and optical data is obtained with multiple concentric cylinders for a rolling vector with the stacks running at an angle of 21° to the cylinder axis and with the BChl dipole moments running at an angle ß ∼ 55° to the tube axis, in accordance with optical data. A packing mode involving alternating syn and anti parallel stacks that is at variance with EM appears higher in energy. A weak cross-peak at -6 ppm in the MAS NMR with 50 kHz spinning, assigned to C-181, matches the shift of antiparallel dimers, which possibly reflects a minor impurity-type fraction in the self-assembled BChl c.
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Affiliation(s)
- Yuliya A Miloslavina
- Institute of Chemistry, Leiden University, Box 9502, 2300 RA, Leiden, The Netherlands
- Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Am Faßberg 11, 37077, Göttingen, Germany
- Eduard-Zintl-Institut für Anorganische and Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str, 64287, Darmstadt, Germany
| | - Brijith Thomas
- Institute of Chemistry, Leiden University, Box 9502, 2300 RA, Leiden, The Netherlands
- Science Division, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Michael Reus
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim a. d. Ruhr, Germany
| | | | - Gert T Oostergetel
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Loren B Andreas
- Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Am Faßberg 11, 37077, Göttingen, Germany
| | - Alfred R Holzwarth
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim a. d. Ruhr, Germany
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Huub J M de Groot
- Institute of Chemistry, Leiden University, Box 9502, 2300 RA, Leiden, The Netherlands.
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2
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Wi S, Li C, Pham K, Lee W, Frydman L. Short and long range 2D 15N- 15N NMR correlations among peptide groups by novel solid state dipolar mixing schemes. JOURNAL OF BIOMOLECULAR NMR 2024; 78:19-30. [PMID: 38102490 DOI: 10.1007/s10858-023-00429-0] [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: 07/04/2023] [Accepted: 11/06/2023] [Indexed: 12/17/2023]
Abstract
A recently developed homonuclear dipolar recoupling scheme, Adiabatic Linearly FREquency Swept reCOupling (AL FRESCO), was applied to record two-dimensional (2D) 15N-15N correlations on uniformly 15N-labeled GB1 powders. A major feature exploited in these 15N-15N correlations was AL FRESCO's remarkably low RF power demands, which enabled seconds-long mixing schemes when establishing direct correlations. These 15N-15N mixing schemes proved efficient regardless of the magic-angle spinning (MAS) rate and, being nearly free from dipolar truncation effects, they enabled the detection of long-range, weak dipolar couplings, even in the presence of strong short-range dipolar couplings. This led to a connectivity information that was significantly better than that obtained with spontaneously proton-driven, 15N spin-diffusion experiments. An indirect approach producing long-range 15N-15N correlations was also tested, relying on short (ms-long) 1HN-1HN mixings schemes while applying AL FRESCO chirped pulses along the 15N channel. These indirect mixing schemes produced numerous long-distance Ni-Ni±n (n = 2 - 5) correlations, that might be useful for characterizing three-dimensional arrangements in proteins. Once again, these AL FRESCO mediated experiments proved more informative than variants based on spin-diffusion-based 1HN-1HN counterparts.
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Affiliation(s)
- Sungsool Wi
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32304, USA.
| | - Conggang Li
- 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, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Karen Pham
- Department of Chemistry, University of Colorado at Denver, Denver, CO, 80217-3364, USA
| | - Woonghee Lee
- Department of Chemistry, University of Colorado at Denver, Denver, CO, 80217-3364, USA
| | - Lucio Frydman
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32304, USA.
- Department of Chemical and Biological Physics, Weizmann Institute of Sciences, Rehovot, Israel.
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Tatman BP, Franks WT, Brown SP, Lewandowski JR. Nuclear spin diffusion under fast magic-angle spinning in solid-state NMR. J Chem Phys 2023; 158:2890210. [PMID: 37171196 DOI: 10.1063/5.0142201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
Solid-state nuclear spin diffusion is the coherent and reversible process through which spin order is transferred via dipolar couplings. With the recent increases in magic-angle spinning (MAS) frequencies and magnetic fields becoming routinely applied in solid-state nuclear magnetic resonance, understanding how the increased 1H resolution obtained affects spin diffusion is necessary for interpretation of several common experiments. To investigate the coherent contributions to spin diffusion with fast MAS, we have developed a low-order correlation in Liouville space model based on the work of Dumez et al. (J. Chem. Phys. 33, 224501, 2010). Specifically, we introduce a new method for basis set selection, which accounts for the resonance-offset dependence at fast MAS. Furthermore, we consider the necessity of including chemical shift, both isotropic and anisotropic, in the modeling of spin diffusion. Using this model, we explore how different experimental factors change the nature of spin diffusion. Then, we show case studies to exemplify the issues that arise in using spin diffusion techniques at fast spinning. We show that the efficiency of polarization transfer via spin diffusion occurring within a deuterated and 100% back-exchanged protein sample at 60 kHz MAS is almost entirely dependent on resonance offset. We additionally identify temperature-dependent magnetization transfer in beta-aspartyl L-alanine, which could be explained by the influence of an incoherent relaxation-based nuclear Overhauser effect.
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Affiliation(s)
- Ben P Tatman
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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Shamir Y, Goldbourt A. Atomic-Resolution Structure of the Protein Encoded by Gene V of fd Bacteriophage in Complex with Viral ssDNA Determined by Magic-Angle Spinning Solid-State NMR. J Am Chem Soc 2022; 145:300-310. [PMID: 36542094 PMCID: PMC9837838 DOI: 10.1021/jacs.2c09957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
F-specific filamentous phages, elongated particles with circular single-stranded DNA encased in a symmetric protein capsid, undergo an intermediate step, where thousands of homodimers of a non-structural protein, gVp, bind to newly synthesized strands of DNA, preventing further DNA replication and preparing the circular genome in an elongated conformation for assembly of a new virion structure at the membrane. While the structure of the free homodimer is known, the ssDNA-bound conformation has yet to be determined. We report an atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage in the nucleoprotein complex elucidated via magic-angle spinning solid-state NMR. The model presents significant conformational changes with respect to the free form. These modifications facilitate the binding mechanism and possibly promote cooperative binding in the assembly of the gVp-ssDNA complex.
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Deligey F, Frank MA, Cho SH, Kirui A, Mentink-Vigier F, Swulius MT, Nixon BT, Wang T. Structure of In Vitro-Synthesized Cellulose Fibrils Viewed by Cryo-Electron Tomography and 13C Natural-Abundance Dynamic Nuclear Polarization Solid-State NMR. Biomacromolecules 2022; 23:2290-2301. [PMID: 35341242 PMCID: PMC9198983 DOI: 10.1021/acs.biomac.1c01674] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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Cellulose, the most
abundant biopolymer, is a central source for
renewable energy and functionalized materials. In vitro synthesis of cellulose microfibrils (CMFs) has become possible using
purified cellulose synthase (CESA) isoforms from Physcomitrium
patens and hybrid aspen. The exact nature of these in vitro fibrils remains unknown. Here, we characterize in vitro-synthesized fibers made by CESAs present in membrane
fractions of P. patens over-expressing
CESA5 by cryo-electron tomography and dynamic nuclear polarization
(DNP) solid-state NMR. DNP enabled measuring two-dimensional 13C–13C correlation spectra without isotope-labeling
of the fibers. Results show structural similarity between in vitro fibrils and native CMF in plant cell walls. Intensity
quantifications agree with the 18-chain structural model for plant
CMF and indicate limited fibrillar bundling. The in vitro system thus reveals insights into cell wall synthesis and may contribute
to novel cellulosic materials. The integrated DNP and cryo-electron
tomography methods are also applicable to structural studies of other
carbohydrate-based biomaterials.
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Affiliation(s)
- Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Mark A Frank
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sung Hyun Cho
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alex Kirui
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Matthew T Swulius
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, Pennsylvania 17033, United States
| | - B Tracy Nixon
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Ghassemi N, Poulhazan A, Deligey F, Mentink-Vigier F, Marcotte I, Wang T. Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants. Chem Rev 2021; 122:10036-10086. [PMID: 34878762 DOI: 10.1021/acs.chemrev.1c00669] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.
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Affiliation(s)
- Nader Ghassemi
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Alexandre Poulhazan
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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7
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Mathew R, Stevensson B, Edén M. Refined Structures of O-Phospho-l-serine and Its Calcium Salt by New Multinuclear Solid-State NMR Crystallography Methods. J Phys Chem B 2021; 125:10985-11004. [PMID: 34553936 PMCID: PMC8503883 DOI: 10.1021/acs.jpcb.1c05587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 12/17/2022]
Abstract
O-phospho-l-serine (Pser) and its Ca salt, Ca[O-phospho-l-serine]·H2O (CaPser), play important roles for bone mineralization and were recently also proposed to account for the markedly improved bone-adhesive properties of Pser-doped calcium phosphate-based cements for biomedical implants. However, the hitherto few proposed structural models of Pser and CaPser were obtained by X-ray diffraction, thereby leaving the proton positions poorly defined. Herein, we refine the Pser and CaPser structures by density functional theory (DFT) calculations and contrast them with direct interatomic-distance constraints from two-dimensional (2D) nuclear magnetic resonance (NMR) correlation experimentation at fast magic-angle spinning (MAS), encompassing double-quantum-single-quantum (2Q-1Q) 1H NMR along with heteronuclear 13C{1H} and 31P{1H} correlation NMR experiments. The Pser and CaPser structures before and after refinements by DFT were validated against sets of NMR-derived effective 1H-1H, 1H-31P, and 1H-13C distances, which confirmed the improved accuracy of the refined structures. Each distance set was derived from one sole 2D NMR experiment applied to a powder without isotopic enrichment. The distances were extracted without invoking numerical spin-dynamics simulations or approximate phenomenological models. We highlight the advantages and limitations of the new distance-extraction procedure. Isotropic 1H, 13C, and 31P chemical shifts obtained by DFT calculations using the gauge including projector augmented wave (GIPAW) method agreed very well with the experimental results. We discuss the isotropic and anisotropic 13C and 31P chemical-shift parameters in relation to the previous literature, where most data on CaPser are reported herein for the first time.
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Affiliation(s)
- Renny Mathew
- Department of Materials and Environmental
Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Baltzar Stevensson
- Department of Materials and Environmental
Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mattias Edén
- Department of Materials and Environmental
Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
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8
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Paluch P, Kupče Ē, Trébosc J, Lafon O, Amoureux JP. Hadamard acquisition of 13 C- 13 C 2-D correlation NMR spectra. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:247-256. [PMID: 31714638 DOI: 10.1002/mrc.4969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
We show that a multiselective excitation with Hadamard encoding is a powerful tool for 2-D acquisition of 13 C─13 C homonuclear correlations. This method is not designed to improve the sensitivity, but rather to reduce the experiment time, provided there is sufficient sensitivity. Therefore, it allows fast acquisition of such 2-D spectra in labeled molecules. The technique has been demonstrated using a U─13 C─15 N histidine hydrochloride monohydrate sample allowing each point of the build-up curves of the 13 C─13 C cross-peaks to be recorded within 4 min 35 s, which is very difficult with conventional methods. Using the U─13 C─15 N f-MLF sample, we have demonstrated that the method can be applied to molecules with 14 13 C resonances with a minimum frequency separation of 240 Hz.
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Affiliation(s)
- Piotr Paluch
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
- CNRS-8181, Unit of Catalysis and Chemistry of Solids, University of Lille, Lille, France
| | | | - Julien Trébosc
- CNRS-8181, Unit of Catalysis and Chemistry of Solids, University of Lille, Lille, France
- CNRS-2638, Fédération Chevreul, University of Lille, Lille, France
| | - Olivier Lafon
- CNRS-8181, Unit of Catalysis and Chemistry of Solids, University of Lille, Lille, France
- Department of Chemistry, Institut Universitaire de France, Paris, France
| | - Jean-Paul Amoureux
- CNRS-8181, Unit of Catalysis and Chemistry of Solids, University of Lille, Lille, France
- Bruker Biospin, Wissembourg, France
- NMR Science and Development Division, RIKEN, Yokohama, Japan
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9
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Zhao W, Kirui A, Deligey F, Mentink-Vigier F, Zhou Y, Zhang B, Wang T. Solid-state NMR of unlabeled plant cell walls: high-resolution structural analysis without isotopic enrichment. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:14. [PMID: 33413580 PMCID: PMC7792314 DOI: 10.1186/s13068-020-01858-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/11/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Multidimensional solid-state nuclear magnetic resonance (ssNMR) spectroscopy has emerged as an indispensable technique for resolving polymer structure and intermolecular packing in primary and secondary plant cell walls. Isotope (13C) enrichment provides feasible sensitivity for measuring 2D/3D correlation spectra, but this time-consuming procedure and its associated expenses have restricted the application of ssNMR in lignocellulose analysis. RESULTS Here, we present a method that relies on the sensitivity-enhancing technique Dynamic Nuclear Polarization (DNP) to eliminate the need for 13C-labeling. With a 26-fold sensitivity enhancement, a series of 2D 13C-13C correlation spectra were successfully collected using the unlabeled stems of wild-type Oryza sativa (rice). The atomic resolution allows us to observe a large number of intramolecular cross peaks for fully revealing the polymorphic structure of cellulose and xylan. NMR relaxation and dipolar order parameters further suggest a sophisticated change of molecular motions in a ctl1 ctl2 double mutant: both cellulose and xylan have become more dynamic on the nanosecond and microsecond timescale, but the motional amplitudes are uniformly small for both polysaccharides. CONCLUSIONS By skipping isotopic labeling, the DNP strategy demonstrated here is universally extendable to all lignocellulose materials. This time-efficient method has landed the technical foundation for understanding polysaccharide structure and cell wall assembly in a large variety of plant tissues and species.
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Affiliation(s)
- Wancheng Zhao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Alex Kirui
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | | | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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10
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Grosu IG, Filip X, Miclăuș MO, Filip C. Hydrogen-Mediated Noncovalent Interactions in Solids: What Can NMR Crystallography Tell About? Molecules 2020; 25:E3757. [PMID: 32824749 PMCID: PMC7463941 DOI: 10.3390/molecules25163757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/15/2020] [Accepted: 08/16/2020] [Indexed: 12/18/2022] Open
Abstract
Hydrogen atoms play a crucial role in the aggregation of organic (bio)molecules through diverse number of noncovalent interactions that they mediate, such as electrostatic in proton transfer systems, hydrogen bonding, and CH-π interactions, to mention only the most prominent. To identify and adequately describe such low-energy interactions, increasingly sensitive methods have been developed over time, among which quantum chemical computations have witnessed impressive advances in recent years. For reaching the present state-of-the-art, computations had to rely on a pool of relevant experimental data, needed at least for validation, if not also for other purposes. In the case of molecular crystals, the best illustration for the synergy between computations and experiment is given by the so-called NMR crystallography approach. Originally designed to increase the confidence level in crystal structure determination of organic compounds from powders, NMR crystallography is able now to offer also a wealth of information regarding the noncovalent interactions that drive molecules to pack in a given crystalline pattern or another. This is particularly true for the noncovalent interactions which depend on the exact location of labile hydrogen atoms in the system: in such cases, NMR crystallography represents a valuable characterization tool, in some cases complementing even the standard single-crystal X-ray diffraction technique. A concise introduction in the field is made in this mini-review, which is aimed at providing a comprehensive picture with respect to the current accuracy level reached by NMR crystallography in the characterization of hydrogen-mediated noncovalent interactions in organic solids. Different types of practical applications are illustrated with the example of molecular crystals studied by our research group, but references to other representative developments reported in the literature are also made. By summarizing the major concepts and methodological progresses, the present work is also intended to be a guide to the practical potential of this relatively recent analytical tool for the scientists working in areas where crystal engineering represents the main approach for rational design of novel materials.
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Affiliation(s)
| | | | | | - Claudiu Filip
- National Institute for R&D of Isotopic and Molecular Technologies, 400293 Cluj, Romania; (I.G.G.); (X.F.); (M.O.M.)
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11
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Yu Y, Stevensson B, Pujari-Palmer M, Guo H, Engqvist H, Edén M. The Monetite Structure Probed by Advanced Solid-State NMR Experimentation at Fast Magic-Angle Spinning. Int J Mol Sci 2019; 20:ijms20246356. [PMID: 31861132 PMCID: PMC6940740 DOI: 10.3390/ijms20246356] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 01/29/2023] Open
Abstract
We present a solid-state nuclear magnetic resonance (NMR) spectroscopy study of the local 31P and 1H environments in monetite [CaHPO4; dicalcium phosphate anhydrous (DCPA)], as well as their relative spatial proximities. Each of the three 1H NMR peaks was unambiguously assigned to its respective crystallographically unique H site of monetite, while their pairwise spatial proximities were probed by homonuclear 1H–1H double quantum–single quantum NMR experimentation under fast magic-angle spinning (MAS) of 66 kHz. We also examined the relative 1H–31P proximities among the inequivalent {P1, P2} and {H1, H2, H3} sites in monetite; the corresponding shortest internuclear 1H–31P distances accorded well with those of a previous neutron diffraction study. The NMR results from the monetite phase were also contrasted with those observed from the monetite component present in a pyrophosphate-bearing calcium phosphate cement, demonstrating that while the latter represents a disordered form of monetite, it shares all essential local features of the monetite structure.
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Affiliation(s)
- Yang Yu
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden; (Y.Y.); (B.S.); (H.G.)
| | - Baltzar Stevensson
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden; (Y.Y.); (B.S.); (H.G.)
| | - Michael Pujari-Palmer
- Applied Material Science, Department of Engineering, Uppsala University, SE-751 21 Uppsala, Sweden; (M.P.-P.); (H.E.)
| | - Hua Guo
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden; (Y.Y.); (B.S.); (H.G.)
| | - Håkan Engqvist
- Applied Material Science, Department of Engineering, Uppsala University, SE-751 21 Uppsala, Sweden; (M.P.-P.); (H.E.)
| | - Mattias Edén
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden; (Y.Y.); (B.S.); (H.G.)
- Correspondence:
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12
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Vosegaard T. Fast simulations of multidimensional NMR spectra of proteins and peptides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:438-448. [PMID: 28879664 DOI: 10.1002/mrc.4663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/28/2017] [Accepted: 09/01/2017] [Indexed: 06/07/2023]
Abstract
To simulate full multidimensional nuclear magnetic resonance spectra of peptides and proteins in a reasonable time frame, a strategy for separating the time-consuming full-density matrix calculations from the chemical shift prediction and calculation of coupling patterns is presented. The simulation setup uses SIMulation Program for SOlid-state NMR (SIMPSON) to calculate total correlation spectroscopy transfer amplitudes and average distances as a source for nuclear Overhauser effect spectroscopy transfer amplitudes. Simulated 1 H 1D, 2D total correlation spectroscopy, and 2D nuclear Overhauser effect spectroscopy nuclear magnetic resonance spectra of peptides with sequence Pro─Ala─Gly─Tyr─Asn and Asn─Phe─Gly─Ala─Ile─Leu and of ubiquitin are presented. In all cases, the simulations lasted from a few seconds to tens of seconds on a normal laptop computer.
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Affiliation(s)
- Thomas Vosegaard
- Danish Center for Ultrahigh-Field NMR Spectroscopy, Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, DK-8000, Aarhus, Denmark
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13
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Phyo P, Wang T, Yang Y, O’Neill H, Hong M. Direct Determination of Hydroxymethyl Conformations of Plant Cell Wall Cellulose Using 1H Polarization Transfer Solid-State NMR. Biomacromolecules 2018; 19:1485-1497. [DOI: 10.1021/acs.biomac.8b00039] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pyae Phyo
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Yu Yang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Hugh O’Neill
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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Sardo M, Santos SM, Babaryk AA, López C, Alkorta I, Elguero J, Claramunt RM, Mafra L. Diazole-based powdered cocrystal featuring a helical hydrogen-bonded network: structure determination from PXRD, solid-state NMR and computer modeling. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 65:49-63. [PMID: 25604487 DOI: 10.1016/j.ssnmr.2014.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/07/2014] [Indexed: 06/04/2023]
Abstract
We present the structure of a new equimolar 1:1 cocrystal formed by 3,5-dimethyl-1H-pyrazole (dmpz) and 4,5-dimethyl-1H-imidazole (dmim), determined by means of powder X-ray diffraction data combined with solid-state NMR that provided insight into topological details of hydrogen bonding connectivities and weak interactions such as CH···π contacts. The use of various 1D/2D (13)C, (15)N and (1)H high-resolution solid-state NMR techniques provided structural insight on local length scales revealing internuclear proximities and relative orientations between the dmim and dmpz molecular building blocks of the studied cocrystal. Molecular modeling and DFT calculations were also employed to generate meaningful structures. DFT refinement was able to decrease the figure of merit R(F(2)) from ~11% (PXRD only) to 5.4%. An attempt was made to rationalize the role of NH···N and CH···π contacts in stabilizing the reported cocrystal. For this purpose four imidazole derivatives with distinct placement of methyl substituents were reacted with dmpz to understand the effect of methylation in blocking or enabling certain intermolecular contacts. Only one imidazole derivative (dmim) was able to incorporate into the dmpz trimeric motif thus resulting in a cocrystal, which contains both hydrophobic (methyl groups) and hydrophilic components that self-assemble to form an atypical 1D network of helicoidal hydrogen bonded pattern, featuring structural similarities with alpha-helix arrangements in proteins. The 1:1 dmpz···dmim compound I is the first example of a cocrystal formed by two different azoles.
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Affiliation(s)
- Mariana Sardo
- Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Sérgio M Santos
- Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Artem A Babaryk
- Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal; Faculty of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska s. 64/13, 01601 Kyiv, Ukraine
| | - Concepción López
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, UNED, Senda del Rey 9, E-28040 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Rosa M Claramunt
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, UNED, Senda del Rey 9, E-28040 Madrid, Spain.
| | - Luís Mafra
- Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal.
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Filip X, Filip C. Can the conformation of flexible hydroxyl groups be constrained by simple NMR crystallography approaches? The case of the quercetin solid forms. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 65:21-28. [PMID: 25465481 DOI: 10.1016/j.ssnmr.2014.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/08/2014] [Accepted: 10/23/2014] [Indexed: 06/04/2023]
Abstract
Hydrogen atoms in systems with many flexible hydroxyl side-groups are difficult to be exactly located from experimental X-Ray diffraction and/or solid-state NMR data, thus often leading to wrong conclusions with respect to the hydrogen bonding network established in crystal lattice. A simple computational method is proposed in the present work to tackle this problem, which may be readily incorporated in conventional NMR crystallography protocols. The method is based on ranking all possible conformations of the flexible hydroxyls according to their lattice energy in crystalline environments. Its effectiveness is investigated on two distinct solid forms of quercetin, for which only two out of the five hydroxyl side-groups can be well constrained from experimental/theoretical data. For this purpose, first-principle quantum-mechanical computations were combined with calculations at the molecular mechanics (MM) level of theory, and previous ss-NMR and X-Ray diffraction data. To assess accuracy in ranking the identified conformers, tests have been performed first on quercetin dihydrate, for which an X-Ray single-crystal structure is available. The possibility of applying this method in a real NMR crystallography context has been investigated finally on anhydrous quercetin, for which only powder X-Ray crystal structure has been reported so far.
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Affiliation(s)
- Xenia Filip
- National Institute for R&D of Isotopic and Molecular Technologies, P.O. Box 700, 400293 Cluj, Romania
| | - Claudiu Filip
- National Institute for R&D of Isotopic and Molecular Technologies, P.O. Box 700, 400293 Cluj, Romania.
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Miclaus M, Grosu IG, Filip X, Tripon C, Filip C. Optimizing structure determination from powders of crystalline organic solids with high molecular flexibility: the case of lisinopril dihydrate. CrystEngComm 2014. [DOI: 10.1039/c3ce41890a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Celinski VR, Weber J, Schmedt Auf der Günne J. C-REDOR curves of extended spin systems. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2013; 49-50:12-22. [PMID: 23141477 DOI: 10.1016/j.ssnmr.2012.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 09/28/2012] [Accepted: 10/01/2012] [Indexed: 06/01/2023]
Abstract
The convergence of simulated C-REDOR curves of (infinitely) large spin systems is investigated with respect to the number of spins considered in the calculations. Taking a sufficiently large number of spins (>20,000 spins) into account enables the simulation of converged C-REDOR curves over the entire time period and not only the initial regime. The calculations are based on an existing approximation within first order average Hamiltonian theory (AHT), which assumes the absence of homonuclear dipole-dipole interactions. The C-REDOR experiment generates an average Hamiltonian close to the idealized AHT behavior even for multiple spin systems including multiple homonuclear dipole-dipole interactions which is shown from numerically exact calculations of the spin dynamics. Experimentally it is shown that calculations accurately predict the full, experimental C-REDOR curves of the multi-spin systems (31)P-(19)F in apatite, (31)P-(1)H in potassium trimetaphosphimate and (1)H-(31)P in potassium dihydrogen phosphate. We also present (13)C-(1)H and (15)N-(1)H data for the organic compounds glycine, l-alanine and l-histidine hydrochloride monohydrate which require consideration of molecular motion. Furthermore, we investigated the current limits of the method from systematic errors and we suggest a simple way to calculate errors for homogeneous and heterogeneous samples from experimental data.
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Filip X, Grosu IG, Miclăuş M, Filip C. NMR crystallography methods to probe complex hydrogen bonding networks: application to structure elucidation of anhydrous quercetin. CrystEngComm 2013. [DOI: 10.1039/c3ce40299a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Hu B, Trébosc J, Lafon O, Chen Q, Masuda Y, Takegoshi K, Amoureux JP. Very-Long-Distance Correlations in Proteins Revealed by Solid-State NMR Spectroscopy. Chemphyschem 2012; 13:3585-8. [DOI: 10.1002/cphc.201200548] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Indexed: 11/11/2022]
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20
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Veshtort M, Griffin RG. Proton-driven spin diffusion in rotating solids via reversible and irreversible quantum dynamics. J Chem Phys 2012; 135:134509. [PMID: 21992326 DOI: 10.1063/1.3635374] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proton-driven spin diffusion (PDSD) experiments in rotating solids have received a great deal of attention as a potential source of distance constraints in large biomolecules. However, the quantitative relationship between the molecular structure and observed spin diffusion has remained obscure due to the lack of an accurate theoretical description of the spin dynamics in these experiments. We start with presenting a detailed relaxation theory of PDSD in rotating solids that provides such a description. The theory applies to both conventional and radio-frequency-assisted PDSD experiments and extends to the non-Markovian regime to include such phenomena as rotational resonance (R(2)). The basic kinetic equation of the theory in the non-Markovian regime has the form of a memory function equation, with the role of the memory function played by the correlation function. The key assumption used in the derivation of this equation expresses the intuitive notion of the irreversible dissipation of coherences in macroscopic systems. Accurate expressions for the correlation functions and for the spin diffusion constants are given. The theory predicts that the spin diffusion constants governing the multi-site PDSD can be approximated by the constants observed in the two-site diffusion. Direct numerical simulations of PDSD dynamics via reversible Liouville-von Neumann equation are presented to support and compliment the theory. Remarkably, an exponential decay of the difference magnetization can be observed in such simulations in systems consisting of only 12 spins. This is a unique example of a real physical system whose typically macroscopic and apparently irreversible behavior can be traced via reversible microscopic dynamics. An accurate value for the spin diffusion constant can be usually obtained through direct simulations of PDSD in systems consisting of two (13)C nuclei and about ten (1)H nuclei from their nearest environment. Spin diffusion constants computed by this method are in excellent agreement with the spin diffusion constants obtained through equations given by the relaxation theory of PDSD. The constants resulting from these two approaches were also in excellent agreement with the results of 2D rotary resonance recoupling proton-driven spin diffusion (R(3)-PDSD) experiments performed in three model compounds, where magnetization exchange occurred over distances up to 4.9 Å. With the methodology presented, highly accurate internuclear distances can be extracted from such data. Relayed transfer of magnetization between distant nuclei appears to be the main (and apparently resolvable) source of uncertainty in such measurements. The non-Markovian kinetic equation was applied to the analysis of the R(2) spin dynamics. The conventional semi-phenomenological treatment of relxation in R(2) has been shown to be equivalent to the assumption of the Lorentzian spectral density function in the relaxatoin theory of PDSD. As this assumption is a poor approximation in real physical systems, the conventional R(2) treatment is likely to carry a significant model error that has not been recognized previously. The relaxation theory of PDSD appears to provide an accurate, parameter-free alternative. Predictions of this theory agreed well with the full quantum mechanical simulations of the R(2) dynamics in the few simple model systems we considered.
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Affiliation(s)
- Mikhail Veshtort
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Filip X, Borodi G, Filip C. Testing the limits of sensitivity in a solid-state structural investigation by combined X-ray powder diffraction, solid-state NMR, and molecular modelling. Phys Chem Chem Phys 2011; 13:17978-86. [DOI: 10.1039/c1cp21878f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Dumez JN, Butler MC, Emsley L. Numerical simulation of free evolution in solid-state nuclear magnetic resonance using low-order correlations in Liouville space. J Chem Phys 2010; 133:224501. [DOI: 10.1063/1.3505455] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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23
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Vosegaard T. Challenges in numerical simulations of solid-state NMR experiments: spin exchange pulse sequences. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2010; 38:77-83. [PMID: 21330113 DOI: 10.1016/j.ssnmr.2011.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/14/2011] [Accepted: 01/24/2011] [Indexed: 05/30/2023]
Abstract
While simulations are essential for interpretation of solid-state NMR experiments, large spin systems involved in e.g. spin-diffusion experiments and/or dynamic effects like chemical exchange pose great challenges for the numerical simulations, where we typically want to include effects of finite pulses and other external manipulations in the simulation. In this paper, these topics are reviewed and addressed by simple numerical simulations. The numerical simulations comprise a 2-spin simulation of (2)H two-site jumps and a 332-spin simulation of a CHHC experiment for a small protein.
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Affiliation(s)
- Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark.
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24
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Bradley JP, Tripon C, Filip C, Brown SP. Determining relative proton-proton proximities from the build-up of two-dimensional correlation peaks in 1H double-quantum MAS NMR: insight from multi-spin density-matrix simulations. Phys Chem Chem Phys 2009; 11:6941-52. [PMID: 19652828 DOI: 10.1039/b906400a] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The build-up of intensity-as a function of the number, n(rcpl), of POST-C7 elements used for the excitation and reconversion of double-quantum (DQ) coherence (DQC)-is analysed for the fifteen distinct DQ correlation peaks that are observed experimentally for the eight separate (1)H resonances in a (1)H (500 MHz) DQ CRAMPS solid-state (12.5 kHz MAS) NMR spectrum of the dipeptide beta-AspAla (S. P. Brown, A. Lesage, B. Elena, and L. Emsley, J. Am. Chem. Soc., 2004, 126, 13230). The simulation in SPINEVOLUTION (M. Veshtort and R. G. Griffin, J. Magn. Reson., 2006, 178, 248) of t(1) ((1)H DQ evolution) FIDs for clusters of eight dipolar-coupled protons gives separate simulated (1)H DQ build-up curves for the CH(2)(a), CH(2)(b), CH(Asp), CH(Ala), NH and OH (1)H single-quantum (SQ) (1)H resonances. An analysis of both the simulated and experimental (1)H DQ build-up leads to the following general observations: (i) considering the build-up of (1)H DQ peaks at a particular SQ frequency, maximum intensity is observed for the DQC corresponding to the shortest H-H distance; (ii) for the maximum intensity (1)H DQ peak at a particular SQ frequency, the recoupling time for the observed maximum intensity depends on the corresponding H-H distance, e.g., maximum intensity for the CH(2)(a)-CH(2)(b) (H-H distance = 1.55 A) and OH-CH(Asp) (H-H distance = 2.49 A) DQ peaks is observed at n(rcpl) = 2 and 3, respectively; (iii) for DQ peaks involving a CH(2) proton at a non-CH(2) SQ frequency, there is much reduced intensity and a maximum intensity at a short recoupling time; (iv) for the other lower intensity (1)H DQ peaks at a particular SQ frequency, maximum intensity is observed for the same (or close to the same) recoupling time, but the relative intensity of the DQ peaks is a reliable indicator of the relative H-H distance-the ratio of the maximum intensities for the peaks at the CH(Ala) SQ frequency due to the two DQCs with the NH and OH protons are found to be approximately in the ratio of the squares of the corresponding dipolar coupling constants. While the simulated (1)H DQ build-up curves reproduce most of the features of the experimental curves, maximum intensity is often observed at a longer recoupling time in simulations. In this respect, simulations for two to eight spins show a trend towards a faster decay for an increasing number of considered spins. Finally, simulations show that increasing either the Larmor frequency (to 1 GHz) or the MAS frequency (to 125 kHz) does not lead to changes in the marked differences between the (1)H DQ build-up curves at the CH(Asp) SQ frequency for DQCs to the CH(2)(a) and OH protons that correspond to similar H-H distances (2.39 A and 2.49 A, respectively).
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