1
|
Zimmermann J, Mayer RJ, Moran J. A single phosphorylation mechanism in early metabolism - the case of phosphoenolpyruvate. Chem Sci 2023; 14:14100-14108. [PMID: 38098731 PMCID: PMC10717536 DOI: 10.1039/d3sc04116f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Phosphorylation is thought to be one of the fundamental reactions for the emergence of metabolism. Nearly all enzymatic phosphorylation reactions in the anabolic core of microbial metabolism act on carboxylates to give acyl phosphates, with a notable exception - the phosphorylation of pyruvate to phosphoenolpyruvate (PEP), which involves an enolate. We wondered whether an ancestral mechanism for the phosphorylation of pyruvate to PEP could also have involved carboxylate phosphorylation rather than the modern enzymatic form. The phosphorylation of pyruvate with P4O10 as a model phosphorylating agent was found to indeed occur via carboxylate phosphorylation, as verified by mechanistic studies using model substrates, time course experiments, liquid and solid-state NMR spectroscopy, and DFT calculations. The in situ generated acyl phosphate subsequently undergoes an intramolecular phosphoryl transfer to yield PEP. A single phosphorylation mechanism acting on carboxylates appears sufficient to initiate metabolic networks that include PEP, strengthening the case that metabolism emerged from self-organized chemistry.
Collapse
Affiliation(s)
- Joris Zimmermann
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
| | - Robert J Mayer
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
| | - Joseph Moran
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
- Institut Universitaire de France (IUF) France
- Department of Chemistry and Biomolecular Sciences, University of Ottawa Ottawa Ontario K1N 6N5 Canada
| |
Collapse
|
2
|
Mroue KH, Nishiyama Y, Kumar Pandey M, Gong B, McNerny E, Kohn DH, Morris MD, Ramamoorthy A. Proton-Detected Solid-State NMR Spectroscopy of Bone with Ultrafast Magic Angle Spinning. Sci Rep 2015; 5:11991. [PMID: 26153138 PMCID: PMC4495383 DOI: 10.1038/srep11991] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/05/2015] [Indexed: 01/26/2023] Open
Abstract
While obtaining high-resolution structural details from bone is highly important to better understand its mechanical strength and the effects of aging and disease on bone ultrastructure, it has been a major challenge to do so with existing biophysical techniques. Though solid-state NMR spectroscopy has the potential to reveal the structural details of bone, it suffers from poor spectral resolution and sensitivity. Nonetheless, recent developments in magic angle spinning (MAS) NMR technology have made it possible to spin solid samples up to 110 kHz frequency. With such remarkable capabilities, (1)H-detected NMR experiments that have traditionally been challenging on rigid solids can now be implemented. Here, we report the first application of multidimensional (1)H-detected NMR measurements on bone under ultrafast MAS conditions to provide atomistic-level elucidation of the complex heterogeneous structure of bone. Our investigations demonstrate that two-dimensional (1)H/(1)H chemical shift correlation spectra for bone are obtainable using fp-RFDR (finite-pulse radio-frequency-driven dipolar recoupling) pulse sequence under ultrafast MAS. Our results infer that water exhibits distinct (1)H-(1)H dipolar coupling networks with the backbone and side-chain regions in collagen. These results show the promising potential of proton-detected ultrafast MAS NMR for monitoring structural and dynamic changes caused by mechanical loading and disease in bone.
Collapse
Affiliation(s)
- Kamal H. Mroue
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109-1055, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109-1055, United States
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan
- RIKEN CLST-JEOL Collaboration Center, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Manoj Kumar Pandey
- RIKEN CLST-JEOL Collaboration Center, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Bo Gong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109-1055, United States
| | - Erin McNerny
- School of Dentistry, University of Michigan, Ann Arbor, Michigan, 48109-1078, United States
| | - David H. Kohn
- School of Dentistry, University of Michigan, Ann Arbor, Michigan, 48109-1078, United States
| | - Michael D. Morris
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109-1055, United States
| | - Ayyalusamy Ramamoorthy
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109-1055, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109-1055, United States
| |
Collapse
|
3
|
Kotler SA, Brender JR, Vivekanandan S, Suzuki Y, Yamamoto K, Monette M, Krishnamoorthy J, Walsh P, Cauble M, Holl MMB, Marsh ENG, Ramamoorthy A. High-resolution NMR characterization of low abundance oligomers of amyloid-β without purification. Sci Rep 2015; 5:11811. [PMID: 26138908 PMCID: PMC4490348 DOI: 10.1038/srep11811] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/21/2015] [Indexed: 01/30/2023] Open
Abstract
Alzheimer's disease is characterized by the misfolding and self-assembly of the amyloidogenic protein amyloid-β (Aβ). The aggregation of Aβ leads to diverse oligomeric states, each of which may be potential targets for intervention. Obtaining insight into Aβ oligomers at the atomic level has been a major challenge to most techniques. Here, we use magic angle spinning recoupling (1)H-(1)H NMR experiments to overcome many of these limitations. Using (1)H-(1)H dipolar couplings as a NMR spectral filter to remove both high and low molecular weight species, we provide atomic-level characterization of a non-fibrillar aggregation product of the Aβ1-40 peptide using non-frozen samples without isotopic labeling. Importantly, this spectral filter allows the detection of the specific oligomer signal without a separate purification procedure. In comparison to other solid-state NMR techniques, the experiment is extraordinarily selective and sensitive. A resolved 2D spectra could be acquired of a small population of oligomers (6 micrograms, 7% of the total) amongst a much larger population of monomers and fibers (93% of the total). By coupling real-time (1)H-(1)H NMR experiments with other biophysical measurements, we show that a stable, primarily disordered Aβ1-40 oligomer 5-15 nm in diameter can form and coexist in parallel with the well-known cross-β-sheet fibrils.
Collapse
Affiliation(s)
- Samuel A. Kotler
- Biophysics, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
| | - Jeffrey R. Brender
- Biophysics, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
- Department of Chemistry, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
| | | | - Yuta Suzuki
- Department of Chemistry, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
| | - Kazutoshi Yamamoto
- Biophysics, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
- Department of Chemistry, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
| | - Martine Monette
- Bruker BioSpin Ltd., Bruker Corporation, 555 E Steeles Ave, Milton, ON, Canada
| | - Janarthanan Krishnamoorthy
- Biophysics, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
- Department of Chemistry, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
| | - Patrick Walsh
- Biophysics, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
- Department of Chemistry, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
| | - Meagan Cauble
- Department of Chemistry, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
| | - Mark M. Banaszak Holl
- Department of Chemistry, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
| | - E. Neil. G. Marsh
- Department of Chemistry, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
| | - Ayyalusamy Ramamoorthy
- Biophysics, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
- Department of Chemistry, University of Michigan-Ann Arbor, Ann Arbor, Michigan 48109, U.S.A
| |
Collapse
|
4
|
Pandey MK, Vivekanandan S, Yamamoto K, Im S, Waskell L, Ramamoorthy A. Proton-detected 2D radio frequency driven recoupling solid-state NMR studies on micelle-associated cytochrome-b(5). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 242:169-79. [PMID: 24657390 PMCID: PMC4020179 DOI: 10.1016/j.jmr.2014.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 02/06/2014] [Accepted: 02/10/2014] [Indexed: 05/08/2023]
Abstract
Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled ((13)C, (15)N and (2)H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged (1)H-(1)H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross-peak intensities against the mixing time - obtained from 2D (1)H-(1)H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure (1)H-(1)H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent (1)H-(1)H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from (1)H-(1)H RFDR experiments. The appearance of resonances with distinct chemical shift values in (1)H-(1)H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles.
Collapse
Affiliation(s)
- Manoj Kumar Pandey
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Subramanian Vivekanandan
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Kazutoshi Yamamoto
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Sangchoul Im
- Department of Anesthesiology, University of Michigan, VA Medical Center, Ann Arbor, MI 48105, United States
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, VA Medical Center, Ann Arbor, MI 48105, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States.
| |
Collapse
|
5
|
Aucoin D, Camenares D, Zhao X, Jung J, Sato T, Smith SO. High-resolution 1H MAS RFDR NMR of biological membranes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 197:77-86. [PMID: 19121592 PMCID: PMC2802820 DOI: 10.1016/j.jmr.2008.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 12/02/2008] [Accepted: 12/05/2008] [Indexed: 05/08/2023]
Abstract
The combination of magic angle spinning (MAS) with the high-resolution (1)H NOESY NMR experiment is an established method for measuring through-space (1)H...(1)H dipolar couplings in biological membranes. The segmental motion of the lipid acyl chains along with the overall rotational diffusion of the lipids provides sufficient motion to average the (1)H dipolar interaction to within the range where MAS can be effective. One drawback of the approach is the relatively long NOESY mixing times needed for relaxation processes to generate significant crosspeak intensity. In order to drive magnetization transfer more rapidly, we use solid-state radiofrequency driven dipolar recoupling (RFDR) pulses during the mixing time. We compare the (1)H MAS NOESY experiment with a (1)H MAS RFDR experiment on dimyristoylphosphocholine, a bilayer-forming lipid and show that the (1)H MAS RFDR experiment provides considerably faster magnetization exchange than the standard (1)H MAS NOESY experiment. We apply the method to model compounds containing basic and aromatic amino acids bound to membrane bilayers to illustrate the ability to locate the position of aromatic groups that have penetrated to below the level of the lipid headgroups.
Collapse
Affiliation(s)
- Darryl Aucoin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5115
| | - Devin Camenares
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5115
| | - Xin Zhao
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Jay Jung
- Department of Physics and Astronomy Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5115
| | - Takeshi Sato
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Steven O. Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5115
- Corresponding author. Tel.: 631-632-1210; Fax: 631-632-8575;
| |
Collapse
|
6
|
Alam TM, Holland GP. (1)H-(13)C INEPT MAS NMR correlation experiments with (1)H-(1)H mediated magnetization exchange to probe organization in lipid biomembranes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 180:210-21. [PMID: 16563820 DOI: 10.1016/j.jmr.2006.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 02/18/2006] [Accepted: 02/20/2006] [Indexed: 05/08/2023]
Abstract
Two-dimensional (1)H-(13)C INEPT MAS NMR experiments utilizing a (1)H-(1)H magnetization exchange mixing period are presented for characterization of lipid systems. The introduction of the exchange period allows for structural information to be obtained via (1)H-(1)H dipolar couplings but with (13)C chemical shift resolution. It is shown that utilizing a RFDR recoupling sequence with short mixing times in place of the more standard NOE cross-relaxation for magnetization exchange during the mixing period allowed for the identification and separation of close (1)H-(1)H dipolar contacts versus longer-range inter-molecular (1)H-(1)H dipolar cross-relaxation. These 2D INEPT experiments were used to address both intra- and inter-molecular contacts in lipid and lipid/cholesterol mixtures.
Collapse
Affiliation(s)
- T M Alam
- Department of Electronic and Nanostructured Materials, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | | |
Collapse
|
7
|
Brenna S, Posset T, Furrer J, Blümel J. 14N NMR and Two-Dimensional Suspension1H and13C HRMAS NMR Spectroscopy of Ionic Liquids Immobilized on Silica. Chemistry 2006; 12:2880-8. [PMID: 16419143 DOI: 10.1002/chem.200501193] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A variety of popular ionic liquids have been synthesized and characterized, including by optimized (14)N NMR spectroscopy of the neat and dissolved ionic liquids. Ionic liquids incorporating Si(OEt)(3) groups have been immobilized on silica in a well-defined manner with the imidazolium moiety remaining intact. This has been proved by optimized one- and two-dimensional (1)H and (13)C HRMAS NMR spectroscopy of the materials suspended in suitable solvents.
Collapse
Affiliation(s)
- Stefano Brenna
- Organic Chemistry Department, University of Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | | | | | | |
Collapse
|
8
|
Elbayed K, Dillmann B, Raya J, Piotto M, Engelke F. Field modulation effects induced by sample spinning: application to high-resolution magic angle spinning NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 174:2-26. [PMID: 15809168 DOI: 10.1016/j.jmr.2004.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Indexed: 05/09/2023]
Abstract
High-resolution magic angle spinning (HRMAS) has become an extremely versatile tool to study heterogeneous systems. HRMAS relies on magic angle spinning of the sample and on pulse sequences originally developed for liquid state NMR. In most cases the outcome of the experiment is conform to what is expected from high-resolution liquid state NMR spectroscopy. However in some instances, experiments run under MAS can produce some very puzzling results. After reviewing the basic hardware which is at the heart of HRMAS spectroscopy, we show that the origin of this behavior lies in the natural time-dependence of some physical quantities imparted by the rotation. We focus in particular on the effects of B1 inhomogeneities on the nutation, the (90 degrees)+x-t-(90 degrees )-x and the MLEV16 experiments. Different models of radiofrequency distribution of B1 fields in a solenoidal coil are derived from simple geometrical considerations. These models are shown by NMR spin dynamics calculations to reproduce the experimental NMR results. They are also consistent with electromagnetic simulations of the B1 field distribution inside a solenoidal coil.
Collapse
Affiliation(s)
- Karim Elbayed
- Institut de Chimie, FRE 2446, Université Louis Pasteur, Strasbourg, France.
| | | | | | | | | |
Collapse
|
9
|
Furrer J, Kramer F, Marino JP, Glaser SJ, Luy B. Homonuclear Hartmann-Hahn transfer with reduced relaxation losses by use of the MOCCA-XY16 multiple pulse sequence. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 166:39-46. [PMID: 14675818 DOI: 10.1016/j.jmr.2003.09.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Homonuclear Hartmann-Hahn transfer is one of the most important building blocks in modern high-resolution NMR. It constitutes a very efficient transfer element for the assignment of proteins, nucleic acids, and oligosaccharides. Nevertheless, in macromolecules exceeding approximately 10 kDa TOCSY-experiments can show decreasing sensitivity due to fast transverse relaxation processes that are active during the mixing periods. In this article we propose the MOCCA-XY16 multiple pulse sequence, originally developed for efficient TOCSY transfer through residual dipolar couplings, as a homonuclear Hartmann-Hahn sequence with improved relaxation properties. A theoretical analysis of the coherence transfer via scalar couplings and its relaxation behavior as well as experimental transfer curves for MOCCA-XY16 relative to the well-characterized DIPSI-2 multiple pulse sequence are given.
Collapse
Affiliation(s)
- Julien Furrer
- Institut für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | | | | | | | | |
Collapse
|