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Crha R, Kozeleková A, Hofrová A, Iľkovičová L, Gašparik N, Kadeřávek P, Hritz J. Hiding in plain sight: Complex interaction patterns between Tau and 14-3-3ζ protein variants. Int J Biol Macromol 2024; 266:130802. [PMID: 38492709 DOI: 10.1016/j.ijbiomac.2024.130802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 03/18/2024]
Abstract
Tau protein is an intrinsically disordered protein that plays a key role in Alzheimer's disease (AD). In brains of AD patients, Tau occurs abnormally phosphorylated and aggregated in neurofibrillary tangles (NFTs). Together with Tau, 14-3-3 proteins - abundant cytosolic dimeric proteins - were found colocalized in the NFTs. However, so far, the molecular mechanism of the process leading to pathological changes in Tau structure as well as the direct involvement of 14-3-3 proteins are not well understood. Here, we aimed to reveal the effects of phosphorylation by protein kinase A (PKA) on Tau structural preferences and provide better insight into the interaction between Tau and 14-3-3 proteins. We also addressed the impact of monomerization-inducing phosphorylation of 14-3-3 at S58 on the binding to Tau protein. Using multidimensional nuclear magnetic resonance spectroscopy (NMR), chemical cross-linking analyzed by mass spectrometry (MS) and PAGE, we unveiled differences in their binding affinity, stoichiometry, and interfaces with single-residue resolution. We revealed that the interaction between 14-3-3 and Tau proteins is mediated not only via the 14-3-3 amphipathic binding grooves, but also via less specific interactions with 14-3-3 protein surface and, in the case of monomeric 14-3-3, also partially via the exposed dimeric interface. In addition, the hyperphosphorylation of Tau changes its affinity to 14-3-3 proteins. In conclusion, we propose quite complex interaction mode between the Tau and 14-3-3 proteins.
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Affiliation(s)
- Radek Crha
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Aneta Kozeleková
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Alena Hofrová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lucia Iľkovičová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Norbert Gašparik
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Kadeřávek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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Wolff WW, Pellizzari J, Soong R, Lysak DH, Steiner K, Ronda K, Costa P, Downey K, Moxley-Paquette V, Suszczynski C, Boehmer S, Prat JR, Simpson AJ. 13 C-depleted algae as food: Permitting background free in-vivo nuclear magnetic resonance of Daphnia magna at natural abundance. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:11-18. [PMID: 37984890 DOI: 10.1002/mrc.5409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
Affiliation(s)
- William W Wolff
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Jacob Pellizzari
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Daniel H Lysak
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Katrina Steiner
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Kiera Ronda
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Peter Costa
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Katelyn Downey
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | | | - Chris Suszczynski
- ISOTEC Stable Isotope Division, Millipore Sigma, Burlington, Massachusetts, USA
| | - Steven Boehmer
- ISOTEC Stable Isotope Division, Millipore Sigma, Burlington, Massachusetts, USA
| | - Jacob R Prat
- ISOTEC Stable Isotope Division, Millipore Sigma, Burlington, Massachusetts, USA
| | - Andre J Simpson
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
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3
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Craft DL, Schuyler AD. nus-tool: A unified program for generating and analyzing sample schedules for nonuniformly sampled NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 352:107458. [PMID: 37146525 PMCID: PMC10330440 DOI: 10.1016/j.jmr.2023.107458] [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: 02/16/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 05/07/2023]
Abstract
Increases in digital resolution achieved by high-field NMR require increases in spectral width. Additionally, the ability to resolve two overlapping peaks requires a sufficiently long acquisition time. These constraints combine, so that achieving high resolution spectra on high-field magnets requires long experiment times when employing uniform sampling and Fourier Transform processing. These limitations may be addressed by using nonuniform sampling (NUS), but the complexity of the parameter space across the variety of available NUS schemes greatly hinders the establishment of optimal approaches and best practices. We address these challenges with nus-tool, which is a software package for generating and analyzing NUS schedules. The nus-tool software internally implements random sampling and exponentially biased sampling. Through pre-configured plug-ins, it also provides access to quantile sampling and Poisson gap sampling. The software computes the relative sensitivity, mean evolution time, point spread function, and peak-to-sidelobe ratio; all of which can be determined for a candidate sample schedule prior to running an experiment to verify expected sensitivity, resolution, and artifact suppression. The nus-tool package is freely available on the NMRbox platform through an interactive GUI and via the command line, which is especially useful for scripted workflows that investigate the effectiveness of various NUS schemes.
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Affiliation(s)
- D Levi Craft
- UConn Health, Molecular Biology and Biophysics, Farmington 06030, CT, USA
| | - Adam D Schuyler
- UConn Health, Molecular Biology and Biophysics, Farmington 06030, CT, USA.
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Negroni M, Kurzbach D. Missing Pieces in Structure Puzzles: How Hyperpolarized NMR Spectroscopy Can Complement Structural Biology and Biochemistry. Chembiochem 2023; 24:e202200703. [PMID: 36624049 DOI: 10.1002/cbic.202200703] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Structure determination lies at the heart of many biochemical research programs. However, the "giants": X-ray diffraction, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, among others, leave quite a few dark spots on the structural pictures drawn of proteins, nucleic acids, membranes, and other biomacromolecules. For example, structural models under physiological conditions or of short-lived intermediates often remain out of reach of the established experimental methods. This account frames the possibility of including hyperpolarized, that is, dramatically signal-enhanced NMR in existing workflows to fill these spots with detailed depictions. We highlight how integrating methods based on dissolution dynamic nuclear polarization can provide valuable complementary information about formerly inaccessible conformational spaces for many systems. A particular focus will be on hyperpolarized buffers to facilitate the NMR structure determination of challenging systems.
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Affiliation(s)
- Mattia Negroni
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
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Conformational Dynamics of Phytoglobin BvPgb1.2 from Beta vulgaris ssp. vulgaris. Int J Mol Sci 2023; 24:ijms24043973. [PMID: 36835381 PMCID: PMC9961634 DOI: 10.3390/ijms24043973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Plant hemoglobins, often referred to as phytoglobins, play important roles in abiotic stress tolerance. Several essential small physiological metabolites can be bound to these heme proteins. In addition, phytoglobins can catalyze a range of different oxidative reactions in vivo. These proteins are often oligomeric, but the degree and relevance of subunit interactions are largely unknown. In this study, we delineate which residues are involved in dimer formation of a sugar beet phytoglobin type 1.2 (BvPgb1.2) using NMR relaxation experiments. E. coli cells harboring a phytoglobin expression vector were cultivated in isotope-labeled (2H, 13C and 15N) M9 medium. The triple-labeled protein was purified to homogeneity using two chromatographic steps. Two forms of BvPgb1.2 were examined, the oxy-form and the more stable cyanide-form. Using three-dimensional triple-resonance NMR experiments, sequence-specific assignments for CN-bound BvPgb1.2 were achieved for 137 backbone amide cross-peaks in the 1H-15N TROSY spectrum, which amounts to 83% of the total number of 165 expected cross-peaks. A large proportion of the non-assigned residues are located in α-helixes G and H, which are proposed to be involved in protein dimerization. Such knowledge around dimer formation will be instrumental for developing a better understanding of phytoglobins' roles in planta.
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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7
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Kristinaityte K, Mames A, Pietrzak M, Westermair FF, Silva W, Gschwind RM, Ratajczyk T, Urbańczyk M. Deeper Insight into Photopolymerization: The Synergy of Time-Resolved Nonuniform Sampling and Diffusion NMR. J Am Chem Soc 2022; 144:13938-13945. [PMID: 35852987 PMCID: PMC9354252 DOI: 10.1021/jacs.2c05944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The comprehensive real-time in situ monitoring of chemical
processes
is a crucial requirement for the in-depth understanding of these processes.
This monitoring facilitates an efficient design of chemicals and materials
with the precise properties that are desired. This work presents the
simultaneous utilization and synergy of two novel time-resolved NMR
methods, i.e., time-resolved diffusion NMR and time-resolved nonuniform
sampling. The first method allows the average diffusion coefficient
of the products to be followed, while the second method enables the
particular products to be monitored. Additionally, the average mass
of the system is calculated with excellent resolution using both techniques.
Employing both methods at the same time and comparing their results
leads to the unequivocal validation of the assignment in the second
method. Importantly, such validation is possible only via the simultaneous
combination of both approaches. While the presented methodology was
utilized for photopolymerization, it can also be employed for any
other polymerization process, complexation, or, in general, chemical
reactions in which the evolution of mass in time is of importance.
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Affiliation(s)
- Kristina Kristinaityte
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Adam Mames
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Mariusz Pietrzak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Franz F. Westermair
- Faculty of Chemistry and Pharmacy, Univeristy of Regensburg, Universitätsstraßze 31, 93053 Regensburg, Germany
| | - Wagner Silva
- Faculty of Chemistry and Pharmacy, Univeristy of Regensburg, Universitätsstraßze 31, 93053 Regensburg, Germany
| | - Ruth M. Gschwind
- Faculty of Chemistry and Pharmacy, Univeristy of Regensburg, Universitätsstraßze 31, 93053 Regensburg, Germany
| | - Tomasz Ratajczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Mateusz Urbańczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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8
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Lhoste C, Lorandel B, Praud C, Marchand A, Mishra R, Dey A, Bernard A, Dumez JN, Giraudeau P. Ultrafast 2D NMR for the analysis of complex mixtures. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:1-46. [PMID: 36113916 DOI: 10.1016/j.pnmrs.2022.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 06/15/2023]
Abstract
2D NMR is extensively used in many different fields, and its potential for the study of complex biochemical or chemical mixtures has been widely demonstrated. 2D NMR gives the ability to resolve peaks that overlap in 1D spectra, while providing both structural and quantitative information. However, complex mixtures are often analysed in situations where the data acquisition time is a crucial limitation, due to an ongoing chemical reaction or a moving sample from a hyphenated technique, or to the high-throughput requirement associated with large sample collections. Among the great diversity of available fast 2D methods, ultrafast (or single-scan) 2D NMR is probably the most general and versatile approach for complex mixture analysis. Indeed, ultrafast NMR has undergone an impressive number of methodological developments that have helped turn it into an efficient analytical tool, and numerous applications to the analysis of mixtures have been reported. This review first summarizes the main concepts, features and practical limitations of ultrafast 2D NMR, as well as the methodological developments that improved its analytical potential. Then, a detailed description of the main applications of ultrafast 2D NMR to mixture analysis is given. The two major application fields of ultrafast 2D NMR are first covered, i.e., reaction/process monitoring and metabolomics. Then, the potential of ultrafast 2D NMR for the analysis of hyperpolarized mixtures is described, as well as recent developments in oriented media. This review focuses on high-resolution liquid-state 2D experiments (including benchtop NMR) that include at least one spectroscopic dimension (i.e., 2D spectroscopy and DOSY) but does not cover in depth applications without spectral resolution and/or in inhomogeneous fields.
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Affiliation(s)
- Célia Lhoste
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | | | - Clément Praud
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | - Achille Marchand
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | - Rituraj Mishra
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | - Arnab Dey
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | - Aurélie Bernard
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
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9
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Ben-Tal Y, Boaler PJ, Dale HJA, Dooley RE, Fohn NA, Gao Y, García-Domínguez A, Grant KM, Hall AMR, Hayes HLD, Kucharski MM, Wei R, Lloyd-Jones GC. Mechanistic analysis by NMR spectroscopy: A users guide. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 129:28-106. [PMID: 35292133 DOI: 10.1016/j.pnmrs.2022.01.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
A 'principles and practice' tutorial-style review of the application of solution-phase NMR in the analysis of the mechanisms of homogeneous organic and organometallic reactions and processes. This review of 345 references summarises why solution-phase NMR spectroscopy is uniquely effective in such studies, allowing non-destructive, quantitative analysis of a wide range of nuclei common to organic and organometallic reactions, providing exquisite structural detail, and using instrumentation that is routinely available in most chemistry research facilities. The review is in two parts. The first comprises an introduction to general techniques and equipment, and guidelines for their selection and application. Topics include practical aspects of the reaction itself, reaction monitoring techniques, NMR data acquisition and processing, analysis of temporal concentration data, NMR titrations, DOSY, and the use of isotopes. The second part comprises a series of 15 Case Studies, each selected to illustrate specific techniques and approaches discussed in the first part, including in situ NMR (1/2H, 10/11B, 13C, 15N, 19F, 29Si, 31P), kinetic and equilibrium isotope effects, isotope entrainment, isotope shifts, isotopes at natural abundance, scalar coupling, kinetic analysis (VTNA, RPKA, simulation, steady-state), stopped-flow NMR, flow NMR, rapid injection NMR, pure shift NMR, dynamic nuclear polarisation, 1H/19F DOSY NMR, and in situ illumination NMR.
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Affiliation(s)
- Yael Ben-Tal
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Patrick J Boaler
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Harvey J A Dale
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Ruth E Dooley
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom; Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Nicole A Fohn
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Yuan Gao
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Andrés García-Domínguez
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Katie M Grant
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Andrew M R Hall
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Hannah L D Hayes
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Maciej M Kucharski
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Ran Wei
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Guy C Lloyd-Jones
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom.
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10
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Boll E, Cantrelle FX, Lamotte O, Aimé S, Wendehenne D, Trivelli X. 1H, 13C and 15N chemical shift backbone resonance NMR assignment of tobacco calmodulin 2. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:63-66. [PMID: 35020112 DOI: 10.1007/s12104-021-10060-5] [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: 08/30/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Calcium is a ubiquitous second messenger regulating numbers of cellular processes in living organisms. It encodes and transmits information perceived by cells to downstream sensors, including calmodulin (CaM), that initiate cellular responses. In plants, CaM has been involved in the regulation of plant responses to biotic and abiotic environmental cues. Plant CaMs possess a cysteine residue in their first calcium-binding motif EF-hand, which is not conserved in other eucaryotic organisms. In this work, we report the near-complete backbone chemical shift assignment of tobacco CaM2 with calcium. These results will be useful to study the impact of this particular EF-hand domain regarding CaM interaction with partners involved in stress responses.
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Affiliation(s)
- Emmanuelle Boll
- ERL9002-Integrative Structural Biology, CNRS, F-59000, Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Francois-Xavier Cantrelle
- ERL9002-Integrative Structural Biology, CNRS, F-59000, Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Olivier Lamotte
- AgroSup Dijon, CNRS, INRAE, Université de Bourgogne, Univ. Bourgogne Franche-Comté, Agroécologie, 17 Rue de Sully, BP 86510, F-21065, Dijon, France
| | - Sébastien Aimé
- AgroSup Dijon, CNRS, INRAE, Université de Bourgogne, Univ. Bourgogne Franche-Comté, Agroécologie, 17 Rue de Sully, BP 86510, F-21065, Dijon, France
| | - David Wendehenne
- AgroSup Dijon, CNRS, INRAE, Université de Bourgogne, Univ. Bourgogne Franche-Comté, Agroécologie, 17 Rue de Sully, BP 86510, F-21065, Dijon, France
| | - Xavier Trivelli
- Univ. Lille, CNRS, INRAE, Centrale Lille, Univ. Artois, FR-2638-IMEC-Institut Michel-Eugène Chevreul, F-59000, Lille, France.
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11
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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12
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Kitoka K, Skrabana R, Gasparik N, Hritz J, Jaudzems K. NMR Studies of Tau Protein in Tauopathies. Front Mol Biosci 2021; 8:761227. [PMID: 34859051 PMCID: PMC8632555 DOI: 10.3389/fmolb.2021.761227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Tauopathies, including Alzheimer's disease (AD), are the most troublesome of all age-related chronic conditions, as there are no well-established disease-modifying therapies for their prevention and treatment. Spatio-temporal distribution of tau protein pathology correlates with cognitive decline and severity of the disease, therefore, tau protein has become an appealing target for therapy. Current knowledge of the pathological effects and significance of specific species in the tau aggregation pathway is incomplete although more and more structural and mechanistic insights are being gained using biophysical techniques. Here, we review the application of NMR to structural studies of various tau forms that appear in its aggregation process, focusing on results obtained from solid-state NMR. Furthermore, we discuss implications from these studies and their prospective contribution to the development of new tauopathy therapies.
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Affiliation(s)
- Kristine Kitoka
- Laboratory of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Rostislav Skrabana
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
- AXON Neuroscience R&D Services SE, Bratislava, Slovakia
| | - Norbert Gasparik
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristaps Jaudzems
- Laboratory of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
- Faculty of Chemistry, University of Latvia, Riga, Latvia
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13
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Lesovoy DM, Georgoulia PS, Diercks T, Matečko‐Burmann I, Burmann BM, Bocharov EV, Bermel W, Orekhov VY. Unambiguous Tracking of Protein Phosphorylation by Fast High‐Resolution FOSY NMR**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dmitry M. Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS 117997 Moscow Russia
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases Moscow Institute of Physics and Technology (State University) 141700 Dolgoprudny Russia
| | - Panagiota S. Georgoulia
- Department of Chemistry and Molecular Biology University of Gothenburg Box 465 40530 Gothenburg Sweden
| | - Tammo Diercks
- NMR Platform CiC bioGUNE Bld. 800, Parque Tecnológico de Bizkaia 48160 Derio Spain
| | - Irena Matečko‐Burmann
- Department of Psychiatry and Neurochemistry University of Gothenburg 40530 Gothenburg Sweden
- Wallenberg Centre for Molecular and Translational Medicine University of Gothenburg 40530 Gothenburg Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology University of Gothenburg Box 465 40530 Gothenburg Sweden
- Wallenberg Centre for Molecular and Translational Medicine University of Gothenburg 40530 Gothenburg Sweden
| | - Eduard V. Bocharov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS 117997 Moscow Russia
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases Moscow Institute of Physics and Technology (State University) 141700 Dolgoprudny Russia
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 4 76287 Rheinstetten Germany
| | - Vladislav Y. Orekhov
- Department of Chemistry and Molecular Biology University of Gothenburg Box 465 40530 Gothenburg Sweden
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14
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Lesovoy DM, Georgoulia PS, Diercks T, Matečko‐Burmann I, Burmann BM, Bocharov EV, Bermel W, Orekhov VY. Unambiguous Tracking of Protein Phosphorylation by Fast High-Resolution FOSY NMR*. Angew Chem Int Ed Engl 2021; 60:23540-23544. [PMID: 34143912 PMCID: PMC8596425 DOI: 10.1002/anie.202102758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/30/2021] [Indexed: 12/12/2022]
Abstract
Dysregulation of post-translational modifications (PTMs) like phosphorylation is often involved in disease. NMR may elucidate exact loci and time courses of PTMs at atomic resolution and near-physiological conditions but requires signal assignment to individual atoms. Conventional NMR methods for this base on tedious global signal assignment that may often fail, as for large intrinsically disordered proteins (IDPs). We present a sensitive, robust alternative to rapidly obtain only the local assignment near affected signals, based on FOcused SpectroscopY (FOSY) experiments using selective polarisation transfer (SPT). We prove its efficiency by identifying two phosphorylation sites of glycogen synthase kinase 3 beta (GSK3β) in human Tau40, an IDP of 441 residues, where the extreme spectral dispersion in FOSY revealed unprimed phosphorylation also of Ser409. FOSY may broadly benefit NMR studies of PTMs and other hotspots in IDPs, including sites involved in molecular interactions.
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Affiliation(s)
- Dmitry M. Lesovoy
- Department of Structural Biology, Shemyakin-OvchinnikovInstitute of Bioorganic Chemistry RAS117997MoscowRussia
- Research Center for Molecular Mechanisms of Aging and Age-related DiseasesMoscow Institute of Physics and Technology (State University)141700DolgoprudnyRussia
| | - Panagiota S. Georgoulia
- Department of Chemistry and Molecular BiologyUniversity of GothenburgBox 46540530GothenburgSweden
| | - Tammo Diercks
- NMR PlatformCiC bioGUNEBld. 800, Parque Tecnológico de Bizkaia48160DerioSpain
| | - Irena Matečko‐Burmann
- Department of Psychiatry and NeurochemistryUniversity of Gothenburg40530GothenburgSweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of Gothenburg40530GothenburgSweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular BiologyUniversity of GothenburgBox 46540530GothenburgSweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of Gothenburg40530GothenburgSweden
| | - Eduard V. Bocharov
- Department of Structural Biology, Shemyakin-OvchinnikovInstitute of Bioorganic Chemistry RAS117997MoscowRussia
- Research Center for Molecular Mechanisms of Aging and Age-related DiseasesMoscow Institute of Physics and Technology (State University)141700DolgoprudnyRussia
| | | | - Vladislav Y. Orekhov
- Department of Chemistry and Molecular BiologyUniversity of GothenburgBox 46540530GothenburgSweden
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15
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Telkki VV, Urbańczyk M, Zhivonitko V. Ultrafast methods for relaxation and diffusion. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 126-127:101-120. [PMID: 34852922 DOI: 10.1016/j.pnmrs.2021.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Relaxation and diffusion NMR measurements offer an approach to studying rotational and translational motion of molecules non-invasively, and they also provide chemical resolution complementary to NMR spectra. Multidimensional experiments enable the correlation of relaxation and diffusion parameters as well as the observation of molecular exchange phenomena through relaxation or diffusion contrast. This review describes how to accelerate multidimensional relaxation and diffusion measurements significantly through spatial encoding. This so-called ultrafast Laplace NMR approach shortens the experiment time to a fraction and makes even single-scan experiments possible. Single-scan experiments, in turn, significantly facilitate the use of nuclear spin hyperpolarization methods to boost sensitivity. The ultrafast Laplace NMR method is also applicable with low-field, mobile NMR instruments, and it can be exploited in many disciplines. For example, it has been used in studies of the dynamics of fluids in porous materials, identification of intra- and extracellular metabolites in cancer cells, and elucidation of aggregation phenomena in atmospheric surfactant solutions.
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Affiliation(s)
| | - Mateusz Urbańczyk
- NMR Research Unit, University of Oulu, P.O. Box 3000, FIN-90014, Finland; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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16
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Definition of the immune evasion-replication interface of rabies virus P protein. PLoS Pathog 2021; 17:e1009729. [PMID: 34237115 PMCID: PMC8291714 DOI: 10.1371/journal.ppat.1009729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/20/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022] Open
Abstract
Rabies virus phosphoprotein (P protein) is a multifunctional protein that plays key roles in replication as the polymerase cofactor that binds to the complex of viral genomic RNA and the nucleoprotein (N protein), and in evading the innate immune response by binding to STAT transcription factors. These interactions are mediated by the C-terminal domain of P (PCTD). The colocation of these binding sites in the small globular PCTD raises the question of how these interactions underlying replication and immune evasion, central to viral infection, are coordinated and, potentially, coregulated. While direct data on the binding interface of the PCTD for STAT1 is available, the lack of direct structural data on the sites that bind N protein limits our understanding of this interaction hub. The PCTD was proposed to bind via two sites to a flexible loop of N protein (Npep) that is not visible in crystal structures, but no direct analysis of this interaction has been reported. Here we use Nuclear Magnetic Resonance, and molecular modelling to show N protein residues, Leu381, Asp383, Asp384 and phosphor-Ser389, are likely to bind to a ‘positive patch’ of the PCTD formed by Lys211, Lys214 and Arg260. Furthermore, in contrast to previous predictions we identify a single site of interaction on the PCTD by this Npep. Intriguingly, this site is proximal to the defined STAT1 binding site that includes Ile201 to Phe209. However, cell-based assays indicate that STAT1 and N protein do not compete for P protein. Thus, it appears that interactions critical to replication and immune evasion can occur simultaneously with the same molecules of P protein so that the binding of P protein to activated STAT1 can potentially occur without interrupting interactions involved in replication. These data suggest that replication complexes might be directly involved in STAT1 antagonism. For viruses to infect cells and generate progeny, they must be able to mediate replication, while simultaneously evading the innate immune system. Viruses with small genomes often achieve this through multifunctional proteins that have roles in both replication and immune evasion, such as the phosphoprotein (P protein) of rabies virus. P protein is an essential cofactor in genome replication and transcription, dependent on the well-folded C-terminal domain (PCTD), which binds to the nucleoprotein (N protein) when complexed with RNA. The PCTD can also bind and antagonize signal transducers and activators of transcription (STAT) proteins, that are essential for activating antiviral mechanisms. Here we show using Nuclear Magnetic Resonance spectroscopy and cell-based assays, that the STAT1-binding and N-binding interfaces are proximal but, nevertheless, it appears that the same molecule of PCTD can simultaneously bind STAT1 and N protein. These data suggest that P-protein-STAT1 interaction, critical to immune evasion, can occur without interrupting interactions underlying replication, and so replication complexes might be directly involved in STAT1 antagonism.
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17
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Fischer ES, Yu CWH, Bellini D, McLaughlin SH, Orr CM, Wagner A, Freund SMV, Barford D. Molecular mechanism of Mad1 kinetochore targeting by phosphorylated Bub1. EMBO Rep 2021; 22:e52242. [PMID: 34013668 PMCID: PMC8391104 DOI: 10.15252/embr.202052242] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/02/2021] [Accepted: 04/13/2021] [Indexed: 01/10/2023] Open
Abstract
During metaphase, in response to improper kinetochore-microtubule attachments, the spindle assembly checkpoint (SAC) activates the mitotic checkpoint complex (MCC), an inhibitor of the anaphase-promoting complex/cyclosome (APC/C). This process is orchestrated by the kinase Mps1, which initiates the assembly of the MCC onto kinetochores through a sequential phosphorylation-dependent signalling cascade. The Mad1-Mad2 complex, which is required to catalyse MCC formation, is targeted to kinetochores through a direct interaction with the phosphorylated conserved domain 1 (CD1) of Bub1. Here, we present the crystal structure of the C-terminal domain of Mad1 (Mad1CTD ) bound to two phosphorylated Bub1CD1 peptides at 1.75 Å resolution. This interaction is mediated by phosphorylated Bub1 Thr461, which not only directly interacts with Arg617 of the Mad1 RLK (Arg-Leu-Lys) motif, but also directly acts as an N-terminal cap to the CD1 α-helix dipole. Surprisingly, only one Bub1CD1 peptide binds to the Mad1 homodimer in solution. We suggest that this stoichiometry is due to inherent asymmetry in the coiled-coil of Mad1CTD and has implications for how the Mad1-Bub1 complex at kinetochores promotes efficient MCC assembly.
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Affiliation(s)
| | | | - Dom Bellini
- MRC Laboratory of Molecular BiologyCambridgeUK
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18
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Long M, Cantrelle FX, Robert X, Boll E, Sierra N, Gouet P, Hanoulle X, Alvarez GI, Guillon C. Identification of a Potential Inhibitor of the FIV p24 Capsid Protein and Characterization of Its Binding Site. Biochemistry 2021; 60:1896-1908. [PMID: 34096272 DOI: 10.1021/acs.biochem.1c00228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Feline immunodeficiency virus (FIV) is a veterinary infective agent for which there is currently no efficient drug available. Drugs targeting the lentivirus capsid are currently under development for the treatment of human immunodeficiency virus 1 (HIV-1). Here we describe a lead compound that interacts with the FIV capsid. This compound, 696, modulates the in vitro assembly of and stabilizes the assembled capsid protein. To decipher the mechanism of binding of this compound to the protein, we performed the first nuclear magnetic resonance (NMR) assignment of the FIV p24 capsid protein. Experimental NMR chemical shift perturbations (CSPs) observed after the addition of 696 enabled the characterization of a specific binding site for 696 on p24. This site was further analyzed by molecular modeling of the protein:compound interaction, demonstrating a strong similarity with the binding sites of existing drugs targeting the HIV-1 capsid protein. Taken together, we characterized a promising capsid-interacting compound with a low cost of synthesis, for which derivatives could lead to the development of efficient treatments for FIV infection. More generally, our strategy combining the NMR assignment of FIV p24 with NMR CSPs and molecular modeling will be useful for the analysis of future compounds targeting p24 in the quest to identify an efficient treatment for FIV.
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Affiliation(s)
- Mathieu Long
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
| | - François-Xavier Cantrelle
- CNRS, ERL9002, Integrative Structural Biology, F-59000 Lille, France.,Univ. Lille, INSERM, CHU Lille University Hospital, Institut Pasteur de Lille, UMR1167-RID-AGE-Risk factors and molecular determinants of aging-related, F-59000 Lille, France
| | - Xavier Robert
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
| | - Emmanuelle Boll
- CNRS, ERL9002, Integrative Structural Biology, F-59000 Lille, France.,Univ. Lille, INSERM, CHU Lille University Hospital, Institut Pasteur de Lille, UMR1167-RID-AGE-Risk factors and molecular determinants of aging-related, F-59000 Lille, France
| | - Natalia Sierra
- Laboratorio de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, 60000 Paysandú, Uruguay
| | - Patrice Gouet
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
| | - Xavier Hanoulle
- CNRS, ERL9002, Integrative Structural Biology, F-59000 Lille, France.,Univ. Lille, INSERM, CHU Lille University Hospital, Institut Pasteur de Lille, UMR1167-RID-AGE-Risk factors and molecular determinants of aging-related, F-59000 Lille, France
| | - Guzmán I Alvarez
- Laboratorio de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, 60000 Paysandú, Uruguay
| | - Christophe Guillon
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
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19
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Matveeva AG, Syryamina VN, Nekrasov VM, Bowman MK. Non-uniform sampling in pulse dipolar spectroscopy by EPR: the redistribution of noise and the optimization of data acquisition. Phys Chem Chem Phys 2021; 23:10335-10346. [PMID: 33881433 DOI: 10.1039/d1cp00705j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pulse dipolar spectroscopy (PDS) in Electron Paramagnetic Resonance (EPR) is the method of choice for determining the distance distribution function for mono-, bi- or multi- spin-labeled macromolecules and nanostructures. PDS acquisition schemes conventionally use uniform sampling of the dipolar trace, but non-uniform sampling (NUS) schemes can decrease the total measurement time or increase the accuracy of the resulting distance distributions. NUS requires optimization of the data acquisition scheme, as well as changes in data processing algorithms to accommodate the non-uniformly sampled data. We investigate in silico the applicability of the NUS approach in PDS, considering its effect on random, truncation and sampling noise in the experimental data. Each type of noise in the time-domain data propagates differently and non-uniformly into the distance spectrum as errors in the distance distribution. NUS schemes seem to be a valid approach for increasing sensitivity and/or throughput in PDS by decreasing and redistributing noise in the distance spectrum so that it has less impact on the distance spectrum.
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Affiliation(s)
- Anna G Matveeva
- Institute of Solid State Chemistry and Mechanochemistry of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia and Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Victoria N Syryamina
- Voevodsky Institute of Chemical Kinetics and Combustion of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Vyacheslav M Nekrasov
- Novosibirsk State University, 630090 Novosibirsk, Russia and Voevodsky Institute of Chemical Kinetics and Combustion of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Michael K Bowman
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia and Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL 35487, USA.
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20
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Steimers E, Matviychuk Y, Friebel A, Münnemann K, von Harbou E, Holland DJ. A comparison of non-uniform sampling and model-based analysis of NMR spectra for reaction monitoring. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:221-236. [PMID: 32892425 DOI: 10.1002/mrc.5095] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is widely used for applications in the field of reaction and process monitoring. When complex reaction mixtures are studied, NMR spectra often suffer from low resolution and overlapping peaks, which places high demands on the method used to acquire or to analyse the NMR spectra. This work presents two NMR methods that help overcome these challenges: 2D non-uniform sampling (NUS) and a recently proposed model-based fitting approach for the analysis of 1D NMR spectra. We use the reaction of glycerol with acetic acid as it produces five reaction products that are all chemically similar and, hence, challenging to distinguish. The reaction was measured on a high-field 400 MHz NMR spectrometer with a 2D NUS-heteronuclear single quantum coherence (HSQC) and a conventional 1D 1 H NMR sequence. We show that comparable results can be obtained using both 2D and 1D methods, if the 2D volume integrals of the 2D NUS-HSQC NMR spectra are calibrated. Further, we monitor the same reaction on a low-field 43 MHz benchtop NMR spectrometer and analyse the acquired 1D 1 H NMR spectra with the model-based approach and with partial least-squares regression (PLS-R), both trained using a single, calibrated data set. Both methods achieve results that are in good quantitative agreement with the high-field data. However, the model-based method was found to be less sensitive to the training data set used than PLS-R and, hence, was more robust when the reaction conditions differed from that of the training data.
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Affiliation(s)
- Ellen Steimers
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern (TUK), Kaiserslautern, Germany
| | - Yevgen Matviychuk
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Anne Friebel
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern (TUK), Kaiserslautern, Germany
| | - Kerstin Münnemann
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern (TUK), Kaiserslautern, Germany
| | - Erik von Harbou
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern (TUK), Kaiserslautern, Germany
- BASF SE, Research and Development, Ludwigshafen, Germany
| | - Daniel J Holland
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
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21
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Gołowicz D, Kaźmierczak M, Kazimierczuk K. Benefits of time-resolved nonuniform sampling in reaction monitoring: The case of aza-Michael addition of benzylamine and acrylamide. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:213-220. [PMID: 33016346 DOI: 10.1002/mrc.5105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/01/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
Monitoring of chemical reactions is best carried out using methods that sample the test object at a rate greater than the time scale of the processes taking place. The recently proposed time-resolved nonuniform sampling (TR-NUS) method allows the use of two-dimensional (2D) nuclear magnetic resonance (NMR) spectra for this purpose and provides a time resolution equivalent to that achievable using one-dimensional spectra. Herein, we show that TR-NUS acquired data eliminates 2D spectral line disturbances and enables more accurate signal integration and kinetics conclusions. The considerations are exemplified with a seemingly simple aza-Michael reaction of benzylamine and acrylamide. Surprisingly, the product identification is possible only using 2D spectra, although credible monitoring requires TR-NUS.
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Affiliation(s)
- Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Magdalena Kaźmierczak
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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22
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Pedersen CP, Prestel A, Teilum K. Software for reconstruction of nonuniformly sampled NMR data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:315-323. [PMID: 32516838 DOI: 10.1002/mrc.5060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Nonuniform sampling (NUS) of multidimensional NMR experiments is a powerful tool to obtain high-resolution spectra with less instrument time. With NUS, only a subset of the points needed for conventional Fourier transformation is recorded, and sophisticated algorithms are needed to reconstruct the missing data points. During the last decade, several software packages implementing the reconstruction algorithms have emerged and been refined and now result in spectra of almost similar quality as spectra from conventionally recorded and processed data. However, from the number of literature references to the reconstruction methods, many more multidimensional NMR spectra could presumably be recorded with NUS. To help researchers considering to start using NUS for their NMR experiments, we here review 13 different reconstruction methods found in five software packages (CambridgeCS, hmsIST, MddNMR, NESTA-NMR, and SMILE). We have compared how the methods run with the provided example scripts for reconstructing a nonuniform sampled three-dimensional 15 N-NOESY-HSQC at sampling densities from 5% to 50%. Overall, the spectra are all of similar quality above 20% sampling density. Thus, without any particular knowledge about the details of the reconstruction algorithms, significant reduction in the experiment time can be achieved. Below 20% sampling density, the intensities of particular weak peaks start being affected. MddNMR's IST with virtual echo and the SMILE algorithms still reproduced the spectra with the highest accuracy of peak intensities.
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Affiliation(s)
- Christian Parsbaek Pedersen
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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23
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Shchukina A, Małecki P, Mateos B, Nowakowski M, Urbańczyk M, Kontaxis G, Kasprzak P, Conrad-Billroth C, Konrat R, Kazimierczuk K. Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy. Chemistry 2021; 27:1753-1767. [PMID: 32985764 DOI: 10.1002/chem.202003678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 11/07/2022]
Abstract
NMR spectroscopy is a particularly informative method for studying protein structures and dynamics in solution; however, it is also one of the most time-consuming. Modern approaches to biomolecular NMR spectroscopy are based on lengthy multidimensional experiments, the duration of which grows exponentially with the number of dimensions. The experimental time may even be several days in the case of 3D and 4D spectra. Moreover, the experiment often has to be repeated under several different conditions, for example, to measure the temperature-dependent effects in a spectrum (temperature coefficients (TCs)). Herein, a new approach that involves joint sampling of indirect evolution times and temperature is proposed. This allows TCs to be measured through 3D spectra in even less time than that needed to acquire a single spectrum by using the conventional approach. Two signal processing methods that are complementary, in terms of sensitivity and resolution, 1) dividing data into overlapping subsets followed by compressed sensing reconstruction, and 2) treating the complete data set with a variant of the Radon transform, are proposed. The temperature-swept 3D HNCO spectra of two intrinsically disordered proteins, osteopontin and CD44 cytoplasmic tail, show that this new approach makes it possible to determine TCs and their non-linearities effectively. Non-linearities, which indicate the presence of a compact state, are particularly interesting. The complete package of data acquisition and processing software for this new approach are provided.
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Affiliation(s)
- Alexandra Shchukina
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Paweł Małecki
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Michał Nowakowski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Paweł Kasprzak
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland.,Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Clara Conrad-Billroth
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
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24
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Boll E, Cantrelle FX, Landrieu I, Hirel M, Sinnaeve D, Levy G. 1H, 13C, and 15N chemical shift assignment of human PACSIN1/syndapin I SH3 domain in solution. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:175-178. [PMID: 32236802 DOI: 10.1007/s12104-020-09940-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Human neuron-specific PACSIN1 plays a key role in synaptic vesicle recycling and endocytosis, as well as reorganization of the microtubule dynamics to maintain axonal plasticity. PACSIN1 contains a highly conserved C-terminal SH3 domain and an F-bar domain at its N-terminus. Due to its remarkable interaction network, PACSIN1 plays a central role in key neuronal functions. Here, we present a robust backbone and side-chain assignment of PACSIN1 SH3 domain based on 2D [1H,15N] HSQC or HMQC, and 3D BEST-HNCO, -HNCACB, -HN(CO)CACB, -HN(CA)CO, and standard (H)CC(CO)NH, HN(CA)NNH, HN(COCA)NH, HBHANNH, HNHA, HBHA(CO)NH, H(CC)(CO)NH, HCCH-TOCSY, that covers 96% for all 13CO, 13Cα and 13Cβ, 28% of 13Cγδε, and 95% of 1HN and 15N chemical shifts. Modelling based on sequence homology with a known related structure, and chemical shift-based secondary structure predictions, identified the presence of five β-strands linked by flexible loops. Taken together, these results open up new avenues to investigate and develop new therapeutic strategies.
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Affiliation(s)
- Emmanuelle Boll
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France
- CNRS ERL Integrative Structural Biology, 59000, Lille, France
| | - Francois-Xavier Cantrelle
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France
- CNRS ERL Integrative Structural Biology, 59000, Lille, France
| | - Isabelle Landrieu
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France
- CNRS ERL Integrative Structural Biology, 59000, Lille, France
| | - Matthieu Hirel
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France
- CNRS ERL Integrative Structural Biology, 59000, Lille, France
| | - Davy Sinnaeve
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France
- CNRS ERL Integrative Structural Biology, 59000, Lille, France
| | - Géraldine Levy
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France.
- CNRS ERL Integrative Structural Biology, 59000, Lille, France.
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Isaksson L, Gustavsson E, Persson C, Brath U, Vrhovac L, Karlsson G, Orekhov V, Westenhoff S. Signaling Mechanism of Phytochromes in Solution. Structure 2020; 29:151-160.e3. [PMID: 32916102 DOI: 10.1016/j.str.2020.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/19/2020] [Accepted: 08/21/2020] [Indexed: 12/31/2022]
Abstract
Phytochrome proteins guide the red/far-red photoresponse of plants, fungi, and bacteria. Crystal structures suggest that the mechanism of signal transduction from the chromophore to the output domains involves refolding of the so-called PHY tongue. It is currently not clear how the two other notable structural features of the phytochrome superfamily, the so-called helical spine and a knot in the peptide chain, are involved in photoconversion. Here, we present solution NMR data of the complete photosensory core module from Deinococcus radiodurans. Photoswitching between the resting and the active states induces changes in amide chemical shifts, residual dipolar couplings, and relaxation dynamics. All observables indicate a photoinduced structural change in the knot region and lower part of the helical spine. This implies that a conformational signal is transduced from the chromophore to the helical spine through the PAS and GAF domains. The discovered pathway underpins functional studies of plant phytochromes and may explain photosensing by phytochromes under biological conditions.
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Affiliation(s)
- Linnéa Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Emil Gustavsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Cecilia Persson
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Ulrika Brath
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Göran Karlsson
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden.
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26
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The native structure of the assembled matrix protein 1 of influenza A virus. Nature 2020; 587:495-498. [PMID: 32908308 DOI: 10.1038/s41586-020-2696-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/19/2020] [Indexed: 02/03/2023]
Abstract
Influenza A virus causes millions of severe cases of disease during annual epidemics. The most abundant protein in influenza virions is matrix protein 1 (M1), which mediates virus assembly by forming an endoskeleton beneath the virus membrane1. The structure of full-length M1, and how it oligomerizes to mediate the assembly of virions, is unknown. Here we determine the complete structure of assembled M1 within intact virus particles, as well as the structure of M1 oligomers reconstituted in vitro. We find that the C-terminal domain of M1 is disordered in solution but can fold and bind in trans to the N-terminal domain of another M1 monomer, thus polymerizing M1 into linear strands that coat the interior surface of the membrane of the assembling virion. In the M1 polymer, five histidine residues-contributed by three different monomers of M1-form a cluster that can serve as the pH-sensitive disassembly switch after entry into a target cell. These structures therefore reveal mechanisms of influenza virus assembly and disassembly.
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27
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Urbańczyk M, Kharbanda Y, Mankinen O, Telkki VV. Accelerating Restricted Diffusion NMR Studies with Time-Resolved and Ultrafast Methods. Anal Chem 2020; 92:9948-9955. [PMID: 32551510 PMCID: PMC7439255 DOI: 10.1021/acs.analchem.0c01523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Restricted
diffusion of fluids in porous materials can be studied
by pulsed field gradient nuclear magnetic resonance (NMR) non-invasively
and without tracers. If the experiment is repeated many times with
varying diffusion delays, detailed information about pore sizes and
tortuosity can be recorded. However, the measurements are very time-consuming
because numerous repetitions are needed for gradient ramping and varying
diffusion delays. In this paper, we demonstrate two different strategies
for acceleration of the restricted diffusion NMR measurements: time-resolved
diffusion NMR and ultrafast Laplace NMR. The former is based on time-resolved
non-uniform sampling, while the latter relies on spatial encoding
of two-dimensional data. Both techniques allow similar 1–2
order of magnitude acceleration of acquisition, but they have different
strengths and weaknesses, which we discuss in detail. The feasibility
of the methods was proven by investigating restricted diffusion of
water inside tracheid cells of thermally modified pine wood.
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Affiliation(s)
| | | | - Otto Mankinen
- NMR Research Unit, University of Oulu, 90014 Oulu, Finland.,Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, Medical Research Center Oulu, University of Oulu and Oulu University Hospital, 90029 Oulu, Finland
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28
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Lane D, Bermel W, Ning P, Jeong TY, Martin R, Soong R, Wu B, Tabatabaei-Anaraki M, Heumann H, Gundy M, Boenisch H, Adamo A, Arhonditsis G, Simpson AJ. Targeting the Lowest Concentration of a Toxin That Induces a Detectable Metabolic Response in Living Organisms: Time-Resolved In Vivo 2D NMR during a Concentration Ramp. Anal Chem 2020; 92:9856-9865. [DOI: 10.1021/acs.analchem.0c01370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Daniel Lane
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Paris Ning
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Tae-Yong Jeong
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Richard Martin
- IMicrosolder, 57 Marshall Street West, Meaford, Ontario, Canada N4L 1E4
| | - Ronald Soong
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Bing Wu
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Maryam Tabatabaei-Anaraki
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | | | | | | | - Antonio Adamo
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - George Arhonditsis
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - André J. Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6
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29
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Patel DS, Blasco P, Widmalm G, Im W. Escherichia coli O176 LPS structure and dynamics: A NMR spectroscopy and MD simulation study. Curr Res Struct Biol 2020; 2:79-88. [PMID: 34235471 PMCID: PMC8244359 DOI: 10.1016/j.crstbi.2020.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/06/2020] [Accepted: 04/08/2020] [Indexed: 01/30/2023] Open
Abstract
A lipopolysaccharide (LPS) molecule is a key component of the bacterial outer membrane used to protect the bacterium and to interact with the environment. To gain insight into its function, the study of the LPS conformation and dynamics at the molecular and cellular levels is necessary, but these highly diverse and dynamic membrane-LPS systems are difficult to study. In this work, by using NMR spectroscopy and molecular dynamics (MD) simulations, we determined the conformational preferences of an E. coli O176 O-antigen polysaccharide at the atomic level. Moreover, we analyzed the use of non-uniform sampling (NUS) for the acquisition of high dynamic range spectra, like 1H,1H-NOESY NMR experiments. A comparison of the effective transglycosidic distances derived from conventional uniformly sampled and NUS 1H,1H-NOESY data showed high similarity under equal measuring time conditions. Furthermore, the experimentally derived internuclear distances of the O-antigen polysaccharide with ten repeating units (RUs) showed very good agreement to those calculated from the MD simulations of the same O-antigen polysaccharide in solution. Analysis of the LPS bilayer simulations with five and with ten RUs revealed that, although similar with respect to populated states in solution, the O-antigen in LPS bilayers had more extended chains as a result of spatial limitations due to close packing. Additional MD simulations of O-antigen polysaccharides from E. coli O6 (branched repeating unit) and O91 (negatively charged linear repeating unit) in solution and LPS bilayers were performed and compared to those of O176 (linear polymer). For all three O-antigens, the ensemble of structures present for the polysaccharides in solution were consistent with the results from their 1H,1H-NOESY experiments. In addition, the similarities between the O-antigen on its own and as a constituent of the full LPS in bilayer environment makes it possible to realistically describe the LPS conformation and dynamics from the MD simulations. Uniform and non-uniform sampled NOESY NMR data yield similar internuclear distances. O-antigen internuclear distances from NMR and MD show excellent agreement. O-antigen ensemble structures from MD are consistent with NMR observations. O-antigen structures are more extended in LPS bilayers than in solution. MD simulations can describe realistic LPS conformation and dynamics.
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Affiliation(s)
- Dhilon S Patel
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, PA, 18015, USA
| | - Pilar Blasco
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, PA, 18015, USA
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30
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Alik A, Bouguechtouli C, Julien M, Bermel W, Ghouil R, Zinn‐Justin S, Theillet F. Sensitivity‐Enhanced
13
C‐NMR Spectroscopy for Monitoring Multisite Phosphorylation at Physiological Temperature and pH. Angew Chem Int Ed Engl 2020; 59:10411-10415. [DOI: 10.1002/anie.202002288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/12/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Ania Alik
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Chafiaa Bouguechtouli
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Manon Julien
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten Germany
| | - Rania Ghouil
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Sophie Zinn‐Justin
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Francois‐Xavier Theillet
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
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31
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Alik A, Bouguechtouli C, Julien M, Bermel W, Ghouil R, Zinn‐Justin S, Theillet F. Sensitivity‐Enhanced
13
C‐NMR Spectroscopy for Monitoring Multisite Phosphorylation at Physiological Temperature and pH. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ania Alik
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Chafiaa Bouguechtouli
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Manon Julien
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten Germany
| | - Rania Ghouil
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Sophie Zinn‐Justin
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Francois‐Xavier Theillet
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
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32
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Olsen GL, Szekely O, Mateos B, Kadeřávek P, Ferrage F, Konrat R, Pierattelli R, Felli IC, Bodenhausen G, Kurzbach D, Frydman L. Sensitivity-enhanced three-dimensional and carbon-detected two-dimensional NMR of proteins using hyperpolarized water. JOURNAL OF BIOMOLECULAR NMR 2020; 74:161-171. [PMID: 32040802 PMCID: PMC7080779 DOI: 10.1007/s10858-020-00301-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/27/2020] [Indexed: 05/11/2023]
Abstract
Signal enhancements of up to two orders of magnitude in protein NMR can be achieved by employing HDO as a vector to introduce hyperpolarization into folded or intrinsically disordered proteins. In this approach, hyperpolarized HDO produced by dissolution-dynamic nuclear polarization (D-DNP) is mixed with a protein solution waiting in a high-field NMR spectrometer, whereupon amide proton exchange and nuclear Overhauser effects (NOE) transfer hyperpolarization to the protein and enable acquisition of a signal-enhanced high-resolution spectrum. To date, the use of this strategy has been limited to 1D and 1H-15N 2D correlation experiments. Here we introduce 2D 13C-detected D-DNP, to reduce exchange-induced broadening and other relaxation penalties that can adversely affect proton-detected D-DNP experiments. We also introduce hyperpolarized 3D spectroscopy, opening the possibility of D-DNP studies of larger proteins and IDPs, where assignment and residue-specific investigation may be impeded by spectral crowding. The signal enhancements obtained depend in particular on the rates of chemical and magnetic exchange of the observed residues, thus resulting in non-uniform 'hyperpolarization-selective' signal enhancements. The resulting spectral sparsity, however, makes it possible to resolve and monitor individual amino acids in IDPs of over 200 residues at acquisition times of just over a minute. We apply the proposed experiments to two model systems: the compactly folded protein ubiquitin, and the intrinsically disordered protein (IDP) osteopontin (OPN).
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Affiliation(s)
- Gregory L Olsen
- Faculty of Chemistry, Institute for Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria.
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Or Szekely
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Borja Mateos
- Department of Structural and Computational Biology, University of Vienna, Vienna BioCenter 5, 1030, Vienna, Austria
| | - Pavel Kadeřávek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Fabien Ferrage
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Robert Konrat
- Department of Structural and Computational Biology, University of Vienna, Vienna BioCenter 5, 1030, Vienna, Austria
| | - Roberta Pierattelli
- Magnetic Resonance Center and Department of Chemistry Ugo Schiff, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Isabella C Felli
- Magnetic Resonance Center and Department of Chemistry Ugo Schiff, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Geoffrey Bodenhausen
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute for Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria.
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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33
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Gołowicz D, Kasprzak P, Orekhov V, Kazimierczuk K. Fast time-resolved NMR with non-uniform sampling. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:40-55. [PMID: 32130958 DOI: 10.1016/j.pnmrs.2019.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
NMR spectroscopy is a versatile tool for studying time-dependent processes: chemical reactions, phase transitions or macromolecular structure changes. However, time-resolved NMR is usually based on the simplest among available techniques - one-dimensional spectra serving as "snapshots" of the studied process. One of the reasons is that multidimensional experiments are very time-expensive due to costly sampling of evolution time space. In this review we summarize efforts to alleviate the problem of limited applicability of multidimensional NMR in time-resolved studies. We focus on techniques based on sparse or non-uniform sampling (NUS), which lead to experimental time reduction by omitting a significant part of the data during measurement and reconstructing it mathematically, adopting certain assumptions about the spectrum. NUS spectra are faster to acquire than conventional ones and thus better suited to the role of "snapshots", but still suffer from non-stationarity of the signal i.e. amplitude and frequency variations within a dataset. We discuss in detail how these instabilities affect the spectra, and what are the optimal ways of sampling the non-stationary FID signal. Finally, we discuss related areas of NMR where serial experiments are exploited and how they can benefit from the same NUS-based approaches.
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Affiliation(s)
- Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland; Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland.
| | - Paweł Kasprzak
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland; Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Vladislav Orekhov
- Department of Chemistry & Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden.
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34
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Nawrocka EK, Kasprzak P, Zawada K, Sadło J, Grochala W, Kazimierczuk K, Leszczyński PJ. Nonstationary Two-Dimensional Nuclear Magnetic Resonance: A Method for Studying Reaction Mechanisms in Situ. Anal Chem 2019; 91:11306-11315. [PMID: 31387347 DOI: 10.1021/acs.analchem.9b02414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear magnetic resonance spectroscopy (NMR) is a versatile tool of chemical analysis allowing one to determine structures of molecules with atomic resolution. Particularly informative are two-dimensional (2D) experiments that directly identify atoms coupled by chemical bonds or a through-space interaction. Thus, NMR could potentially be powerful tool to study reactions in situ and explain their mechanisms. Unfortunately, 2D NMR is very time-consuming and thus often cannot serve as a "snapshot" technique for in situ reaction monitoring. Particularly difficult is the case of spectra, in which resonance frequencies vary in the course of reaction. This leads to resolution and sensitivity loss, often hindering the detection of transient products. In this paper we introduce a novel approach to correct such nonstationary 2D NMR signals and raise the detection limits over 10 times. We demonstrate success of its application for studying the mechanism of the reaction of AgSO4-induced synthesis of diphenylmethane-type compounds. Several reactions occur in the studied mixture of benzene and toluene, all with rather low yield and leading to compounds with similar chemical shifts. Nevertheless, with the use of a proposed 2D NMR approach we were able to describe complex mechanisms of diphenylmethane formation involving AgSO4-induced toluene deprotonation and formation of benzyl carbocation, followed by nucleophilic attacks.
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Affiliation(s)
- Ewa Klaudia Nawrocka
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-089 Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2C , 02-097 Warsaw , Poland
| | - Paweł Kasprzak
- Centre of New Technologies , University of Warsaw , Banacha 2C , 02-097 Warsaw , Poland.,Department of Mathematical Methods in Physics, Faculty of Physics , University of Warsaw , Pasteura 5 , 02-093 Warsaw , Poland
| | - Katarzyna Zawada
- Department of Physical Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division , Medical University of Warsaw , Banacha 1 , 02-097 Warsaw , Poland
| | - Jarosław Sadło
- Institute of Nuclear Chemistry and Technology , Dorodna 16 , 03-195 Warsaw , Poland
| | - Wojciech Grochala
- Centre of New Technologies , University of Warsaw , Banacha 2C , 02-097 Warsaw , Poland
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35
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Ying J, Barnes CA, Louis JM, Bax A. Importance of time-ordered non-uniform sampling of multi-dimensional NMR spectra of Aβ 1-42 peptide under aggregating conditions. JOURNAL OF BIOMOLECULAR NMR 2019; 73:429-441. [PMID: 31407200 PMCID: PMC6819256 DOI: 10.1007/s10858-019-00235-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/09/2019] [Indexed: 06/02/2023]
Abstract
Although the order of the time steps in which the non-uniform sampling (NUS) schedule is implemented when acquiring multi-dimensional NMR spectra is of limited importance when sample conditions remain unchanged over the course of the experiment, it is shown to have major impact when samples are unstable. In the latter case, time-ordering of the NUS data points by the normalized radial length yields a reduction of sampling artifacts, regardless of the spectral reconstruction algorithm. The disadvantage of time-ordered NUS sampling is that halting the experiment prior to its completion will result in lower spectral resolution, rather than a sparser data matrix. Alternatively, digitally correcting for sample decay prior to reconstruction of randomly ordered NUS data points can mitigate reconstruction artifacts, at the cost of somewhat lower sensitivity. Application of these sampling schemes to the Alzheimer's amyloid beta (Aβ1-42) peptide at an elevated concentration, low temperature, and 3 kbar of pressure, where approximately 75% of the peptide reverts to an NMR-invisible state during the collection of a 3D 15N-separated NOESY spectrum, highlights the improvement in artifact suppression and reveals weak medium-range NOE contacts in several regions, including the C-terminal region of the peptide.
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Affiliation(s)
- Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - C Ashley Barnes
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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36
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Matviychuk Y, Bostock MJ, Nietlispach D, Holland DJ. Time-domain signal modelling in multidimensional NMR experiments for estimation of relaxation parameters. JOURNAL OF BIOMOLECULAR NMR 2019; 73:93-104. [PMID: 31055682 DOI: 10.1007/s10858-018-00224-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
We present a model-based method for estimation of relaxation parameters from time-domain NMR data specifically suitable for processing data in popular 2D phase-sensitive experiments. Our model is formulated in terms of commutative bicomplex algebra, which allows us to use the complete information available in an NMR signal acquired with principles of quadrature detection without disregarding any of its dimensions. Compared to the traditional intensity-analysis method, our model-based approach offers an important advantage for the analysis of overlapping peaks and is robust over a wide range of signal-to-noise ratios. We assess its performance with simulated experiments and then apply it for determination of [Formula: see text], [Formula: see text], and [Formula: see text] relaxation rates in datasets of a protein with more than 100 cross peaks.
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Affiliation(s)
- Yevgen Matviychuk
- Department of Chemical and Process Engineering, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Mark J Bostock
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Daniel J Holland
- Department of Chemical and Process Engineering, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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37
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Selenko P. Quo Vadis Biomolecular NMR Spectroscopy? Int J Mol Sci 2019; 20:ijms20061278. [PMID: 30875725 PMCID: PMC6472163 DOI: 10.3390/ijms20061278] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) spectroscopy offers the possibility to study proteins and other biomolecules at atomic resolution directly in cells. As such, it provides compelling means to complement existing tools in cellular structural biology. Given the dominance of electron microscopy (EM)-based methods in current structure determination routines, I share my personal view about the role of biomolecular NMR spectroscopy in the aftermath of the revolution in resolution. Specifically, I focus on spin-off applications that in-cell NMR has helped to develop and how they may provide broader and more generally applicable routes for future NMR investigations. I discuss the use of ‘static’ and time-resolved solution NMR spectroscopy to detect post-translational protein modifications (PTMs) and to investigate structural consequences that occur in their response. I argue that available examples vindicate the need for collective and systematic efforts to determine post-translationally modified protein structures in the future. Furthermore, I explain my reasoning behind a Quinary Structure Assessment (QSA) initiative to interrogate cellular effects on protein dynamics and transient interactions present in physiological environments.
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Affiliation(s)
- Philipp Selenko
- Weizmann Institute of Science, Department of Biological Regulation, 234 Herzl Street, Rehovot 76100, Israel.
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38
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MacDonald TSC, Price WS, Beves JE. Time‐Resolved Diffusion NMR Measurements for Transient Processes. Chemphyschem 2019; 20:926-930. [DOI: 10.1002/cphc.201900150] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 11/06/2022]
Affiliation(s)
| | - William S. Price
- Nanoscale Organisation and Dynamics Group School of Science and Health Western Sydney University Penrith NSW 2751 Australia
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39
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Gołowicz D, Kazimierczuk K, Urbańczyk M, Ratajczyk T. Monitoring Hydrogenation Reactions using Benchtop 2D NMR with Extraordinary Sensitivity and Spectral Resolution. ChemistryOpen 2019; 8:196-200. [PMID: 30815327 PMCID: PMC6376214 DOI: 10.1002/open.201800294] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/21/2019] [Indexed: 12/02/2022] Open
Abstract
Low-field benchtop nuclear magnetic resonance (BT-NMR) spectrometers with Halbach magnets are being increasingly used in science and industry as cost-efficient tools for the monitoring of chemical reactions, including hydrogenation. However, their use of low-field magnets limits both resolution and sensitivity. In this paper, we show that it is possible to alleviate these two problems through the combination of parahydrogen-induced polarization (PHIP) and fast correlation spectroscopy with time-resolved non-uniform sampling (TR-NUS). PHIP can enhance NMR signals so that substrates are easily detectable on BT-NMR spectrometers. The interleaved acquisition of one- and two-dimensional spectra with TR-NUS provides unique insight into the consecutive moments of hydrogenation reactions, with a spectral resolution unachievable in a standard approach. We illustrate the potential of the technique with two examples: the hydrogenation of ethylphenyl propiolate and the hydrogenation of a mixture of two substrates - ethylphenyl propiolate and ethyl 2-butynoate.
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Affiliation(s)
- Dariusz Gołowicz
- Faculty of Chemistry, Biological and Chemical Research CentreUniversity of WarsawŻwirki i Wigury 10102-089WarsawPoland
- Centre of New TechnologiesUniversity of WarsawBanacha 2 C02-097WarsawPoland
| | | | - Mateusz Urbańczyk
- Centre of New TechnologiesUniversity of WarsawBanacha 2 C02-097WarsawPoland
- NMR Research UnitUniversity of Oulu90014OuluFinland
| | - Tomasz Ratajczyk
- Institute of Physical ChemistryPolish Academy of SciencesKasprzaka 44/5201-224WarsawPoland
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40
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Urbańczyk M, Shchukina A, Gołowicz D, Kazimierczuk K. TReNDS-Software for reaction monitoring with time-resolved non-uniform sampling. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:4-12. [PMID: 30255516 DOI: 10.1002/mrc.4796] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
NMR spectroscopy, used routinely for structure elucidation, has also become a widely applied tool for process and reaction monitoring. However, the most informative of NMR methods-correlation experiments-are often useless in this kind of applications. The traditional sampling of a multidimensional FID is usually time-consuming, and thus, the reaction-monitoring toolbox was practically limited to 1D experiments (with rare exceptions, e.g., single-scan or fast-sampling experiments). Recently, the technique of time-resolved non-uniform sampling (TR-NUS) has been proposed, which allows to use standard multidimensional pulse sequences preserving the temporal resolution close to that achievable in 1D experiments. However, the method existed only as a prototype and did not allow on-the-fly processing during the reaction. In this paper, we introduce TReNDS: free, user-friendly software kit for acquisition and processing of TR-NUS data. The program works on Bruker, Agilent, and Magritek spectrometers, allowing to carry out up to four experiments with interleaved TR-NUS. The performance of the program is demonstrated on the example of enzymatic hydrolysis of sucrose.
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Affiliation(s)
- Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Spektrino Sp. z o.o., Warsaw, Poland
- NMR Research Unit, University of Oulu, Oulu, Finland
| | | | - Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
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41
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Limatola A, Eichmann C, Jacob RS, Ben-Nissan G, Sharon M, Binolfi A, Selenko P. Time-Resolved NMR Analysis of Proteolytic α-Synuclein Processing in vitro and in cellulo. Proteomics 2018; 18:e1800056. [PMID: 30260559 DOI: 10.1002/pmic.201800056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/14/2018] [Indexed: 11/07/2022]
Abstract
Targeted proteolysis of the disordered Parkinson's disease protein alpha-synuclein (αSyn) constitutes an important event under physiological and pathological cell conditions. In this work, site-specific αSyn cleavage by different endopeptidases in vitro and by endogenous proteases in extracts of challenged and unchallenged cells was studied by time-resolved NMR spectroscopy. Specifically, proteolytic processing was monitored under neutral and low pH conditions and in response to Rotenone-induced oxidative stress. Further, time-dependent degradation of electroporation-delivered αSyn in intact SH-SY5Y and A2780 cells was analyzed. Results presented here delineate a general framework for NMR-based proteolysis studies in vitro and in cellulo, and confirm earlier reports pertaining to the exceptional proteolytic stability of αSyn under physiological cell conditions. However, experimental findings also reveal altered protease susceptibilities in selected mammalian cell lines and upon induced cell stress.
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Affiliation(s)
- Antonio Limatola
- Leibniz Institute of Molecular Pharmacology (FMP-Berlin), In-cell NMR Group,, Robert-Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biology, Stanford University, Stanford, CA, 94305-5430, USA
| | - Cédric Eichmann
- Leibniz Institute of Molecular Pharmacology (FMP-Berlin), In-cell NMR Group,, Robert-Rössle Strasse 10, 13125, Berlin, Germany
| | - Reeba Susan Jacob
- Leibniz Institute of Molecular Pharmacology (FMP-Berlin), In-cell NMR Group,, Robert-Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl Street, 761000, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, 234 Herzl Street, 761000, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, 234 Herzl Street, 761000, Rehovot, Israel
| | - Andres Binolfi
- Leibniz Institute of Molecular Pharmacology (FMP-Berlin), In-cell NMR Group,, Robert-Rössle Strasse 10, 13125, Berlin, Germany.,Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) and Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Ocampo y Esmeralda, 2000, Rosario, Argentina
| | - Philipp Selenko
- Leibniz Institute of Molecular Pharmacology (FMP-Berlin), In-cell NMR Group,, Robert-Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl Street, 761000, Rehovot, Israel
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42
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Concilio MG, Jacquemmoz C, Boyarskaya D, Masson G, Dumez JN. Ultrafast Maximum-Quantum NMR Spectroscopy for the Analysis of Aromatic Mixtures. Chemphyschem 2018; 19:3310-3317. [PMID: 30239108 DOI: 10.1002/cphc.201800667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Indexed: 12/24/2022]
Abstract
Maximum-quantum (MaxQ) NMR experiments have been introduced to overcome issues related to peak overlap and high spectral density in the NMR spectra of aromatic mixtures. In MaxQ NMR, spin systems are separated on the basis of the highest-quantum coherence that they can form. MaxQ experiments are however time consuming and methods have been introduced to accelerate them. In this article, we demonstrate the ultrafast, single-scan acquisition of MaxQ NMR spectra using spatial encoding of the multiple-quantum dimension. So far, the spatial encoding methodology has been applied only for the encoding of up to double-quantum coherences, and here we show that it can be extended to higher coherence orders, to yield a massive reduction of the acquisition time of multi-quantum spectra of aromatic mixtures, and also to monitor chemical reactions.
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Affiliation(s)
- Maria Grazia Concilio
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Corentin Jacquemmoz
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Dina Boyarskaya
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Géraldine Masson
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Jean-Nicolas Dumez
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
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43
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Gołowicz D, Urbańczyk M, Shchukina A, Kazimierczuk K. SCoT: Swept coherence transfer for quantitative heteronuclear 2D NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 294:1-6. [PMID: 29960129 DOI: 10.1016/j.jmr.2018.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/08/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is frequently applied in quantitative chemical analysis (qNMR). It is easy to measure one-dimensional (1D) NMR spectra in a quantitative regime (with appropriately long relaxation delays and acquisition times); however, their applicability is limited in the case of complex samples with severe peak overlap. Two-dimensional (2D) NMR solves the overlap problem, but at the cost of biasing peak intensities and hence quantitativeness. This is partly due to the uneven coherence transfer between excited/detected 1H nuclei and the heteronuclei coupled to them (typically 13C). In the traditional approach, the transfer occurs via the evolution of a spin system state under the J-coupling Hamiltonian during a delay of a fixed length. The delay length is set on the basis of the predicted average coupling constant in the sample. This leads to disturbances for pairs of nuclei with coupling constants deviating from this average. Here, we present a novel approach based on non-standard processing of the data acquired in experiments, where the coherence transfer delay is co-incremented with non-uniformly sampled evolution time. This method allows us to obtain the optimal transfer for all resonances, which improves quantitativeness. We demonstrate the concept for the coherence transfer and multiplicity-edit delays in a heteronuclear single-quantum correlation experiment (HSQC).
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Affiliation(s)
- Dariusz Gołowicz
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland; Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Alexandra Shchukina
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland; Institute for Spectroscopy, Russian Academy of Sciences, Fizicheskaya 5, Troitsk, 108840 Moscow, Russia
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44
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Schlippenbach TV, Oefner PJ, Gronwald W. Systematic Evaluation of Non-Uniform Sampling Parameters in the Targeted Analysis of Urine Metabolites by 1H, 1H 2D NMR Spectroscopy. Sci Rep 2018; 8:4249. [PMID: 29523811 PMCID: PMC5844889 DOI: 10.1038/s41598-018-22541-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/23/2018] [Indexed: 11/15/2022] Open
Abstract
Non-uniform sampling (NUS) allows the accelerated acquisition of multidimensional NMR spectra. The aim of this contribution was the systematic evaluation of the impact of various quantitative NUS parameters on the accuracy and precision of 2D NMR measurements of urinary metabolites. Urine aliquots spiked with varying concentrations (15.6-500.0 µM) of tryptophan, tyrosine, glutamine, glutamic acid, lactic acid, and threonine, which can only be resolved fully by 2D NMR, were used to assess the influence of the sampling scheme, reconstruction algorithm, amount of omitted data points, and seed value on the quantitative performance of NUS in 1H,1H-TOCSY and 1H,1H-COSY45 NMR spectroscopy. Sinusoidal Poisson-gap sampling and a compressed sensing approach employing the iterative re-weighted least squares method for spectral reconstruction allowed a 50% reduction in measurement time while maintaining sufficient quantitative accuracy and precision for both types of homonuclear 2D NMR spectroscopy. Together with other advances in instrument design, such as state-of-the-art cryogenic probes, use of 2D NMR spectroscopy in large biomedical cohort studies seems feasible.
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Affiliation(s)
- Trixi von Schlippenbach
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany
| | - Wolfram Gronwald
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany.
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45
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Rao Kakita VM, Bopardikar M, Kumar Shukla V, Rachineni K, Ranjan P, Singh JS, Hosur R. An efficient combination of BEST and NUS methods in multidimensional NMR spectroscopy for high throughput analysis of proteins. RSC Adv 2018; 8:17616-17621. [PMID: 35542095 PMCID: PMC9080477 DOI: 10.1039/c8ra00527c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/01/2018] [Indexed: 11/23/2022] Open
Abstract
Application of Non Uniform Sampling (NUS) along with Band-selective Excitation Short-Transient (BEST) NMR experiments has been demonstrated for obtaining the important residue-specific atomic level backbone chemical shift values in short durations of time. This application has been demonstrated with both well-folded (ubiquitin) and unfolded (α-synuclein) proteins alike. With this strategy, the experiments required for determining backbone chemical shifts can be performed very rapidly, i.e., in ∼2 hours of spectrometer time, and this data can be used to calculate the backbone folds of proteins using well established algorithms. This will be of great value for structural proteomic investigations on one hand, where the speed of structure determination is a limiting factor and for application in the study of slow kinetic processes involving proteins, such as fibrillization, on the other hand. Application of NUS along with BEST NMR experiments has been demonstrated for obtaining the important residue-specific atomic level backbone chemical shift values in short durations of time.![]()
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Affiliation(s)
| | - Mandar Bopardikar
- Department of Chemical Sciences
- Tata Institute of Fundamental Research (TIFR)
- Mumbai 400 005
- India
| | - Vaibhav Kumar Shukla
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Mumbai 400 098
- India
| | - Kavitha Rachineni
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Mumbai 400 098
- India
| | - Priyatosh Ranjan
- Department of Biosciences & Bioengineering
- Indian Institute of Technology-Bombay (IIT-B)
- Mumbai 400076
- India
| | - Jai Shankar Singh
- Department of Biosciences & Bioengineering
- Indian Institute of Technology-Bombay (IIT-B)
- Mumbai 400076
- India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Mumbai 400 098
- India
- Department of Chemical Sciences
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46
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Qu X, Qiu T, Guo D, Lu H, Ying J, Shen M, Hu B, Orekhov V, Chen Z. High-fidelity spectroscopy reconstruction in accelerated NMR. Chem Commun (Camb) 2018; 54:10958-10961. [DOI: 10.1039/c8cc06132g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
High-fidelity spectra, particularly low intensity peaks, are reconstructed for fast NMR with better rank approximation in the EnhanCed Low Rank (ECLR) method.
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Affiliation(s)
- Xiaobo Qu
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- Xiamen University
- Xiamen 361005
- China
| | - Tianyu Qiu
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- Xiamen University
- Xiamen 361005
- China
| | - Di Guo
- School of Computer and Information Engineering
- Xiamen University of Technology
- Xiamen 361024
- China
| | - Hengfa Lu
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- Xiamen University
- Xiamen 361005
- China
| | - Jiaxi Ying
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- Xiamen University
- Xiamen 361005
- China
| | - Ming Shen
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- East China Normal University
- Shanghai 200062
- China
| | - Bingwen Hu
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- East China Normal University
- Shanghai 200062
- China
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology and Swedish NMR Centre
- University of Gothenburg
- Gothenburg 40530
- Sweden
| | - Zhong Chen
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- Xiamen University
- Xiamen 361005
- China
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47
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Ghosh S, Sengupta A, Chandra K. SOFAST-HMQC-an efficient tool for metabolomics. Anal Bioanal Chem 2017; 409:6731-6738. [PMID: 29030664 DOI: 10.1007/s00216-017-0676-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/13/2017] [Accepted: 09/22/2017] [Indexed: 11/25/2022]
Abstract
Nuclear magnetic resonance (NMR)-based metabolomics relies mostly on 1D NMR; however, the technique is limited by overlap of the signals from the metabolites. In order to circumvent this problem, 2D 1H-13C correlation spectroscopy techniques are often used. However owing to poorer natural abundance and gyromagnetic ratio of 13C, the acquisition time for 2D 1H-13C heteronuclear single quantum coherence spectroscopy (HSQC) is long. This makes it almost impossible to be used in high throughput study. We have reported the application of selective optimized flip angle short transient (SOFAST) technique coupled to heteronuclear multiple quantum correlation (HMQC) along with nonlinear sampling (NUS) in urine and serum samples. This technique takes sevenfold less experimental time than the conventional 1H-13C HSQC experiment with retention of almost all molecular information. Hence, this can be used for high throughput study. Graphical abstract SOFAST-HMQC is a two-dimensional NMR technique that significantly decreases experimental time without loss of information. This technique is applied in complex biofluid samples that are used for high throughput metabolomics studies and shows promise of better information recovery than conventional two-dimensional NMR technique in shorter time.
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Affiliation(s)
- Soumita Ghosh
- Department of Systems Pharmacology and Systems and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, 421 Curie Blvd., Philadelphia, PA, 19104-6160, USA
| | - Arjun Sengupta
- Department of Systems Pharmacology and Systems and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, 421 Curie Blvd., Philadelphia, PA, 19104-6160, USA
| | - Kousik Chandra
- Indian Institute of Science, CV Raman Rd., Bangalore, Karnataka, 560012, India.
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48
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Mayzel M, Ahlner A, Lundström P, Orekhov VY. Measurement of protein backbone 13CO and 15N relaxation dispersion at high resolution. JOURNAL OF BIOMOLECULAR NMR 2017; 69:1-12. [PMID: 28864905 PMCID: PMC5626786 DOI: 10.1007/s10858-017-0127-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/26/2017] [Indexed: 05/31/2023]
Abstract
Peak overlap in crowded regions of two-dimensional spectra prevents characterization of dynamics for many sites of interest in globular and intrinsically disordered proteins. We present new three-dimensional pulse sequences for measurement of Carr-Purcell-Meiboom-Gill relaxation dispersions at backbone nitrogen and carbonyl positions. To alleviate increase in the measurement time associated with the additional spectral dimension, we use non-uniform sampling in combination with two distinct methods of spectrum reconstruction: compressed sensing and co-processing with multi-dimensional decomposition. The new methodology was validated using disordered protein CD79A from B-cell receptor and an SH3 domain from Abp1p in exchange between its free form and bound to a peptide from the protein Ark1p. We show that, while providing much better resolution, the 3D NUS experiments give the similar accuracy and precision of the dynamic parameters to ones obtained using traditional 2D experiments. Furthermore, we show that jackknife resampling of the spectra yields robust estimates of peak intensities errors, eliminating the need for recording duplicate data points.
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Affiliation(s)
- Maxim Mayzel
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530, Göteborg, Sweden
| | - Alexandra Ahlner
- Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, 58183, Linköping, Sweden
| | - Patrik Lundström
- Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, 58183, Linköping, Sweden
| | - Vladislav Y Orekhov
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530, Göteborg, Sweden.
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Göteborg, Sweden.
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49
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Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. SCOPE OF REVIEW In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. MAJOR CONCLUSIONS Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. GENERAL SIGNIFICANCE For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Teppei Ikeya
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori 3-1, Mizuho-ku, Nagoya 467-8603, Japan
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
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Dass R, Grudzia Ż K, Ishikawa T, Nowakowski M, Dȩbowska R, Kazimierczuk K. Fast 2D NMR Spectroscopy for In vivo Monitoring of Bacterial Metabolism in Complex Mixtures. Front Microbiol 2017; 8:1306. [PMID: 28769889 PMCID: PMC5509914 DOI: 10.3389/fmicb.2017.01306] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/28/2017] [Indexed: 01/28/2023] Open
Abstract
The biological toolbox is full of techniques developed originally for analytical chemistry. Among them, spectroscopic experiments are very important source of atomic-level structural information. Nuclear magnetic resonance (NMR) spectroscopy, although very advanced in chemical and biophysical applications, has been used in microbiology only in a limited manner. So far, mostly one-dimensional 1H experiments have been reported in studies of bacterial metabolism monitored in situ. However, low spectral resolution and limited information on molecular topology limits the usability of these methods. These problems are particularly evident in the case of complex mixtures, where spectral peaks originating from many compounds overlap and make the interpretation of changes in a spectrum difficult or even impossible. Often a suite of two-dimensional (2D) NMR experiments is used to improve resolution and extract structural information from internuclear correlations. However, for dynamically changing sample, like bacterial culture, the time-consuming sampling of so-called indirect time dimensions in 2D experiments is inefficient. Here, we propose the technique known from analytical chemistry and structural biology of proteins, i.e., time-resolved non-uniform sampling. The method allows application of 2D (and multi-D) experiments in the case of quickly varying samples. The indirect dimension here is sparsely sampled resulting in significant reduction of experimental time. Compared to conventional approach based on a series of 1D measurements, this method provides extraordinary resolution and is a real-time approach to process monitoring. In this study, we demonstrate the usability of the method on a sample of Escherichia coli culture affected by ampicillin and on a sample of Propionibacterium acnes, an acne causing bacterium, mixed with a dose of face tonic, which is a complicated, multi-component mixture providing complex NMR spectrum. Through our experiments we determine the exact concentration and time at which the anti-bacterial agents affect the bacterial metabolism. We show, that it is worth to extend the NMR toolbox for microbiology by including techniques of 2D z-TOCSY, for total "fingerprinting" of a sample and 2D 13C-edited HSQC to monitor changes in concentration of metabolites in selected metabolic pathways.
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Affiliation(s)
- Rupashree Dass
- Centre of New Technologies, University of WarsawWarsaw, Poland
| | - Katarzyna Grudzia Ż
- Faculty of Chemistry, Biological and Chemical Research Centre, University of WarsawWarsaw, Poland
| | - Takao Ishikawa
- Department of Molecular Biology, Faculty of Biology, Institute of Biochemistry, University of WarsawWarsaw, Poland
| | | | - Renata Dȩbowska
- Dr Irena Eris Cosmetic Laboratories, Centre for Science and ResearchWarsaw, Poland
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