CoChat
Sign Up
Cited by 0Advanced NMR Techniques and ApplicationsMicrobial Natural Products and BiosynthesisMetabolomics and Mass Spectrometry Studies

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

NMR as a readout to monitor and restore the integrity of complex chemoenzymatic reactions

Open access
Marincin, Kenneth A., Hwang, Yousang, Kengmana, Everett S., Meyers, David J., Frueh, Dominique P.·2022·Journal of Magnetic Resonance
DOI 10.1016/j.jmr.2022.107265PMC PMC9463103

Published version of a preprint

Open this paper in CoChat — free account

Abstract

The non-invasive nature of NMR offers a means to monitor biochemical reactions in situ at the atomic level. We harness this advantage to monitor a complex chemoenzymatic reaction that sequentially modifies reagents and loads the product on a nonribosomal peptide synthetase carrier protein. We present a protocol including a pulse sequence that permits to assess both the integrity of reagents and the completion of each step in the reaction, thus alleviating otherwise time-consuming and costly approaches to debug and repeat inefficient reactions. This study highlights the importance of NMR as a tool to establish reliable and reproducible experimental conditions in biochemical studies.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.jmr.2022.107265

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 44

  1. Nakane, 2020, Single-particle cryo-EM at atomic resolution, Nature, 587, 152, 10.1038/s41586-020-2829-0 · DOI
  2. Henzler-Wildman, 2007, Dynamic personalities of proteins, Nature, 450, 964, 10.1038/nature06522 · DOI · Paper page
  3. Iwahara, 2006, Detecting transient intermediates in macromolecular binding by paramagnetic NMR, Nature, 440, 1227, 10.1038/nature04673 · DOI
  4. Goodrich, 2015, A nuclear magnetic resonance method for probing molecular influences of substrate loading in nonribosomal peptide synthetase carrier proteins, Biochemistry, 54, 1154, 10.1021/bi501433r · DOI
  5. Serber, 2001, In-Cell NMR Spectroscopy, Biochemistry, 40, 14317, 10.1021/bi011751w · DOI
  6. Whittier, 2013, Conformational Motions Regulate Phosphoryl Transfer in Related Protein Tyrosine Phosphatases, Science (80-.), 341, 899, 10.1126/science.1241735 · DOI
  7. Bozhüyük, 2019, Engineering enzymatic assembly lines to produce new antibiotics, Curr. Opin. Microbiol., 51, 88, 10.1016/j.mib.2019.10.007 · DOI
  8. Finking, 2004, Biosynthesis of nonribosomal peptides, Annu. Rev. Microbiol., 58, 453, 10.1146/annurev.micro.58.030603.123615 · DOI
  9. Süssmuth, 2017, Nonribosomal Peptide Synthesis—Principles and Prospects, Angew. Chemie - Int. Ed., 56, 3770, 10.1002/anie.201609079 · DOI
  10. Reimer, 2019, Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility, Science (80-.), 366
  11. Izoré, 2021, Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity, Nat. Commun., 12, 1, 10.1038/s41467-021-22623-0 · DOI
  12. Tarry, 2017, X-Ray Crystallography and Electron Microscopy of Cross- and Multi-Module Nonribosomal Peptide Synthetase Proteins Reveal a Flexible Architecture, Structure., 25, 783, 10.1016/j.str.2017.03.014 · DOI
  13. Goodrich, 2015, Solution Structure of a Nonribosomal Peptide Synthetase Carrier Protein Loaded with Its Substrate Reveals Transient, Well-Defined Contacts, J. Am. Chem. Soc., 137, 12100, 10.1021/jacs.5b07772 · DOI
  14. Jaremko, 2015, Structure and Substrate Sequestration in the Pyoluteorin Type II Peptidyl Carrier Protein PltL, J. Am. Chem. Soc., 137, 11546, 10.1021/jacs.5b04525 · DOI
  15. Worthington, 2006, One-pot chemo-enzymatic synthesis of reporter-modified proteins, Org. Biomol. Chem., 4, 44, 10.1039/B512735A · DOI
  16. Nazi, 2004, One-pot chemoenzymatic preparation of coenzyme A analogues, Anal. Biochem., 324, 100, 10.1016/j.ab.2003.09.005 · DOI
  17. Lambalot, 1996, A new enzyme superfamily - The phosphopantetheinyl transferases, Chem. Biol., 3, 923, 10.1016/S1074-5521(96)90181-7 · DOI
  18. Hur, 2009, Crosslinking Studies of Protein-Protein Interactions in Nonribosomal Peptide Biosynthesis, Chem. Biol., 16, 372, 10.1016/j.chembiol.2009.02.009 · DOI
  19. Goodrich, 2017, Molecular impact of covalent modifications on nonribosomal peptide synthetase carrier protein communication, J. Biol. Chem., 292, 10002, 10.1074/jbc.M116.766220 · DOI
  20. Kosa, 2014, Chemoenzymatic exchange of phosphopantetheine on protein and peptide, Chem. Sci., 5, 1179, 10.1039/C3SC53154F · DOI
  21. Zou, 2009, Phosphopantetheinyl transferase catalyzed site-specific protein labeling with ADP conjugated chemical probes, J. Am. Chem. Soc., 131, 7548, 10.1021/ja902464v · DOI
  22. Kittilä, 2018, An enhanced chemoenzymatic method for loading substrates onto carrier protein domains, Biochem. Cell Biol., 96, 372, 10.1139/bcb-2017-0275 · DOI
  23. Miller, 2007, Phosphopantetheine adenylyltransferase from Escherichia coli: Investigation of the kinetic mechanism and role in regulation of coenzyme A biosynthesis, J. Bacteriol., 189, 8196, 10.1128/JB.00732-07 · DOI
  24. Geerlof, 1999, Purification and characterization of phosphopantetheine adenylyltransferase from Escherichia coli, J. Biol. Chem., 274, 27105, 10.1074/jbc.274.38.27105 · DOI
  25. Rootman, 2010, Creating cellulose-binding domain fusions of the coenzymea biosynthetic enzymes to enable reactor-based biotransformations, ChemCatChem, 2, 1239, 10.1002/cctc.201000197 · DOI
  26. Strauss, 2010, Biocatalytic Production of Coenzyme A Analogues, ChemCatChem, 2, 929, 10.1002/cctc.201000139 · DOI
  27. Gehring, 1998, The nonribosomal peptide synthetase HMWP2 forms a thiazoline ring during biogenesis of yersiniabactin, an iron-chelating virulence factor of Yersinia pestis, Biochemistry, 37, 11637, 10.1021/bi9812571 · DOI
  28. Marincin, 2021, Using delayed decoupling to attenuate residual signals in editing filters, Magn. Reson., 2, 475, 10.5194/mr-2-475-2021 · DOI
  29. Breeze, 2000, Isotope-filtered NMR methods for the study of biomolecular structure and interactions, Prog. Nucl. Magn. Reson. Spectrosc., 36, 323, 10.1016/S0079-6565(00)00020-0 · DOI
  30. Gemmecker, 1992, An Improved Method for Selectively Observing Protons Attached to 12C in the Presence of 1H–13C Spin Pairs, J. Magn. Reson., 96, 199
  31. Zangger, 2003, X-filtering for a range of coupling constants: Application to the detection of intermolecular NOEs, J. Magn. Reson., 160, 97, 10.1016/S1090-7807(02)00176-3 · DOI
  32. Stejskal, 1965, Spin diffusion measurements: Spin echoes in the presence of a time-dependent field gradient, J. Chem. Phys., 42, 288, 10.1063/1.1695690 · DOI
  33. Tanner, 1970, Use of the stimulated echo in nmr diffusion studies, J. Chem. Phys., 52, 2523, 10.1063/1.1673336 · DOI
  34. Johnson, 1999, Diffusion ordered nuclear magnetic resonance spectroscopy: Principles and applications, Prog. Nucl. Magn. Reson. Spectrosc., 34, 203, 10.1016/S0079-6565(99)00003-5 · DOI
  35. Gonnella, 1998, Isotope-Filtered Affinity NMR, J. Magn. Reson., 131, 336, 10.1006/jmre.1997.1376 · DOI
  36. Wu, 1995, An Improved Diffusion-Ordered Spectroscopy Experiment Incorporating Bipolar-Gradient Pulses, J. Magn. Reson. Ser. A., 115, 260, 10.1006/jmra.1995.1176 · DOI
  37. Yao, 2014, Measuring translational diffusion coefficients of peptides and proteins by pfg-nmr using band-selective rf pulses, Eur. Biophys. J., 43, 331, 10.1007/s00249-014-0965-x · DOI
  38. Böhlen, 1993, Experimental aspects of chirp NMR spectroscopy, J. Magn. Reson. - Ser. A., 102, 293, 10.1006/jmra.1993.1107 · DOI
  39. Shaka, 1985, Computer-optimized decoupling scheme for wideband applications and low-level operation, J. Magn. Reson., 64, 547
  40. Yin, 2006, Site-specific protein labeling by Sfp phosphopantetheinyl transferase, Nat. Protoc., 1, 280, 10.1038/nprot.2006.43 · DOI
  41. Meier, 2006, Synthesis and evaluation of bioorthogonal pantetheine analogues for in vivo protein modification, J. Am. Chem. Soc., 128, 12174, 10.1021/ja063217n · DOI
  42. Wishart, 2009, HMDB: A knowledgebase for the human metabolome, Nucleic Acids Res., 37, 603, 10.1093/nar/gkn810 · DOI
  43. Gowda, 2019, Extending the Scope of 1 H NMR Spectroscopy for the Analysis of Cellular, Anal. Chem., 91, 2464, 10.1021/acs.analchem.8b05286 · DOI
  44. Rucker, 1989, Broadband homonuclear cross polarization in 2D N.M.R. using DIPSI-2, Mol. Phys., 68, 509, 10.1080/00268978900102331 · DOI

Metadata

Authors
Marincin, K. A., Hwang, Y., Kengmana, E. S., Meyers, D. J., & Frueh, D. P.
Affiliations
Johns Hopkins University (US)
Corresponding author
Frueh, Dominique P.
ORCID
Venue
Journal of Magnetic Resonance
Publisher
Elsevier BV
Published
2022-09
Volume
342
Pages
107265
ISSN
1090-7807 (ISSN-L)
DOI
10.1016/j.jmr.2022.107265
PMC
PMC9463103
OpenAlex
W4284881971
Cited by
0
References
1
FWCI
0.00
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Magnetic Resonance (acceptedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Institute for Clinical and Translational Research, University of Maryland, Baltimore
  • National Institutes of Health (UL1TR003098)
  • National Institute of General Medical Sciences (R01GM104257)
  • Flight Attendant Medical Research Institute
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
  • Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Microbial Natural Products and Biosynthesis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
Keywords
chemoenzymatic synthesis, nonribosomal peptide synthetase, NMR pulse sequences, reaction monitoring, in situ NMR, reproducibility, pulse sequence design
MeSH terms
Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review