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Cited by 8Advanced Fluorescence Microscopy TechniquesProtein Structure and DynamicsPhotochemistry and Electron Transfer Studies

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Conformational Dynamics of mCherry Variants: A Link between Side-Chain Motions and Fluorescence Brightness

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Mukherjee, Srijit, Manna, Premashis, Douglas, Nancy, Chapagain, Prem P., Jimenez, Ralph·2023·The Journal of Physical Chemistry B
DOI 10.1021/acs.jpcb.2c05584

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Abstract

The 3-fold higher brightness of the recently developed mCherry-XL red fluorescent protein (FP) compared to its progenitor, mCherry, is due to a significant decrease in the nonradiative decay rate underlying its increased fluorescence quantum yield. To examine the structural and dynamic role of the four mutations that distinguish the two FPs and closely related variants, we employed microsecond time scale, all-atom molecular dynamics simulations. The simulations revealed that the I197R mutation leads to the formation of multiple hydrogen-bonded contacts and increased rigidity of the β-barrel. In particular, mCherryXL showed reduced nanosecond time scale breathing of the gap between the β7 and β10-strands, which was previously shown to be the most flexible region of mCherry. Together with experimental results, the simulations also reveal steric interactions of residue 161 and a network of hydrogen-bonding interactions of the chromophore with residues at positions 59, 143, and 163 that are critical in perturbing the chromophore electronic structure. Finally, we shed light on the conformational dynamics of the conserved residues R95 and S146, which are hydrogen-bonded to the chromophore, and provide physical insights into the observed photophysics. To the best of our knowledge, this is the first study that evaluates the conformational space for a set of closely related FPs generated by directed evolution.

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  1. 10.1146/annurev.biochem.67.1.509 · DOI
  2. 10.1038/nmeth819 · DOI
  3. 10.1038/s41592-018-0211-z · DOI
  4. 10.3390/chemosensors5040032 · DOI
  5. 10.1021/acs.chemrev.6b00700 · DOI
  6. 10.1038/s41467-020-14559-8 · DOI
  7. 10.1021/acscentsci.1c01233 · DOI
  8. 10.1073/pnas.2000942117 · DOI
  9. 10.1021/acs.jpcb.1c05629 · DOI
  10. 10.1038/s41467-022-30685-x · DOI
  11. 10.1038/s41596-019-0250-7 · DOI
  12. 10.1039/C8IB00103K · DOI
  13. 10.1021/acs.analchem.5b00607 · DOI
  14. 10.1039/C9LC00790C · DOI
  15. 10.1016/j.bbrc.2022.01.044 · DOI
  16. 10.1073/pnas.2024034118 · DOI
  17. 10.1073/pnas.1323440111 · DOI
  18. 10.1073/pnas.0709599105 · DOI
  19. 10.1021/ct100227k · DOI
  20. 10.1021/jp2020269 · DOI
  21. 10.1021/jacs.2c02946 · DOI
  22. 10.1126/science.aax1898 · DOI
  23. 10.1021/jacs.9b07152 · DOI
  24. 10.1016/j.bpj.2011.06.055 · DOI
  25. 10.1021/acs.chemrev.6b00238 · DOI
  26. 10.1021/jacs.9b08356 · DOI
  27. 10.1021/jacs.1c12305 · DOI
  28. 10.1039/D2CP00889K · DOI
  29. 10.3389/fmolb.2021.633217 · DOI
  30. 10.1039/D1SC05849E · DOI
  31. 10.1021/acs.jpcb.1c08570 · DOI
  32. 10.3390/chemosensors9080234 · DOI
  33. 10.1038/nmeth.4074 · DOI
  34. 10.1021/ar2001556 · DOI
  35. 10.1126/sciadv.aax0024 · DOI
  36. 10.1021/acs.chemrev.8b00026 · DOI
  37. 10.3389/fmolb.2020.569990 · DOI
  38. 10.1021/acs.chemrev.7b00427 · DOI
  39. 10.1016/j.jmgm.2010.06.010 · DOI
  40. 10.1038/s41586-022-04637-w · DOI
  41. 10.1021/acs.jpcb.2c01956 · DOI
  42. 10.1021/acs.biochem.0c00484 · DOI
  43. 10.1063/5.0014475 · DOI
  44. 10.1002/jcc.20289 · DOI · Paper page
  45. 10.1002/prot.24852 · DOI
  46. 10.1021/jp014476w · DOI
  47. 10.1016/0263-7855(96)00018-5 · DOI · Paper page
  48. 10.1063/1.3660197 · DOI
  49. 10.1021/jp308366y · DOI
  50. 10.1039/C4IB00251B · DOI
  51. 10.1021/bi060773l · DOI
  52. 10.1021/ja2114568 · DOI
  53. 10.1038/nbt1037 · DOI · Paper page
  54. 10.1073/pnas.1013910107 · DOI
  55. 10.1073/pnas.082243699 · DOI
  56. 10.1021/jp3060944 · DOI
  57. 10.1021/jp306093h · DOI
  58. 10.1016/j.ijbiomac.2020.03.244 · DOI
  59. 10.1021/acs.jpclett.0c00105 · DOI
  60. 10.1021/acs.jctc.9b00070 · DOI
  61. 10.1021/acs.jpcb.1c10516 · DOI
  62. 10.1021/jacs.0c01880 · DOI

Metadata

Authors
Mukherjee, S., Manna, P., Douglas, N., Chapagain, P. P., & Jimenez, R.
Affiliations
  • National Institute of Standards and Technology (US)
  • Massachusetts Institute of Technology (US)
  • University of Colorado Boulder (US)
  • Florida International University (US)
Corresponding author
Jimenez, Ralph
ORCID
Venue
The Journal of Physical Chemistry B
Publisher
American Chemical Society (ACS)
Published
2022-12-27
Volume
127
Issue
1
Pages
52-61
ISSN
  • 1520-5207 (ISSN-L)
  • 1520-6106
DOI
10.1021/acs.jpcb.2c05584
OpenAlex
W4313237746
Cited by
8
References
2
Citations by year
2026: 3 · 2025: 2 · 2024: 3
FWCI
0.55
Type
journal article
Language
en
Open access
Licence
Locations
  • The Journal of Physical Chemistry B (publishedVersion)
  • ChemRxiv (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health (T32)
  • Division of Physics (PHY 1734006)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Photochemistry and Electron Transfer Studies
Keywords
mCherry, red fluorescent protein, conformational dynamics, fluorescence intensity, quantum yield, hydrogen bond network, nonradiative decay
MeSH terms
Fluorescence, Hydrogen, Mutation, Protein Conformation, Molecular Dynamics Simulation

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