Cited by 6Photoreceptor and optogenetics researchProtein Structure and DynamicsReceptor Mechanisms and Signaling

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

Engineering of soluble bacteriorhodopsin

Open access

Published version of a preprint

Abstract

Analogues of membrane protein bacteriorhodopsin are reported that are soluble and stable, bind retinal and exhibit photocycles under illumination, highlighting the power of modern protein engineering approaches.

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 · 10.1039/d5sc02453f

Cites

3 of 3 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: 64

  1. Levental, 2023, Nat. Rev. Mol. Cell Biol., 24, 107, 10.1038/s41580-022-00524-4 · DOI
  2. Privé, 2007, Methods, 41, 388, 10.1016/j.ymeth.2007.01.007 · DOI
  3. Serebryany, 2012, Biochim. Biophys. Acta, 1818, 225, 10.1016/j.bbamem.2011.07.047 · DOI
  4. Pandey, 2016, Biochem. Cell Biol., 94, 507, 10.1139/bcb-2015-0143 · DOI
  5. Zhang, 2019, Curr. Opin. Struct. Biol., 58, 278, 10.1016/j.sbi.2019.06.002 · DOI
  6. Qing, 2022, Chem. Rev., 122, 14085, 10.1021/acs.chemrev.1c00757 · DOI
  7. Slovic, 2004, Proc. Natl. Acad. Sci. U. S. A., 101, 1828, 10.1073/pnas.0306417101 · DOI
  8. Ma, 2008, Proc. Natl. Acad. Sci. U. S. A., 105, 16537, 10.1073/pnas.0805501105 · DOI
  9. Cui, 2012, Biochim. Biophys. Acta, Biomembr., 1818, 617, 10.1016/j.bbamem.2011.11.021 · DOI
  10. Zhang, 2018, Proc. Natl. Acad. Sci. U. S. A., 115, E8652, 10.1073/pnas.1810662115 · DOI
  11. Sumida, 2024, J. Am. Chem. Soc., 146, 2054, 10.1021/jacs.3c10941 · DOI
  12. Goverde, 2024, Nature, 631, 449, 10.1038/s41586-024-07601-y · DOI
  13. Oesterhelt, 1971, Nature, 233, 149
  14. Grote, 2014, Biochim. Biophys. Acta, Bioenerg., 1837, 533, 10.1016/j.bbabio.2013.08.006 · DOI
  15. Gordeliy, 2022, Methods Mol. Biol., 2501, 1, 10.1007/978-1-0716-2329-9_1 · DOI
  16. Rozenberg, 2021, Annu. Rev. Microbiol., 75, 427, 10.1146/annurev-micro-031721-020452 · DOI
  17. Kojima, 2020, Biochemistry, 59, 218, 10.1021/acs.biochem.9b00768 · DOI
  18. A.Alekseev , V.Gordeliy and E.Bamberg , in Rhodopsin: Methods and Protocols , ed. V. Gordeliy , Springer US , New York, NY , 2022 , pp. 71–100 · DOI
  19. Baker, 2024, Research Square, 10.21203/rs.3.rs-4652998/v1 · DOI
  20. Borshchevskiy, 2022, Nat. Struct. Mol. Biol., 29, 440, 10.1038/s41594-022-00762-2 · DOI
  21. Nikolaev, 2024, Protein Sci., 33, e4958, 10.1002/pro.4958 · DOI
  22. Nikolaev, 2024, Protein Sci., 33, e5216, 10.1002/pro.5216 · DOI
  23. Mirdita, 2022, Nat. Methods, 19, 679, 10.1038/s41592-022-01488-1 · DOI · Paper page
  24. Dencher, 1978, FEBS Lett., 96, 322, 10.1016/0014-5793(78)80427-X · DOI
  25. Ernst, 2014, Chem. Rev., 114, 126, 10.1021/cr4003769 · DOI
  26. Chizhov, 1996, Biophys. J., 71, 2329, 10.1016/S0006-3495(96)79475-4 · DOI
  27. Wickstrand, 2019, Annu. Rev. Biochem., 88, 59, 10.1146/annurev-biochem-013118-111327 · DOI
  28. Butt, 1989, EMBO J., 8, 1657, 10.1002/j.1460-2075.1989.tb03556.x · DOI
  29. Holz, 1989, Proc. Natl. Acad. Sci. U. S. A., 86, 2167, 10.1073/pnas.86.7.2167 · DOI
  30. Liao, 1984, J. Biol. Chem., 259, 4200, 10.1016/S0021-9258(17)43030-4 · DOI
  31. Kahn, 1992, Biochemistry, 31, 6144, 10.1021/bi00141a027 · DOI
  32. Popot, 2000, Annu. Rev. Biochem., 69, 881, 10.1146/annurev.biochem.69.1.881 · DOI
  33. Mitra, 2002, Protein Eng., 15, 485, 10.1093/protein/15.6.485 · DOI
  34. Schafmeister, 1993, Science, 262, 734, 10.1126/science.8235592 · DOI
  35. Gibas, 1997, Protein Eng., 10, 1175, 10.1093/protein/10.10.1175 · DOI
  36. Frank, 2000, Biochemistry, 39, 6825, 10.1021/bi0000972 · DOI
  37. Li, 2001, Biochemistry, 40, 6636, 10.1021/bi0026573 · DOI
  38. Kim, 2025, Annu. Rev. Biophys., 54, 141, 10.1146/annurev-biophys-070524-100658 · DOI
  39. Abraham, 2015, SoftwareX, 1–2, 19, 10.1016/j.softx.2015.06.001 · DOI · Paper page
  40. Wang, 2012, Science, 338, 1340, 10.1126/science.1226135 · DOI
  41. W. L.DeLano , San Carlos: DeLano Scientific , 2012
  42. Olsson, 2011, J. Chem. Theory Comput., 7, 525, 10.1021/ct100578z · DOI
  43. Best, 2012, J. Chem. Theory Comput., 8, 3257, 10.1021/ct300400x · DOI
  44. Jorgensen, 1983, J. Chem. Phys., 79, 926, 10.1063/1.445869 · DOI
  45. Zhu, 2013, J. Am. Chem. Soc., 135, 9391, 10.1021/ja4002986 · DOI
  46. Evans, 1985, J. Chem. Phys., 83, 4069, 10.1063/1.449071 · DOI
  47. Parrinello, 1981, J. Appl. Phys., 52, 7182, 10.1063/1.328693 · DOI
  48. Hess, 1997, J. Comput. Chem., 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H · DOI
  49. Essmann, 1995, J. Chem. Phys., 103, 8577, 10.1063/1.470117 · DOI
  50. Michaud-Agrawal, 2011, J. Comput. Chem., 32, 2319, 10.1002/jcc.21787 · DOI
  51. Katoh, 2013, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010 · DOI · Paper page
  52. Nguyen, 2015, Mol. Biol. Evol., 32, 268, 10.1093/molbev/msu300 · DOI · Paper page
  53. Bianchini, 2024, Ecol. Evol., 14, e10873, 10.1002/ece3.10873 · DOI
  54. D.Soloviov , V.Borshchevskiy and I.Chizhov , in Rhodopsin: Methods and Protocols , ed. V. Gordeliy , Springer US , New York, NY , 2022 , pp. 169–179 · DOI
  55. Müller, 1991, Eur. Biophys. J., 19, 231, 10.1007/BF00183531 · DOI
  56. Evans, 2006, Acta Crystallogr., Sect. D:Struct. Biol., 62, 72, 10.1107/S0907444905036693 · DOI
  57. Winter, 2010, J. Appl. Crystallogr., 43, 186, 10.1107/S0021889809045701 · DOI
  58. Winter, 2018, Acta Crystallogr., Sect. D:Struct. Biol., 74, 85, 10.1107/S2059798317017235 · DOI
  59. Winn, 2011, Acta Crystallogr., Sect. D:Struct. Biol., 67, 235, 10.1107/S0907444910045749 · DOI · Paper page
  60. Evans, 2013, Acta Crystallogr., Sect. D:Struct. Biol., 69, 1204, 10.1107/S0907444913000061 · DOI
  61. I. J.Tickle , C.Flensburg , P.Keller , W.Paciorek , A.Sharff , C.Vonrhein and G.Bricogne , STARANISO Global Phasing Ltd , Cambridge, United Kingdom , 2016
  62. McCoy, 2007, J. Appl. Crystallogr., 40, 658, 10.1107/S0021889807021206 · DOI · Paper page
  63. Vagin, 2004, Acta Crystallogr., Sect. D:Struct. Biol., 60, 2184, 10.1107/S0907444904023510 · DOI
  64. Agirre, 2023, Acta Crystallogr., Sect. D:Struct. Biol., 79, 449, 10.1107/S2059798323003595 · DOI

Metadata

Authors
Nikolaev, A., Orlov, Y., Tsybrov, F., Kuznetsova, E., Shishkin, P., Kuzmin, A., Mikhailov, A., Nikolaeva, Y. S., Anuchina, A., Chizhov, I., Semenov, O., Kapranov, I., Borshchevskiy, V., Remeeva, A., & Gushchin, I.
Affiliations
Moscow Institute of Physics and Technology (RU)
Corresponding author
Gushchin, Ivan
Venue
Chemical Science
Published
2025
Volume
16
Issue
24
Pages
11067-11076
ISSN
  • 2041-6520 (ISSN-L)
  • 2041-6539
OpenAlex
W4410338897
Cited by
6
References
3
Citations by year
2026: 5 · 2025: 1
FWCI
2.35
Type
journal article
Language
en
Open access
Locations
  • Chemical Science (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • Russian Science Foundation (21-64-00018)
  • Ministry of Science and Higher Education of the Russian Federation (075-15-2021-1354, FSMG-2025-0003)
Topics
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Photoreceptor and optogenetics research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
Keywords
bacteriorhodopsin, retinal binding pocket, chromophore binding, photocycle, crystal structure, optogenetics, light-driven proton pump

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