001     607037
005     20250723171737.0
024 7 _ |a 10.1038/s41467-024-47469-0
|2 doi
024 7 _ |a 10.3204/PUBDB-2024-01742
|2 datacite_doi
024 7 _ |a altmetric:162182590
|2 altmetric
024 7 _ |a pmid:38600129
|2 pmid
024 7 _ |a WOS:001202408400026
|2 WOS
024 7 _ |a openalex:W4394674430
|2 openalex
037 _ _ |a PUBDB-2024-01742
041 _ _ |a English
082 _ _ |a 500
100 1 _ |a Podoliak, E.
|0 P:(DE-HGF)0
|b 0
245 _ _ |a A subgroup of light-driven sodium pumps with an additional Schiff base counterion
260 _ _ |a [London]
|c 2024
|b Nature Publishing Group UK
336 7 _ |a article
|2 DRIVER
336 7 _ |a Output Types/Journal article
|2 DataCite
336 7 _ |a Journal Article
|b journal
|m journal
|0 PUB:(DE-HGF)16
|s 1741773768_1487754
|2 PUB:(DE-HGF)
336 7 _ |a ARTICLE
|2 BibTeX
336 7 _ |a JOURNAL_ARTICLE
|2 ORCID
336 7 _ |a Journal Article
|0 0
|2 EndNote
520 _ _ |a Light-driven sodium pumps (NaRs) are unique ion-transporting microbial rhodopsins. The major group of NaRs is characterized by an NDQ motif and has two aspartic acid residues in the central region essential for sodium transport. Here we identify a subgroup of the NDQ rhodopsins bearing an additional glutamic acid residue in the close vicinity to the retinal Schiff base. We thoroughly characterize a member of this subgroup, namely the protein ErNaR from Erythrobacter sp. HL-111 and show that the additional glutamic acid results in almost complete loss of pH sensitivity for sodium-pumping activity, which is in contrast to previously studied NaRs. ErNaR is capable of transporting sodium efficiently even at acidic pH levels. X-ray crystallography and single particle cryo-electron microscopy reveal that the additional glutamic acid residue mediates the connection between the other two Schiff base counterions and strongly interacts with the aspartic acid of the characteristic NDQ motif. Hence, it reduces its pKa. Our findings shed light on a subgroup of NaRs and might serve as a basis for their rational optimization for optogenetics.
536 _ _ |a 6G3 - PETRA III (DESY) (POF4-6G3)
|0 G:(DE-HGF)POF4-6G3
|c POF4-6G3
|f POF IV
|x 0
536 _ _ |a DFG project G:(GEPRIS)390729940 - EXC 2067: Multiscale Bioimaging: Von molekularen Maschinen zu Netzwerken erregbarer Zellen (390729940)
|0 G:(GEPRIS)390729940
|c 390729940
|x 1
536 _ _ |a DFG project G:(GEPRIS)390873048 - EXC 2151: ImmunoSensation2 - the immune sensory system (390873048)
|0 G:(GEPRIS)390873048
|c 390873048
|x 2
542 _ _ |i 2024-04-10
|2 Crossref
|u https://creativecommons.org/licenses/by/4.0
542 _ _ |i 2024-04-10
|2 Crossref
|u https://creativecommons.org/licenses/by/4.0
588 _ _ |a Dataset connected to CrossRef, Journals: bib-pubdb1.desy.de
693 _ _ |a PETRA III
|f PETRA Beamline P14
|1 EXP:(DE-H253)PETRAIII-20150101
|0 EXP:(DE-H253)P-P14-20150101
|6 EXP:(DE-H253)P-P14-20150101
|x 0
700 1 _ |a Lamm, G. H. U.
|0 P:(DE-HGF)0
|b 1
700 1 _ |a Marin, E.
|b 2
700 1 _ |a Schellbach, A. V.
|b 3
700 1 _ |a Fedotov, D. A.
|0 P:(DE-HGF)0
|b 4
700 1 _ |a Stetsenko, A.
|0 P:(DE-HGF)0
|b 5
700 1 _ |a Asido, M.
|0 0000-0003-3181-0236
|b 6
700 1 _ |a Maliar, N.
|b 7
700 1 _ |a Bourenkov, G.
|0 P:(DE-H253)PIP1007425
|b 8
700 1 _ |a Balandin, T.
|0 0000-0001-8471-8041
|b 9
700 1 _ |a Baeken, C.
|b 10
700 1 _ |a Astashkin, R.
|b 11
700 1 _ |a Schneider, T. R.
|0 P:(DE-H253)PIP1005932
|b 12
700 1 _ |a Bateman, A.
|0 0000-0002-6982-4660
|b 13
700 1 _ |a Wachtveitl, J.
|0 0000-0002-8496-8240
|b 14
700 1 _ |a Schapiro, I.
|0 0000-0001-8536-6869
|b 15
700 1 _ |a Busskamp, V.
|0 0000-0001-7517-8944
|b 16
700 1 _ |a Guskov, A.
|0 P:(DE-HGF)0
|b 17
700 1 _ |a Gordeliy, V.
|b 18
700 1 _ |a Alekseev, A.
|0 P:(DE-HGF)0
|b 19
|e Corresponding author
700 1 _ |a Kovalev, K.
|0 P:(DE-HGF)0
|b 20
|e Corresponding author
773 1 8 |a 10.1038/s41467-024-47469-0
|b Springer Science and Business Media LLC
|d 2024-04-10
|n 1
|p 3119
|3 journal-article
|2 Crossref
|t Nature Communications
|v 15
|y 2024
|x 2041-1723
773 _ _ |a 10.1038/s41467-024-47469-0
|g Vol. 15, no. 1, p. 3119
|0 PERI:(DE-600)2553671-0
|n 1
|p 3119
|t Nature Communications
|v 15
|y 2024
|x 2041-1723
856 4 _ |u https://www.nature.com/articles/s41467-024-47469-0
856 4 _ |u https://bib-pubdb1.desy.de/record/607037/files/A%20subgroup%20of%20light-driven%20sodium%20pumps%20with%20an%20additional%20Schiff%20base%20counterion.pdf
|y OpenAccess
856 4 _ |u https://bib-pubdb1.desy.de/record/607037/files/A%20subgroup%20of%20light-driven%20sodium%20pumps%20with%20an%20additional%20Schiff%20base%20counterion.pdf?subformat=pdfa
|x pdfa
|y OpenAccess
909 C O |o oai:bib-pubdb1.desy.de:607037
|p openaire
|p open_access
|p VDB
|p driver
|p dnbdelivery
910 1 _ |a European Molecular Biology Laboratory
|0 I:(DE-588b)235011-7
|k EMBL
|b 8
|6 P:(DE-H253)PIP1007425
910 1 _ |a European XFEL
|0 I:(DE-588)1043621512
|k XFEL.EU
|b 8
|6 P:(DE-H253)PIP1007425
910 1 _ |a European Molecular Biology Laboratory
|0 I:(DE-588b)235011-7
|k EMBL
|b 12
|6 P:(DE-H253)PIP1005932
910 1 _ |a European Molecular Biology Laboratory
|0 I:(DE-588b)235011-7
|k EMBL
|b 20
|6 P:(DE-HGF)0
913 1 _ |a DE-HGF
|b Forschungsbereich Materie
|l Großgeräte: Materie
|1 G:(DE-HGF)POF4-6G0
|0 G:(DE-HGF)POF4-6G3
|3 G:(DE-HGF)POF4
|2 G:(DE-HGF)POF4-600
|4 G:(DE-HGF)POF
|v PETRA III (DESY)
|x 0
914 1 _ |y 2024
915 _ _ |a Article Processing Charges
|0 StatID:(DE-HGF)0561
|2 StatID
|d 2023-08-29
915 _ _ |a WoS
|0 StatID:(DE-HGF)0113
|2 StatID
|b Science Citation Index Expanded
|d 2023-08-29
915 _ _ |a Fees
|0 StatID:(DE-HGF)0700
|2 StatID
|d 2023-08-29
915 _ _ |a OpenAccess
|0 StatID:(DE-HGF)0510
|2 StatID
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)1190
|2 StatID
|b Biological Abstracts
|d 2023-08-29
915 _ _ |a Creative Commons Attribution CC BY 4.0
|0 LIC:(DE-HGF)CCBY4
|2 HGFVOC
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)0160
|2 StatID
|b Essential Science Indicators
|d 2023-08-29
915 _ _ |a JCR
|0 StatID:(DE-HGF)0100
|2 StatID
|b NAT COMMUN : 2022
|d 2025-01-02
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)0200
|2 StatID
|b SCOPUS
|d 2025-01-02
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)0300
|2 StatID
|b Medline
|d 2025-01-02
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)0501
|2 StatID
|b DOAJ Seal
|d 2024-01-30T07:48:07Z
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)0500
|2 StatID
|b DOAJ
|d 2024-01-30T07:48:07Z
915 _ _ |a Peer Review
|0 StatID:(DE-HGF)0030
|2 StatID
|b DOAJ : Peer review
|d 2024-01-30T07:48:07Z
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)0199
|2 StatID
|b Clarivate Analytics Master Journal List
|d 2025-01-02
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)1040
|2 StatID
|b Zoological Record
|d 2025-01-02
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)1060
|2 StatID
|b Current Contents - Agriculture, Biology and Environmental Sciences
|d 2025-01-02
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)1150
|2 StatID
|b Current Contents - Physical, Chemical and Earth Sciences
|d 2025-01-02
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)1050
|2 StatID
|b BIOSIS Previews
|d 2025-01-02
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)1030
|2 StatID
|b Current Contents - Life Sciences
|d 2025-01-02
915 _ _ |a DBCoverage
|0 StatID:(DE-HGF)0150
|2 StatID
|b Web of Science Core Collection
|d 2025-01-02
915 _ _ |a IF >= 15
|0 StatID:(DE-HGF)9915
|2 StatID
|b NAT COMMUN : 2022
|d 2025-01-02
920 1 _ |0 I:(DE-H253)EMBL-User-20120814
|k EMBL-User
|l EMBL-User
|x 0
920 1 _ |0 I:(DE-H253)EMBL-20120731
|k EMBL
|l EMBL
|x 1
980 _ _ |a journal
980 _ _ |a VDB
980 _ _ |a I:(DE-H253)EMBL-User-20120814
980 _ _ |a I:(DE-H253)EMBL-20120731
980 _ _ |a UNRESTRICTED
980 1 _ |a FullTexts
999 C 5 |a 10.1038/ncomms2689
|1 K Inoue
|9 -- missing cx lookup --
|2 Crossref
|u Inoue, K. et al. A light-driven sodium ion pump in marine bacteria. Nat. Commun. 4, 1678 (2013).
|t Nat. Commun.
|v 4
|y 2013
999 C 5 |a 10.1021/acs.chemrev.7b00548
|9 -- missing cx lookup --
|1 H Kandori
|p 10646 -
|2 Crossref
|u Kandori, H., Inoue, K. & Tsunoda, S. P. Light-driven sodium-pumping rhodopsin: A new concept of active transport. Chem. Rev. 118, 10646–10658 (2018).
|t Chem. Rev.
|v 118
|y 2018
999 C 5 |a 10.1021/bi501064n
|9 -- missing cx lookup --
|1 SP Balashov
|p 7549 -
|2 Crossref
|u Balashov, S. P. et al. Light-driven Na+pump from Gillisia limnaea: A high-affinity Na+binding site is formed transiently in the photocycle. Biochemistry 53, 7549–7561 (2014).
|t Biochemistry
|v 53
|y 2014
999 C 5 |a 10.1134/S0006297915040082
|9 -- missing cx lookup --
|1 YV Bertsova
|p 449 -
|2 Crossref
|u Bertsova, Y. V., Bogachev, A. V. & Skulachev, V. P. Proteorhodopsin from Dokdonia sp. PRO95 is a light-driven Na+-pump. Biochem. Mosc. 80, 449–454 (2015).
|t Biochem. Mosc.
|v 80
|y 2015
999 C 5 |a 10.1073/pnas.1403051111
|1 S Yoshizawa
|9 -- missing cx lookup --
|2 Crossref
|u Yoshizawa, S. et al. Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria. Proc. Natl. Acad. Sci. USA. https://doi.org/10.1073/pnas.1403051111 (2014).
|t Proc. Natl. Acad. Sci. USA.
|y 2014
999 C 5 |a 10.1371/journal.pone.0179232
|9 -- missing cx lookup --
|1 SP Tsunoda
|p e0179232 -
|2 Crossref
|u Tsunoda, S. P. et al. Functional characterization of sodium-pumping rhodopsins with different pumping properties. PLOS ONE 12, e0179232 (2017).
|t PLOS ONE
|v 12
|y 2017
999 C 5 |a 10.1038/newbio233149a0
|9 -- missing cx lookup --
|1 D Oesterhelt
|p 149 -
|2 Crossref
|u Oesterhelt, D. & Stoeckenius, W. Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat. New Biol. 233, 149–152 (1971).
|t Nat. New Biol.
|v 233
|y 1971
999 C 5 |a 10.1016/j.jphotobiol.2021.112285
|1 S-G Cho
|9 -- missing cx lookup --
|2 Crossref
|u Cho, S.-G. et al. Discovery of a new light-driven Li+/Na+-pumping rhodopsin with DTG motif. J. Photochem. Photobiol. B 223, 112285 (2021).
|t J. Photochem. Photobiol. B
|v 223
|y 2021
999 C 5 |a 10.1038/nsmb.3002
|9 -- missing cx lookup --
|1 I Gushchin
|p 390 -
|2 Crossref
|u Gushchin, I. et al. Crystal structure of a light-driven sodium pump. Nat. Struct. Mol. Biol. 22, 390–396 (2015).
|t Nat. Struct. Mol. Biol.
|v 22
|y 2015
999 C 5 |a 10.1038/nature14322
|9 -- missing cx lookup --
|1 HE Kato
|p 48 -
|2 Crossref
|u Kato, H. E. et al. Structural basis for Na+ transport mechanism by a light-driven Na+ pump. Nature 521, 48–53 (2015).
|t Nature
|v 521
|y 2015
999 C 5 |a 10.1038/s41598-018-26606-y
|1 M Shibata
|9 -- missing cx lookup --
|2 Crossref
|u Shibata, M. et al. Oligomeric states of microbial rhodopsins determined by high-speed atomic force microscopy and circular dichroic spectroscopy. Sci. Rep. 8, 8262 (2018).
|t Sci. Rep.
|v 8
|y 2018
999 C 5 |a 10.1126/sciadv.aav2671
|9 -- missing cx lookup --
|1 K Kovalev
|p eaav2671 -
|2 Crossref
|u Kovalev, K. et al. Structure and mechanisms of sodium-pumping KR2 rhodopsin. Sci. Adv. 5, eaav2671 (2019).
|t Sci. Adv.
|v 5
|y 2019
999 C 5 |a 10.1371/journal.pone.0166820
|9 -- missing cx lookup --
|1 MR Hoque
|p e0166820 -
|2 Crossref
|u Hoque, M. R. et al. A chimera Na+-pump rhodopsin as an effective optogenetic silencer. PLOS ONE 11, e0166820 (2016).
|t PLOS ONE
|v 11
|y 2016
999 C 5 |a 10.1038/s41586-020-2307-8
|9 -- missing cx lookup --
|1 P Skopintsev
|p 314 -
|2 Crossref
|u Skopintsev, P. et al. Femtosecond-to-millisecond structural changes in a light-driven sodium pump. Nature 583, 314–318 (2020).
|t Nature
|v 583
|y 2020
999 C 5 |a 10.1016/j.jbc.2021.100792
|9 -- missing cx lookup --
|1 T Kato
|p 100792 -
|2 Crossref
|u Kato, T., Tsukamoto, T., Demura, M. & Kikukawa, T. Real-time identification of two substrate-binding intermediates for the light-driven sodium pump rhodopsin. J. Biol. Chem. 296, 100792 (2021).
|t J. Biol. Chem.
|v 296
|y 2021
999 C 5 |a 10.1016/j.jbc.2021.100459
|9 -- missing cx lookup --
|1 M Tsujimura
|p 100459 -
|2 Crossref
|u Tsujimura, M. & Ishikita, H. Identification of intermediate conformations in the photocycle of the light-driven sodium-pumping rhodopsin KR2. J. Biol. Chem. 296, 100459 (2021).
|t J. Biol. Chem.
|v 296
|y 2021
999 C 5 |a 10.1016/j.jbc.2022.102366
|9 -- missing cx lookup --
|1 T Fujisawa
|p 102366 -
|2 Crossref
|u Fujisawa, T., Kinoue, K., Seike, R., Kikukawa, T. & Unno, M. Reisomerization of retinal represents a molecular switch mediating Na+ uptake and release by a bacterial sodium-pumping rhodopsin. J. Biol. Chem. 298, 102366 (2022).
|t J. Biol. Chem.
|v 298
|y 2022
999 C 5 |9 -- missing cx lookup --
|a 10.1021/acs.jpcb.2c08933
|2 Crossref
|u Photochemistry of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2 and Its Implications on Microbial Rhodopsin Research: Retrospective and Perspective | The Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.2c08933.
999 C 5 |a 10.1038/s41467-020-16032-y
|1 K Kovalev
|9 -- missing cx lookup --
|2 Crossref
|u Kovalev, K. et al. Molecular mechanism of light-driven sodium pumping. Nat. Commun. 11, 2137 (2020).
|t Nat. Commun.
|v 11
|y 2020
999 C 5 |a 10.1021/acs.biochem.6b00741
|9 -- missing cx lookup --
|1 R Abe-Yoshizumi
|p 5790 -
|2 Crossref
|u Abe-Yoshizumi, R., Inoue, K., Kato, H. E., Nureki, O. & Kandori, H. Role of Asn112 in a light-driven sodium ion-pumping Rhodopsin. Biochemistry 55, 5790–5797 (2016).
|t Biochemistry
|v 55
|y 2016
999 C 5 |a 10.1002/ange.201504549
|9 -- missing cx lookup --
|1 K Inoue
|p 11698 -
|2 Crossref
|u Inoue, K., Konno, M., Abe‐Yoshizumi, R. & Kandori, H. The role of the NDQ motif in sodium-pumping rhodopsins. Angew. Chem. 127, 11698–11701 (2015).
|t Angew. Chem.
|v 127
|y 2015
999 C 5 |a 10.1038/s41598-018-27690-w
|1 C Grimm
|9 -- missing cx lookup --
|2 Crossref
|u Grimm, C., Silapetere, A., Vogt, A., Bernal Sierra, Y. A. & Hegemann, P. Electrical properties, substrate specificity and optogenetic potential of the engineered light-driven sodium pump eKR2. Sci. Rep. 8, 9316 (2018).
|t Sci. Rep.
|v 8
|y 2018
999 C 5 |a 10.1021/bi048318h
|9 -- missing cx lookup --
|1 R Huber
|p 1800 -
|2 Crossref
|u Huber, R. et al. pH-dependent photoisomerization of retinal in proteorhodopsin. Biochemistry 44, 1800–1806 (2005).
|t Biochemistry
|v 44
|y 2005
999 C 5 |a 10.1021/acs.jpclett.5b01994
|9 -- missing cx lookup --
|1 S Tahara
|p 4481 -
|2 Crossref
|u Tahara, S. et al. Ultrafast photoreaction dynamics of a light-driven sodium-ion-pumping retinal protein from krokinobacter eikastus revealed by femtosecond time-resolved absorption spectroscopy. J. Phys. Chem. Lett. 6, 4481–4486 (2015).
|t J. Phys. Chem. Lett.
|v 6
|y 2015
999 C 5 |a 10.1021/jp4112662
|9 -- missing cx lookup --
|1 Y Sudo
|p 1510 -
|2 Crossref
|u Sudo, Y. et al. The early steps in the photocycle of a photosensor protein sensory rhodopsin I from Salinibacter ruber. J. Phys. Chem. B 118, 1510–1518 (2014).
|t J. Phys. Chem. B
|v 118
|y 2014
999 C 5 |a 10.1021/jp803282s
|9 -- missing cx lookup --
|1 T Nakamura
|p 12795 -
|2 Crossref
|u Nakamura, T. et al. Ultrafast pump−probe study of the primary photoreaction process in pharaonis halorhodopsin: halide ion dependence and isomerization dynamics. J. Phys. Chem. B 112, 12795–12800 (2008).
|t J. Phys. Chem. B
|v 112
|y 2008
999 C 5 |a 10.1126/science.3363359
|9 -- missing cx lookup --
|1 RA Mathies
|p 777 -
|2 Crossref
|u Mathies, R. A., Brito Cruz, C. H., Pollard, W. T. & Shank, C. V. Direct observation of the femtosecond excited-state cis-trans isomerization in Bacteriorhodopsin. Science 240, 777–779 (1988).
|t Science
|v 240
|y 1988
999 C 5 |a 10.1016/j.bpj.2020.12.011
|9 -- missing cx lookup --
|1 P Eberhardt
|p 568 -
|2 Crossref
|u Eberhardt, P. et al. Temperature dependence of the krokinobacter rhodopsin 2 Kinetics. Biophys. J. 120, 568–575 (2021).
|t Biophys. J.
|v 120
|y 2021
999 C 5 |a 10.1002/anie.202103882
|9 -- missing cx lookup --
|1 J Weissbecker
|p 23010 -
|2 Crossref
|u Weissbecker, J. et al. The voltage dependent sidedness of the reprotonation of the retinal schiff base determines the unique inward pumping of xenorhodopsin. Angew. Chem. Int. Ed. 60, 23010–23017 (2021).
|t Angew. Chem. Int. Ed.
|v 60
|y 2021
999 C 5 |a 10.1021/acs.jpclett.1c01436
|9 -- missing cx lookup --
|1 M Asido
|p 6284 -
|2 Crossref
|u Asido, M. et al. Transient near-UV absorption of the light-driven sodium pump Krokinobacter eikastus Rhodopsin 2: A spectroscopic marker for retinal configuration. J. Phys. Chem. Lett. 12, 6284–6291 (2021).
|t J. Phys. Chem. Lett.
|v 12
|y 2021
999 C 5 |a 10.1016/j.jmb.2024.168447
|9 -- missing cx lookup --
|1 M Asido
|p 168447 -
|2 Crossref
|u Asido, M., Boumrifak, C., Weissbecker, J., Bamberg, E. & Wachtveitl, J. Vibrational study of the inward proton pump Xenorhodopsin NsXeR: switch order determines vectoriality. J. Mol. Biol. 436, 168447 (2024).
|t J. Mol. Biol.
|v 436
|y 2024
999 C 5 |a 10.1021/acs.jpclett.5b02371
|9 -- missing cx lookup --
|1 Y Kato
|p 5111 -
|2 Crossref
|u Kato, Y., Inoue, K. & Kandori, H. Kinetic analysis of H+-Na+ selectivity in a light-driven Na+-pumping rhodopsin. J. Phys. Chem. Lett. 6, 5111–5115 (2015).
|t J. Phys. Chem. Lett.
|v 6
|y 2015
999 C 5 |a 10.1073/pnas.1710702114
|9 -- missing cx lookup --
|1 OA Sineshchekov
|p E9512 -
|2 Crossref
|u Sineshchekov, O. A., Govorunova, E. G., Li, H. & Spudich, J. L. Bacteriorhodopsin-like channelrhodopsins: Alternative mechanism for control of cation conductance. Proc. Natl. Acad. Sci. 114, E9512–E9519 (2017).
|t Proc. Natl. Acad. Sci.
|v 114
|y 2017
999 C 5 |a 10.1016/j.bpj.2022.12.023
|9 -- missing cx lookup --
|1 CN Kriebel
|p 1003 -
|2 Crossref
|u Kriebel, C. N. et al. Structural and functional consequences of the H180A mutation of the light-driven sodium pump KR2. Biophys. J. 122, 1003–1017 (2023).
|t Biophys. J.
|v 122
|y 2023
999 C 5 |a 10.1021/acs.jpcb.2c08933
|9 -- missing cx lookup --
|1 M Asido
|p 3766 -
|2 Crossref
|u Asido, M. & Wachtveitl, J. Photochemistry of the light-driven sodium pump krokinobacter eikastus rhodopsin 2 and its implications on microbial rhodopsin research: Retrospective and perspective. J. Phys. Chem. B 127, 3766–3773 (2023).
|t J. Phys. Chem. B
|v 127
|y 2023
999 C 5 |9 -- missing cx lookup --
|a 10.1063/1.4892418
|2 Crossref
|u Harbach, P. H. P., Wormit, M. & Dreuw, A. The third-order algebraic diagrammatic construction method (ADC(3)) for the polarization propagator for closed-shell molecules: Efficient implementation and benchmarkinga). J. Chem. Phys. 141, 064113 (2014).
999 C 5 |a 10.1038/s41594-022-00762-2
|9 -- missing cx lookup --
|1 V Borshchevskiy
|p 440 -
|2 Crossref
|u Borshchevskiy, V. et al. True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins. Nat. Struct. Mol. Biol. 29, 440–450 (2022).
|t Nat. Struct. Mol. Biol.
|v 29
|y 2022
999 C 5 |a 10.1111/febs.13585
|9 -- missing cx lookup --
|1 I Gushchin
|p 1232 -
|2 Crossref
|u Gushchin, I. et al. Structure of the light-driven sodium pump KR2 and its implications for optogenetics. FEBS J 283, 1232–1238 (2016).
|t FEBS J
|v 283
|y 2016
999 C 5 |a 10.1093/nar/gkh340
|9 -- missing cx lookup --
|1 RC Edgar
|p 1792 -
|2 Crossref
|u Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
|t Nucleic Acids Res
|v 32
|y 2004
999 C 5 |a 10.1093/nar/gkw256
|9 -- missing cx lookup --
|1 J Trifinopoulos
|p W232 -
|2 Crossref
|u Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A. & Minh, B. Q. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 44, W232–W235 (2016).
|t Nucleic Acids Res.
|v 44
|y 2016
999 C 5 |a 10.1093/nar/gkab301
|9 -- missing cx lookup --
|1 I Letunic
|p W293 -
|2 Crossref
|u Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
|t Nucleic Acids Res.
|v 49
|y 2021
999 C 5 |a 10.1093/bioinformatics/bts565
|9 -- missing cx lookup --
|1 L Fu
|p 3150 -
|2 Crossref
|u Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).
|t Bioinformatics
|v 28
|y 2012
999 C 5 |a 10.1016/j.pep.2005.01.016
|9 -- missing cx lookup --
|1 FW Studier
|p 207 -
|2 Crossref
|u Studier, F. W. Protein production by auto-induction in high-density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005).
|t Protein Expr. Purif.
|v 41
|y 2005
999 C 5 |a 10.1021/ac504348h
|9 -- missing cx lookup --
|1 C Slavov
|p 2328 -
|2 Crossref
|u Slavov, C., Hartmann, H. & Wachtveitl, J. Implementation and evaluation of data analysis strategies for time-resolved optical spectroscopy. Anal. Chem. 87, 2328–2336 (2015).
|t Anal. Chem.
|v 87
|y 2015
999 C 5 |a 10.1038/nmeth.4169
|9 -- missing cx lookup --
|1 A Punjani
|p 290 -
|2 Crossref
|u Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
|t Nat. Methods
|v 14
|y 2017
999 C 5 |a 10.1038/s41592-019-0575-8
|9 -- missing cx lookup --
|1 T Bepler
|p 1153 -
|2 Crossref
|u Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).
|t Nat. Methods
|v 16
|y 2019
999 C 5 |a 10.1002/pro.3235
|9 -- missing cx lookup --
|1 TD Goddard
|p 14 -
|2 Crossref
|u Goddard, T. D. et al. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
|t Protein Sci.
|v 27
|y 2018
999 C 5 |a 10.1038/s41586-021-03819-2
|9 -- missing cx lookup --
|1 J Jumper
|p 583 -
|2 Crossref
|u Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
|t Nature
|v 596
|y 2021
999 C 5 |a 10.1107/S2059798318006551
|9 -- missing cx lookup --
|1 PV Afonine
|p 531 -
|2 Crossref
|u Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. Sect. Struct. Biol. 74, 531–544 (2018).
|t Acta Crystallogr. Sect. Struct. Biol.
|v 74
|y 2018
999 C 5 |a 10.1107/S2059798318009324
|9 -- missing cx lookup --
|1 PV Afonine
|p 814 -
|2 Crossref
|u Afonine, P. V. et al. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Crystallogr. Sect. Struct. Biol. 74, 814–840 (2018).
|t Acta Crystallogr. Sect. Struct. Biol.
|v 74
|y 2018
999 C 5 |a 10.1107/S0907444910007493
|9 -- missing cx lookup --
|1 P Emsley
|p 486 -
|2 Crossref
|u Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
|t Acta Crystallogr. D Biol. Crystallogr.
|v 66
|y 2010
999 C 5 |a 10.1002/jcc.20084
|9 -- missing cx lookup --
|1 EF Pettersen
|p 1605 -
|2 Crossref
|u Pettersen, E. F. et al. UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
|t J. Comput. Chem.
|v 25
|y 2004
999 C 5 |a 10.1073/pnas.93.25.14532
|9 -- missing cx lookup --
|1 EM Landau
|p 14532 -
|2 Crossref
|u Landau, E. M. & Rosenbusch, J. P. Lipidic cubic phases: A novel concept for the crystallization of membrane proteins. Proc. Natl. Acad. Sci. 93, 14532–14535 (1996).
|t Proc. Natl. Acad. Sci.
|v 93
|y 1996
999 C 5 |a 10.1107/S0907444909047337
|9 -- missing cx lookup --
|1 W Kabsch
|p 125 -
|2 Crossref
|u Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).
|t Acta Crystallogr. D Biol. Crystallogr.
|v 66
|y 2010
999 C 5 |2 Crossref
|u Tickle, I. J. et al. STARANISO. Cambridge, United Kingdom: Global Phasing Ltd. (2018).
999 C 5 |a 10.1107/S0907444909042589
|9 -- missing cx lookup --
|1 A Vagin
|p 22 -
|2 Crossref
|u Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D Biol. Crystallogr. 66, 22–25 (2010).
|t Acta Crystallogr. D Biol. Crystallogr.
|v 66
|y 2010
999 C 5 |a 10.1107/S0907444910045749
|9 -- missing cx lookup --
|1 MD Winn
|p 235 -
|2 Crossref
|u Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).
|t Acta Crystallogr. D Biol. Crystallogr.
|v 67
|y 2011
999 C 5 |a 10.1107/S0907444911001314
|9 -- missing cx lookup --
|1 GN Murshudov
|p 355 -
|2 Crossref
|u Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011).
|t Acta Crystallogr. D Biol. Crystallogr.
|v 67
|y 2011
999 C 5 |a 10.1107/S0907444904019158
|9 -- missing cx lookup --
|1 P Emsley
|p 2126 -
|2 Crossref
|u Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
|t Acta Crystallogr. D Biol. Crystallogr.
|v 60
|y 2004
999 C 5 |a 10.1002/prot.22102
|9 -- missing cx lookup --
|1 DC Bas
|p 765 -
|2 Crossref
|u Bas, D. C., Rogers, D. M. & Jensen, J. H. Very fast prediction and rationalization of pKa values for protein–ligand complexes. Proteins Struct. Funct. Bioinforma. 73, 765–783 (2008).
|t Proteins Struct. Funct. Bioinforma.
|v 73
|y 2008
999 C 5 |a 10.1021/acs.jcim.3c01153
|9 -- missing cx lookup --
|1 DA Case
|p 6183 -
|2 Crossref
|u Case, D. A. et al. AmberTools. J. Chem. Inf. Model. 63, 6183–6191 (2023).
|t J. Chem. Inf. Model.
|v 63
|y 2023
999 C 5 |a 10.1002/wcms.1121
|9 -- missing cx lookup --
|1 R Salomon-Ferrer
|p 198 -
|2 Crossref
|u Salomon-Ferrer, R., Case, D. A. & Walker, R. C. An overview of the Amber biomolecular simulation package. WIREs Comput. Mol. Sci. 3, 198–210 (2013).
|t WIREs Comput. Mol. Sci.
|v 3
|y 2013
999 C 5 |a 10.1016/0022-2836(76)90311-9
|9 -- missing cx lookup --
|1 A Warshel
|p 227 -
|2 Crossref
|u Warshel, A. & Levitt, M. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103, 227–249 (1976).
|t J. Mol. Biol.
|v 103
|y 1976
999 C 5 |9 -- missing cx lookup --
|a 10.1016/S0065-3233(03)66007-9
|2 Crossref
|u Shurki, A. & Warshel, A. Structure⧸Function Correlations of Proteins using MM, QM⧸MM, and Related Approaches: Methods, Concepts, Pitfalls, and Current Progress. In Advances in Protein Chemistry 66 249–313 (Academic Press, 2003).
999 C 5 |a 10.1090/S0025-5718-1980-0572855-7
|9 -- missing cx lookup --
|1 J Nocedal
|p 773 -
|2 Crossref
|u Nocedal, J. Updating quasi-Newton matrices with limited storage. Math. Comput. 35, 773–782 (1980).
|t Math. Comput.
|v 35
|y 1980
999 C 5 |a 10.1103/PhysRevLett.52.997
|9 -- missing cx lookup --
|1 E Runge
|p 997 -
|2 Crossref
|u Runge, E. & Gross, E. K. U. Density-functional theory for time-dependent systems. Phys. Rev. Lett. 52, 997–1000 (1984).
|t Phys. Rev. Lett.
|v 52
|y 1984
999 C 5 |a 10.1016/0009-2614(93)89151-7
|9 -- missing cx lookup --
|1 O Vahtras
|p 514 -
|2 Crossref
|u Vahtras, O., Almlöf, J. & Feyereisen, M. W. Integral approximations for LCAO-SCF calculations. Chem. Phys. Lett. 213, 514–518 (1993).
|t Chem. Phys. Lett.
|v 213
|y 1993
999 C 5 |a 10.1002/jcc.20495
|9 -- missing cx lookup --
|1 S Grimme
|p 1787 -
|2 Crossref
|u Grimme, S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J. Comput. Chem. 27, 1787–1799 (2006).
|t J. Comput. Chem.
|v 27
|y 2006
999 C 5 |a 10.1063/1.456153
|9 -- missing cx lookup --
|1 TH Dunning Jr
|p 1007 -
|2 Crossref
|u Dunning, T. H. Jr Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys. 90, 1007–1023 (1989).
|t J. Chem. Phys.
|v 90
|y 1989
999 C 5 |a 10.1016/0009-2614(82)85016-1
|9 -- missing cx lookup --
|1 JE Hahn
|p 595 -
|2 Crossref
|u Hahn, J. E. et al. Observation of an electric quadrupole transition in the X-ray absorption spectrum of a Cu(II) complex. Chem. Phys. Lett. 88, 595–598 (1982).
|t Chem. Phys. Lett.
|v 88
|y 1982
999 C 5 |a 10.1002/wcms.1606
|9 -- missing cx lookup --
|1 F Neese
|p e1606 -
|2 Crossref
|u Neese, F. Software update: The ORCA program system—Version 5.0. WIREs Comput. Mol. Sci. 12, e1606 (2022).
|t WIREs Comput. Mol. Sci.
|v 12
|y 2022
999 C 5 |a 10.1063/5.0004635
|9 -- missing cx lookup --
|1 SG Balasubramani
|p 184107 -
|2 Crossref
|u Balasubramani, S. G. et al. TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations. J. Chem. Phys. 152, 184107 (2020).
|t J. Chem. Phys.
|v 152
|y 2020


LibraryCollectionCLSMajorCLSMinorLanguageAuthor
Marc 21