Home > Publications database > A subgroup of light-driven sodium pumps with an additional Schiff base counterion > print |
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 |
Library | Collection | CLSMajor | CLSMinor | Language | Author |
---|