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000607037 1001_ $$0P:(DE-HGF)0$$aPodoliak, E.$$b0
000607037 245__ $$aA subgroup of light-driven sodium pumps with an additional Schiff base counterion
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000607037 520__ $$aLight-driven sodium pumps (NaRs) are unique ion-transporting microbial rhodopsins. The major group of NaRs is characterized by an NDQ motif and has two aspartic acid residues in the central region essential for sodium transport. Here we identify a subgroup of the NDQ rhodopsins bearing an additional glutamic acid residue in the close vicinity to the retinal Schiff base. We thoroughly characterize a member of this subgroup, namely the protein ErNaR from Erythrobacter sp. HL-111 and show that the additional glutamic acid results in almost complete loss of pH sensitivity for sodium-pumping activity, which is in contrast to previously studied NaRs. ErNaR is capable of transporting sodium efficiently even at acidic pH levels. X-ray crystallography and single particle cryo-electron microscopy reveal that the additional glutamic acid residue mediates the connection between the other two Schiff base counterions and strongly interacts with the aspartic acid of the characteristic NDQ motif. Hence, it reduces its pKa. Our findings shed light on a subgroup of NaRs and might serve as a basis for their rational optimization for optogenetics.
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000607037 7001_ $$0P:(DE-HGF)0$$aLamm, G. H. U.$$b1
000607037 7001_ $$aMarin, E.$$b2
000607037 7001_ $$aSchellbach, A. V.$$b3
000607037 7001_ $$0P:(DE-HGF)0$$aFedotov, D. A.$$b4
000607037 7001_ $$0P:(DE-HGF)0$$aStetsenko, A.$$b5
000607037 7001_ $$00000-0003-3181-0236$$aAsido, M.$$b6
000607037 7001_ $$aMaliar, N.$$b7
000607037 7001_ $$0P:(DE-H253)PIP1007425$$aBourenkov, G.$$b8
000607037 7001_ $$00000-0001-8471-8041$$aBalandin, T.$$b9
000607037 7001_ $$aBaeken, C.$$b10
000607037 7001_ $$aAstashkin, R.$$b11
000607037 7001_ $$0P:(DE-H253)PIP1005932$$aSchneider, T. R.$$b12
000607037 7001_ $$00000-0002-6982-4660$$aBateman, A.$$b13
000607037 7001_ $$00000-0002-8496-8240$$aWachtveitl, J.$$b14
000607037 7001_ $$00000-0001-8536-6869$$aSchapiro, I.$$b15
000607037 7001_ $$00000-0001-7517-8944$$aBusskamp, V.$$b16
000607037 7001_ $$0P:(DE-HGF)0$$aGuskov, A.$$b17
000607037 7001_ $$aGordeliy, V.$$b18
000607037 7001_ $$0P:(DE-HGF)0$$aAlekseev, A.$$b19$$eCorresponding author
000607037 7001_ $$0P:(DE-HGF)0$$aKovalev, K.$$b20$$eCorresponding author
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000607037 999C5 $$1K Inoue$$2Crossref$$9-- missing cx lookup --$$a10.1038/ncomms2689$$tNat. Commun.$$uInoue, K. et al. A light-driven sodium ion pump in marine bacteria. Nat. Commun. 4, 1678 (2013).$$v4$$y2013
000607037 999C5 $$1H Kandori$$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.chemrev.7b00548$$p10646 -$$tChem. Rev.$$uKandori, H., Inoue, K. & Tsunoda, S. P. Light-driven sodium-pumping rhodopsin: A new concept of active transport. Chem. Rev. 118, 10646–10658 (2018).$$v118$$y2018
000607037 999C5 $$1SP Balashov$$2Crossref$$9-- missing cx lookup --$$a10.1021/bi501064n$$p7549 -$$tBiochemistry$$uBalashov, S. P. et al. Light-driven Na+pump from Gillisia limnaea: A high-affinity Na+binding site is formed transiently in the photocycle. Biochemistry 53, 7549–7561 (2014).$$v53$$y2014
000607037 999C5 $$1YV Bertsova$$2Crossref$$9-- missing cx lookup --$$a10.1134/S0006297915040082$$p449 -$$tBiochem. Mosc.$$uBertsova, 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).$$v80$$y2015
000607037 999C5 $$1S Yoshizawa$$2Crossref$$9-- missing cx lookup --$$a10.1073/pnas.1403051111$$tProc. Natl. Acad. Sci. USA.$$uYoshizawa, 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).$$y2014
000607037 999C5 $$1SP Tsunoda$$2Crossref$$9-- missing cx lookup --$$a10.1371/journal.pone.0179232$$pe0179232 -$$tPLOS ONE$$uTsunoda, S. P. et al. Functional characterization of sodium-pumping rhodopsins with different pumping properties. PLOS ONE 12, e0179232 (2017).$$v12$$y2017
000607037 999C5 $$1D Oesterhelt$$2Crossref$$9-- missing cx lookup --$$a10.1038/newbio233149a0$$p149 -$$tNat. New Biol.$$uOesterhelt, D. & Stoeckenius, W. Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat. New Biol. 233, 149–152 (1971).$$v233$$y1971
000607037 999C5 $$1S-G Cho$$2Crossref$$9-- missing cx lookup --$$a10.1016/j.jphotobiol.2021.112285$$tJ. Photochem. Photobiol. B$$uCho, S.-G. et al. Discovery of a new light-driven Li+/Na+-pumping rhodopsin with DTG motif. J. Photochem. Photobiol. B 223, 112285 (2021).$$v223$$y2021
000607037 999C5 $$1I Gushchin$$2Crossref$$9-- missing cx lookup --$$a10.1038/nsmb.3002$$p390 -$$tNat. Struct. Mol. Biol.$$uGushchin, I. et al. Crystal structure of a light-driven sodium pump. Nat. Struct. Mol. Biol. 22, 390–396 (2015).$$v22$$y2015
000607037 999C5 $$1HE Kato$$2Crossref$$9-- missing cx lookup --$$a10.1038/nature14322$$p48 -$$tNature$$uKato, H. E. et al. Structural basis for Na+ transport mechanism by a light-driven Na+ pump. Nature 521, 48–53 (2015).$$v521$$y2015
000607037 999C5 $$1M Shibata$$2Crossref$$9-- missing cx lookup --$$a10.1038/s41598-018-26606-y$$tSci. Rep.$$uShibata, M. et al. Oligomeric states of microbial rhodopsins determined by high-speed atomic force microscopy and circular dichroic spectroscopy. Sci. Rep. 8, 8262 (2018).$$v8$$y2018
000607037 999C5 $$1K Kovalev$$2Crossref$$9-- missing cx lookup --$$a10.1126/sciadv.aav2671$$peaav2671 -$$tSci. Adv.$$uKovalev, K. et al. Structure and mechanisms of sodium-pumping KR2 rhodopsin. Sci. Adv. 5, eaav2671 (2019).$$v5$$y2019
000607037 999C5 $$1MR Hoque$$2Crossref$$9-- missing cx lookup --$$a10.1371/journal.pone.0166820$$pe0166820 -$$tPLOS ONE$$uHoque, M. R. et al. A chimera Na+-pump rhodopsin as an effective optogenetic silencer. PLOS ONE 11, e0166820 (2016).$$v11$$y2016
000607037 999C5 $$1P Skopintsev$$2Crossref$$9-- missing cx lookup --$$a10.1038/s41586-020-2307-8$$p314 -$$tNature$$uSkopintsev, P. et al. Femtosecond-to-millisecond structural changes in a light-driven sodium pump. Nature 583, 314–318 (2020).$$v583$$y2020
000607037 999C5 $$1T Kato$$2Crossref$$9-- missing cx lookup --$$a10.1016/j.jbc.2021.100792$$p100792 -$$tJ. Biol. Chem.$$uKato, T., Tsukamoto, T., Demura, M. & Kikukawa, T. Real-time identification of two substrate-binding intermediates for the light-driven sodium pump rhodopsin. J. Biol. Chem. 296, 100792 (2021).$$v296$$y2021
000607037 999C5 $$1M Tsujimura$$2Crossref$$9-- missing cx lookup --$$a10.1016/j.jbc.2021.100459$$p100459 -$$tJ. Biol. Chem.$$uTsujimura, M. & Ishikita, H. Identification of intermediate conformations in the photocycle of the light-driven sodium-pumping rhodopsin KR2. J. Biol. Chem. 296, 100459 (2021).$$v296$$y2021
000607037 999C5 $$1T Fujisawa$$2Crossref$$9-- missing cx lookup --$$a10.1016/j.jbc.2022.102366$$p102366 -$$tJ. Biol. Chem.$$uFujisawa, T., Kinoue, K., Seike, R., Kikukawa, T. & Unno, M. Reisomerization of retinal represents a molecular switch mediating Na+ uptake and release by a bacterial sodium-pumping rhodopsin. J. Biol. Chem. 298, 102366 (2022).$$v298$$y2022
000607037 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.jpcb.2c08933$$uPhotochemistry of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2 and Its Implications on Microbial Rhodopsin Research: Retrospective and Perspective | The Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.2c08933.
000607037 999C5 $$1K Kovalev$$2Crossref$$9-- missing cx lookup --$$a10.1038/s41467-020-16032-y$$tNat. Commun.$$uKovalev, K. et al. Molecular mechanism of light-driven sodium pumping. Nat. Commun. 11, 2137 (2020).$$v11$$y2020
000607037 999C5 $$1R Abe-Yoshizumi$$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.biochem.6b00741$$p5790 -$$tBiochemistry$$uAbe-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).$$v55$$y2016
000607037 999C5 $$1K Inoue$$2Crossref$$9-- missing cx lookup --$$a10.1002/ange.201504549$$p11698 -$$tAngew. Chem.$$uInoue, K., Konno, M., Abe‐Yoshizumi, R. & Kandori, H. The role of the NDQ motif in sodium-pumping rhodopsins. Angew. Chem. 127, 11698–11701 (2015).$$v127$$y2015
000607037 999C5 $$1C Grimm$$2Crossref$$9-- missing cx lookup --$$a10.1038/s41598-018-27690-w$$tSci. Rep.$$uGrimm, C., Silapetere, A., Vogt, A., Bernal Sierra, Y. A. & Hegemann, P. Electrical properties, substrate specificity and optogenetic potential of the engineered light-driven sodium pump eKR2. Sci. Rep. 8, 9316 (2018).$$v8$$y2018
000607037 999C5 $$1R Huber$$2Crossref$$9-- missing cx lookup --$$a10.1021/bi048318h$$p1800 -$$tBiochemistry$$uHuber, R. et al. pH-dependent photoisomerization of retinal in proteorhodopsin. Biochemistry 44, 1800–1806 (2005).$$v44$$y2005
000607037 999C5 $$1S Tahara$$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.jpclett.5b01994$$p4481 -$$tJ. Phys. Chem. Lett.$$uTahara, S. et al. Ultrafast photoreaction dynamics of a light-driven sodium-ion-pumping retinal protein from krokinobacter eikastus revealed by femtosecond time-resolved absorption spectroscopy. J. Phys. Chem. Lett. 6, 4481–4486 (2015).$$v6$$y2015
000607037 999C5 $$1Y Sudo$$2Crossref$$9-- missing cx lookup --$$a10.1021/jp4112662$$p1510 -$$tJ. Phys. Chem. B$$uSudo, 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).$$v118$$y2014
000607037 999C5 $$1T Nakamura$$2Crossref$$9-- missing cx lookup --$$a10.1021/jp803282s$$p12795 -$$tJ. Phys. Chem. B$$uNakamura, T. et al. Ultrafast pump−probe study of the primary photoreaction process in pharaonis halorhodopsin: halide ion dependence and isomerization dynamics. J. Phys. Chem. B 112, 12795–12800 (2008).$$v112$$y2008
000607037 999C5 $$1RA Mathies$$2Crossref$$9-- missing cx lookup --$$a10.1126/science.3363359$$p777 -$$tScience$$uMathies, 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).$$v240$$y1988
000607037 999C5 $$1P Eberhardt$$2Crossref$$9-- missing cx lookup --$$a10.1016/j.bpj.2020.12.011$$p568 -$$tBiophys. J.$$uEberhardt, P. et al. Temperature dependence of the krokinobacter rhodopsin 2 Kinetics. Biophys. J. 120, 568–575 (2021).$$v120$$y2021
000607037 999C5 $$1J Weissbecker$$2Crossref$$9-- missing cx lookup --$$a10.1002/anie.202103882$$p23010 -$$tAngew. Chem. Int. Ed.$$uWeissbecker, 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).$$v60$$y2021
000607037 999C5 $$1M Asido$$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.jpclett.1c01436$$p6284 -$$tJ. Phys. Chem. Lett.$$uAsido, M. et al. Transient near-UV absorption of the light-driven sodium pump Krokinobacter eikastus Rhodopsin 2: A spectroscopic marker for retinal configuration. J. Phys. Chem. Lett. 12, 6284–6291 (2021).$$v12$$y2021
000607037 999C5 $$1M Asido$$2Crossref$$9-- missing cx lookup --$$a10.1016/j.jmb.2024.168447$$p168447 -$$tJ. Mol. Biol.$$uAsido, 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).$$v436$$y2024
000607037 999C5 $$1Y Kato$$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.jpclett.5b02371$$p5111 -$$tJ. Phys. Chem. Lett.$$uKato, Y., Inoue, K. & Kandori, H. Kinetic analysis of H+-Na+ selectivity in a light-driven Na+-pumping rhodopsin. J. Phys. Chem. Lett. 6, 5111–5115 (2015).$$v6$$y2015
000607037 999C5 $$1OA Sineshchekov$$2Crossref$$9-- missing cx lookup --$$a10.1073/pnas.1710702114$$pE9512 -$$tProc. Natl. Acad. Sci.$$uSineshchekov, 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).$$v114$$y2017
000607037 999C5 $$1CN Kriebel$$2Crossref$$9-- missing cx lookup --$$a10.1016/j.bpj.2022.12.023$$p1003 -$$tBiophys. J.$$uKriebel, C. N. et al. Structural and functional consequences of the H180A mutation of the light-driven sodium pump KR2. Biophys. J. 122, 1003–1017 (2023).$$v122$$y2023
000607037 999C5 $$1M Asido$$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.jpcb.2c08933$$p3766 -$$tJ. Phys. Chem. B$$uAsido, 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).$$v127$$y2023
000607037 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1063/1.4892418$$uHarbach, 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).
000607037 999C5 $$1V Borshchevskiy$$2Crossref$$9-- missing cx lookup --$$a10.1038/s41594-022-00762-2$$p440 -$$tNat. Struct. Mol. Biol.$$uBorshchevskiy, V. et al. True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins. Nat. Struct. Mol. Biol. 29, 440–450 (2022).$$v29$$y2022
000607037 999C5 $$1I Gushchin$$2Crossref$$9-- missing cx lookup --$$a10.1111/febs.13585$$p1232 -$$tFEBS J$$uGushchin, I. et al. Structure of the light-driven sodium pump KR2 and its implications for optogenetics. FEBS J 283, 1232–1238 (2016).$$v283$$y2016
000607037 999C5 $$1RC Edgar$$2Crossref$$9-- missing cx lookup --$$a10.1093/nar/gkh340$$p1792 -$$tNucleic Acids Res$$uEdgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).$$v32$$y2004
000607037 999C5 $$1J Trifinopoulos$$2Crossref$$9-- missing cx lookup --$$a10.1093/nar/gkw256$$pW232 -$$tNucleic Acids Res.$$uTrifinopoulos, 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).$$v44$$y2016
000607037 999C5 $$1I Letunic$$2Crossref$$9-- missing cx lookup --$$a10.1093/nar/gkab301$$pW293 -$$tNucleic Acids Res.$$uLetunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).$$v49$$y2021
000607037 999C5 $$1L Fu$$2Crossref$$9-- missing cx lookup --$$a10.1093/bioinformatics/bts565$$p3150 -$$tBioinformatics$$uFu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).$$v28$$y2012
000607037 999C5 $$1FW Studier$$2Crossref$$9-- missing cx lookup --$$a10.1016/j.pep.2005.01.016$$p207 -$$tProtein Expr. Purif.$$uStudier, F. W. Protein production by auto-induction in high-density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005).$$v41$$y2005
000607037 999C5 $$1C Slavov$$2Crossref$$9-- missing cx lookup --$$a10.1021/ac504348h$$p2328 -$$tAnal. Chem.$$uSlavov, C., Hartmann, H. & Wachtveitl, J. Implementation and evaluation of data analysis strategies for time-resolved optical spectroscopy. Anal. Chem. 87, 2328–2336 (2015).$$v87$$y2015
000607037 999C5 $$1A Punjani$$2Crossref$$9-- missing cx lookup --$$a10.1038/nmeth.4169$$p290 -$$tNat. Methods$$uPunjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).$$v14$$y2017
000607037 999C5 $$1T Bepler$$2Crossref$$9-- missing cx lookup --$$a10.1038/s41592-019-0575-8$$p1153 -$$tNat. Methods$$uBepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).$$v16$$y2019
000607037 999C5 $$1TD Goddard$$2Crossref$$9-- missing cx lookup --$$a10.1002/pro.3235$$p14 -$$tProtein Sci.$$uGoddard, T. D. et al. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).$$v27$$y2018
000607037 999C5 $$1J Jumper$$2Crossref$$9-- missing cx lookup --$$a10.1038/s41586-021-03819-2$$p583 -$$tNature$$uJumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).$$v596$$y2021
000607037 999C5 $$1PV Afonine$$2Crossref$$9-- missing cx lookup --$$a10.1107/S2059798318006551$$p531 -$$tActa Crystallogr. Sect. Struct. Biol.$$uAfonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. Sect. Struct. Biol. 74, 531–544 (2018).$$v74$$y2018
000607037 999C5 $$1PV Afonine$$2Crossref$$9-- missing cx lookup --$$a10.1107/S2059798318009324$$p814 -$$tActa Crystallogr. Sect. Struct. Biol.$$uAfonine, 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).$$v74$$y2018
000607037 999C5 $$1P Emsley$$2Crossref$$9-- missing cx lookup --$$a10.1107/S0907444910007493$$p486 -$$tActa Crystallogr. D Biol. Crystallogr.$$uEmsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).$$v66$$y2010
000607037 999C5 $$1EF Pettersen$$2Crossref$$9-- missing cx lookup --$$a10.1002/jcc.20084$$p1605 -$$tJ. Comput. Chem.$$uPettersen, E. F. et al. UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).$$v25$$y2004
000607037 999C5 $$1EM Landau$$2Crossref$$9-- missing cx lookup --$$a10.1073/pnas.93.25.14532$$p14532 -$$tProc. Natl. Acad. Sci.$$uLandau, E. M. & Rosenbusch, J. P. Lipidic cubic phases: A novel concept for the crystallization of membrane proteins. Proc. Natl. Acad. Sci. 93, 14532–14535 (1996).$$v93$$y1996
000607037 999C5 $$1W Kabsch$$2Crossref$$9-- missing cx lookup --$$a10.1107/S0907444909047337$$p125 -$$tActa Crystallogr. D Biol. Crystallogr.$$uKabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).$$v66$$y2010
000607037 999C5 $$2Crossref$$uTickle, I. J. et al. STARANISO. Cambridge, United Kingdom: Global Phasing Ltd. (2018).
000607037 999C5 $$1A Vagin$$2Crossref$$9-- missing cx lookup --$$a10.1107/S0907444909042589$$p22 -$$tActa Crystallogr. D Biol. Crystallogr.$$uVagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D Biol. Crystallogr. 66, 22–25 (2010).$$v66$$y2010
000607037 999C5 $$1MD Winn$$2Crossref$$9-- missing cx lookup --$$a10.1107/S0907444910045749$$p235 -$$tActa Crystallogr. D Biol. Crystallogr.$$uWinn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).$$v67$$y2011
000607037 999C5 $$1GN Murshudov$$2Crossref$$9-- missing cx lookup --$$a10.1107/S0907444911001314$$p355 -$$tActa Crystallogr. D Biol. Crystallogr.$$uMurshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011).$$v67$$y2011
000607037 999C5 $$1P Emsley$$2Crossref$$9-- missing cx lookup --$$a10.1107/S0907444904019158$$p2126 -$$tActa Crystallogr. D Biol. Crystallogr.$$uEmsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).$$v60$$y2004
000607037 999C5 $$1DC Bas$$2Crossref$$9-- missing cx lookup --$$a10.1002/prot.22102$$p765 -$$tProteins Struct. Funct. Bioinforma.$$uBas, D. C., Rogers, D. M. & Jensen, J. H. Very fast prediction and rationalization of pKa values for protein–ligand complexes. Proteins Struct. Funct. Bioinforma. 73, 765–783 (2008).$$v73$$y2008
000607037 999C5 $$1DA Case$$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.jcim.3c01153$$p6183 -$$tJ. Chem. Inf. Model.$$uCase, D. A. et al. AmberTools. J. Chem. Inf. Model. 63, 6183–6191 (2023).$$v63$$y2023
000607037 999C5 $$1R Salomon-Ferrer$$2Crossref$$9-- missing cx lookup --$$a10.1002/wcms.1121$$p198 -$$tWIREs Comput. Mol. Sci.$$uSalomon-Ferrer, R., Case, D. A. & Walker, R. C. An overview of the Amber biomolecular simulation package. WIREs Comput. Mol. Sci. 3, 198–210 (2013).$$v3$$y2013
000607037 999C5 $$1A Warshel$$2Crossref$$9-- missing cx lookup --$$a10.1016/0022-2836(76)90311-9$$p227 -$$tJ. Mol. Biol.$$uWarshel, 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).$$v103$$y1976
000607037 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/S0065-3233(03)66007-9$$uShurki, 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).
000607037 999C5 $$1J Nocedal$$2Crossref$$9-- missing cx lookup --$$a10.1090/S0025-5718-1980-0572855-7$$p773 -$$tMath. Comput.$$uNocedal, J. Updating quasi-Newton matrices with limited storage. Math. Comput. 35, 773–782 (1980).$$v35$$y1980
000607037 999C5 $$1E Runge$$2Crossref$$9-- missing cx lookup --$$a10.1103/PhysRevLett.52.997$$p997 -$$tPhys. Rev. Lett.$$uRunge, E. & Gross, E. K. U. Density-functional theory for time-dependent systems. Phys. Rev. Lett. 52, 997–1000 (1984).$$v52$$y1984
000607037 999C5 $$1O Vahtras$$2Crossref$$9-- missing cx lookup --$$a10.1016/0009-2614(93)89151-7$$p514 -$$tChem. Phys. Lett.$$uVahtras, O., Almlöf, J. & Feyereisen, M. W. Integral approximations for LCAO-SCF calculations. Chem. Phys. Lett. 213, 514–518 (1993).$$v213$$y1993
000607037 999C5 $$1S Grimme$$2Crossref$$9-- missing cx lookup --$$a10.1002/jcc.20495$$p1787 -$$tJ. Comput. Chem.$$uGrimme, S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J. Comput. Chem. 27, 1787–1799 (2006).$$v27$$y2006
000607037 999C5 $$1TH Dunning Jr$$2Crossref$$9-- missing cx lookup --$$a10.1063/1.456153$$p1007 -$$tJ. Chem. Phys.$$uDunning, T. H. Jr Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys. 90, 1007–1023 (1989).$$v90$$y1989
000607037 999C5 $$1JE Hahn$$2Crossref$$9-- missing cx lookup --$$a10.1016/0009-2614(82)85016-1$$p595 -$$tChem. Phys. Lett.$$uHahn, 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).$$v88$$y1982
000607037 999C5 $$1F Neese$$2Crossref$$9-- missing cx lookup --$$a10.1002/wcms.1606$$pe1606 -$$tWIREs Comput. Mol. Sci.$$uNeese, F. Software update: The ORCA program system—Version 5.0. WIREs Comput. Mol. Sci. 12, e1606 (2022).$$v12$$y2022
000607037 999C5 $$1SG Balasubramani$$2Crossref$$9-- missing cx lookup --$$a10.1063/5.0004635$$p184107 -$$tJ. Chem. Phys.$$uBalasubramani, S. G. et al. TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations. J. Chem. Phys. 152, 184107 (2020).$$v152$$y2020