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Volumn 1837, Issue 5, 2014, Pages 643-655

Channelrhodopsins: A bioinformatics perspective

Author keywords

Bioinformatics; Channelrhodopsin; Membrane protein; Protein structure and dynamics

Indexed keywords

CALCIUM CHANNEL L TYPE; CALCIUM CHANNEL T TYPE; CHANNELRHODOPSIN; RHODOPSIN; UNCLASSIFIED DRUG;

EID: 84897112563     PISSN: 00052728     EISSN: 18792650     Source Type: Journal    
DOI: 10.1016/j.bbabio.2013.11.005     Document Type: Review
Times cited : (13)

References (107)
  • 1
    • 34247548430 scopus 로고    scopus 로고
    • Channelrhodopsin-2-assisted circuit mapping of long-range callosal projections
    • DOI 10.1038/nn1891, PII NN1891
    • L. Petreanu, D. Huber, A. Sobczyk, and K. Svoboda Channelrhodopsin-2- assisted circuit mapping of long-range callosal projections Nat. Neurosci. 10 2007 663 668 (Pubitemid 46652447)
    • (2007) Nature Neuroscience , vol.10 , Issue.5 , pp. 663-668
    • Petreanu, L.1    Huber, D.2    Sobczyk, A.3    Svoboda, K.4
  • 3
    • 84873298804 scopus 로고    scopus 로고
    • From channelrhodopsins to optogenetics
    • P. Hegemann, and G. Nagel From channelrhodopsins to optogenetics EMBO Mol. Med. 5 2013 173 176
    • (2013) EMBO Mol. Med. , vol.5 , pp. 173-176
    • Hegemann, P.1    Nagel, G.2
  • 5
    • 0037189362 scopus 로고    scopus 로고
    • Channelrhodopsin-1: A light-gated proton channel in green algae
    • DOI 10.1126/science.1072068
    • G. Nagel, D. Ollig, M. Fuhrmann, S. Kateriya, A.M. Musti, E. Bamberg, and P. Hegemann Channelrhodopsin-1: a light-gated proton channel in green algae Science 296 2002 2395 2398 (Pubitemid 34734214)
    • (2002) Science , vol.296 , Issue.5577 , pp. 2395-2398
    • Nagel, G.1    Ollig, D.2    Fuhrmann, M.3    Kateriya, S.4    Musti, A.M.5    Bamberg, E.6    Hegemann, P.7
  • 7
    • 29044433616 scopus 로고    scopus 로고
    • Light activation of Channelrhodopsin-2 in excitable cells of caenorhabditis elegans triggers rapid behavioral responses
    • DOI 10.1016/j.cub.2005.11.032, PII S0960982205014077
    • G. Nagel, M. Brauner, J.F. Liewald, N. Adeishvili, E. Bamberg, and A. Gooschalk Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral response Curr. Biol. 15 2005 2279 2284 (Pubitemid 41790623)
    • (2005) Current Biology , vol.15 , Issue.24 , pp. 2279-2284
    • Nagel, G.1    Brauner, M.2    Liewald, J.F.3    Adeishvili, N.4    Bamberg, E.5    Gottschalk, A.6
  • 8
    • 71749109952 scopus 로고    scopus 로고
    • The retinal structure of channelrhodopsin-2 assessed by resonance Raman spectroscopy
    • M. Nack, I. Radu, C. Bamann, E. Bamberg, and J. Heberle The retinal structure of channelrhodopsin-2 assessed by resonance Raman spectroscopy FEBS Lett. 583 2009 3676 3680
    • (2009) FEBS Lett. , vol.583 , pp. 3676-3680
    • Nack, M.1    Radu, I.2    Bamann, C.3    Bamberg, E.4    Heberle, J.5
  • 10
    • 58049216319 scopus 로고    scopus 로고
    • Monitoring light-induced structural changes of channelrhodopsin-2 by UV-visible and Fourier transform infrared spectroscopy
    • 350033-35041
    • E. Ritter, K. Stehfest, A. Berndt, P. Hegemann, and F. Bartl Monitoring light-induced structural changes of channelrhodopsin-2 by UV-visible and Fourier transform infrared spectroscopy J. Biol. Chem. 283 2008 350033-35041
    • (2008) J. Biol. Chem. , vol.283
    • Ritter, E.1    Stehfest, K.2    Berndt, A.3    Hegemann, P.4    Bartl, F.5
  • 14
    • 67349185408 scopus 로고    scopus 로고
    • Ion channels versus ion pumps: The principal difference, in principle
    • D.C. Gadsby Ion channels versus ion pumps: the principal difference, in principle Nat. Rev. Mol. Cell Biol. 10 2009 344 352
    • (2009) Nat. Rev. Mol. Cell Biol. , vol.10 , pp. 344-352
    • Gadsby, D.C.1
  • 15
    • 84874187340 scopus 로고    scopus 로고
    • The thin line between channels and pumps
    • L.S. Brown The thin line between channels and pumps Biophys. J. 104 2013 739 740
    • (2013) Biophys. J. , vol.104 , pp. 739-740
    • Brown, L.S.1
  • 18
    • 77952304469 scopus 로고    scopus 로고
    • The branched photocycle of the slow-cycling channelrhodopsin-2 mutant C128T
    • K. Stehfest, E. Ritter, A. Berndt, F. Bartl, and P. Hegemann The branched photocycle of the slow-cycling channelrhodopsin-2 mutant C128T J. Mol. Biol. 398 2010 690 702
    • (2010) J. Mol. Biol. , vol.398 , pp. 690-702
    • Stehfest, K.1    Ritter, E.2    Berndt, A.3    Bartl, F.4    Hegemann, P.5
  • 19
    • 75349085542 scopus 로고    scopus 로고
    • Structural guidance of the photocycle of channelrhodopsin-2 by an interhelical hydrogen bond
    • C. Bamann, R. Gueta, S. Kleinlogel, G. Nagel, and E. Bamberg Structural guidance of the photocycle of channelrhodopsin-2 by an interhelical hydrogen bond Biochemistry 49 2010 267 278
    • (2010) Biochemistry , vol.49 , pp. 267-278
    • Bamann, C.1    Gueta, R.2    Kleinlogel, S.3    Nagel, G.4    Bamberg, E.5
  • 21
    • 84855190225 scopus 로고    scopus 로고
    • New channelrhodopsins with a red-shifted spectrum and rapid kinetics from Mesostigma viride
    • 1-9
    • E.G. Govorunova, E.N. Spudich, C.E. Lane, O.A. Sineshchekov, and J.L. Spudich New channelrhodopsins with a red-shifted spectrum and rapid kinetics from Mesostigma viride mBio 2 2011 e00115-11 1-9
    • (2011) MBio , vol.2 , pp. 00115-00211
    • Govorunova, E.G.1    Spudich, E.N.2    Lane, C.E.3    Sineshchekov, O.A.4    Spudich, J.L.5
  • 22
    • 80052461748 scopus 로고    scopus 로고
    • Rectification of the channelrhodopsin early conductance
    • D. Gradmann, A. Berndt, F. Schneider, and P. Hegemann Rectification of the channelrhodopsin early conductance Biophys. J. 101 2011 1057 1068
    • (2011) Biophys. J. , vol.101 , pp. 1057-1068
    • Gradmann, D.1    Berndt, A.2    Schneider, F.3    Hegemann, P.4
  • 23
    • 65549100187 scopus 로고    scopus 로고
    • Characterization of engineered channelrhodopsin variants with improved properties and kinetics
    • J.Y. Lin, M.Z. Lin, P. Steinbach, and R.Y. Tsien Characterization of engineered channelrhodopsin variants with improved properties and kinetics Biophys. J. 96 2009 1803 1814
    • (2009) Biophys. J. , vol.96 , pp. 1803-1814
    • Lin, J.Y.1    Lin, M.Z.2    Steinbach, P.3    Tsien, R.Y.4
  • 25
    • 84869784276 scopus 로고    scopus 로고
    • Re-introduction of transmembrane serine residues reduce the minimum pore diameter of channelrhodopsin-2
    • R. Richards, and R.E. Dempski Re-introduction of transmembrane serine residues reduce the minimum pore diameter of channelrhodopsin-2 PLoS One 7 2012 e50018
    • (2012) PLoS One , vol.7 , pp. 50018
    • Richards, R.1    Dempski, R.E.2
  • 26
    • 81055155876 scopus 로고    scopus 로고
    • Projection structure of channelrhodopsin-2 at 6 Å resolution by electron crystallography
    • M. Müller, C. Bamann, E. Bamberg, and W. Kühlbrandt Projection structure of channelrhodopsin-2 at 6 Å resolution by electron crystallography J. Mol. Biol. 414 2011 86 95
    • (2011) J. Mol. Biol. , vol.414 , pp. 86-95
    • Müller, M.1    Bamann, C.2    Bamberg, E.3    Kühlbrandt, W.4
  • 28
    • 60749095002 scopus 로고    scopus 로고
    • Multiple sequence alignment using ClustalW and ClustalX
    • (Chapter 2, Unit 2.3).
    • J.D. Thomson, J.D. Gibson, and D.G. Higgins Multiple sequence alignment using ClustalW and ClustalX Curr. Protoc. Bioinforma. 2002 (Chapter 2, Unit 2.3). http://dx.doi.org/10.1002/0471250953.bi0203s00
    • (2002) Curr. Protoc. Bioinforma.
    • Thomson, J.D.1    Gibson, J.D.2    Higgins, D.G.3
  • 29
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • DOI 10.1093/bib/bbn013, Special Issue: Critical Technologies for Bioinformatics
    • K. Katoh, and H. Toh Recent developments in the MAFFT multiple sequence alignment program Brief Bioinform. 9 2008 286 298 (Pubitemid 351890825)
    • (2008) Briefings in Bioinformatics , vol.9 , Issue.4 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 30
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • R.C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797 (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 31
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • C. Notredame, D.G. Higgins, and J. Heringa T-Coffee: a novel method for fast and accurate multiple sequence alignment J. Mol. Biol. 302 2000 205 217
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 32
    • 0021160693 scopus 로고
    • The alignment of sets of sequences and the construction of phyletic trees: An integrated method
    • P. Hogeweg, and B. Hesper The alignment of sets of sequences and the construction of phyletic trees: An integrated method J. Mol. Evol. 20 1984 175 186 (Pubitemid 14058167)
    • (1984) Journal of Molecular Evolution , vol.20 , Issue.2 , pp. 175-186
    • Hogeweg, P.1    Hesper, B.2
  • 33
    • 33748940447 scopus 로고    scopus 로고
    • Analysis and comparison of benchmarks for multiple sequence alignment
    • G. Blackshields, I.M. Wallace, M. Larkin, and D.G. Higgins Analysis and comparison of benchmarks for multiple sequence alignment In Silico Biol. 6 2006 321 339 (Pubitemid 44430621)
    • (2006) In Silico Biology , vol.6 , Issue.4 , pp. 321-339
    • Blackshields, G.1    Wallace, I.M.2    Larkin, M.3    Higgins, D.G.4
  • 34
    • 34548400364 scopus 로고    scopus 로고
    • Recent evolutions of multiple sequence alignment algorithms
    • C. Notredame Recent evolutions of multiple sequence alignment algorithms PLoS Comput. Biol. 3 2007 e123
    • (2007) PLoS Comput. Biol. , vol.3 , pp. 123
    • Notredame, C.1
  • 35
    • 0033567092 scopus 로고    scopus 로고
    • Protein, lipid and water organization in bacteriorhodopsin crystals: A molecular view of the purple membrane at 1.9 A resolution
    • DOI 10.1016/S0969-2126(99)80118-X
    • H. Belrhali, P. Nollert, A. Royant, C. Menzel, J.P. Rosenbusch, E.M. Landau, and E. Pebay-Peyroula Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 Å resolution Structure 7 1999 909 917 (Pubitemid 29372513)
    • (1999) Structure , vol.7 , Issue.8 , pp. 909-917
    • Belrhali, H.1    Nollert, P.2    Royant, A.3    Menzel, C.4    Rosenbusch, J.P.5    Landau, E.M.6    Pebay-Peyroula, E.7
  • 36
    • 0345059376 scopus 로고    scopus 로고
    • Announcing the worldwide Protein Data Bank
    • DOI 10.1038/nsb1203-980
    • H.M. Berman, K. Henrick, and H. Nakamura Announcing the worldwide Protein Data Bank Nat. Struct. Biol. 10 2003 980 (Pubitemid 37500485)
    • (2003) Nature Structural Biology , vol.10 , Issue.12 , pp. 980
    • Berman, H.1    Henrick, K.2    Nakamura, H.3
  • 38
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • P. Rice, I. Longden, and A. Bleasby EMBOSS: The European Molecular Biology Open Software Suite Trends Genet. 16 2000 276 277
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 39
    • 13444280419 scopus 로고    scopus 로고
    • PDB-TM: Selection and membrane localization of transmembrane proteins in the protein data bank
    • G.E. Tusnady, Z.S. Dosztanyi, and I. Simon PDB-TM: selection and membrane localization of transmembrane proteins in the protein data bank Nucleic Acids Res. 33 2005 D275 D278
    • (2005) Nucleic Acids Res. , vol.33
    • Tusnady, G.E.1    Dosztanyi, Z.S.2    Simon, I.3
  • 40
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT Suite: A web server for clustering and comparing biological sequences
    • Y. Huang, B. Niu, Y. Gao, L. Fu, and W. Li CD-HIT Suite: a web server for clustering and comparing biological sequences Bioinformatics 26 2010 680 682
    • (2010) Bioinformatics , vol.26 , pp. 680-682
    • Huang, Y.1    Niu, B.2    Gao, Y.3    Fu, L.4    Li, W.5
  • 41
    • 0023042012 scopus 로고
    • Information content of binding sites on nucleotide sequences
    • T.D. Schneider, G.D. Stormo, L. Gold, and A. Ehrenfeucht Information content of binding sites on nucleotide sequences J. Mol. Biol. 188 1986 415 431
    • (1986) J. Mol. Biol. , vol.188 , pp. 415-431
    • Schneider, T.D.1    Stormo, G.D.2    Gold, L.3    Ehrenfeucht, A.4
  • 42
    • 2142738304 scopus 로고    scopus 로고
    • WebLogo: A sequence logo generator
    • DOI 10.1101/gr.849004
    • G.E. Crooks, G. Hon, J.-M. Chandonia, and S.E. Brenner WebLogo: a sequence logo generator Genome Res. 14 2004 1188 1190 (Pubitemid 38811555)
    • (2004) Genome Research , vol.14 , Issue.6 , pp. 1188-1190
    • Crooks, G.E.1    Hon, G.2    Chandonia, J.-M.3    Brenner, S.E.4
  • 44
    • 13744252339 scopus 로고    scopus 로고
    • Accuracy of structure-derived properties in simple comparative models of protein structures
    • DOI 10.1093/nar/gki162
    • S. Chakravarty, L. Wang, and R. Sanchez Accuracy of structure-derived properties in simple comparative models of protein structures Nucleic Acids Res. 33 2005 244 259 (Pubitemid 40276946)
    • (2005) Nucleic Acids Research , vol.33 , Issue.1 , pp. 244-259
    • Chakravarty, S.1    Wang, L.2    Sanchez, R.3
  • 46
    • 78149236789 scopus 로고    scopus 로고
    • Medeller: Homology-based coordinate generation for membrane proteins
    • S. Kelm, J. Shi, and C.M. Deane Medeller: homology-based coordinate generation for membrane proteins Bioinformatics 26 2010 2833 2840
    • (2010) Bioinformatics , vol.26 , pp. 2833-2840
    • Kelm, S.1    Shi, J.2    Deane, C.M.3
  • 47
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the web: A case study using the Phyre server
    • L.A. Kelley, and M.J.E. Sternberg Protein structure prediction on the web: a case study using the Phyre server Nat. Protoc. 4 2009 363 371
    • (2009) Nat. Protoc. , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.E.2
  • 49
    • 37349063087 scopus 로고    scopus 로고
    • Features of transmembrane segments that promote the lateral release from the translocase into the lipid phase
    • DOI 10.1021/bi701398y
    • K. Xie, T. Hessa, S. Seppälä, M. Rapp, G. von Heijne, and R.E. Dalbey RE Features of transmembrane segments that promote the lateral release from the translocase into the lipid phase Biochemistry 46 2007 15153 15161 (Pubitemid 350308906)
    • (2007) Biochemistry , vol.46 , Issue.51 , pp. 15153-15161
    • Xie, K.1    Hessa, T.2    Seppala, S.3    Rapp, M.4    Von Heijne, G.5    Dalbey, R.E.6
  • 51
    • 0007949690 scopus 로고    scopus 로고
    • Interhelical hydrogen bonding drives strong interactions in membrane proteins
    • DOI 10.1038/72430
    • F.X. Zhou, M.J. Cocco, W.P. Russ, A.T. Brunger, and D.M. Engelman Interhelical hydrogen bonding drives strong interactions in membrane proteins Nat. Struct. Biol. 7 2000 154 160 (Pubitemid 30082514)
    • (2000) Nature Structural Biology , vol.7 , Issue.2 , pp. 154-160
    • Zhou, F.X.1    Cocco, M.J.2    Russ, W.P.3    Brunger, A.T.4    Engelman, D.M.5
  • 54
    • 0242551561 scopus 로고    scopus 로고
    • Inter-helical hydrogen bond formation during membrane protein integration into the ER membrane
    • DOI 10.1016/j.jmb.2003.10.019
    • M. Hermansson, and G. von Heijne Inter-helical hydrogen bond formation during membrane protein integration into the ER membrane J. Mol. Biol. 334 2003 803 809 (Pubitemid 37433893)
    • (2003) Journal of Molecular Biology , vol.334 , Issue.4 , pp. 803-809
    • Hermansson, M.1    Von Heijne, G.2
  • 55
    • 0036301006 scopus 로고    scopus 로고
    • Motifs of serine and threonine can drive association of transmembrane helices
    • DOI 10.1006/jmbi.2001.5353
    • J.P. Dawson, J.S. Weineger, and D.M. Engelman Motifs of serine and threonine can drive association of membrane helices J. Mol. Biol. 316 2002 799 805 (Pubitemid 34729255)
    • (2002) Journal of Molecular Biology , vol.316 , Issue.3 , pp. 799-805
    • Dawson, J.P.1    Weinger, J.S.2    Engelman, D.M.3
  • 56
    • 33644772377 scopus 로고    scopus 로고
    • Kinetics of an individual transmembrane helix during bacteriorhodopsin folding
    • DOI 10.1016/j.jmb.2005.12.042, PII S0022283605016141
    • E.L.R. Compton, N.A. Farmer, M. Lorch, J.M. Mason, K.M. Moreton, and P.J. Booth Kinetics of an individual transmembrane helix during bacteriorhodopsin folding J. Mol. Biol. 357 2006 325 338 (Pubitemid 43339334)
    • (2006) Journal of Molecular Biology , vol.357 , Issue.1 , pp. 325-338
    • Compton, E.L.R.1    Farmer, N.A.2    Lorch, M.3    Mason, J.M.4    Moreton, K.M.5    Booth, P.J.6
  • 58
    • 20044389842 scopus 로고    scopus 로고
    • Membrane insertion of a potassium-channel voltage sensor
    • DOI 10.1126/science.1109176
    • T. Hessa, S.H. White, and G. von Heijne Membrane insertion of a potassium-channel voltage sensor Science 307 2005 1427 (Pubitemid 40321932)
    • (2005) Science , vol.307 , Issue.5714 , pp. 1427
    • Hessa, T.1    White, S.H.2    Von Heijne, G.3
  • 60
    • 0344335730 scopus 로고
    • Aspartic acids 96 and 85 play a central role in the function of bacteriorhodopsin as a proton pump
    • H.J. Butt, K. Fendler, E. Bamberg, J. Tittor, and D. Oesterhelt Aspartic acids 96 and 85 play a central role in the function of bacteriorhodopsin as a proton pump EMBO J. 8 1989 1657 1663
    • (1989) EMBO J. , vol.8 , pp. 1657-1663
    • Butt, H.J.1    Fendler, K.2    Bamberg, E.3    Tittor, J.4    Oesterhelt, D.5
  • 61
    • 0025016817 scopus 로고
    • Substitution of amino acids Asp-85, Asp-212, and Arg-82 in bacteriorhodopsin affects the proton release phase of the pump and the pK of the Schiff base
    • H. Otto, T. Marti, M. Holtz, T. Mogi, L.J. Stern, F. Engel, H.G. Khorana, and M.P. Heyn Substitution of amino acids Asp-85, Asp-212, and Arg-82 in bacteriorhodopsin affects the proton release phase of the pump and the pK of the Schiff base Proc. Natl. Acad. Sci. U. S. A. 87 1990 1018 1022
    • (1990) Proc. Natl. Acad. Sci. U. S. A. , vol.87 , pp. 1018-1022
    • Otto, H.1    Marti, T.2    Holtz, M.3    Mogi, T.4    Stern, L.J.5    Engel, F.6    Khorana, H.G.7    Heyn, M.P.8
  • 62
    • 0026557012 scopus 로고
    • Influence of the size and protonation state of acidic residue 85 on the absorption spectrum and photoreaction of the bacteriorhodopsin chromophore
    • J.K. Lanyi, J. Tittor, G. Váró, G. Krippahl, and D. Oesterhelt Influence of the size and protonation state of acidic residue 85 on the absorption spectrum and photoreaction of the bacteriorhodopsin chromophore Biochim. Biophys. Acta 1099 1992 102 110
    • (1992) Biochim. Biophys. Acta , vol.1099 , pp. 102-110
    • Lanyi, J.K.1    Tittor, J.2    Váró, G.3    Krippahl, G.4    Oesterhelt, D.5
  • 63
    • 0027051284 scopus 로고
    • Effect of introducing different carboxylate-containing side chains at position 85 on chromophore formation and proton transport in bacteriorhodopsin
    • D.A. Greenhalgh, S. Subramaniam, U. Alexiev, H. Otto, M.P. Heyn, and H.G. Khorana Effect of introducing different carboxylate-containing side chains at position 85 on chromophore formation and proton transport in bacteriorhodopsin J. Biol. Chem. 267 1992 25734 25738 (Pubitemid 23013969)
    • (1992) Journal of Biological Chemistry , vol.267 , Issue.36 , pp. 25734-25738
    • Greenhalgh, D.A.1    Subramaniam, S.2    Alexiev, U.3    Otto, H.4    Heyn, M.P.5    Khorana, H.G.6
  • 64
    • 0027249907 scopus 로고
    • Decoupling of photo- and proton cycle in the Asp85 → Glu mutant of bacteriorhodopsin
    • J. Heberle, D. Oesterhelt, and N.A. Dencher Decoupling of photo- and proton cycle in the Asp85 → Glu mutant of bacteriorhodopsin EMBO J. 12 1993 3721 3727 (Pubitemid 23282747)
    • (1993) EMBO Journal , vol.12 , Issue.10 , pp. 3721-3727
    • Heberle, J.1    Oesterhelt, D.2    Dencher, N.A.3
  • 65
    • 33745099339 scopus 로고    scopus 로고
    • Structural and energetic determinants of primary proton transfer in bacteriorhodopsin
    • DOI 10.1039/b516451f
    • A.-N. Bondar, J.C. Smith, and S. Fischer Structural and energetic determinants of primary proton transfer in bacteriorhodopsin Photochem. Photobiol. Sci. 5 2006 547 552 (Pubitemid 43885918)
    • (2006) Photochemical and Photobiological Sciences , vol.5 , Issue.6 , pp. 547-552
    • Bondar, A.-N.1    Smith, J.C.2    Fischer, S.3
  • 66
  • 69
    • 0028946790 scopus 로고
    • Effects of substitution of tyrosine 57 with asparagine and phenylalanine on the properties of bacteriorhodopsin
    • R. Govindjee, M. Kono, S.P. Balashov, E. Imasheva, M. Sheves, and T.G. Ebrey Effects of substitution of tyrosine 57 with asparagine and phenylalanine on the properties of bacteriorhodopsin Biochemistry 34 1995 4828 4838
    • (1995) Biochemistry , vol.34 , pp. 4828-4838
    • Govindjee, R.1    Kono, M.2    Balashov, S.P.3    Imasheva, E.4    Sheves, M.5    Ebrey, T.G.6
  • 70
    • 0027474325 scopus 로고
    • Fourier transform Raman spectroscopy of the bacteriorhodopsin mutant Tyr- 185→Phe: Formation of a stable O-like species during light adaptation and detection of its transient N-like photoproduct
    • P. Rath, M.P. Krebs, Y. He, H.G. Khorana, and K.J. Rotschild Fourier Transform Raman Spectroscopy of the bacteriorhodopsin mutant Tyr-185 Phe: formation of a stable O-like species during light adaptation and detection of its transient N-like photoproduct Biochemistry 32 1993 2272 2281 (Pubitemid 23094889)
    • (1993) Biochemistry , vol.32 , Issue.9 , pp. 2272-2281
    • Rath, P.1    Krebs, M.P.2    He, Y.3    Khorana, H.G.4    Rothschild, K.J.5
  • 71
    • 79959928058 scopus 로고    scopus 로고
    • Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers
    • C.P. Moon, and K.G. Fleming Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers Proc. Natl. Acad. Sci. U. S. A. 108 2011 10174 10177
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , pp. 10174-10177
    • Moon, C.P.1    Fleming, K.G.2
  • 72
    • 0033104768 scopus 로고    scopus 로고
    • Hydrogen bonds between short polar side chains and peptide backbone: Prevalence in proteins and effects on helix-forming propensities
    • DOI 10.1002/(SICI)1097-0134(19990301)34:4<497::AID-PROT9>3.0.CO;2-G
    • M. Vijayakumar, H. Qian, and H.-X. Zhou Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities Proteins Struct. Funct. Genet. 34 1999 497 507 (Pubitemid 29129700)
    • (1999) Proteins: Structure, Function and Genetics , vol.34 , Issue.4 , pp. 497-507
    • Vijayakumar, M.1    Qian, H.2    Zhou, H.-X.3
  • 73
    • 0033544689 scopus 로고    scopus 로고
    • KPROT: A knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction
    • DOI 10.1006/jmbi.1999.3257
    • Y. Pilpel, N. Ben-Tal, and D. Lancet KPROT: a knowledge-based scale for the propensity of residue orientation in transmembrane segments, application to membrane protein structure prediction J. Mol. Biol. 294 1999 921 935 (Pubitemid 30000385)
    • (1999) Journal of Molecular Biology , vol.294 , Issue.4 , pp. 921-935
    • Pilpel, Y.1    Ben-Tal, N.2    Lancet, D.3
  • 74
    • 84871272778 scopus 로고    scopus 로고
    • Ser/Thr motifs in transmembrane proteins: Conservation patterns and effects on local protein structure and dynamics
    • C. del Val, S.H. White, and A.-N. Bondar Ser/Thr motifs in transmembrane proteins: conservation patterns and effects on local protein structure and dynamics J. Membr. Biol. 245 2012 717 730
    • (2012) J. Membr. Biol. , vol.245 , pp. 717-730
    • Del Val, C.1    White, S.H.2    Bondar, A.-N.3
  • 75
    • 0036568229 scopus 로고    scopus 로고
    • Interhelical hydrogen bonds and spatial motifs in membrane proteins: Polar clamps and serine zippers
    • DOI 10.1002/prot.10071
    • L. Adamian, and J. Liang Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers Proteins Struct. Funct. Genet. 47 2002 209 218 (Pubitemid 34266091)
    • (2002) Proteins: Structure, Function and Genetics , vol.47 , Issue.2 , pp. 209-218
    • Adamian, L.1    Liang, J.2
  • 76
    • 0021755525 scopus 로고
    • Intrahelical hydrogen bonds of serine, threonine and cysteine residues within a-helices and its relevance to membrane-bound proteins
    • T.M. Gray, and B.W. Mathews Intrahelical hydrogen bonds of serine, threonine and cysteine residues within a-helices and its relevance to membrane-bound proteins J. Mol. Biol. 175 1984 75 81
    • (1984) J. Mol. Biol. , vol.175 , pp. 75-81
    • Gray, T.M.1    Mathews, B.W.2
  • 77
    • 0024290488 scopus 로고
    • Helix signals in proteins
    • L.G. Presta, and G.D. Rose Helix signals in proteins Science 240 1988 1632 1641
    • (1988) Science , vol.240 , pp. 1632-1641
    • Presta, L.G.1    Rose, G.D.2
  • 78
    • 0024290472 scopus 로고
    • Amino acid preferences for specific location at the ends of helices
    • J.S. Richardson, and D.C. Richardson Amino acid preferences for specific location at the ends of helices Science 240 1988 1648 1652
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 80
    • 0032101291 scopus 로고    scopus 로고
    • Dissecting α-helices: Position-specific analysis of α-helices in globular proteins
    • DOI 10.1002/(SICI)1097-0134(19980601)31:4<460::AID-PROT12>3.0.CO;2- D
    • S. Kumar, and M. Bansal Dissecting a-helices: position-specific analysis of a-helices in globular proteins Proteins Struct. Funct. Genet. 31 1998 460 476 (Pubitemid 28265563)
    • (1998) Proteins: Structure, Function and Genetics , vol.31 , Issue.4 , pp. 460-476
    • Kumar, S.1    Bansal, M.2
  • 82
    • 84876717781 scopus 로고    scopus 로고
    • QM/MM simulations of vibrational spectra of bacteriorhodopsin and channelrhodopsin-2
    • K. Welke, H.C. Watanabe, T. Wolter, M. Gaus, and M. Elstner QM/MM simulations of vibrational spectra of bacteriorhodopsin and channelrhodopsin-2 Phys. Chem. Chem. Phys. 15 2013 6651 6659
    • (2013) Phys. Chem. Chem. Phys. , vol.15 , pp. 6651-6659
    • Welke, K.1    Watanabe, H.C.2    Wolter, T.3    Gaus, M.4    Elstner, M.5
  • 83
    • 84877578341 scopus 로고    scopus 로고
    • Towards an understanding of channelrhodopsin function: Simulations lead to novel insights of the channel mechanism
    • H.C. Watanabe, K. Welke, D.J. Sindhikara, P. Hegemann, and M. Elstner Towards an understanding of channelrhodopsin function: simulations lead to novel insights of the channel mechanism J. Mol. Biol. 425 2013 1795 1814
    • (2013) J. Mol. Biol. , vol.425 , pp. 1795-1814
    • Watanabe, H.C.1    Welke, K.2    Sindhikara, D.J.3    Hegemann, P.4    Elstner, M.5
  • 84
    • 22144464025 scopus 로고    scopus 로고
    • A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues
    • DOI 10.1529/biophysj.104.047639
    • B. Nie, J. Stutzman, and A. Xie A vibrational spectra marker for probing the hydrogen-bonding statis of protonated Asp and Glu residues Biophys. J. 88 2005 2833 2847 (Pubitemid 40976149)
    • (2005) Biophysical Journal , vol.88 , Issue.4 , pp. 2833-2847
    • Nie, B.1    Stutzman, J.2    Xie, A.3
  • 86
    • 0030840715 scopus 로고    scopus 로고
    • Localization and orientation of functional water molecules in bacteriorhodopsin as revealed by polarized Fourier transform infrared spectroscopy
    • M. Hatanaka, H. Kandori, and A. Maeda Localization and orientation of functional water molecules in bacteriorhodopsin as revealed by polarized Fourier transform infrared spectroscopy Biophys. J. 72 1997 1001 1006 (Pubitemid 27337635)
    • (1997) Biophysical Journal , vol.73 , Issue.2 , pp. 1001-1006
    • Hatanaka, M.1    Kandori, H.2    Maeda, A.3
  • 88
    • 0034734246 scopus 로고    scopus 로고
    • Atomic resolution structures of bacteriorhodopsin photocycle intermediates: The role of discrete water molecules in the function of this light-driven proton pump
    • H. Luecke Atomic resolution structures of bacteriorhodopsin photocycle intermediates: the role of discrete water molecules in the function of this light-driven proton pump Biochim. Biophys. Acta 1460 2000 133 156
    • (2000) Biochim. Biophys. Acta , vol.1460 , pp. 133-156
    • Luecke, H.1
  • 89
    • 30144445932 scopus 로고    scopus 로고
    • Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy
    • DOI 10.1038/nature04231
    • F. Garczareck, and K. Gerwert Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy Nature 439 2005 109 112 (Pubitemid 43053638)
    • (2006) Nature , vol.439 , Issue.7072 , pp. 109-112
    • Garczarek, F.1    Gerwert, K.2
  • 90
    • 67249096746 scopus 로고    scopus 로고
    • Functional and shunt states of bacteriorhodopsin revealed by 250 GHz dynamics nuclear polarization-enhanced solid-state NMR
    • V.S. Bajaj, M.L. Mak-Jurkausas, M. Belenky, J. Herzfeld, and R.G. Griffin Functional and shunt states of bacteriorhodopsin revealed by 250 GHz dynamics nuclear polarization-enhanced solid-state NMR Proc. Natl. Acad. Sci. U. S. A. 9 2009 9244 9249
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.9 , pp. 9244-9249
    • Bajaj, V.S.1    Mak-Jurkausas, M.L.2    Belenky, M.3    Herzfeld, J.4    Griffin, R.G.5
  • 91
    • 3543020365 scopus 로고    scopus 로고
    • Hydration switch model for the proton transfer in the Schiff base region of bacteriorhodopsin
    • H. Kandori Hydration switch model for the proton transfer in the Schiff base region of bacteriorhodopsin Biochim. Biophys. Acta 1658 2000 72 79
    • (2000) Biochim. Biophys. Acta , vol.1658 , pp. 72-79
    • Kandori, H.1
  • 92
    • 0346366810 scopus 로고    scopus 로고
    • Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle
    • DOI 10.1016/j.jmb.2003.10.068
    • T. Kouyama, T. Nischikawa, T. Tokuhisa, and H. Okumura Crystal structure of the L intermediate of bacteriorhodopsin: evidence for vertical translocation of a water molecule during the proton pumping cycle J. Mol. Biol. 335 2004 531 546 (Pubitemid 37532654)
    • (2004) Journal of Molecular Biology , vol.335 , Issue.2 , pp. 531-546
    • Kouyama, T.1    Nishikawa, T.2    Tokuhisa, T.3    Okumura, H.4
  • 93
    • 0034321020 scopus 로고    scopus 로고
    • Proton transfer in bacteriorhodopsin: Structure, excitation, IR spectra, and potential energy surface analyses by an ab initio QM/MM method
    • DOI 10.1021/jp001508r
    • S. Hayashi, and I. Ohmine Proton transfer in bacteriorhodopsin: structure, excitation, IR spectra, and potential energy surface analyses by an ab initio QM/MM method J. Phys. Chem. B 104 2000 10678 10691 (Pubitemid 32021481)
    • (2000) Journal of Physical Chemistry B , vol.104 , Issue.45 , pp. 10678-10691
    • Hayashi, S.1    Ohmine, I.2
  • 94
    • 0033884808 scopus 로고    scopus 로고
    • A study on the mechanism of the proton transport in bacteriorhodopsin: The importance of the water molecule
    • K. Murata, Y. Fujii, N. Enomoto, M. Hata, T. Hoshino, and M. Tsuda A study on the mechanism of the proton transport in bacteriorhodopsin: the importance of the water molecule Biophys. J. 79 2000 982 991 (Pubitemid 30626189)
    • (2000) Biophysical Journal , vol.79 , Issue.2 , pp. 982-991
    • Murata, K.1    Fujii, Y.2    Enomoto, N.3    Hata, M.4    Hoshino, T.5    Tsuda, M.6
  • 96
    • 3142613053 scopus 로고    scopus 로고
    • Mechanism of primary proton transfer in bacteriorhodopsin
    • DOI 10.1016/j.str.2004.04.016, PII S0969212604001637
    • A.-N. Bondar, M. Elstner, S. Suhai, J.C. Smith, and S. Fischer Mechanism of primary proton transfer in bacteriorhodopsin Structure 12 2004 1281 1288 (Pubitemid 38900770)
    • (2004) Structure , vol.12 , Issue.7 , pp. 1281-1288
    • Bondar, A.-N.1    Elstner, M.2    Suhai, S.3    Smith, J.C.4    Fischer, S.5
  • 97
    • 57449095198 scopus 로고    scopus 로고
    • Key role of active-site water molecules in bacteriorhodopsin proton transfer
    • A.-N. Bondar, J. Baudry, S. Suhai, S. Fischer, and J.C. Smith Key role of active-site water molecules in bacteriorhodopsin proton transfer J. Phys. Chem. B 112 2008 14729 14741
    • (2008) J. Phys. Chem. B , vol.112 , pp. 14729-14741
    • Bondar, A.-N.1    Baudry, J.2    Suhai, S.3    Fischer, S.4    Smith, J.C.5
  • 98
    • 69249213570 scopus 로고    scopus 로고
    • Water molecules in short- and long-distance proton transfer steps of bacteriorhodopsin proton pumping
    • A.-N. Bondar, and J.C. Smith Water molecules in short- and long-distance proton transfer steps of bacteriorhodopsin proton pumping Isr. J. Chem. 49 2009 155-161
    • (2009) Isr. J. Chem. , vol.49 , pp. 155-161
    • Bondar, A.-N.1    Smith, J.C.2
  • 99
    • 79955667818 scopus 로고    scopus 로고
    • Water pathways in the bacteriorhodopsin proton pump
    • A.-N. Bondar, S. Fischer, and J.C. Smith Water pathways in the bacteriorhodopsin proton pump J. Membr. Biol. 239 2011 73 84
    • (2011) J. Membr. Biol. , vol.239 , pp. 73-84
    • Bondar, A.-N.1    Fischer, S.2    Smith, J.C.3
  • 100
    • 61549125968 scopus 로고    scopus 로고
    • Rhomboid protease dynamics and lipid interactions
    • A.-N. Bondar, C. del Val, and S.H. White Rhomboid protease dynamics and lipid interactions Structure 17 2009 395 405
    • (2009) Structure , vol.17 , pp. 395-405
    • Bondar, A.-N.1    Del Val, C.2    White, S.H.3
  • 101
    • 84857650478 scopus 로고    scopus 로고
    • Hydrogen bond dynamics in membrane protein function
    • A.-N. Bondar, and S.H. White Hydrogen bond dynamics in membrane protein function Biochim. Biophys. Acta 1818 2012 942 950
    • (2012) Biochim. Biophys. Acta , vol.1818 , pp. 942-950
    • Bondar, A.-N.1    White, S.H.2
  • 104
    • 84884906995 scopus 로고    scopus 로고
    • Structural differences between the closed and open states of channelrhodopsin-2 as observed by EPR spectroscopy
    • N. Krause, C. Engelhardt, J. Heberle, R. Schlesinger, and R. Bittl Structural differences between the closed and open states of channelrhodopsin-2 as observed by EPR spectroscopy FEBS Lett. 587 2013 3309 3313
    • (2013) FEBS Lett. , vol.587 , pp. 3309-3313
    • Krause, N.1    Engelhardt, C.2    Heberle, J.3    Schlesinger, R.4    Bittl, R.5
  • 105
    • 0020475449 scopus 로고
    • A simple method for displaying the hydrophatic character of a protein
    • J. Kyte, and R.F. Doolittle A simple method for displaying the hydrophatic character of a protein J. Mol. Biol. 157 1982 105 132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 107
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building for molecular graphics
    • P. Emsley, and K. Cowtan Coot: model-building for molecular graphics Acta Crystallogr. D60 2004 2126 2132
    • (2004) Acta Crystallogr. , vol.60 D , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2


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