Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology.
暂无分享,去创建一个
Hideki Kandori | Yoshitaka Kato | Massimo Olivucci | Silvia Rinaldi | Xuchun Yang | Nicolas Ferré | Michael Stenrup | Alessio Valentini | N. Ferré | M. Olivucci | S. Rinaldi | H. Luk | H. Kandori | Hoi Ling Luk | Federico Melaccio | María Del Carmen Marín | Fabio Montisci | Marco Cherubini | Yoelvis Orozco-Gonzalez | M. Stenrup | A. Valentini | F. Melaccio | Xuchun Yang | Y. Orozco-Gonzalez | Yoshitaka Kato | M. del Carmen Marín | Fabio Montisci | Marco Cherubini | Silvia Rinaldi | Federico Melaccio
[1] G. Wald,et al. Pre-Lumirhodopsin and the Bleaching of Visual Pigments , 1963, Nature.
[2] M. Levitt,et al. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.
[3] L. Stryer,et al. Retinal has a highly dipolar vertically excited singlet state: implications for vision. , 1976, Proceedings of the National Academy of Sciences of the United States of America.
[4] J. Michl,et al. Prediction of structural and environmental effects on the S1S0 energy gap and jump probability in double-bond cis—trans photoisomeriz , 1984 .
[5] U. Singh,et al. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .
[6] J. Ponder,et al. An efficient newton‐like method for molecular mechanics energy minimization of large molecules , 1987 .
[7] Kerstin Andersson,et al. Second-order perturbation theory with a CASSCF reference function , 1990 .
[8] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[9] Keiji Morokuma,et al. The IMOMO method: Integration of different levels of molecular orbital approximations for geometry optimization of large systems: Test for n‐butane conformation and SN2 reaction: RCl+Cl− , 1996 .
[10] J Hermans,et al. Hydrophilicity of cavities in proteins , 1996, Proteins.
[11] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[12] W. P. Hayes,et al. Melanopsin: An opsin in melanophores, brain, and eye. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[13] H Luecke,et al. Structure of bacteriorhodopsin at 1.55 A resolution. , 1999, Journal of molecular biology.
[14] J. Spudich,et al. Retinylidene proteins: structures and functions from archaea to humans. , 2000, Annual review of cell and developmental biology.
[15] Roland Lindh,et al. Analytical gradients of a state average MCSCF state and a state average diagnostic , 2001 .
[16] N. Kamo,et al. Structural changes of pharaonis phoborhodopsin upon photoisomerization of the retinal chromophore: infrared spectral comparison with bacteriorhodopsin. , 2001, Biochemistry.
[17] János G. Ángyán,et al. Approximate electrostatic interaction operator for QM/MM calculations , 2002 .
[18] Massimo Olivucci,et al. Probing the rhodopsin cavity with reduced retinal models at the CASPT2//CASSCF/AMBER level of theory. , 2003, Journal of the American Chemical Society.
[19] J. Spudich,et al. Demonstration of a sensory rhodopsin in eubacteria , 2003, Molecular microbiology.
[20] Massimo Olivucci,et al. Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[21] N. Ferré,et al. Complete-active-space self-consistent-field/Amber parameterization of the Lys296–retinal–Glu113 rhodopsin chromophore-counterion system , 2004 .
[22] Marcus Elstner,et al. The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. , 2004, Journal of molecular biology.
[23] K. Deisseroth,et al. Millisecond-timescale, genetically targeted optical control of neural activity , 2005, Nature Neuroscience.
[24] K. Jung,et al. FTIR spectroscopy of the all-trans form of Anabaena sensory rhodopsin at 77 K: hydrogen bond of a water between the Schiff base and Asp75. , 2005, Biochemistry.
[25] M. Murakami,et al. Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state. , 2005, Journal of molecular biology.
[26] T. Okada,et al. Crystallographic analysis of primary visual photochemistry. , 2006, Angewandte Chemie.
[27] V. Buss,et al. Quantum mechanical studies on the crystallographic model of bathorhodopsin. , 2006, Angewandte Chemie.
[28] J. Lanyi,et al. Proton transfers in the bacteriorhodopsin photocycle. , 2006, Biochimica et biophysica acta.
[29] K. Jung,et al. FTIR study of the photoisomerization processes in the 13-cis and all-trans forms of Anabaena sensory rhodopsin at 77 K. , 2006, Biochemistry.
[30] N. Ferré,et al. The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution , 2006, Proceedings of the National Academy of Sciences.
[31] Jie Liang,et al. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues , 2006, Nucleic Acids Res..
[32] Jun-Ya Hasegawa,et al. Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins. , 2007, Journal of chemical theory and computation.
[33] K. Bravaya,et al. An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase. , 2007, Journal of the American Chemical Society.
[34] J. Spudich,et al. Crystal structure of the Anabaena sensory rhodopsin transducer. , 2007, Journal of molecular biology.
[35] N. Ferré,et al. Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry , 2007, Proceedings of the National Academy of Sciences.
[36] V. Buss,et al. Origin of spectral tuning in rhodopsin--it is not the binding pocket. , 2007, Angewandte Chemie.
[37] E. Boyden,et al. Multiple-Color Optical Activation, Silencing, and Desynchronization of Neural Activity, with Single-Spike Temporal Resolution , 2007, PloS one.
[38] M. Frisch,et al. Three-layer ONIOM studies of the dark state of rhodopsin: the protonation state of Glu181. , 2008, Journal of molecular biology.
[39] M. Olivucci,et al. Origin of the absorption maxima of the photoactive yellow protein resolved via ab initio multiconfigurational methods. , 2008, The journal of physical chemistry. B.
[40] Keiji Morokuma,et al. Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants. , 2008, The journal of physical chemistry. B.
[41] Ehud Y. Isacoff,et al. Optical Switches for Remote and Noninvasive Control of Cell Signaling , 2008, Science.
[42] Keiji Morokuma,et al. Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies. , 2008, The journal of physical chemistry. B.
[43] Tsutomu Kouyama,et al. Crystal structure of squid rhodopsin , 2008, Nature.
[44] Massimo Olivucci,et al. Relationship between the excited state relaxation paths of rhodopsin and isorhodopsin. , 2008, Journal of the American Chemical Society.
[45] Marco Garavelli,et al. Electrostatic control of the photoisomerization efficiency and optical properties in visual pigments: on the role of counterion quenching. , 2009, Journal of the American Chemical Society.
[46] D. Tobias,et al. Dynamics of the internal water molecules in squid rhodopsin. , 2009, Biophysical journal.
[47] Roland L. Dunbrack,et al. proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improved prediction of protein side-chain conformations with SCWRL4 , 2022 .
[48] L. Serrano-Andrés,et al. Deciphering intrinsic deactivation/isomerization routes in a phytochrome chromophore model. , 2009, The journal of physical chemistry. B.
[49] Thomas G. Oertner,et al. Temporal Control of Immediate Early Gene Induction by Light , 2009, PloS one.
[50] Mikhail N. Ryazantsev,et al. Computational Photobiology and Beyond , 2010 .
[51] M. Elstner,et al. The protonation state of Glu181 in rhodopsin revisited: interpretation of experimental data on the basis of QM/MM calculations. , 2010, The journal of physical chemistry. B.
[52] N. Ferré,et al. Anabaena sensory rhodopsin is a light-driven unidirectional rotor , 2010, Proceedings of the National Academy of Sciences.
[53] K. Morokuma,et al. Photochemistry of visual pigment in a G(q) protein-coupled receptor (GPCR)--insights from structural and spectral tuning studies on squid rhodopsin. , 2010, Chemistry.
[54] R. Mathies,et al. Conical intersection dynamics of the primary photoisomerization event in vision , 2010, Nature.
[55] FRANCESCO AQUILANTE,et al. MOLCAS 7: The Next Generation , 2010, J. Comput. Chem..
[56] Ana-Nicoleta Bondar,et al. Coupling of retinal, protein, and water dynamics in squid rhodopsin. , 2010, Biophysical journal.
[57] Martin Kircher,et al. High‐throughput DNA sequencing – concepts and limitations , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.
[58] Marco Garavelli,et al. Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping , 2010, Proceedings of the National Academy of Sciences.
[59] N. Ferré,et al. Color-tuning mechanism of firefly investigated by multi-configurational perturbation method. , 2010, Journal of the American Chemical Society.
[60] R. Birge,et al. Glutamic acid 181 is negatively charged in the bathorhodopsin photointermediate of visual rhodopsin. , 2011, Journal of the American Chemical Society.
[61] Jan H. Jensen,et al. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. , 2011, Journal of chemical theory and computation.
[62] N. Ferré,et al. Unique QM/MM Potential Energy Surface Exploration Using Microiterations , 2011 .
[63] Roland Lindh,et al. The ultrafast photoisomerizations of rhodopsin and bathorhodopsin are modulated by bond length alternation and HOOP driven electronic effects. , 2011, Journal of the American Chemical Society.
[64] A. Granovsky,et al. Extended multi-configuration quasi-degenerate perturbation theory: the new approach to multi-state multi-reference perturbation theory. , 2011, The Journal of chemical physics.
[65] Hideaki E. Kato,et al. Crystal structure of the channelrhodopsin light-gated cation channel , 2012, Nature.
[66] N. Ferré,et al. Quantum chemical modeling of rhodopsin mutants displaying switchable colors. , 2012, Physical chemistry chemical physics : PCCP.
[67] Y. Shichida,et al. Photochemical properties of mammalian melanopsin. , 2012, Biochemistry.
[68] Roland Lindh,et al. Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model. , 2012, Journal of chemical theory and computation.
[69] V. Batista,et al. The active site of melanopsin: the biological clock photoreceptor. , 2012, Journal of the American Chemical Society.
[70] J. Spudich,et al. Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes. , 2013, Acta crystallographica. Section D, Biological crystallography.
[71] Robert J. Lucas,et al. Human melanopsin forms a pigment maximally sensitive to blue light (λmax ≈ 479 nm) supporting activation of Gq/11 and Gi/o signalling cascades , 2013, Proceedings of the Royal Society B: Biological Sciences.
[72] Massimo Olivucci,et al. Toward an understanding of the retinal chromophore in rhodopsin mimics. , 2013, The journal of physical chemistry. B.
[73] Ivano Tavernelli,et al. Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls. , 2013, Journal of chemical theory and computation.
[74] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[75] R. Lindh,et al. Mapping the Excited State Potential Energy Surface of a Retinal Chromophore Model with Multireference and Equation-of-Motion Coupled-Cluster Methods. , 2013, Journal of chemical theory and computation.
[76] M. Olivucci,et al. Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins , 2014, Proceedings of the National Academy of Sciences.
[77] I. Tavernelli,et al. Origin of the spectral shifts among the early intermediates of the rhodopsin photocycle. , 2014, Journal of the American Chemical Society.
[78] P. Hegemann,et al. Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms , 2013, Chemical reviews.
[79] S. Hayashi,et al. Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II. , 2015, Journal of the American Chemical Society.
[80] Hideaki E. Kato,et al. Atomistic design of microbial opsin-based blue-shifted optogenetics tools , 2015, Nature Communications.
[81] Markus Reiher,et al. Automated Selection of Active Orbital Spaces. , 2016, Journal of chemical theory and computation.
[82] Hiroshi C. Watanabe,et al. Active site structure and absorption spectrum of channelrhodopsin-2 wild-type and C128T mutant , 2016, Chemical science.