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For: Huntress MM, Gozem S, Malley KR, Jailaubekov AE, Vasileiou C, Vengris M, Geiger JH, Borhan B, Schapiro I, Larsen DS, Olivucci M. Toward an Understanding of the Retinal Chromophore in Rhodopsin Mimics. J Phys Chem B 2013;117:10053-70. [DOI: 10.1021/jp305935t] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Li G, Meng J, Yu S, Bai X, Dai J, Song Y, Peng X, Zhao Q. Excited-State Dynamics of a CRABPII-Based Microbial Rhodopsin Mimic. J Phys Chem B 2024;128:7712-7721. [PMID: 38940335 DOI: 10.1021/acs.jpcb.4c01296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
2
Malakar P, Gholami S, Aarabi M, Rivalta I, Sheves M, Garavelli M, Ruhman S. Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct. Nat Commun 2024;15:2136. [PMID: 38459010 PMCID: PMC10923925 DOI: 10.1038/s41467-024-46061-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024]  Open
3
Li G, Hu Y, Pei S, Meng J, Wang J, Wang J, Yue S, Wang Z, Wang S, Liu X, Weng Y, Peng X, Zhao Q. Excited-state dynamics of all-trans protonated retinal Schiff base in CRABPII-based rhodopsin mimics. Biophys J 2022;121:4109-4118. [PMID: 36181266 PMCID: PMC9675042 DOI: 10.1016/j.bpj.2022.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/06/2022] [Accepted: 09/26/2022] [Indexed: 11/20/2022]  Open
4
Tassone G, Paolino M, Pozzi C, Reale A, Salvini L, Giorgi G, Orlandini M, Galvagni F, Mangani S, Yang X, Carlotti B, Ortica F, Latterini L, Olivucci M, Cappelli A. Xanthopsin-Like Systems via Site-Specific Click-Functionalization of a Retinoic Acid Binding Protein. Chembiochem 2022;23:e202100449. [PMID: 34647400 PMCID: PMC8934143 DOI: 10.1002/cbic.202100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/12/2021] [Indexed: 01/07/2023]
5
Demoulin B, Maiuri M, Berbasova T, Geiger JH, Borhan B, Garavelli M, Cerullo G, Rivalta I. Control of Protonated Schiff Base Excited State Decay within Visual Protein Mimics: A Unified Model for Retinal Chromophores. Chemistry 2021;27:16389-16400. [PMID: 34653286 DOI: 10.1002/chem.202102383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 11/07/2022]
6
Pro219 is an electrostatic color determinant in the light-driven sodium pump KR2. Commun Biol 2021;4:1185. [PMID: 34645937 PMCID: PMC8514524 DOI: 10.1038/s42003-021-02684-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 09/19/2021] [Indexed: 11/13/2022]  Open
7
Liang R, Yu JK, Meisner J, Liu F, Martinez TJ. Electrostatic Control of Photoisomerization in Channelrhodopsin 2. J Am Chem Soc 2021;143:5425-5437. [PMID: 33794085 DOI: 10.1021/jacs.1c00058] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
8
El‐Tahawy MMT, Conti I, Bonfanti M, Nenov A, Garavelli M. Tailoring Spectral and Photochemical Properties of Bioinspired Retinal Mimics by in Silico Engineering. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
9
El‐Tahawy MMT, Conti I, Bonfanti M, Nenov A, Garavelli M. Tailoring Spectral and Photochemical Properties of Bioinspired Retinal Mimics by in Silico Engineering. Angew Chem Int Ed Engl 2020;59:20619-20627. [DOI: 10.1002/anie.202008644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 11/08/2022]
10
Lin CY, Boxer SG. Mechanism of Color and Photoacidity Tuning for the Protonated Green Fluorescent Protein Chromophore. J Am Chem Soc 2020;142:11032-11041. [PMID: 32453950 DOI: 10.1021/jacs.0c02796] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
11
Manathunga M, Jenkins AJ, Orozco-Gonzalez Y, Ghanbarpour A, Borhan B, Geiger JH, Larsen DS, Olivucci M. Computational and Spectroscopic Characterization of the Photocycle of an Artificial Rhodopsin. J Phys Chem Lett 2020;11:4245-4252. [PMID: 32374610 PMCID: PMC9272672 DOI: 10.1021/acs.jpclett.0c00751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
12
Santos EM, Berbasova T, Wang W, Salmani RE, Sheng W, Vasileiou C, Geiger JH, Borhan B. Engineering of a Red Fluorogenic Protein/Merocyanine Complex for Live-Cell Imaging. Chembiochem 2020;21:723-729. [PMID: 31482666 PMCID: PMC7379159 DOI: 10.1002/cbic.201900428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Indexed: 12/25/2022]
13
Pedraza-González L, De Vico L, del Carmen Marín M, Fanelli F, Olivucci M. a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement. J Chem Theory Comput 2019;15:3134-3152. [PMID: 30916955 PMCID: PMC7141608 DOI: 10.1021/acs.jctc.9b00061] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
14
Orozco-Gonzalez Y, Kabir MP, Gozem S. Electrostatic Spectral Tuning Maps for Biological Chromophores. J Phys Chem B 2019;123:4813-4824. [DOI: 10.1021/acs.jpcb.9b00489] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
15
Ghanbarpour A, Nairat M, Nosrati M, Santos EM, Vasileiou C, Dantus M, Borhan B, Geiger JH. Mimicking Microbial Rhodopsin Isomerization in a Single Crystal. J Am Chem Soc 2019;141:1735-1741. [PMID: 30580520 DOI: 10.1021/jacs.8b12493] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
16
Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018;118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
17
Pomogaev VA, Ramazanov RR, Ruud K, Artyukhov VY. Insight into the fluorescence quenching of Trp214 at HSA by the Dimetridazole ligand from simulation. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.08.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
18
Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017;117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
19
Demoulin B, Altavilla SF, Rivalta I, Garavelli M. Fine Tuning of Retinal Photoinduced Decay in Solution. J Phys Chem Lett 2017;8:4407-4412. [PMID: 28853582 DOI: 10.1021/acs.jpclett.7b01780] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
20
Shu Y, Fales BS, Peng WT, Levine BG. Understanding Nonradiative Recombination through Defect-Induced Conical Intersections. J Phys Chem Lett 2017;8:4091-4099. [PMID: 28799771 DOI: 10.1021/acs.jpclett.7b01707] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
21
Varsano D, Caprasecca S, Coccia E. Theoretical description of protein field effects on electronic excitations of biological chromophores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017;29:013002. [PMID: 27830666 DOI: 10.1088/0953-8984/29/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
22
Stenrup M, Pieri E, Ledentu V, Ferré N. pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin. Phys Chem Chem Phys 2017;19:14073-14084. [DOI: 10.1039/c7cp00991g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
23
Melaccio F, del Carmen Marín M, Valentini A, Montisci F, Rinaldi S, Cherubini M, Yang X, Kato Y, Stenrup M, Orozco-Gonzalez Y, Ferré N, Luk HL, Kandori H, Olivucci M. Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology. J Chem Theory Comput 2016;12:6020-6034. [DOI: 10.1021/acs.jctc.6b00367] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
24
Assar Z, Nossoni Z, Wang W, Santos EM, Kramer K, McCornack C, Vasileiou C, Borhan B, Geiger JH. Domain-Swapped Dimers of Intracellular Lipid-Binding Proteins: Evidence for Ordered Folding Intermediates. Structure 2016;24:1590-8. [PMID: 27524203 PMCID: PMC5330279 DOI: 10.1016/j.str.2016.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 11/29/2022]
25
Suomivuori CM, Lang L, Sundholm D, Gamiz-Hernandez AP, Kaila VRI. Tuning the Protein-Induced Absorption Shifts of Retinal in Engineered Rhodopsin Mimics. Chemistry 2016;22:8254-61. [DOI: 10.1002/chem.201505126] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/23/2016] [Indexed: 11/12/2022]
26
Bonvicini A, Demoulin B, Altavilla SF, Nenov A, El-Tahawy MMT, Segarra-Martí J, Giussani A, Batista VS, Garavelli M, Rivalta I. Ultraviolet vision: photophysical properties of the unprotonated retinyl Schiff base in the Siberian hamster cone pigment. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1869-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
27
Berbasova T, Santos EM, Nosrati M, Vasileiou C, Geiger JH, Borhan B. Light-Activated Reversible Imine Isomerization: Towards a Photochromic Protein Switch. Chembiochem 2016;17:407-14. [PMID: 26684483 PMCID: PMC4835339 DOI: 10.1002/cbic.201500613] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 01/07/2023]
28
Saini P, Banerjee M, Chattopadhyay A. Computational Investigation of the Photochemical Reaction Path of Some Synthesized and Experimentally Analyzed Small-Chain Conjugated Nitrones. J Phys Chem A 2016;120:396-406. [PMID: 26697926 DOI: 10.1021/acs.jpca.5b11069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
29
Cheng C, Kamiya M, Uchida Y, Hayashi S. Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II. J Am Chem Soc 2015;137:13362-70. [PMID: 26418582 DOI: 10.1021/jacs.5b08316] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
30
Hofmann L, Palczewski K. Advances in understanding the molecular basis of the first steps in color vision. Prog Retin Eye Res 2015;49:46-66. [PMID: 26187035 DOI: 10.1016/j.preteyeres.2015.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/05/2023]
31
SORCI for photochemical and thermal reaction paths: A benchmark study. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
32
Callis PR. Simulating electrostatic effects on electronic transitions in proteins. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923571] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
33
Caprasecca S, Jurinovich S, Viani L, Curutchet C, Mennucci B. Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation. J Chem Theory Comput 2014;10:1588-98. [DOI: 10.1021/ct500021d] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
34
Gozem S, Melaccio F, Lindh R, Krylov AI, Granovsky AA, Angeli C, Olivucci M. Mapping the Excited State Potential Energy Surface of a Retinal Chromophore Model with Multireference and Equation-of-Motion Coupled-Cluster Methods. J Chem Theory Comput 2013;9:4495-506. [DOI: 10.1021/ct400460h] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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