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For: Callis PR, Liu T. Short range photoinduced electron transfer in proteins: QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2006.01.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Number Cited by Other Article(s)
1
Understanding flavin electronic structure and spectra. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1541] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
2
Factors deciding the assembly and thermostability of the DmrB cage. Int J Biol Macromol 2021;182:959-967. [PMID: 33872614 DOI: 10.1016/j.ijbiomac.2021.04.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 11/20/2022]
3
Viquez Rojas CI, Slipchenko LV. Exchange Repulsion in Quantum Mechanical/Effective Fragment Potential Excitation Energies: Beyond Polarizable Embedding. J Chem Theory Comput 2020;16:6408-6417. [PMID: 32786899 DOI: 10.1021/acs.jctc.9b01156] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
4
Parson WW. Generalizing the Marcus equation. J Chem Phys 2020;152:184106. [DOI: 10.1063/5.0007569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
5
Zanetti-Polzi L, Daidone I, Corni S. Evidence of a Thermodynamic Ramp for Hole Hopping to Protect a Redox Enzyme from Oxidative Damage. J Phys Chem Lett 2019;10:1450-1456. [PMID: 30855973 DOI: 10.1021/acs.jpclett.9b00403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
6
Hong Yang, Jia-Bao Li, Muhammad Kamran Siddiqui, Waqas Nazeer, Meysam Najafi. A Theoretical Examination of the Antioxidant Activity of NH2, OMe, and tert-Butyl Sesamol Derivatives and Their Drug Delivery with C60 Nanocage. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s0036024418130216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
7
Zanetti-Polzi L, Del Galdo S, Daidone I, D'Abramo M, Barone V, Aschi M, Amadei A. Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory. Phys Chem Chem Phys 2018;20:24369-24378. [PMID: 30215645 DOI: 10.1039/c8cp04190c] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
8
Valenti G, Iurlo M, Claramunt RM, Accorsi G, Paolucci F, Farrán MÁ, Marcaccio M. Redox Properties and Interchromophoric Electronic Interactions in Isoalloxazine−Anthraquinone Dyads. ChemElectroChem 2018. [DOI: 10.1002/celc.201701374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
9
Higgins SA, Ouonkap SVY, Savage DF. Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering. ACS Synth Biol 2017;6:1825-1833. [PMID: 28707884 DOI: 10.1021/acssynbio.7b00112] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
10
Zanetti-Polzi L, Aschi M, Amadei A, Daidone I. Alternative Electron-Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Excited States in Riboflavin Binding Protein. J Phys Chem Lett 2017;8:3321-3327. [PMID: 28665138 DOI: 10.1021/acs.jpclett.7b01575] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
11
Parson WW. Vibrational Relaxations and Dephasing in Electron-Transfer Reactions. J Phys Chem B 2016;120:11412-11418. [DOI: 10.1021/acs.jpcb.6b08803] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
12
Callis PR. Binding phenomena and fluorescence quenching. II: Photophysics of aromatic residues and dependence of fluorescence spectra on protein conformation. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.04.051] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
13
Hardman SJO, Pudney CR, Hay S, Scrutton NS. Excited state dynamics can be used to probe donor-acceptor distances for H-tunneling reactions catalyzed by flavoproteins. Biophys J 2014;105:2549-58. [PMID: 24314085 DOI: 10.1016/j.bpj.2013.10.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/09/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022]  Open
14
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: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
15
MD + QM correlations with tryptophan fluorescence spectral shifts and lifetimes. Methods Mol Biol 2014;1076:171-214. [PMID: 24108627 DOI: 10.1007/978-1-62703-649-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
16
Nunthaboot N, Lugsanangarm K, Nueangaudom A, Pianwanit S, Kokpol S, Tanaka F. Role of the electrostatic energy between the photo-products and ionic groups on the photoinduced electron transfer rates from aromatic amino acids to the excited flavin in five single-point substitution isoforms of the charged amino acid residue-13 in the FMN-binding protein. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.902534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
17
Farmanzadeh D, Najafi M. On the Antioxidant Activity of the Tryptophan Derivatives. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20130035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
18
Laptenok SP, Bouzhir-Sima L, Lambry JC, Myllykallio H, Liebl U, Vos MH. Ultrafast real-time visualization of active site flexibility of flavoenzyme thymidylate synthase ThyX. Proc Natl Acad Sci U S A 2013;110:8924-9. [PMID: 23671075 PMCID: PMC3670337 DOI: 10.1073/pnas.1218729110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
19
Recent Progress in Density Functional Methodology for Biomolecular Modeling. STRUCTURE AND BONDING 2013. [DOI: 10.1007/978-3-642-32750-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
20
Tusell JR, Callis PR. Simulations of tryptophan fluorescence dynamics during folding of the villin headpiece. J Phys Chem B 2012;116:2586-94. [PMID: 22256973 DOI: 10.1021/jp211217w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
21
Sun Q, Lu R, Yu A. Structural Heterogeneity in the Collision Complex between Organic Dyes and Tryptophan in Aqueous Solution. J Phys Chem B 2011;116:660-6. [DOI: 10.1021/jp2100304] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
22
Merkley ED, Daggett V, Parson WW. A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8. Proteins 2011;80:546-55. [PMID: 22081476 DOI: 10.1002/prot.23219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/04/2011] [Accepted: 10/07/2011] [Indexed: 11/10/2022]
23
Zieba AA, Richardson C, Lucero C, Dieng SD, Gindt YM, Schelvis JPM. Evidence for concerted electron proton transfer in charge recombination between FADH- and 306Trp• in Escherichia coli photolyase. J Am Chem Soc 2011;133:7824-36. [PMID: 21534528 DOI: 10.1021/ja2001488] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
24
Predicting Fluorescence Lifetimes and Spectra of Biopolymers. Methods Enzymol 2011. [DOI: 10.1016/b978-0-12-381270-4.00001-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
25
Chosrowjan H, Taniguchi S, Mataga N, Nakanishi T, Haruyama Y, Sato S, Kitamura M, Tanaka F. Effects of the disappearance of one charge on ultrafast fluorescence dynamics of the FMN binding protein. J Phys Chem B 2010;114:6175-82. [PMID: 20397678 DOI: 10.1021/jp912137s] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Electrochromism and Solvatochromism in Fluorescence Response of Organic Dyes: A Nanoscopic View. SPRINGER SERIES ON FLUORESCENCE 2010. [DOI: 10.1007/978-3-642-04702-2_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
27
Zhang R, Lev B, Cuervo JE, Noskov SY, Salahub DR. A Guide to QM/MM Methodology and Applications. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59010-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
28
Xu J, Chen J, Toptygin D, Tcherkasskaya O, Callis P, King J, Brand L, Knutson JR. Femtosecond fluorescence spectra of tryptophan in human gamma-crystallin mutants: site-dependent ultrafast quenching. J Am Chem Soc 2009;131:16751-7. [PMID: 19919143 PMCID: PMC3439204 DOI: 10.1021/ja904857t] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
29
Accorsi G, Barigelletti F, Farrán A, Herranz F, Claramunt RM, Marcaccio M, Valenti G, Paolucci F, Pinilla E, Torres MR. Intramolecular interactions and photoinduced electron transfer in isoalloxazine-naphthalene bichromophores. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2009.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
30
Senn HM, Thiel W. QM/MM methods for biomolecular systems. Angew Chem Int Ed Engl 2009;48:1198-229. [PMID: 19173328 DOI: 10.1002/anie.200802019] [Citation(s) in RCA: 1892] [Impact Index Per Article: 118.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
31
Senn H, Thiel W. QM/MM-Methoden für biomolekulare Systeme. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200802019] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
32
Callis PR. Exploring the Electrostatic Landscape of Proteins with Tryptophan Fluorescence. REVIEWS IN FLUORESCENCE 2009. [DOI: 10.1007/978-0-387-88722-7_10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
33
Nunthaboot N, Tanaka F, Kokpol S, Chosrowjan H, Taniguchi S, Mataga N. Quantum Mechanical Study of Photoinduced Charge Transfer in FMN Binding Protein. J Phys Chem B 2008;112:15837-43. [DOI: 10.1021/jp806272v] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
34
Nunthaboot N, Tanaka F, Kokpol S, Chosrowjan H, Taniguchi S, Mataga N. Simultaneous analysis of ultrafast fluorescence decays of FMN binding protein and its mutated proteins by molecular dynamic simulation and electron transfer theory. J Phys Chem B 2008;112:13121-7. [PMID: 18800855 DOI: 10.1021/jp804130j] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
35
Hernández-Alcántara G, Rodríguez-Romero A, Reyes-Vivas H, Peon J, Cabrera N, Ortiz C, Enríquez-Flores S, De la Mora-De la Mora I, López-Velázquez G. Unraveling the mechanisms of tryptophan fluorescence quenching in the triosephosphate isomerase from Giardia lamblia. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008;1784:1493-500. [PMID: 18620084 DOI: 10.1016/j.bbapap.2008.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2007] [Revised: 05/09/2008] [Accepted: 05/29/2008] [Indexed: 10/21/2022]
36
Tanaka F, Rujkorakarn R, Chosrowjan H, Taniguchi S, Mataga N. Analyses of donor–acceptor distance-dependent rates of photo-induced electron transfer in flavoproteins with three kinds of electron transfer theories. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
37
Chosrowjan H, Taniguchi S, Mataga N, Tanaka F, Todoroki D, Kitamura M. Comparison between Ultrafast Fluorescence Dynamics of FMN Binding Protein from Desulfovibrio vulgaris, Strain Miyazaki, in Solution vs Crystal Phases. J Phys Chem B 2007;111:8695-7. [PMID: 17608527 DOI: 10.1021/jp073702k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
38
Iavarone AT, Patriksson A, van der Spoel D, Parks JH. Fluorescence probe of Trp-cage protein conformation in solution and in gas phase. J Am Chem Soc 2007;129:6726-35. [PMID: 17487969 DOI: 10.1021/ja065092s] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
39
Iavarone AT, Duft D, Parks JH. Shedding Light on Biomolecule Conformational Dynamics Using Fluorescence Measurements of Trapped Ions. J Phys Chem A 2006;110:12714-27. [PMID: 17125284 DOI: 10.1021/jp064933e] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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