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Im J, Lee J, Lee JH. Surface Accessibility of an Intrinsically Disordered Protein Probed by 2D Time-Resolved Laser-Assisted NMR Spectroscopy. J Am Chem Soc 2022; 144:17010-17021. [PMID: 36083135 DOI: 10.1021/jacs.2c06309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Probing the protein surface accessibility of different residues is a powerful way of characterizing the overall conformation of intrinsically disordered proteins (IDPs). We present a two-dimensional (2D) time-resolved photo-CIDNP (TR-CIDNP) experiment suitable for IDP analysis. Pulse stretching of high-power laser pulses, band-selective decoupling of 13Cα, and simultaneous application of radiofrequency and laser pulses were implemented to quantitatively analyze the IDP surface at ultrahigh resolution. Comparative analysis with other methods that measure protein surface accessibility validated the newly developed method and emphasized the importance of dye charge in photo-CIDNP. Using the neutral riboflavin dye, surface accessibilities were measured to be nearly identical for the four Tyr residues of α-synuclein (α-Syn), whose 1Hα-13Cα correlations were well-resolved in the 2D TR-CIDNP spectrum. Having confirmed the similarity between the time-resolved and steady-state photo-CIDNP results for α-Syn, we used the more sensitive latter method to show that divalent cations induce compaction of the C-terminal region and release of the N-terminal region of α-Syn. The photo-CIDNP method presented herein can be used as an orthogonal and independent method for investigating important biological processes associated with changes in the overall IDP conformation.
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Affiliation(s)
- Jonghyuk Im
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jongchan Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jung Ho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea.,Advanced Institutes of Convergence Technology, Suwon, Gyeonggi-do 16229, Korea
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2
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Savina ED, Tsentalovich YP, Sherin PS. UV-A induced damage to lysozyme via Type I photochemical reactions sensitized by kynurenic acid. Free Radic Biol Med 2020; 152:482-493. [PMID: 31751763 DOI: 10.1016/j.freeradbiomed.2019.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023]
Abstract
In this work we studied the mechanisms of Type I photodamage to a model protein, hen egg white lysozyme (HEWL), sensitized by kynurenic acid (KNA) - one of the most efficient photosensitizers of the human eye lens present in trace amounts within tissue. The kynurenic acid radical, KNA•-, formed in the quenching of triplet KNA by HEWL, can be readily oxidized by molecular oxygen with the formation of superoxide anion radical O2•-. This leads to two ways of damage to proteins: either via the direct reactions between KNA•- and HEWL• radicals (Type Ia) or via the reactions between superoxide anion O2•- and HEWL• radicals (Type Ib). Our results demonstrate significant degradation of the protein during Type Ia photolysis with the formation of various oligomeric and oxygenated forms of HEWL and several deoxygenated products of KNA. Liquid chromatography-mass spectrometry analysis revealed the cross-linking of HEWL via tryptophan (Trp62) and tyrosine (Tyr23) residues and, for the first time, the covalent binding of KNA to protein via tryptophan (Trp62 and Trp123) residues. It was found that Type Ib reactions lead to substantially smaller damage to HEWL; the degradation quantum yields (Φdeg) of HEWL are 1.3 ± 0.3% and 0.12 ± 0.03% for Type Ia and Ib photolyses, respectively. Low Φdeg values for both types of photolysis indicate the Back Electron Transfer (BET) with the restoration of initial reagents as the main radical decay path with significantly higher BET efficiency in the case of Type Ib reactions. Therefore, in essentially oxygen-free tissues like the eye lens, the direct radical reactions via Type Ia mechanism could induce significantly larger damage to proteins, leading to their cross-linking and oxidation. The accumulation of these modifications can cause the development of various diseases, in particular, cataracts in the eye lens.
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Affiliation(s)
- Ekaterina D Savina
- International Tomography Center SB RAS, Institutskaya str. 3A, 630090, Novosibirsk, Russia; Novosibirsk State University, Pirogova str. 2, 630090, Novosibirsk, Russia
| | - Yuri P Tsentalovich
- International Tomography Center SB RAS, Institutskaya str. 3A, 630090, Novosibirsk, Russia; Novosibirsk State University, Pirogova str. 2, 630090, Novosibirsk, Russia
| | - Peter S Sherin
- International Tomography Center SB RAS, Institutskaya str. 3A, 630090, Novosibirsk, Russia; Novosibirsk State University, Pirogova str. 2, 630090, Novosibirsk, Russia.
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3
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Morozova OB, Ivanov KL. Time-Resolved Chemically Induced Dynamic Nuclear Polarization of Biologically Important Molecules. Chemphyschem 2018; 20:197-215. [DOI: 10.1002/cphc.201800566] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/11/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Olga B. Morozova
- International Tomography Center; Institutskaya 3a 630090 Novosibirsk Russia
- Novosibirsk State University; Pirogova 2 630090 Novosibirsk Russia
| | - Konstantin L. Ivanov
- International Tomography Center; Institutskaya 3a 630090 Novosibirsk Russia
- Novosibirsk State University; Pirogova 2 630090 Novosibirsk Russia
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4
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Morozova OB, Panov MS, Fishman NN, Yurkovskaya AV. Electron transfer vs. proton-coupled electron transfer as the mechanism of reaction between amino acids and triplet-excited benzophenones revealed by time-resolved CIDNP. Phys Chem Chem Phys 2018; 20:21127-21135. [DOI: 10.1039/c8cp03591a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We use proportionality between NMR signal enhancements in geminate products and hyperfine coupling constants in transient radicals to elucidate reaction mechanism in detail.
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Affiliation(s)
- Olga B. Morozova
- International Tomography Center
- 630090 Novosibirsk
- Russia
- Novosibirsk State University
- 630090 Novosibirsk
| | - Mikhail S. Panov
- International Tomography Center
- 630090 Novosibirsk
- Russia
- Novosibirsk State University
- 630090 Novosibirsk
| | - Natalya N. Fishman
- International Tomography Center
- 630090 Novosibirsk
- Russia
- Novosibirsk State University
- 630090 Novosibirsk
| | - Alexandra V. Yurkovskaya
- International Tomography Center
- 630090 Novosibirsk
- Russia
- Novosibirsk State University
- 630090 Novosibirsk
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5
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Sormacheva ED, Sherin PS, Tsentalovich YP. Dimerization and oxidation of tryptophan in UV-A photolysis sensitized by kynurenic acid. Free Radic Biol Med 2017; 113:372-384. [PMID: 29024806 DOI: 10.1016/j.freeradbiomed.2017.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 11/24/2022]
Abstract
Photoinduced generation of radicals in the eye lens may play an important role in the modification of proteins leading to their coloration, aggregation, and insolubilization. The radicals can be formed via the reactions of photoexcited endogenous chromophores of the human lens with lens proteins, in particular with tryptophan residues. In the present work we studied the reactions induced by UV-A (315-400nm) light between kynurenic acid (KNA), an effective photosensitizer present in the human lens, and N-acetyl-L-tryptophan (NTrpH) under aerobic and anaerobic conditions. Our results show that the reaction mechanism strongly depends on the presence of oxygen in solution. Under aerobic conditions, the generation of singlet oxygen is the major channel of the effective NTrpH oxidation. In argon-bubbled solutions, the quenching of triplet KNA by NTrpH results in the formation of KNA•- and NTrp• radicals. Under laser pulse irradiation, when the radical concentration is high, the main pathway of the radical decay is the back electron transfer with the restoration of initial reagents. Other reactions include (i) the radical combination yielding NTrp dimers and (ii) the oxygen atom transfer from KNA•- to NTrp• with the formation of oxidized NTrp species and deoxygenated KNA products. In continuous-wave photolysis, even trace amounts of molecular oxygen are sufficient to oxidize the majority of KNA•- radicals with the rate constant of (2.0 ± 0.2) × 109M-1s-1, leading to the restoration of KNA and the formation of superoxide radical O2•-. The latter reacts with NTrp• via either the radical combination to form oxidized NTrp (minor pathway), or the electron transfer to restore NTrpH in the ground state (major pathway). As the result, the quantum yields of the starting compound decomposition under continuous-wave anaerobic photolysis are rather low: 1.6% for NTrpH and 0.02% for KNA. The photolysis of KNA with alpha-crystallin yields the same deoxygenated KNA products as the photolysis of KNA with NTrpH, indicating the similarity of the photolysis mechanisms. Thus, inside the eye lens KNA can sensitize both protein photooxidation and protein covalent cross-linking with the minor self-degradation. This may play an important role in the lens protein modifications during the normal aging and cataract development.
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Affiliation(s)
- Ekaterina D Sormacheva
- International Tomography Center SB RAS, Institutskaya str. 3A, 630090 Novosibisrk, Russia
| | - Peter S Sherin
- International Tomography Center SB RAS, Institutskaya str. 3A, 630090 Novosibisrk, Russia; Novosibirsk State University, Pirogova str. 2, 630090 Novosibisrk, Russia.
| | - Yuri P Tsentalovich
- International Tomography Center SB RAS, Institutskaya str. 3A, 630090 Novosibisrk, Russia; Novosibirsk State University, Pirogova str. 2, 630090 Novosibisrk, Russia
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6
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Sherin PS, Zelentsova EA, Sormacheva ED, Yanshole VV, Duzhak TG, Tsentalovich YP. Aggregation of α-crystallins in kynurenic acid-sensitized UVA photolysis under anaerobic conditions. Phys Chem Chem Phys 2016; 18:8827-39. [DOI: 10.1039/c5cp06693j] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive protein aggregation is the major outcome of kynurenic acid-sensitized photolysis of α-crystallin under anaerobic conditions. The main lens antioxidants ascorbate and glutathione effectively inhibit the protein aggregation.
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Affiliation(s)
- P. S. Sherin
- International Tomography Center of Siberian Branch of Russian Academy of Science
- Novosibirsk
- Russia
- Novosibirsk State University
- Novosibirsk
| | - E. A. Zelentsova
- International Tomography Center of Siberian Branch of Russian Academy of Science
- Novosibirsk
- Russia
- Novosibirsk State University
- Novosibirsk
| | - E. D. Sormacheva
- International Tomography Center of Siberian Branch of Russian Academy of Science
- Novosibirsk
- Russia
- Novosibirsk State University
- Novosibirsk
| | - V. V. Yanshole
- International Tomography Center of Siberian Branch of Russian Academy of Science
- Novosibirsk
- Russia
- Novosibirsk State University
- Novosibirsk
| | - T. G. Duzhak
- International Tomography Center of Siberian Branch of Russian Academy of Science
- Novosibirsk
- Russia
- Novosibirsk State University
- Novosibirsk
| | - Yu. P. Tsentalovich
- International Tomography Center of Siberian Branch of Russian Academy of Science
- Novosibirsk
- Russia
- Novosibirsk State University
- Novosibirsk
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Abramova TV, Morozova OB, Silnikov VN, Yurkovskaya AV. Synthesis of nucleotide-amino acid conjugates designed for photo-CIDNP experiments by a phosphotriester approach. Beilstein J Org Chem 2013; 9:2898-909. [PMID: 24367455 PMCID: PMC3869286 DOI: 10.3762/bjoc.9.326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/15/2013] [Indexed: 11/23/2022] Open
Abstract
Conjugates of 2’-deoxyguanosine, L-tryptophan and benzophenone designed to study pathways of fast radical reactions by the photo Chemically Induced Dynamic Nuclear Polarization (photo-CIDNP) method were obtained by the phosphotriester block liquid phase synthesis. The phosphotriester approach to the oligonucleotide synthesis was shown to be a versatile and economic strategy for preparing the required amount of high quality samples of nucleotide–amino acid conjugates.
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Affiliation(s)
- Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia ; Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia
| | - Olga B Morozova
- Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia ; International Tomography Center, SB RAS, Institutskaya 3a, Novosibirsk 630090, Russia
| | - Vladimir N Silnikov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
| | - Alexandra V Yurkovskaya
- Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia ; International Tomography Center, SB RAS, Institutskaya 3a, Novosibirsk 630090, Russia
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8
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Nguyen TX, Grampp G, Yurkovskaya A, Lukzen N. Kinetics of the oxidation of thymine and thymidine by triplet 2,2'-dipyridyl in aqueous solutions at different pH values. J Phys Chem A 2013; 117:7655-60. [PMID: 23906227 PMCID: PMC3751068 DOI: 10.1021/jp4022882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 06/21/2013] [Indexed: 01/20/2023]
Abstract
The photo-oxidation of the nucleobase, thymine (Thy), and nucleoside, thymidine (dThy), by dipyridyl (DP) has been investigated in aqueous solution using time-resolved laser flash photolysis. The pH dependence of the oxidation rate constants is measured within a large pH scale. As a consequence, the chemical reactivity of the reactants existing in solution at a certain range of pH is predicted. Bimolecular rate constants of the quenching reactions between triplet dipyridyl and thymine and thymidine are, respectively, kq = 2.4 × 10(7) M(-1) s(-1) (pH < 5.8) and kq = 1.0 × 10(7) M(-1) s(-1) (5.8 < pH < 9.8). Cyclic voltammetry was used to measure the potentials of thymine oxidation and dipyridyl reduction in water at pH < 7. Both results give hints for a proton coupled electron-transfer (PCET) reaction from thymine to triplet dipyridyl.
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Affiliation(s)
- Truong X. Nguyen
- Institute of Physical and Theoretical
Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Günter Grampp
- Institute of Physical and Theoretical
Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Alexandra
V. Yurkovskaya
- International Tomography
Center, Institutskaya 3a, 630090 Novosibirsk, Russia
- Novosibirsk State
University, Pirogova 2, 630090 Novosibirsk, Russia
| | - Nikita Lukzen
- International Tomography
Center, Institutskaya 3a, 630090 Novosibirsk, Russia
- Novosibirsk State
University, Pirogova 2, 630090 Novosibirsk, Russia
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Wallrapp FH, Voityuk AA, Guallar V. In-silico assessment of protein-protein electron transfer. a case study: cytochrome c peroxidase--cytochrome c. PLoS Comput Biol 2013; 9:e1002990. [PMID: 23555224 PMCID: PMC3605091 DOI: 10.1371/journal.pcbi.1002990] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/28/2013] [Indexed: 11/28/2022] Open
Abstract
The fast development of software and hardware is notably helping in closing the gap between macroscopic and microscopic data. Using a novel theoretical strategy combining molecular dynamics simulations, conformational clustering, ab-initio quantum mechanics and electronic coupling calculations, we show how computational methodologies are mature enough to provide accurate atomistic details into the mechanism of electron transfer (ET) processes in complex protein systems, known to be a significant challenge. We performed a quantitative study of the ET between Cytochrome c Peroxidase and its redox partner Cytochrome c. Our results confirm the ET mechanism as hole transfer (HT) through residues Ala194, Ala193, Gly192 and Trp191 of CcP. Furthermore, our findings indicate the fine evolution of the enzyme to approach an elevated turnover rate of 5.47×106 s−1 for the ET between Cytc and CcP through establishment of a localized bridge state in Trp191. We have developed a protocol capable of describing long-range electron transfer mechanisms at an atomic detailed level. We demonstrate the maturity of the computational techniques in obtaining a quantitative view of the Cytochrome c Peroxidase/Cytochrome c electron transfer process, known to be a significant challenge. In excellent agreement with experimental data, our results allow for the description of the electron transfer pathway, its mechanism and the electron transfer rate at a quantitative level. The overall protocol is free of parameterization and can be applied to any complex electron transfer process. Furthermore, the results reveal the fine enzyme evolution of this protein-protein complex to optimize its electron transfer rate by a localized bridge state.
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Affiliation(s)
- Frank H. Wallrapp
- Department of Life Sciences, Barcelona Supercomputing Center, Nexus II Building, Barcelona, Spain
| | - Alexander A. Voityuk
- Department of Computational Chemistry, University of Girona, Girona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Victor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center, Nexus II Building, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- * E-mail:
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Lee M, Urata SM, Aguilera JA, Perry CC, Milligan JR. Modeling the Influence of Histone Proteins on the Sensitivity of DNA to Ionizing Radiation. Radiat Res 2012; 177:152-63. [DOI: 10.1667/rr2812.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Chakraborty B, Roy AS, Dasgupta S, Basu S. Magnetic Field Effect Corroborated with Docking Study to Explore Photoinduced Electron Transfer in Drug−Protein Interaction. J Phys Chem A 2010; 114:13313-25. [DOI: 10.1021/jp109604a] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Brotati Chakraborty
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata-700064, India, and Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
| | - Atanu Singha Roy
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata-700064, India, and Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
| | - Swagata Dasgupta
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata-700064, India, and Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
| | - Samita Basu
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata-700064, India, and Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
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Zhang Y, Görner H. Flavin-sensitized Photo-oxidation of Lysozyme and Serum Albumin. Photochem Photobiol 2009; 85:943-8. [DOI: 10.1111/j.1751-1097.2009.00547.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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ZHAO YY, MA JY, ZHAO XJ, LI XY. Solvent Reorganization Energy of Intramolecular Electron Transfer in Peptides Involving Tryptophan and Tyrosine. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ivanov KL, Yurkovskaya AV, Hore PJ, Lukzen NN. Theoretical study of the CIDNP kinetics of the reaction of a photo-excited dye with a reactive spot on the surface of a sphere: application to CIDNP of proteins. Mol Phys 2006. [DOI: 10.1080/00268970600618442] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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