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Choi J, Cho DW, Tojo S, Fujitsuka M, Majima T. Configurational changes of heme followed by cytochrome c folding reaction. MOLECULAR BIOSYSTEMS 2014; 11:218-22. [PMID: 25358103 DOI: 10.1039/c4mb00551a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although the folding kinetics of cytochrome c (Cyt-c), ferric or ferrous Cyt-c, has been extensively investigated as a paradigm for a protein folding reaction using various time-resolved spectroscopic techniques, the configurational change of heme associated with the folding reaction from a ferric Cyt-c to a ferrous Cyt-c induced by one-electron reduction has not been elucidated. To address this issue, we investigated the configurational change of heme in the Cyt-c folding process induced by one-electron reduction using a combination of time-resolved resonance Raman spectroscopy and pulse radiolysis. The results presented herein reveal that the reduction of ferric Cyt-c and the ligation of Met80 occur simultaneously within a timescale of approximately 2 μs, and that the ligand binding and exchange of heme depend on the initial configuration of the heme. The rapid ligation of Met80 observed in this study may be attributed to the intramolecular diffusion of Met80 into ferrous Cyt-c with a 5-coordinated high-spin configuration. Conversely, the ligand exchange of a ferrous Cyt-c with a 6-coordinated low-spin configuration was significantly slower.
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Affiliation(s)
- Jungkweon Choi
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
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Lobato L, Bouzhir-Sima L, Yamashita T, Wilson MT, Vos MH, Liebl U. Dynamics of the heme-binding bacterial gas-sensing dissimilative nitrate respiration regulator (DNR) and activation barriers for ligand binding and escape. J Biol Chem 2014; 289:26514-26524. [PMID: 25037216 DOI: 10.1074/jbc.m114.571398] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
DNR (dissimilative nitrate respiration regulator) is a heme-binding transcription factor that is involved in the regulation of denitrification in Pseudomonas aeruginosa. In the ferrous deoxy state, the heme is 6-coordinate; external NO and CO can replace an internal ligand. Using fluorescence anisotropy, we show that high-affinity sequence-specific DNA binding occurs only when the heme is nitrosylated, consistent with the proposed function of DNR as NO sensor and transcriptional activator. This role is moreover supported by the NO "trapping" properties revealed by ultrafast spectroscopy that are similar to those of other heme-based NO sensor proteins. Dissociated CO-heme pairs rebind in an essentially barrierless way. This process competes with migration out of the heme pocket. The latter process is thermally activated (Ea ∼ 7 kJ/mol). This result is compared with other heme proteins, including the homologous CO sensor/transcription factor CooA, variants of the 5-coordinate mycobacterial sensor DosT and the electron transfer protein cytochrome c. This comparison indicates that thermal activation of ligand escape from the heme pocket is specific for systems where an external ligand replaces an internal one. The origin of this finding and possible implications are discussed.
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Affiliation(s)
- Laura Lobato
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France
| | - Latifa Bouzhir-Sima
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France
| | - Taku Yamashita
- Laboratory of Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan, and
| | - Michael T Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester C04 3SQ, United Kingdom
| | - Marten H Vos
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France,.
| | - Ursula Liebl
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France,.
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Kim HM, Park J, Noh HC, Lim M, Chung YK, Kang YK. Unidirectional Photo-induced Charge Separation and Thermal Charge Recombination of Cofacially Aligned Donor-Acceptor System Probed by Ultrafast Visible-Pump/Mid-IR-Probe Spectroscopy. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.2.587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Park J, Lee T, Lim M. Direct Observation of the Low-Spin Fe(III)–NO(radical) Intermediate State during Rebinding of NO to Photodeligated Ferric Cytochrome c. J Phys Chem B 2013; 117:12039-50. [DOI: 10.1021/jp407733g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jaeheung Park
- Department of Chemistry and
Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Taegon Lee
- Department of Chemistry and
Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Manho Lim
- Department of Chemistry and
Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
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Park J, Lee T, Lim M. Vibrational relaxation of NO stretching modes in ferrous NO and ferric NO in model heme. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Kim J, Park J, Lee T, Pak Y, Lim M. Dynamics of geminate rebinding of CO to cytochrome c in guanidine HCl probed by femtosecond vibrational spectroscopy. J Phys Chem B 2013; 117:4934-44. [PMID: 23590118 DOI: 10.1021/jp401481q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Femtosecond vibrational spectroscopy was used to probe the rebinding dynamics of CO to cytochrome c (Cytc) in 1.8 and 7 M guanidine HCl (GdnHCl) after photodeligation of the corresponding CO-bound protein in D2O buffer (pD = 7.4) at 283 K. Geminate rebinding (GR) dynamics of CO to the folded Cytc in 1.8 M GdnHCl (nCytc) is similar to that to chemically modified cytochrome c (cCytc), suggesting that the overall conformations of nCytcCO and cCytcCO are similar. About 86% of the dissociated CO molecules were geminately rebound to nCytc nonexponentially within 1 ns. The efficient GR of CO to the folded Cytc can be attributed to the organized protein matrix near the active site of nCytc that provides an efficient trap for the diffusing CO ligand after photodissociation. Although the concentration of nCytc did not affect its GR yield of CO, GR yield of CO to the unfolded Cytc in 7 M GdnHCl (uCytc) increased from 5 to 30% as the protein concentration increased from 0.3 to 9 mM. Time-resolved spectra of the (13)CO dissociated from both 9 mM nCytc(13)CO and 9 mM uCytc(13)CO showed a growing band with a peak at 2090 cm(-1) on the picosecond time scale, which was assigned to (13)CO in D2O solvent. At 1 ns, the fraction of the CO band in the solvent was about 10% of the nascent photodeligated protein in nCytc and more than 50% in the concentrated uCytc. Whereas a small opening in the active site of nCytc is responsible for the ultrafast escape of CO to solution in the folded protein, a large fraction of the CO escape to the solvent in uCytc results from the denatured structure of the active site in the unfolded protein. The spectrum of the CO dissociated from the concentrated uCytcCO contained a band that decayed as efficiently as that for the folded protein, suggesting that some fraction of uCytcCO might form aggregates even in 7 M denaturant, such that the aggregate acts as an efficient trap for the diffusing CO after deligation. No hint of precipitate in the concentrated uCytcCO and protein refolding upon dilution of the GdnHCl indicate that the aggregate does not grow continuously but remains as a soluble oligomer. The delayed appearance of the solvated CO and the inefficient GR of CO in uCytcCO suggest that the monomeric unfolded CytcCO so loosely arranged that the protein matrix cannot trap CO efficiently but the bound CO is still buried within hydrophobic residues even under the harsh denaturation condition.
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Affiliation(s)
- Jooyoung Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 609-735 Korea
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Park J, Lee T, Lim M. Geminate rebinding dynamics of nitric oxide to ferric hemoglobin in D2O solution. Photochem Photobiol Sci 2013; 12:1008-15. [PMID: 23512239 DOI: 10.1039/c3pp50014d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Femtosecond mid-infrared (mid-IR) spectroscopy was used to probe geminate rebinding (GR) dynamics of photo-released nitric oxide (NO) to ferric hemoglobin (Hb(III)) in D2O solution at room temperature. Time-resolved vibrational spectra exhibit two overlapping NO bands for NO-bound Hb(III) (Hb(III)NO), a major band at 1925 cm(-1) (89%) and a minor one at 1905 cm(-1) (11%), suggesting that Hb(III)NO has at least two conformational substates. Both bands decay nonexponentially, each with a different time scale, and the decays are described by a stretched exponential function; the major band's decay is described by 0.96 exp(-t/40 ps)(0.86) + 0.04 and the minor band's decay is described by exp(-t/85 ps)(0.75). These decays arise mainly from the GR of the photo-released NO to Hb(III), indicating that the bound state's conformer influences the NO binding. In particular, the His64 residue, known to have inward conformation in the major band and outward conformation in the minor band, plays a significant role in controlling the binding of NO to Hb(III). The GR of NO to ferric Hb is slower than that to ferrous Hb, which shows fast and efficient GR due to the high reactivity of NO to the heme Fe(ii). The slower GR of NO to Hb(III) may be caused by the lower reactivity of NO to the heme Fe(iii).
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Affiliation(s)
- Jaeheung Park
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
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Rebinding kinetics of dissociated amino acid ligand and carbon monoxide to ferrous microperoxidase-11 in aqueous solution. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4788-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Kim J, Park J, Lee T, Lim M. Dynamics of Geminate Rebinding of NO with Cytochrome c in Aqueous Solution Using Femtosecond Vibrational Spectroscopy. J Phys Chem B 2012; 116:13663-71. [PMID: 23113639 DOI: 10.1021/jp308468j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jooyoung Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735,
Korea
| | - Jaeheung Park
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735,
Korea
| | - Taegon Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735,
Korea
| | - Manho Lim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735,
Korea
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Lapini A, Di Donato M, Patrizi B, Marcelli A, Lima M, Righini R, Foggi P, Sciamanna N, Boffi A. Carbon monoxide recombination dynamics in truncated hemoglobins studied with visible-pump midIR-probe spectroscopy. J Phys Chem B 2012; 116:8753-61. [PMID: 22759230 DOI: 10.1021/jp3019149] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbon monoxide recombination dynamics upon photodissociation with visible light has been characterized by means of ultrafast visible-pump/MidIR probe spectroscopy for the truncated hemoglobins from Thermobifida fusca and Bacillus subtilis. Photodissociation has been induced by exciting the sample at two different wavelengths: 400 nm, corresponding to the heme absorption in the B-band, and 550 nm, in the Q-bands. The bleached iron-CO coordination band located at 1850-1950 cm(-1) and the free CO absorption band in the region 2050-2200 cm(-1) have been observed by probe pulses tuned in the appropriate infrared region. The kinetic traces measured at 1850-1950 cm(-1) reveal multiexponential subnanosecond dynamics that have been interpreted as arising from fast geminate recombination of the photolyzed CO. A compared analysis of the crystal structure of the two proteins reveals a similar structure of their distal heme pocket, which contains conserved polar and aromatic amino acid residues closely interacting with the iron ligand. Although fast geminate recombination is observed in both proteins, several kinetic differences can be evidenced, which can be interpreted in terms of a different structural flexibility of the corresponding heme distal pockets. The analysis of the free CO band-shape and of its dynamic evolution brings out novel features about the nature of the docking site inside the protein cavity.
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Affiliation(s)
- Andrea Lapini
- LENS (European Laboratory for Nonlinear Spectroscopy), via N. Carrara 1, 50019 Sesto Fiorentino (FI), Italy
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Adamczyk K, Candelaresi M, Kania R, Robb K, Bellota-Antón C, Greetham GM, Pollard MR, Towrie M, Parker AW, Hoskisson PA, Tucker NP, Hunt NT. The effect of point mutation on the equilibrium structural fluctuations of ferric Myoglobin. Phys Chem Chem Phys 2012; 14:7411-9. [DOI: 10.1039/c2cp23568d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Nuernberger P, Lee KF, Bonvalet A, Bouzhir-Sima L, Lambry JC, Liebl U, Joffre M, Vos MH. Strong Ligand–Protein Interactions Revealed by Ultrafast Infrared Spectroscopy of CO in the Heme Pocket of the Oxygen Sensor FixL. J Am Chem Soc 2011; 133:17110-3. [DOI: 10.1021/ja204549n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Patrick Nuernberger
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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Choi J, Yang C, Kim J, Ihee H. Protein Folding Dynamics of Cytochrome c Seen by Transient Grating and Transient Absorption Spectroscopies. J Phys Chem B 2011; 115:3127-35. [DOI: 10.1021/jp106588d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jungkweon Choi
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Cheolhee Yang
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Jeongho Kim
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Hyotcherl Ihee
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
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Relationship between protein structural fluctuations and rebinding dynamics in ferric haem nitrosyls. Biochem J 2011; 433:459-68. [DOI: 10.1042/bj20101496] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The interaction of nitric oxide (NO) with haem proteins is widespread in biology. In the current paper, we present the first ultrafast 2D-IR (two-dimensional infrared) spectroscopic analysis of haem nitrosylation, which has been combined with time-resolved IR pump–probe studies to investigate the relationship between equilibrium vibrational dynamics of the haem environment and ligand rebinding behaviour following photolysis of NO from the Fe(III)–NO site. Studies of two haem proteins, Mb (myoglobin) and Cc (cytochrome c), which play different physiological roles, reveal marked contrasts in the ultrafast fluctuations of the protein pockets containing the haem, showing that the Mb pocket is somewhat more flexible than that of Cc. This correlates strongly with slower observed photolysis rebinding kinetics of Mb–NO compared with Cc–NO, and indicates a direct link between ultrafast fluctuations and biological functionality. Furthermore, this indicates the validity of linear response theories in relation to protein ligand binding. Finally, 2D-IR shows that Cc–NO displays two distinct structural sub-sites at room temperature that do not exchange on the timescales accessible via the NO vibrational lifetime.
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Kim JY, Park JH, Chowdhury SA, Lim MH. Picosecond Dynamics of CN--Ligated Ferric Cytochrome c after Photoexcitation Using Time-resolved Vibrational Spectroscopy. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.12.3771] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Park J, Lee T, Lim M. Viscosity-Dependent Dynamics of CO Rebinding to Microperoxidase-8 in Glycerol/Water Solution. J Phys Chem B 2010; 114:10897-904. [DOI: 10.1021/jp1050436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jaeheung Park
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735 Korea
| | - Taegon Lee
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735 Korea
| | - Manho Lim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735 Korea
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Benabbas A, Ye X, Kubo M, Zhang Z, Maes EM, Montfort WR, Champion PM. Ultrafast dynamics of diatomic ligand binding to nitrophorin 4. J Am Chem Soc 2010; 132:2811-20. [PMID: 20121274 DOI: 10.1021/ja910005b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nitrophorin 4 (NP4) is a heme protein that stores and delivers nitric oxide (NO) through pH-sensitive conformational change. This protein uses the ferric state of a highly ruffled heme to bind NO tightly at low pH and release it at high pH. In this work, the rebinding kinetics of NO and CO to NP4 are investigated as a function of iron oxidation state and the acidity of the environment. The geminate recombination process of NO to ferrous NP4 at both pH 5 and pH 7 is dominated by a single approximately 7 ps kinetic phase that we attribute to the rebinding of NO directly from the distal pocket. The lack of pH dependence explains in part why NP4 cannot use the ferrous state to fulfill its function. The kinetic response of ferric NP4NO shows two distinct phases. The relative geminate amplitude of the slower phase increases dramatically as the pH is raised from 5 to 8. We assign the fast phase of NO rebinding to a conformation of the ferric protein with a closed hydrophobic pocket. The slow phase is assigned to the protein in an open conformation with a more hydrophilic heme pocket environment. Analysis of the ultrafast kinetics finds the equilibrium off-rate of NO to be proportional to the open state population as well as the pH-dependent amplitude of escape from the open pocket. When both factors are considered, the off-rate increases by more than an order of magnitude as the pH changes from 5 to 8. The recombination of CO to ferrous NP4 is observed to have a large nonexponential geminate amplitude with rebinding time scales of approximately 10(-11)-10(-9) s at pH 5 and approximately 10(-10)-10(-8) s at pH 7. The nonexponential CO rebinding kinetics at both pH 5 and pH 7 are accounted for using a simple model that has proven effective for understanding CO binding in a variety of other heme systems (Ye, X.; et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14682).
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Affiliation(s)
- Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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