1
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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]
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2
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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]
Abstract
Dihydromethanopterin reductase (DmrB), is a naturally occurring cage protein found in various archaeal and a few bacterial species. It exists as 24mer with cubic geometry where 8 trimeric subunits are present at the corners of each cube. Each trimer is made up of three monomeric units and six FMN, where two molecules of FMN are present at the interface of each monomer. DmrB is involved in the conversion of dihydromethanopterin to tetrahydromethanopterin using FMN as a redox equivalent. In the present study, we have used spectroscopic and biochemical techniques along with complementary bio-informatic work to understand the assembly principles of the DmrB. Our results show a concentration dependant self-assembly of DmrB which is mediated by ionic interactions. The co-factor FMN stabilizes and preserves the secondary and quaternary structure of DmrB against thermal insult, indicating that the higher order assembly of DmrB is very thermostable. Our work provides an interesting piece of information regarding the role of the co-factors in the thermostability of these classes of cage proteins. The understanding of the assembly and disassembly of this thermostable cage would enable the downstream usage of this system in various nano-biotechnological applications.
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3
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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]
Abstract
Hybrid quantum mechanical and molecular mechanical (QM/MM) approaches facilitate computational modeling of large biological and materials systems. Typically, in QM/MM, a small region of the system is modeled with an accurate quantum mechanical method and its surroundings with a more efficient alternative, such as a classical force field or the effective fragment potential (EFP). The reliability of QM/MM calculations depends largely on the treatment of interactions between the two subregions, also known as embedding. The polarizable embedding, which allows mutual polarization between solvent and solute, is considered to be essential for describing electronic excitations in polar solvents. In this work, we employ the QM/EFP model and extend the polarizable embedding by incorporating two short-range terms-a charge penetration correction to the electrostatic term and the exchange-repulsion term-both of which are modeled with one-electron contributions to the quantum Hamiltonian. We evaluate the accuracy of these terms by computing excitation energies across 37 molecular clusters consisting of biologically relevant chromophores surrounded by polar solvent molecules. QM/EFP excitation energies are compared to the fully quantum mechanical calculations with the configuration interaction singles (CIS) method. We find that the charge penetration correction diminishes the accuracy of the QM/EFP calculations. On the other hand, while the effect of exchange-repulsion is negligible for most ππ* transitions, the exchange-repulsion significantly improves description of nπ* transitions with blue solvatochromic shifts. As a result, addition of the exchange-repulsion term improves the overall accuracy of QM/EFP. Performances of QM/EFP models remain similar when excitation energies are modeled with cc-pVDZ and aug-cc-pVDZ basis sets.
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Affiliation(s)
- Claudia I Viquez Rojas
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
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4
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Affiliation(s)
- William W. Parson
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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5
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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]
Abstract
Redox proteins and enzymes are at risk of irreversible oxidative damage from highly oxidizing intermediates generated in the active site in the case of unsuccessful functional reaction. Chains of tyrosine and/or tryptophan residues have been recently proposed to provide protection to the active site and the whole protein by delivering oxidizing equivalents (holes) out of the protein via a multistep hopping mechanism. In the present work we use a hybrid quantum/classical theoretical-computational methodology based on the perturbed matrix method and on molecular dynamics simulations to calculate the oxidation potential difference along a chain of tyrosine and tryptophan residues in a human redox enzyme of major importance, a superoxide dismutase, which acts as antioxidant defense. We show that the hole hopping is thermodynamically favored along such a chain and that the hopping propensity is strongly affected by the protein environment and in particular by the active site and its second coordination sphere.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Stefano Corni
- Department of Chemical Sciences , University of Padova , I-35131 Padova , Italy
- Center S3 , CNR-Institute of Nanoscience , Via Campi 213/A , 41125 Modena , Italy
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6
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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]
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7
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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]
Abstract
Some years ago we developed a theoretical-computational hybrid quantum/classical methodology, the Perturbed Matrix Method (PMM), to be used in conjunction with molecular dynamics simulations for the investigation of chemical processes in complex systems, that proved to be a valuable tool for the simulation of relevant experimental observables, e.g., spectroscopic signals, reduction potentials, kinetic constants. In typical PMM calculations the quantum sub-part of the system, the quantum centre, is embedded into an external perturbing field providing a perturbation operator explicitly calculated up to the dipolar terms. In this paper we further develop the PMM approach, beyond the dipolar terms in the perturbation operator expansion, by including explicitly the quadrupolar terms and/or by expanding the perturbation operator on each atom of the quantum centre. These different levels of the perturbation operator expansion, providing different levels of theory, have been tested by calculating three different spectroscopic observables: the spectral signal of liquid water and aqueous benzene due to the lowest energy electronic excitation and the infrared amide I band of aqueous trans-N-methylacetamide. All the systems tested show that, even though the previous PMM level of theory is already capable of reproducing the main features of the spectral signal, the higher levels of theory improve the quantitative reproduction of the spectral details.
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Affiliation(s)
- Laura Zanetti-Polzi
- Dipartimento di Scienze Fisiche e Chimiche, University of L'Aquila, via Vetoio (Coppito 1), 67010 L'Aquila, Italy
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8
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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]
Affiliation(s)
- Giovanni Valenti
- Department of Chemistry “ G. Ciamician”; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Matteo Iurlo
- Department of Chemistry “ G. Ciamician”; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Rosa María Claramunt
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias; Universidad Nacional de Educación a Distancia (UNED); Paseo Senda del Rey 9 28040 Madrid Spain
| | - Gianluca Accorsi
- CNR NANOTEC, Institute of Nanotechnology c/o Campus Ecotekne; University of Salento; Via Monteroni 73100 Lecce Italy
| | - Francesco Paolucci
- Department of Chemistry “ G. Ciamician”; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - M. Ángeles Farrán
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias; Universidad Nacional de Educación a Distancia (UNED); Paseo Senda del Rey 9 28040 Madrid Spain
| | - Massimo Marcaccio
- Department of Chemistry “ G. Ciamician”; University of Bologna; Via Selmi 2 40126 Bologna Italy
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9
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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]
Abstract
Comprehensive and programmable protein mutagenesis is critical for understanding structure-function relationships and improving protein function. There is thus a need for robust and unbiased molecular biological approaches for the construction of the requisite comprehensive protein libraries. Here we demonstrate that plasmid recombineering is a simple and robust in vivo method for the generation of protein mutants for both comprehensive library generation as well as programmable targeting of sequence space. Using the fluorescent protein iLOV as a model target, we build a complete mutagenesis library and find it to be specific and comprehensive, detecting 99.8% of our intended mutations. We then develop a thermostability screen and utilize our comprehensive mutation data to rapidly construct a targeted and multiplexed library that identifies significantly improved variants, thus demonstrating rapid protein engineering in a simple protocol.
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Affiliation(s)
- Sean A. Higgins
- Department
of Molecular and Cell Biology, and ‡Department of Chemistry, UC Berkeley, Berkeley, California 94720, United States
| | - Sorel V. Y. Ouonkap
- Department
of Molecular and Cell Biology, and ‡Department of Chemistry, UC Berkeley, Berkeley, California 94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, and ‡Department of Chemistry, UC Berkeley, Berkeley, California 94720, United States
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10
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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]
Abstract
Flavoproteins, containing flavin chromophores, are enzymes capable of transferring electrons at very high speeds. The ultrafast photoinduced electron-transfer (ET) kinetics of riboflavin binding protein to the excited riboflavin was studied by femtosecond spectroscopy and found to occur within a few hundred femtoseconds [ Zhong and Zewail, Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11867-11872 ]. This ultrafast kinetics was attributed to the presence of two aromatic rings that could transfer the electron to riboflavin: the side chains of tryptophan 156 and tyrosine 75. However, the underlying ET mechanism remained unclear. Here, using a hybrid quantum mechanical-molecular dynamics approach, we perform ET dynamics simulations taking into account the motion of the protein and the solvent upon ET. This approach reveals that ET occurs via a major reaction channel involving tyrosine 75 (83%) and a minor one involving tryptophan 156 (17%). We also show that the protein environment is designed to ensure the fast quenching of the riboflavin excited state.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00185 Rome, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
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11
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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]
Affiliation(s)
- William W. Parson
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
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12
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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]
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13
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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
Abstract
In enzyme systems where fast motions are thought to contribute to H-transfer efficiency, the distance between hydrogen donor and acceptor is a very important factor. Sub-ångstrom changes in donor-acceptor distance can have a large effect on the rate of reaction, so a sensitive probe of these changes is a vital tool in our understanding of enzyme function. In this study we use ultrafast transient absorption spectroscopy to investigate the photoinduced electron transfer rates, which are also very sensitive to small changes in distance, between coenzyme analog, NAD(P)H4, and the isoalloxazine center in the model flavoenzymes morphinone reductase (wild-type and selected variants) and pentaerythritol tetranitrate reductase (wild-type). It is shown that upon addition of coenzyme to the protein the rate of photoinduced electron transfer is increased. By comparing the magnitude of this increase with existing values for NAD(P)H4-FMN distances, based on charge-transfer complex absorbance and experimental kinetic isotope effect reaction data, we show that this method can be used as a sensitive probe of donor-acceptor distance in a range of enzyme systems.
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Affiliation(s)
- Samantha J O Hardman
- Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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14
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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]
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15
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Abstract
Principles behind quenching of tryptophan (Trp) fluorescence are updated and extended in light of recent 100-ns and 1-μs molecular dynamics (MD) trajectories augmented with quantum mechanical (QM) calculations that consider electrostatic contributions to wavelength shifts and quenching. Four studies are summarized, including (1) new insight into the single exponential decay of NATA, (2) a study revealing how unsuspected rotamer transitions affect quenching of Trp when used as a probe of protein folding, (3) advances in understanding the origin of nonexponential decay from 100-ns simulations on 19 Trps in 16 proteins, and (4) the correlation of wavelength with lifetime for decay-associated spectra (DAS). Each study strongly reinforces the concept that-for Trp-electron transfer-based quenching is controlled much more by environment electrostatic factors affecting the charge transfer (CT) state energy than by distance dependence of electronic coupling. In each case, water plays a large role in unexpected ways.
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16
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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]
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17
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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]
Affiliation(s)
- Davood Farmanzadeh
- Department of Physical Chemistry, Faculty of Chemistry, University of Mazandaran
| | - Meysam Najafi
- Department of Physical Chemistry, Faculty of Chemistry, University of Mazandaran
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18
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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
Abstract
In many bacteria the flavoenzyme thymidylate synthase ThyX produces the DNA nucleotide deoxythymidine monophosphate from dUMP, using methylenetetrahydrofolate as carbon donor and NADPH as hydride donor. Because all three substrates bind in close proximity to the catalytic flavin adenine dinucleotide group, substantial flexibility of the ThyX active site has been hypothesized. Using femtosecond time-resolved fluorescence spectroscopy, we have studied the conformational heterogeneity and the conformational interconversion dynamics in real time in ThyX from the hyperthermophilic bacterium Thermotoga maritima. The dynamics of electron transfer to excited flavin adenine dinucleotide from a neighboring tyrosine residue are used as a sensitive probe of the functional dynamics of the active site. The fluorescence decay spanned a full three orders of magnitude, demonstrating a very wide range of conformations. In particular, at physiological temperatures, multiple angstrom cofactor-residue displacements occur on the picoseconds timescale. These experimental findings are supported by molecular dynamics simulations. Binding of the dUMP substrate abolishes this flexibility and stabilizes the active site in a configuration where dUMP closely interacts with the flavin cofactor and very efficiently quenches fluorescence itself. Our results indicate a dynamic selected-fit mechanism where binding of the first substrate dUMP at high temperature stabilizes the enzyme in a configuration favorable for interaction with the second substrate NADPH, and more generally have important implications for the role of active site flexibility in enzymes interacting with multiple poly-atom substrates and products. Moreover, our data provide the basis for exploring the effect of inhibitor molecules on the active site dynamics of ThyX and other multisubstrate flavoenzymes.
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Affiliation(s)
- Sergey P. Laptenok
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Latifa Bouzhir-Sima
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Jean-Christophe Lambry
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Hannu Myllykallio
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Ursula Liebl
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Marten H. Vos
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
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19
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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]
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20
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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]
Abstract
Protein folding kinetics is commonly monitored by changes in tryptophan (Trp) fluorescence intensity. Considerable recent discussion has centered on whether the fluorescence of the single Trp in the much-studied, fast-folding villin headpiece C-terminal domain (HP35) accurately reflects folding kinetics, given the general view that quenching is by a histidine cation (His(+)) one turn away in an α-helix (helix III) that forms early in the folding process, according to published MD simulations. To help answer this question, we ran 1.0 μs MD simulations on HP35 (N27H) and a faster-folding variant in its folded form at 300 K and used the coordinates and force field charges with quantum calculations to simulate fluorescence quenching caused by electron transfer to the local amide and to the His(+). The simulations demonstrate that quenching by His(+) in the fully formed helix III is possible only during certain Trp and His(+) rotamer and solvent conformations, the propensity of which is a variable that can allow Trp fluorescence to report the global folding rate, as recent experiments imply.
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Affiliation(s)
- Jose R Tusell
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400, USA
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21
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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]
Affiliation(s)
- Qinfang Sun
- Department of Chemistry, Renmin University of China, Beijing 100872, People’s Republic of China
| | - Rong Lu
- Department of Chemistry, Renmin University of China, Beijing 100872, People’s Republic of China
| | - Anchi Yu
- Department of Chemistry, Renmin University of China, Beijing 100872, People’s Republic of China
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22
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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]
Abstract
Using molecular dynamics simulations and steady-state fluorescence spectroscopy, we have identified a conformational change in the active site of a thermophilic flavoenzyme, NADH oxidase from Thermus thermophilus HB8 (NOX). The enzyme's far-UV circular dichroism spectrum, intrinsic tryptophan fluorescence, and apparent molecular weight measured by dynamic light scattering varied little between 25 and 75°C. However, the fluorescence of the tightly bound FAD cofactor increased approximately fourfold over this temperature range. This effect appears not to be due to aggregation, unfolding, cofactor dissociation, or changes in quaternary structure. We therefore attribute the change in flavin fluorescence to a temperature-dependent conformational change involving the NOX active site. Molecular dynamics simulations and the effects of mutating aromatic residues near the flavin suggest that the change in fluorescence results from a decrease in quenching by electron transfer from tyrosine 137 to the flavin.
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Affiliation(s)
- Eric D Merkley
- Department of Biochemistry, University of Washington, Seattle, Washington
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23
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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]
Abstract
Proton-coupled electron-transfer (PCET) is a mechanism of great importance in protein electron transfer and enzyme catalysis, and the involvement of aromatic amino acids in this process is of much interest. The DNA repair enzyme photolyase provides a natural system that allows for the study of PCET using a neutral radical tryptophan (Trp(•)). In Escherichia coli photolyase, photoreduction of the flavin adenine dinucleotide (FAD) cofactor in its neutral radical semiquinone form (FADH(•)) results in the formation of FADH(-) and (306)Trp(•). Charge recombination between these two intermediates requires the uptake of a proton by (306)Trp(•). The rate constant of charge recombination has been measured as a function of temperature in the pH range from 5.5 to 10.0, and the data are analyzed with both classical Marcus and semi-classical Hopfield electron transfer theory. The reorganization energy associated with the charge recombination process shows a pH dependence ranging from 2.3 eV at pH ≤ 7 and 1.2 eV at pH(D) 10.0. These findings indicate that at least two mechanisms are involved in the charge recombination reaction. Global analysis of the data supports the hypothesis that PCET during charge recombination can follow two different mechanisms with an apparent switch around pH 6.5. At lower pH, concerted electron proton transfer (CEPT) is the favorable mechanism with a reorganization energy of 2.1-2.3 eV. At higher pH, a sequential mechanism becomes dominant with rate-limiting electron-transfer followed by proton uptake which has a reorganization energy of 1.0-1.3 eV. The observed 'inverse' deuterium isotope effect at pH < 8 can be explained by a solvent isotope effect that affects the free energy change of the reaction and masks the normal, mass-related kinetic isotope effect that is expected for a CEPT mechanism. To the best of our knowledge, this is the first time that a switch in PCET mechanism has been observed in a protein.
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Affiliation(s)
- Agnieszka A Zieba
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, USA
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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]
Abstract
Crystal structures of E13T (Glu13 was replaced by Thr13) and E13Q (Glu13 was replaced by Gln13) FMN binding proteins (FMN-bp) from Desulfovibrio vulgaris, strain Miyazaki F, were determined by the X-ray diffraction method. Geometrical factors related to photoinduced electron transfer from Trp32, Tyr35, and Trp106 to the excited isoalloxazine (Iso*) were compared among the three forms of FMN-bp. The rate of ET is considered to be fastest from Trp32 to Iso* in FMN-bp and then from Tyr35 and Trp106. The distances between Iso and Trp32 did not change appreciably (0.705-0.712 nm) among WT, E13T, and E13Q FMN-bps, though the distances between Iso and Tyr35 or Trp106 became a little shorter by ca. 0.01 nm in both mutated FMN-bps. The distances between the residue at 13 and the ET donors or acceptor in the mutated proteins, however, changed markedly, compared to WT. Hydrogen bonding pairs and distances between Iso and surrounding amino acids were not modified when Glu13 was replaced by Thr13 or Gln13. Effects of elimination of ionic charge at Glu13 on the ultrafast fluorescence dynamics in E13T and E13Q were investigated comparing to WT, by means of a fluorescence up-conversion method. Fluorescence lifetimes were tau(1) = 107 fs (alpha(1) = 0.86), tau(2) = 475 fs (alpha(2) = 0.12), and tau(3) = 30 ps (alpha(3) = 0.02) in E13T and tau(1) = 134 fs (alpha(1) = 0.85), alpha(2) = 746 fs (alpha(2) = 0.12), and tau(3) = 30 ps (alpha(3) = 0.03) in E13Q, which are compared to the reported lifetimes in WT, tau(1) = 168 fs (alpha(1) = 0.95) and alpha(2) = 1.4 ps (alpha(2) = 0.05). Average lifetimes (tau(AV) = Sigma(i=1)(2or3)alpha(i)tau(i)) were 0.75 ps in E13T, 1.10 ps in E13Q, and 0.23 ps in WT, which implies that tau(AV) was 3.3 times longer in E13T and 4.8 times longer in E13Q, compared to WT. The ultrafast fluorescence dynamics of WT did not change when solvent changed from H(2)O to D(2)O. Static ET rates (inverse of average lifetimes) were analyzed with static structures of the three systems of FMN-bp. Net electrostatic (ES) energies of Iso and Trp32, on which ET rates depend, were 0.0263 eV in WT, 0.322 eV in E13T, and 0.412 eV in E13Q. The calculated ET rates were in excellent agreement with the observed ones in all systems.
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Affiliation(s)
- Haik Chosrowjan
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan
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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]
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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]
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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]
Abstract
The eye lens Crystallin proteins are subject to UV irradiation throughout life, and the photochemistry of damage proceeds through the excited state; thus, their tryptophan (Trp) fluorescence lifetimes are physiologically important properties. The time-resolved fluorescence spectra of single Trps in human gammaD- and gammaS-Crystallins have been measured with both an upconversion spectrophotofluorometer on the 300 fs to 100 ps time scale, and a time correlated single photon counting apparatus on the 100 ps to 10 ns time scale, respectively. Three Trps in each wild type protein were replaced by phenylalanine, leading to single-Trp mutants: W68-only and W156-only of HgammaD- and W72-only and W162-only of HgammaS-Crystallin. These proteins exhibit similar ultrafast signatures: positive definite decay associated spectra (DAS) for 50-65 ps decay constants that indicate dominance of fast, heterogeneous quenching. The quenched population (judged by amplitude) of this DAS differs among mutants. Trps 68, 156 in human gammaD- and Trp72 in human gammaS-Crystallin are buried, but water can reach amide oxygen and ring HE1 atoms through narrow channels. QM-MM simulations of quenching by electron transfer predict heterogeneous decay times from 50-500 ps that agree with our experimental results. Further analysis of apparent radiative lifetimes allow us to deduce that substantial subpopulations of Trp are fully quenched in even faster (sub-300 fs) processes for several of the mutants. The quenching of Trp fluorescence of human gammaD- and gammaS-Crystallin may protect them from ambient light induced photo damage.
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Affiliation(s)
- Jianhua Xu
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1412
| | - Jiejin Chen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Dmitri Toptygin
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218
| | - Olga Tcherkasskaya
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1412
| | - Patrik Callis
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717
| | - Jonathan King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ludwig Brand
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218
| | - Jay R. Knutson
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1412
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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]
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Abstract
Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
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Affiliation(s)
- Hans Martin Senn
- Department of Chemistry, WestCHEM and University of Glasgow, Glasgow G12 8QQ, UK.
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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]
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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]
Affiliation(s)
- Nadtanet Nunthaboot
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
| | - Fumio Tanaka
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
| | - Sirirat Kokpol
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
| | - Haik Chosrowjan
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
| | - Seiji Taniguchi
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
| | - Noboru Mataga
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
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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]
Abstract
Ultrafast fluorescence decays of FMN binding proteins (FBP) from Desulfovibrio vulgaris (Miyazaki F) were analyzed with an electron transfer (ET) theory by Kakitani and Mataga (KM theory). Time-dependent distances among isoalloxazine (Iso) and Trp-32, Tyr-35, and Trp-106 in wild-type FBP (WT), among Iso and Tyr-32, Tyr-35, and Trp-106 in W32Y (Trp-32 was replaced by Tyr-32), and among Iso and Tyr-35 and Trp-106 in W32A (Trp-32 was replaced by Ala-32) were determined by molecular dynamic simulation (MD). Electrostatic energies between Iso anion and all other ionic groups, between Trp-32 cation and all other ionic groups, and between Tyr-32 cation and all other ionic groups were calculated in WT, W32Y, and W32A, from the MD coordinates. ET parameters contained in KM theory, such as frequency (nu 0), a coefficient of the ET process (beta), a critical distance of the ET process ( R 0), standard free energy related to the electron affinity of the excited Iso ( G Iso (0)), and the static dielectric constant in FBP species (epsilon 0), were determined with and without inclusion of the electrostatic energy, so as to fit the calculated fluorescence decays with the observed decays of all FBP species, by a nonlinear least-squares method according to the Marquardt algorithm. In the analyses the parameters, nu 0, beta, and R 0 were determined separately between Trp residues and Tyr residues among all FBP species. Calculated fluorescence intensities with the inclusion of the electrostatic energy fit quite well with the observed ones of all WT, W32Y, and W32A.
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Affiliation(s)
- Nadtanet Nunthaboot
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand
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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]
Abstract
In the native state several proteins exhibit a quenching of fluorescence of their tryptophans. We studied triosephosphate isomerase from Giardia lamblia (GlTIM) to dissect the mechanisms that account for the quenching of fluorescence of its Trp. GlTIM contains four Trp per monomer (Trp75, Trp162, Trp173, and Trp196) distributed throughout the 3D structure. The fluorescence of the denatured enzyme is 3-fold higher than that of native GlTIM. To ascertain the origin of this phenomenon, single and triple mutants of Trp per Phe were made. The intrinsic fluorescence was determined, and the data were interpreted on the basis of the crystal structure of the enzyme. Our data show that the fluorescence of all Trp residues is quenched through two different mechanisms. In one, fluorescence is quenched by aromatic-aromatic interactions due to the proximity and orientation of the indole groups of Trp196 and Trp162. The magnitude of the quenching of fluorescence in Trp162 is higher than in the other three Trp. Fluorescence quenching is also due to energy transfer to the charged residues that surround Trp 75, 173 and 196. Further analysis of the fluorescence of GlTIM showed that, among TIMs from other parasites, Trp at position 12 exhibits rather unique properties.
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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]
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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]
Abstract
Ultrafast fluorescence dynamics of FMN binding protein (FBP) from Desulfobivrio vulgaris, strain Miyaxaki F, were compared in solution and crystal phases. Fluorescence lifetimes of FBP were 167 fs (96%) and 1.5 ps (4%) in solution (tau(av) = 220 fs), and 730 fs (60%) and longer than 10 ps (40%) in crystals (tau(av) = 4.44 ps). The quenching of the fluorescence of flavin in the protein was considered to be due to photoinduced electron transfer (ET) from Trp or Tyr to the excited isoalloxazine (Iso) nearby. The average lifetime was 20 times longer in crystal vs in solution. Averaged distances between Iso and nearby Trp-32, Tyr-35, and Trp-106 were 8.42, 7.36, and 8.15 A in solution, respectively (obtained by NMR spectroscopy), and 7.05, 7.72, and 8.49 A in crystal, respectively (obtained by X-ray crystallography). The prolonged lifetime in crystal cannot be elucidated by the change in the distances between the states. It was suggested that the longer lifetime in crystal was ascribed to the absence of water molecules around FBP with rapid motional freedom, which may be the driving force for the ET in flavoproteins.
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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]
Abstract
Measurements of protein unfolding in the absence of solvent, when combined with unfolding studies in solution, offer a unique opportunity to measure the effects of solvent on protein structure and dynamics. The experiments presented here rely on the fluorescence of an attached dye to probe the local conformational dynamics through interactions with a Trp residue and fields originating on charge sites. We present fluorescence measurements of thermal fluctuations accompanying conformational change of a miniprotein, Trp-cage, in solution and in gas phase. Molecular dynamics (MD) simulations are performed as a function of temperature, charge state, and charge location to elucidate the dye-protein conformational dynamics leading to the changes in measured fluorescence. The results indicate that the stability of the unsolvated protein is dominated by hydrogen bonds. Substituting asparagine for aspartic acid at position 9 results in a dramatic alteration of the solution unfolding curve, indicating that the salt bridge involving Lys8, Asp9, and Arg16 (+ - +) is essential for Trp-cage stability in solution. In contrast, this substitution results in minor changes in the unfolding curve of the unsolvated protein, showing that hydrogen bonds are the major contributor to the stability of Trp-cage in gas phase. Consistent with this hypothesis, the decrease in the number of hydrogen bonds with increasing temperature indicated by MD simulations agrees reasonably well with the experimentally derived enthalpies of conformational change. The simulation results display relatively compact conformations compared with NMR structures that are generally consistent with experimental results. The measured unfolding curves of unsolvated Trp-cage ions are invariant with the acetonitrile content of the solution from which they are formed, possibly as a result of conformational relaxation during or after desolvation. This work demonstrates the power of combined solution and gas-phase studies and of single-point mutations to identify specific noncovalent interactions which contribute to protein-fold stability. The combination of experiment and simulation is particularly useful because these approaches yield complementary information which can be used to deduce the details of structural changes of proteins in the gas phase.
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Affiliation(s)
- Anthony T Iavarone
- Rowland Institute at Harvard, 100 Edwin H. Land Boulevard, Cambridge, Massachusetts 02142, USA
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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]
Abstract
Biomolecule conformational change has been widely investigated in solution using several methods; however, much less experimental data about structural changes are available for completely isolated, gas-phase biomolecules. Studies of conformational change in unsolvated biomolecules are required to complement the interpretation of mass spectrometry measurements and in addition, can provide a means to directly test theoretical simulations of biomolecule structure and dynamics independent of a simulated solvent. In this Feature Article, we review our recent introduction of a fluorescence-based method for probing local conformational dynamics in unsolvated biomolecules through interactions of an attached dye with tryptophan (Trp) residues and fields originating on charge sites. Dye-derivatized biomolecule ions are formed by electrospray ionization and are trapped in a variable-temperature quadrupole ion trap in which they are irradiated with either continuous or short pulse lasers to excite fluorescence. Fluorescence is measured as a function of temperature for different charge states. Optical measurements of the dye fluorescence include average intensity changes, changes in the emission spectrum, and time-resolved measurements of the fluorescence decay. These measurements have been applied to the miniprotein, Trp-cage, polyproline peptides and to a beta-hairpin-forming peptide, and the results are presented as examples of the broad applicability and utility of these methods. Model fits to Trp-cage fluorescence data measured as a function of temperature provide quantitative information on the thermodynamics of conformational changes, which are reproduced well by molecular dynamics. Time-resolved measurements of the fluorescence decays of Trp-cage and small polyproline peptides definitively demonstrate the occurrence of fluorescence quenching by the amino acid Trp in unsolvated biomolecules.
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Affiliation(s)
- Anthony T Iavarone
- The Rowland Institute at Harvard, 100 Edwin H. Land Boulevard, Cambridge, MA 02142, USA
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