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Guo Y, Feng M, Kuang Z, Abeywickrama CS, Pang Y, Xia A. Unveiling Solvation Dynamics of Excited and Ground States via Ultrafast Pump-Dump-Probe Spectroscopy. J Phys Chem B 2023; 127:7764-7771. [PMID: 37656037 DOI: 10.1021/acs.jpcb.3c05450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The conventional ultrafast pump-probe spectroscopy has primarily focused on examining the formation and decay of the excited state intermediates, but it is very difficult to detect those intermediates while the formation is slow and dissipation is much fast because of the limited concentration during the intrinsic photocycle. To address this issue, a multipulse ultrafast pump-dump-probe spectroscopy was employed to generate and probe the short-lived ground state intermediates (GSIs) in an electronic push-pull pyrene derivative (EPP). This particular derivative undergoes planarized intramolecular charge transfer (PICT) in the excited state upon initial femtosecond pulse excitation. After applying the dump pulse once the PICT was formed, the blue-shifted transient absorption GSIs with the ground state dynamics of the structure recovery was directly observed. It is found that GSIs undergo slower reorganization than the PICT formation in the excited state of EPP due to the solvation effect with different dipole moments of ground states and excited states. These findings provide a comprehensive understanding of the full photocycle dynamics of both the ground and excited states, shedding light on the presence of hidden ground state behaviors.
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Affiliation(s)
- Yuanyuan Guo
- School of Science, Beijing University of Posts and Telecommunications (BUPT), Beijing 100876, People's Republic of China
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Minjun Feng
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Zhuoran Kuang
- School of Science, Beijing University of Posts and Telecommunications (BUPT), Beijing 100876, People's Republic of China
| | | | - Yi Pang
- Department of Chemistry, University of Akron, Akron, Ohio 44325, United States
| | - Andong Xia
- School of Science, Beijing University of Posts and Telecommunications (BUPT), Beijing 100876, People's Republic of China
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2
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Coumarin 343 in aqueous solution: theoretical analysis of absorption. J Mol Model 2022; 28:126. [PMID: 35460442 DOI: 10.1007/s00894-022-05122-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/18/2022] [Indexed: 10/18/2022]
Abstract
Vibronic coupling and hydration were taken into account when describing the absorption of coumarin C343 (both neutral and anionic forms) in an aqueous media. It was shown that the B3LYP functional with the 6-31 + + G(d,p) basis set and the IEFPCM solvent continuum model give theoretical vibronic absorption spectra, which are coincide with the experimental ones. Of the structural differences between C3430 and C343-, there is a different twisting of the carboxyl group additionally changing due to excitation. Upon excitation, a significant shift in the electron density occurs from the C10 atom to the C4 atom only. Thus, a charge transfer on the scale of the entire molecule does not occur. Different hydration complexes with strongly bound water molecules have been analyzed.
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3
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Dogra P, Arya S, Singh AK, Datta A, Mukhopadhyay S. Conformational and Solvation Dynamics of an Amyloidogenic Intrinsically Disordered Domain of a Melanosomal Protein. J Phys Chem B 2022; 126:443-452. [PMID: 34986640 DOI: 10.1021/acs.jpcb.1c09304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The conformational plasticity of intrinsically disordered proteins (IDPs) allows them to adopt a range of conformational states that can be important for their biological functions. The driving force for the conformational preference of an IDP emanates from an intricate interplay between chain-chain and chain-solvent interactions. Using ultrafast femtosecond and picosecond time-resolved fluorescence measurements, we characterized the conformational and solvation dynamics around the N- and C-terminal segments of a disordered repeat domain of a melanosomal protein Pmel17 that forms functional amyloid responsible for melanin biosynthesis. Our time-resolved fluorescence anisotropy results revealed slight compaction and slower rotational dynamics around the amyloidogenic C-terminal segment when compared to the proline-rich N-terminal segment of the repeat domain. The compaction of the C-terminal region was also associated with the restrained mobility of hydration water as indicated by our solvation dynamics measurements. Our findings indicate that sequence-dependent chain-solvent interactions govern both the conformational and solvation dynamics that are crucial in directing the conversion of a highly dynamic IDP into an ordered amyloid assembly. Such an interplay of amino acid composition-dependent conformational and solvation dynamics might have important physicochemical consequences in specific water-protein, ion-protein, and protein-protein interactions involved in amyloid formation and phase transitions.
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Affiliation(s)
| | | | - Avinash K Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Anindya Datta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
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4
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Rey R, Hynes JT. Solvation Dynamics in Water. 4. On the Initial Regime of Solvation Relaxation. J Phys Chem B 2020; 124:7668-7681. [PMID: 32790403 DOI: 10.1021/acs.jpcb.0c05706] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is shown, by means of numerical and analytic work, that initial molecular momenta play little significant role in the initial fast solvation relaxation that follows electronic excitation of, and charge creation for, a standard model system of a solute in water. Instead, the nonequilibrium dynamics are predominantly described by noninertial "steering" by the torques directly generated by the newly created charge distribution. It is this process that largely overcomes inertia and drives the relaxation dynamics on a time scale of a few tens of femtoseconds in the key initial regime of the dynamics. These results are discussed in the context of commonly employed descriptions such as inertial, Gaussian, and underdamped dynamical behavior.
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Affiliation(s)
- Rossend Rey
- Departament de Fı́sica, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
| | - James T Hynes
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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5
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Dozova N, Lacombat F, Bou-Nader C, Hamdane D, Plaza P. Ultrafast photoinduced flavin dynamics in the unusual active site of the tRNA methyltransferase TrmFO. Phys Chem Chem Phys 2019; 21:8743-8756. [PMID: 30968076 DOI: 10.1039/c8cp06072j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flavoproteins often stabilize their flavin coenzyme by stacking interactions involving the isoalloxazine moiety of the flavin and an aromatic residue from the apoprotein. The bacterial FAD and folate-dependent tRNA methyltransferase TrmFO has the unique property of stabilizing its FAD coenzyme by an unusual H-bond-assisted π-π stacking interaction, involving a conserved tyrosine (Y346 in Bacillus subtilis TrmFO, BsTrmFO), the isoalloxazine of FAD and the backbone of a catalytic cysteine (C53). Here, the interaction between FAD and Y346 has been investigated by measuring the photoinduced flavin dynamics of BsTrmFO in the wild-type (WT) protein, C53A and several Y346 mutants by ultrafast transient absorption spectroscopy. In C53A, the excited FAD very rapidly (0.43 ps) abstracts an electron from Y346, yielding the FAD˙-/Y346OH˙+ radical pair, while relaxation of the local environment (1.3 ps) of the excited flavin produces a slight Stokes shift of its stimulated emission band. The radical pair then decays via charge recombination, mostly in 3-4 ps, without any deprotonation of the Y346OH˙+ radical. Presumably, the H-bond between Y346 and the amide group of C53 increases the pKa of Y346OH˙+ and slows down its deprotonation. The dynamics of WT BsTrmFO shows additional slow decay components (43 and 700 ps), absent in the C53A mutant, assigned to excited FADox populations not undergoing fast photoreduction. Their presence is likely due to a more flexible structure of the WT protein, favored by the presence of C53. Interestingly, mutations of Y346 canceling its electron donating character lead to multiple slower quenching channels in the ps-ns regime. These channels are proposed to be due to electron abstraction either (i) from the adenine moiety of FAD, a distribution of the isoalloxazine-adenine distance in the absence of Y346 explaining the multiexponential decay, or (ii) from the W286 residue, possibly accounting for one of the decays. This work supports the idea that H-bond-assisted π-π stacking controls TrmFO's active site dynamics, required for competent orientation of the reactive centers during catalysis.
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Affiliation(s)
- Nadia Dozova
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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6
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Kuang Z, Guo Q, Wang X, Song H, Maroncelli M, Xia A. Ultrafast Ground-State Intramolecular Proton Transfer in Diethylaminohydroxyflavone Resolved with Pump-Dump-Probe Spectroscopy. J Phys Chem Lett 2018; 9:4174-4181. [PMID: 29991264 DOI: 10.1021/acs.jpclett.8b01826] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
4'- N, N-Diethylamino-3-hydroxyflavone (DEAHF), due to excited-state intramolecular proton transfer (ESIPT) reaction, exhibits two solvent-dependent emission bands. Because of the slow formation and fast decay of the ground-state tautomer, its population does not accumulate enough for its detection during the normal photocycle. As a result, the details of the ground-state intramolecular proton-transfer (GSIPT) reaction have remained unknown. The present work uses femtosecond pump-dump-probe spectroscopy to prepare the short-lived ground-state tautomer and track this GSIPT process in solution. By simultaneously measuring femtosecond pump-probe and pump-dump-probe spectra, ultrafast kinetics of the ESIPT and GSIPT reactions are obtained. The GSIPT reaction is shown to be a solvent-dependent irreversible two-state process in two solvents, with estimated time constants of 1.7 ps in toluene and 10 ps in the more polar tetrahydrofuran. These results are of great value in both fully describing the photocycle of this four-level proton transfer molecule and for providing a deeper understanding of dynamical solvent effects on tautomerization.
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Affiliation(s)
- Zhuoran Kuang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Qianjin Guo
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
| | - Xian Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Hongwei Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Mark Maroncelli
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Andong Xia
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
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7
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West RG, Fuciman M, Staleva-Musto H, Šebelík V, Bína D, Durchan M, Kuznetsova V, Polívka T. Equilibration Dependence of Fucoxanthin S1 and ICT Signatures on Polarity, Proticity, and Temperature by Multipulse Femtosecond Absorption Spectroscopy. J Phys Chem B 2018; 122:7264-7276. [DOI: 10.1021/acs.jpcb.8b04217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Robert G. West
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Marcel Fuciman
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Hristina Staleva-Musto
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Václav Šebelík
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - David Bína
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
- Institute of Plant Molecular Biology, Biological Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Milan Durchan
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
- Institute of Plant Molecular Biology, Biological Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Valentyna Kuznetsova
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Tomáš Polívka
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
- Institute of Plant Molecular Biology, Biological Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
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8
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Masters TA, Robinson NA, Marsh RJ, Blacker TS, Armoogum DA, Larijani B, Bain AJ. Time-resolved stimulated emission depletion and energy transfer dynamics in two-photon excited EGFP. J Chem Phys 2018; 148:134312. [DOI: 10.1063/1.5011643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- T. A. Masters
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- CoMPLEX, University College London, London WC1E 6BT, United Kingdom
| | - N. A. Robinson
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - R. J. Marsh
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - T. S. Blacker
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- CoMPLEX, University College London, London WC1E 6BT, United Kingdom
| | - D. A. Armoogum
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - B. Larijani
- Cell Biophysics Laboratory, Ikerbasque, Basque Foundation for Science and Unidad de Biofisica (CSIC-UPV/EHU), Bilbao, Spain
| | - A. J. Bain
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- CoMPLEX, University College London, London WC1E 6BT, United Kingdom
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9
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Wendel M, Nizinski S, Prukala D, Sikorski M, Wybraniec S, Burdzinski G. Ultrafast internal conversion in neobetanin in comparison to betacyanins. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2016.09.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Biswas S, Mukherjee SK, Chowdhury PK. Crowder-Induced Rigidity in a Multidomain Protein: Insights from Solvation. J Phys Chem B 2016; 120:12501-12510. [DOI: 10.1021/acs.jpcb.6b10478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saikat Biswas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Sanjib Kumar Mukherjee
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit Kumar Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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11
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Dozova N, Ventelon L, Clermont G, Blanchard-Desce M, Plaza P. Excited-state symmetry breaking of linear quadrupolar chromophores: A transient absorption study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.10.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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12
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Abstract
In this contribution, we report studies of the nature of binding interactions and dynamics of protein histone I (H1) with ligands in solution and as a complex with DNA, an important biological process for the higher-order structure in chromatin. With femtosecond time resolution, we examined the role of solvation by water, the micropolarity at the interface of the binding site(s) of H1, and the rigidity of the complex structure. We used two biologically common fluorescent probes: 2-(p-toluidino)naphthalene-6-sulfonate (TNS) and 5-(dimethylamino)naphthalene-1-sulfonyl chloride (DC). By noncovalently attaching TNS and covalently adducting DC to the binding sites we found that the solvation dynamics, which occur within 1 ps, for the probe at the protein surface and in bulk solution are comparable, indicating the significant contribution of bulk water shells. However, the local polarity changes significantly, reflecting the change in dielectric properties at the protein/water interface. The binding structure of the protein-DNA complex was examined by the local orientational motion of the probe. The covalently bound DC molecule, sandwiched between the protein and DNA, was found to be frozen, revealing the very rigid structure at the recognition site, while, for noncovalently bound TNS, the complexes displace the probe. The dynamical rigidity of the complex, and the role of solvation and interface polarity, elucidate the strong recognition mechanism between DNA and the protein by electrostatic interactions, which are important to the compactness and to chromatin condensation in the biological function.
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Affiliation(s)
- D Zhong
- Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA
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13
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Chevalier K, Grün A, Stamm A, Schmitt Y, Gerhards M, Diller R. ESIPT and Photodissociation of 3-Hydroxychromone in Solution: Photoinduced Processes Studied by Static and Time-Resolved UV/Vis, Fluorescence, and IR Spectroscopy. J Phys Chem A 2013; 117:11233-45. [DOI: 10.1021/jp407252y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katharina Chevalier
- Department of Physics and ‡Department of
Chemistry and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Anneken Grün
- Department of Physics and ‡Department of
Chemistry and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Anke Stamm
- Department of Physics and ‡Department of
Chemistry and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Yvonne Schmitt
- Department of Physics and ‡Department of
Chemistry and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Markus Gerhards
- Department of Physics and ‡Department of
Chemistry and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Rolf Diller
- Department of Physics and ‡Department of
Chemistry and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
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14
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Nanda V, Cristian L, Toptygin D, Brand L, Degrado WF. Nanosecond Dynamics of InfluenzaA/M2TM and an Amantadine Resistant Mutant Probed by Time-Dependent Red Shifts of a Native Tryptophan. Chem Phys 2013; 422:10.1016/j.chemphys.2012.12.018. [PMID: 24273370 PMCID: PMC3833813 DOI: 10.1016/j.chemphys.2012.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Proteins involved in functions such as electron transfer or ion transport must be capable of stabilizing transient charged species on time scales ranging from picoseconds to microseconds. We study the influenza A M2 proton channel, containing a tryptophan residue that serves as an essential part of the proton conduction pathway. We induce a transition dipole in tryptophan by photoexcitation, and then probe the dielectric stabilization of its excited state. The magnitude of the stabilization over this time regime was larger than that generally found for tryptophan in membrane or protein environments. M2 achieves a water-like stabilization over a 25 nanosecond time scale, slower than that of bulk water, but sufficiently rapid to contribute to stabilization of charge as protons diffuse through the channel. These measurements should stimulate future MD studies to clarify the role of sidechain versus non-bulk water in defining the process of relaxation.
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Affiliation(s)
- Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School - UMDNJ, Piscataway, New Jersey 08854 ; Department of Biochemistry, Robert Wood Johnson Medical School - UMDNJ, Piscataway, New Jersey 08854
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15
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Hamm P, Zewail AH, Fleming GR. A tribute to Robin Hochstrasser. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Amaro M, Brezovský J, Kováčová S, Maier L, Chaloupková R, Sýkora J, Paruch K, Damborský J, Hof M. Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore? J Phys Chem B 2013; 117:7898-906. [DOI: 10.1021/jp403708c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mariana Amaro
- J. Heyrovsky Institute of Physical
Chemistry of the ASCR, v. v. i., Academy of Sciences of the Czech Republic, Dolejskova 3, 182 23 Praha, Czech
Republic
| | - Jan Brezovský
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Silvia Kováčová
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
- Department of Chemistry, Faculty
of Science, Masaryk University, Kamenice
5/A8, 625 00 Brno, Czech Republic
| | - Lukáš Maier
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
- Department of Chemistry, Faculty
of Science, Masaryk University, Kamenice
5/A8, 625 00 Brno, Czech Republic
| | - Radka Chaloupková
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jan Sýkora
- J. Heyrovsky Institute of Physical
Chemistry of the ASCR, v. v. i., Academy of Sciences of the Czech Republic, Dolejskova 3, 182 23 Praha, Czech
Republic
| | - Kamil Paruch
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
- Department of Chemistry, Faculty
of Science, Masaryk University, Kamenice
5/A8, 625 00 Brno, Czech Republic
| | - Jiří Damborský
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Martin Hof
- J. Heyrovsky Institute of Physical
Chemistry of the ASCR, v. v. i., Academy of Sciences of the Czech Republic, Dolejskova 3, 182 23 Praha, Czech
Republic
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17
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Sajadi M, Ernsting NP. Excess Dynamic Stokes Shift of Molecular Probes in Solution. J Phys Chem B 2013; 117:7675-84. [DOI: 10.1021/jp400473n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mohsen Sajadi
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
| | - Nikolaus P. Ernsting
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
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18
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Carlson PJ, Bose S, Armstrong DW, Hawkins T, Gordon MS, Petrich JW. Structure and Dynamics of the 1-Hydroxyethyl-4-amino-1,2,4-triazolium Nitrate High-Energy Ionic Liquid System. J Phys Chem B 2011; 116:503-12. [DOI: 10.1021/jp207840q] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Philip J. Carlson
- U.S. Department of Energy Ames Laboratory and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Sayantan Bose
- U.S. Department of Energy Ames Laboratory and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Daniel W. Armstrong
- Department of Chemistry and Biochemistry, University of Texas, Arlington, Box 19065, Arlington, Texas 76019, United States
| | - Tommy Hawkins
- Air Force Research Laboratory, 10 East Saturn Boulevard, Building 8451, Edwards Air Force Base, California 93524, United States
| | - Mark S. Gordon
- U.S. Department of Energy Ames Laboratory and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Jacob W. Petrich
- U.S. Department of Energy Ames Laboratory and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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19
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Sajadi M, Furse KE, Zhang XX, Dehmel L, Kovalenko SA, Corcelli SA, Ernsting NP. Beobachtung einer DNA-Ligand-Schwingung über zeitaufgelöste Fluoreszenzmessung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102942] [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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20
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Sajadi M, Furse KE, Zhang XX, Dehmel L, Kovalenko SA, Corcelli SA, Ernsting NP. Detection of DNA-Ligand Binding Oscillations by Stokes-Shift Measurements. Angew Chem Int Ed Engl 2011; 50:9501-5. [DOI: 10.1002/anie.201102942] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/24/2011] [Indexed: 11/10/2022]
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21
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Zhang XX, Würth C, Zhao L, Resch-Genger U, Ernsting NP, Sajadi M. Femtosecond broadband fluorescence upconversion spectroscopy: improved setup and photometric correction. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:063108. [PMID: 21721675 DOI: 10.1063/1.3597674] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A setup for fluorescence upconversion spectroscopy (FLUPS) is described which has 80 fs temporal response (fwhm) for emission in the spectral range 425-750 nm. Broadband phase matching is achieved with tilted gate pulses at 1340 nm. Background from harmonics of the gate pulse is removed and sensitivity increased compared to previous designs. Photometric calibration of the upconversion process is performed with a set of fluorescent dyes. For Coumarin 153 in methanol the peak position, bandwidth, and asymmetry depending on delay time are reported.
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Affiliation(s)
- X-X Zhang
- Photonics Center, College of Physical Science, Nankai University, Tianjin, China
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22
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van Wilderen LJGW, Lincoln CN, van Thor JJ. Modelling multi-pulse population dynamics from ultrafast spectroscopy. PLoS One 2011; 6:e17373. [PMID: 21445294 PMCID: PMC3061864 DOI: 10.1371/journal.pone.0017373] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 02/01/2011] [Indexed: 01/18/2023] Open
Abstract
Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is essential to model and resolve the details of physical behaviour of populations in ultrafast spectroscopy such as pump-probe, pump-dump-probe and pump-repump-probe experiments.
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Affiliation(s)
- Luuk J. G. W. van Wilderen
- Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Imperial College London, London, United Kingdom
| | - Craig N. Lincoln
- Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Imperial College London, London, United Kingdom
| | - Jasper J. van Thor
- Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Imperial College London, London, United Kingdom
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23
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Toptygin D, Woolf TB, Brand L. Picosecond protein dynamics: the origin of the time-dependent spectral shift in the fluorescence of the single Trp in the protein GB1. J Phys Chem B 2010; 114:11323-37. [PMID: 20701310 DOI: 10.1021/jp104425t] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How a biological system responds to a charge shift is a challenging question directly relevant to biological function. Time-resolved fluorescence of a tryptophan residue reflects protein and solvent response to the difference in pi-electron density between the excited and the ground state. In this study we use molecular dynamics to calculate the time-dependent spectral shift (TDSS) in the fluorescence of Trp-43 in GB1 protein. A new computational method for separating solvent, protein, and fluorophore contributions to TDSS is applied to 100 nonequilibrium trajectories for GB1 in TIP3P water. The results support several nontrivial conclusions. Both longitudinal and transverse relaxation modes of bulk solvent contribute to the TDSS in proteins. All relaxation components slower than the transverse relaxation of bulk solvent have significant contributions from both protein and solvent, with a negative correlation between them. Five exponential terms in the TDSS of GB1 are well separated by their relaxation times. A 0.036 ps term is due to both solvent (60%) and protein (40%). Two exponential terms represent longitudinal (tau(L) approximately = 0.4 ps) and transverse (tau(D) approximately = 5.6 ps) relaxation modes of TIP3P water. A 131 ps term is attributable to a small change in the tertiary structure, with the alpha-helix moving 0.2 A away from the beta-strand containing Trp-43. A 2580 ps term is due to the change in the conformation of the Glu-42 side chain that brings its carboxyl group close to the positively charged end of the excited fluorophore. Interestingly, water cancels 60% of the TDSS resulting from this conformational change.
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Affiliation(s)
- Dmitri Toptygin
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
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25
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Xu J, Wang QD, Zhu Q, Fu KX, He FC, Li XY. Time-Dependent Stokes Shift from Solvent Dielectric Relaxation. CHINESE J CHEM PHYS 2010. [DOI: 10.1088/1674-0068/23/03/297-302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Bose S, Adhikary R, Barnes CA, Fulton DB, Hargrove MS, Song X, Petrich JW. Comparison of the Dielectric Response Obtained from Fluorescence Upconversion Measurements and Molecular Dynamics Simulations for Coumarin 153−Apomyoglobin Complexes and Structural Analysis of the Complexes by NMR and Fluorescence Methods. J Phys Chem A 2010; 115:3630-41. [DOI: 10.1021/jp1008225] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Sayantan Bose
- Department of Chemistry and ‡Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Ramkrishna Adhikary
- Department of Chemistry and ‡Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Charles A. Barnes
- Department of Chemistry and ‡Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - D. Bruce Fulton
- Department of Chemistry and ‡Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Hargrove
- Department of Chemistry and ‡Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Xueyu Song
- Department of Chemistry and ‡Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Jacob W. Petrich
- Department of Chemistry and ‡Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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27
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Zhang L, Yang Y, Kao YT, Wang L, Zhong D. Protein hydration dynamics and molecular mechanism of coupled water-protein fluctuations. J Am Chem Soc 2009; 131:10677-91. [PMID: 19586028 DOI: 10.1021/ja902918p] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein surface hydration is fundamental to its structural stability and flexibility, and water-protein fluctuations are essential to biological function. Here, we report a systematic global mapping of water motions in the hydration layer around a model protein of apomyoglobin in both native and molten globule states. With site-directed mutagenesis, we use intrinsic tryptophan as a local optical probe to scan the protein surface one at a time with single-site specificity. With femtosecond resolution, we examined 16 mutants in two states and observed two types of water-network relaxation with distinct energy and time distributions. The first water motion results from the local collective hydrogen-bond network relaxation and occurs in a few picoseconds. The initial hindered motions, observed in bulk water in femtoseconds, are highly suppressed and drastically slow down due to structured water-network collectivity in the layer. The second water-network relaxation unambiguously results from the lateral cooperative rearrangements in the inner hydration shell and occurs in tens to hundreds of picoseconds. Significantly, this longtime dynamics is the coupled interfacial water-protein motions and is the direct measurement of such cooperative fluctuations. These local protein motions, although highly constrained, are necessary to assist the longtime water-network relaxation. A series of correlations of hydrating water dynamics and coupled fluctuations with local protein's chemical and structural properties were observed. These results are significant and reveal various water behaviors in the hydration layer with wide heterogeneity. We defined a solvation speed and an angular speed to quantify the water-network rigidity and local protein flexibility, respectively. We also observed that the dynamic hydration layer extends to more than 10 A. Finally, from native to molten globule states, the hydration water networks loosen up, and the protein locally becomes more flexible with larger global plasticity and partial unfolding.
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Affiliation(s)
- Luyuan Zhang
- Department of Physics, Program of Biophysics, The Ohio State University, Columbus, Ohio 43210, USA
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28
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Fürstenberg A, Kel O, Gradinaru J, Ward TR, Emery D, Bollot G, Mareda J, Vauthey E. Site-dependent excited-state dynamics of a fluorescent probe bound to avidin and streptavidin. Chemphyschem 2009; 10:1517-32. [PMID: 19565577 DOI: 10.1002/cphc.200900132] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The excited-state dynamics of biotin-spacer-Lucifer-Yellow (LY) constructs bound to avidin (Avi) and streptavidin (Sav) was investigated using femtosecond spectroscopy. Two different locations in the proteins, identified by molecular dynamics simulations of Sav, namely the entrance of the binding pocket and the protein surface, were probed by varying the length of the spacer. A reduction of the excited-state lifetime, stronger in Sav than in Avi, was observed with the long spacer construct. Transient absorption measurements show that this effect originates from an electron transfer quenching of LY, most probably by a nearby tryptophan residue. The local environment of the LY chromophore could be probed by measuring the time-dependent polarisation anisotropy and Stokes shift of the fluorescence. Substantial differences in both dynamics were observed. The fluorescence anisotropy decays analysed by using the wobbling-in-a-cone model reveal a much more constrained environment of the chromophore with the short spacer. Moreover, the dynamic Stokes shift is multiphasic in all cases, with a approximately 1 ps component that can be ascribed to diffusive motion of bulk-like water molecules, and with slower components with time constants varying not only with the spacer, but with the protein as well. These slow components, which depend strongly on the local environment of the probe, are ascribed to the motion of the hydration layer coupled to the conformational dynamics of the protein.
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Affiliation(s)
- Alexandre Fürstenberg
- Department of Physical Chemistry, University of Geneva, 30, quai Ernest-Ansermet, CH-1211 Geneva, 4, Switzerland
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29
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Adhikary R, Barnes CA, Petrich JW. Solvation Dynamics of the Fluorescent Probe PRODAN in Heterogeneous Environments: Contributions from the Locally Excited and Charge-Transferred States. J Phys Chem B 2009; 113:11999-2004. [DOI: 10.1021/jp905139n] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
| | - Charles A. Barnes
- Department of Chemistry, Iowa State University Ames, Iowa 50011-3111
| | - Jacob W. Petrich
- Department of Chemistry, Iowa State University Ames, Iowa 50011-3111
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30
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Zhong D. Hydration Dynamics and Coupled Water-Protein Fluctuations Probed by Intrinsic Tryptophan. ADVANCES IN CHEMICAL PHYSICS 2009. [DOI: 10.1002/9780470508602.ch3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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31
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Bose S, Adhikary R, Mukherjee P, Song X, Petrich JW. Considerations for the Construction of the Solvation Correlation Function and Implications for the Interpretation of Dielectric Relaxation in Proteins. J Phys Chem B 2009; 113:11061-8. [DOI: 10.1021/jp9004345] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Sayantan Bose
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | | | - Prasun Mukherjee
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Xueyu Song
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Jacob W. Petrich
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
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32
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Jesenská A, Sýkora J, Olzyńska A, Brezovský J, Zdráhal Z, Damborský J, Hof M. Nanosecond time-dependent Stokes shift at the tunnel mouth of haloalkane dehalogenases. J Am Chem Soc 2009; 131:494-501. [PMID: 19113888 DOI: 10.1021/ja804020q] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tunnel mouths are evolutionally the most variable regions in the structures of haloalkane dehalogenases originating from different bacterial species, suggesting their importance for adaptation of enzymes to various substrates. We decided to monitor the dynamics of this particular region by means of time-resolved fluorescence spectroscopy and molecular dynamic simulations. To label the enzyme specifically, we adapted a novel procedure that utilizes a coumarin dye containing a halide-hydrocarbon linker, which serves as a substrate for enzymatic reaction. The procedure leads to a coumarin dye covalently attached and specifically located in the tunnel mouth of the enzyme. In this manner, we stained two haloalkane dehalogenase mutants, DbjA-H280F and DhaA-H272F. The measurements of time-resolved fluorescence anisotropy, acrylamide quenching, and time-resolved emission spectra reveal differences in the polarity, accessibility and mobility of the dye and its microenvironment for both of the mutants. The obtained experimental data are consistent with the results obtained by molecular dynamics calculations and correlate with the anatomy of the tunnel mouths, which were proposed to have a strong impact on the catalytic activity and specificity of the examined mutants. Interestingly, the kinetics of the recorded time-dependent Stokes shift is unusual slow; it occurs on the nanosecond time-scale, suggesting that the protein dynamics is extremely slowed down at the region involved in the exchange of ligands between the active-site cavity and bulk solvent.
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Affiliation(s)
- Andrea Jesenská
- Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic
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33
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Sen S, Andreatta D, Ponomarev SY, Beveridge DL, Berg MA. Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments. J Am Chem Soc 2009; 131:1724-35. [PMID: 19191698 PMCID: PMC2750815 DOI: 10.1021/ja805405a] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Time-resolved Stokes-shift experiments measure the dynamics of biomolecules and of the perturbed solvent near them on subnanosecond time scales, but molecular dynamics simulations are needed to provide a clear interpretation of the results. Here we show that simulations using standard methods quantitatively reproduce the main features of TRSS experiments in DNA and provide a molecular assignment for the dynamics. The simulations reproduce the magnitude and unusual power-law dynamics of the Stokes shift seen in recent experiments [ Andreatta, D., et al. J. Am. Chem. Soc. 2005, 127, 7270 ]. A polarization model is introduced to eliminate cross-correlations between the different components contributing to the signal. Using this model, well-defined contributions of the DNA, water, and counterion to the experimental signal are extracted. Water is found to have the largest contribution and to be responsible for the power-law dynamics. The counterions have a smaller, but non-negligible, contribution with a time constant of 220 ps. The contribution to the signal of the DNA itself is minor and fits a 30 ps stretched exponential. Both time-averaged and dynamic distributions are calculated. They show a small subset of ions with a different coupling but no other evidence of substates or rate heterogeneity.
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Affiliation(s)
- Sobhan Sen
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067 India
| | - Daniele Andreatta
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | | | | | - Mark A. Berg
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
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34
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Lindquist BA, Furse KE, Corcelli SA. Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview. Phys Chem Chem Phys 2009; 11:8119-32. [DOI: 10.1039/b908588b] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Pronchik J, Giurleo JT, Talaga DS. Separation and Analysis of Dynamic Stokes Shift with Multiple Fluorescence Environments: Coumarin 153 in Bovine β-Lactoglobulin A. J Phys Chem B 2008; 112:11422-34. [DOI: 10.1021/jp802666n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jeremy Pronchik
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854
| | - Jason T. Giurleo
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854
| | - David S. Talaga
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854
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36
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Thielges MC, Zimmermann J, Yu W, Oda M, Romesberg FE. Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition. Biochemistry 2008; 47:7237-47. [PMID: 18549243 DOI: 10.1021/bi800374q] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The production of antibodies that selectively bind virtually any foreign compound is the hallmark of the immune system. While much is understood about how sequence diversity contributes to this remarkable feat of molecular recognition, little is known about how sequence diversity impacts antibody dynamics, which is also expected to contribute to molecular recognition. Toward this goal, we examined a panel of antibodies elicited to the chromophoric antigen fluorescein. On the basis of isothermal titration calorimetry, we selected six antibodies that bind fluorescein with diverse binding entropies, suggestive of varying contributions of dynamics to molecular recognition. Sequencing revealed that two pairs of antibodies employ homologous heavy chains that were derived from common germline genes, while the other two heavy chains and all six of the light chains were derived from different germline genes and are not homologous. Interestingly, more than half of all the somatic mutations acquired during affinity maturation among the six antibodies are located in positions unlikely to contact fluorescein directly. To quantify and compare the dynamics of the antibody-fluorescein complexes, three-pulse photon echo peak shift and transient grating spectroscopy were employed. All of the antibodies exhibited motions on three distinct time scales, ultrafast motions on the <100 fs time scale, diffusive motions on the picosecond time scale, and motions that occur on time scales longer than nanoseconds and thus appear static. However, the exact frequency of the picosecond time scale motion and the relative contribution of the different motions vary significantly among the antibody-chromophore complexes, revealing a high level of dynamic diversity. Using a hierarchical model, we relate the data to features of the antibodies' energy landscapes as well as their flexibility in terms of elasticity and plasticity. In all, the data provide a consistent picture of antibody flexibility, which interestingly appears to be correlated with binding entropy as well as with germline gene use and the mutations introduced during affinity maturation. The data also provide a gauge of the dynamic diversity of the antibody repertoire and suggest that this diversity might contribute to molecular recognition by facilitating the recognition of the broadest range of foreign molecules.
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Affiliation(s)
- Megan C Thielges
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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37
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Gilmore J, McKenzie RH. Quantum Dynamics of Electronic Excitations in Biomolecular Chromophores: Role of the Protein Environment and Solvent. J Phys Chem A 2008; 112:2162-76. [DOI: 10.1021/jp710243t] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Joel Gilmore
- Department of Physics, University of Queensland, Brisbane 4072 Australia
| | - Ross H. McKenzie
- Department of Physics, University of Queensland, Brisbane 4072 Australia
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38
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van Thor JJ, Zanetti G, Ronayne KL, Towrie M. Structural events in the photocycle of green fluorescent protein. J Phys Chem B 2007; 109:16099-108. [PMID: 16853046 DOI: 10.1021/jp051315+] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Picosecond time-resolved mid-infrared absorption changes of the wild type green fluorescent protein from Aequorea victoria are reported on structural events during the photocycle. Concomitant with rapid H/D transfer following excitation of the neutral A state at 400 nm, a transient signal at 1721/1711 cm(-1) (H/D) developed belonging to protonated glutamate 222, which was definitively assigned using the E222D mutant from the altered proton-transfer kinetics to aspartate in addition to the altered band position and intensity in the spectra. A transient at 1697 cm(-1), assigned to a structural perturbation of glutamine 69, had a H/D kinetic isotope effect of >32, showing the conformational dynamics to be sensitive to the active site H/D vibrations. The kinetic data up to 2 ns after excitation in the 1250-1800 cm(-1) region in D2O provided 10 and 75 ps time constants for the excited-state deuteron transfer and the associated A1* - A1 and A2* - A2 difference spectra and showed the radiative intermediate I state vibrations and the transient accumulation of the long-lived ground-state intermediate I2. Assignments of chromophore modes for the A1, A2, and I2 ground states are proposed on the basis of published model compound studies (Esposito, A. P.; Schellenberg, P.; Parson, W. W.; Reid, P. J. J. Mol. Struct. 2001, 569, 25 and He, X.; Bell, A. F.; Tonge, P. J. J. Phys. Chem. B 2002, 106, 6056). Tentative assignments for the singlet-state intermediates A1*, A2*, and I* are discussed. An unexpected and unassigned band that may be a C=C chromophore vibration was observed in the ground state (1665 cm(-1)) as well as in all photocycle intermediates. Optical dumping of the transient I population was achieved using an additional 532 nm pulse and the directly obtained I2 - I* difference spectrum was highly similar to the I2 - I* photocycle spectrum. The pump-dump-probe spectrum differed from the pump-probe photocycle difference spectrum with respect to the intensity of the phenol 1 mode at 1578 cm(-1), suggesting stronger delocalization of the negative charge onto the phenolic ring of the anionic chromophore in the dumped I2 state. Indication for structural heterogeneity of the chromophore, Glu 222, and the chromophore environment was found in the two parallel proton-transfer reactions and their distinct associated ground- and intermediate-state vibrations. Vibrational spectral markers at 1695 cm(-1) assigned to Gln 69, at 1631 cm(-1) belonging to a C=C mode, and at 1354 cm(-1) belonging to a phenolate vibration further indicated the I2 and I* states to be unrelaxed.
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Affiliation(s)
- Jasper J van Thor
- Laboratory of Molecular Biophysics, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, United Kingdom.
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Kühn O, Wöste L. Biological systems: Applications and perspectives. ANALYSIS AND CONTROL OF ULTRAFAST PHOTOINDUCED REACTIONS 2007. [PMCID: PMC7122019 DOI: 10.1007/978-3-540-68038-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Oliver Kühn
- Institut f. Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, D-14195 Berlin, Germany
| | - Ludger Wöste
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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40
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Abbyad P, Shi X, Childs W, McAnaney TB, Cohen BE, Boxer SG. Measurement of solvation responses at multiple sites in a globular protein. J Phys Chem B 2007; 111:8269-76. [PMID: 17592867 PMCID: PMC2507720 DOI: 10.1021/jp0709104] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins respond to electrostatic perturbations through complex reorganizations of their charged and polar groups, as well as those of the surrounding media. These solvation responses occur both in the protein interior and on its surface, though the exact mechanisms of solvation are not well understood, in part because of limited data on the solvation responses for any given protein. Here, we characterize the solvation kinetics at sites throughout the sequence of a small globular protein, the B1 domain of streptococcal protein G (GB1), using the synthetic fluorescent amino acid Aladan. Aladan was incorporated into seven different GB1 sites, and the time-dependent Stokes shift was measured over the femtosecond to nanosecond time scales by fluorescence upconversion and time-correlated single photon counting. The seven sites range from buried within the protein core to fully solvent-exposed on the protein surface, and are located on different protein secondary structures including beta-sheets, helices, and loops. The dynamics in the protein sites were compared against the free fluorophore in buffer. All protein sites exhibited an initial, ultrafast Stokes shift on the subpicosecond time scale similar to that observed for the free fluorophore, but smaller in magnitude. As the probe is moved from the surface to more buried sites, the dynamics of the solvation response become slower, while no clear correlation between dynamics and secondary structure is observed. We suggest that restricted movements of the surrounding protein residues give rise to the observed long time dynamics and that such movements comprise a large portion of the protein's solvation response. The proper treatment of dynamic Stokes shift data when the time scale for solvation is comparable to the fluorescence lifetime is discussed.
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Affiliation(s)
- Paul Abbyad
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
| | - Xinghua Shi
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
| | - William Childs
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
| | - Tim B. McAnaney
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
| | - Bruce E. Cohen
- Biological Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
- To whom correspondence should be addressed, , Phone: (650)723-4482; fax (650)723-4817
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Chowdhury PK, Halder M, Sanders L, Arnold RA, Liu Y, Armstrong DW, Kundu S, Hargrove MS, Song X, Petrich JW. The Complex of Apomyoglobin with the Fluorescent Dye Coumarin 153¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2004.tb00032.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Golosov AA, Karplus M. Probing Polar Solvation Dynamics in Proteins: A Molecular Dynamics Simulation Analysis. J Phys Chem B 2007; 111:1482-90. [PMID: 17249715 DOI: 10.1021/jp065493u] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Measurements of time-resolved Stokes shifts on picosecond to nanosecond time scales have been used to probe the polar solvation dynamics of biological systems. Since it is difficult to decompose the measurements into protein and solvent contributions, computer simulations are useful to aid in understanding the details of the molecular behavior. Here we report the analysis of simulations of the electrostatic interactions of the rest of the protein and the solvent with 11 residues of the immunoglobulin binding domain B1 of protein G. It is shown that the polar solvation dynamics are position-dependent and highly heterogeneous. The contributions due to interactions with the protein and with the solvent are determined. The solvent contributions are found to vary from negligible after a few picoseconds to dominant on a scale of hundreds of picoseconds. The origin for the latter is found to involve coupled hydration and protein conformational dynamics. The resulting microscopic picture demonstrates that a wide range of possibilities have to be considered in the interpretation of time-resolved Stokes shift measurements.
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Affiliation(s)
- Andrei A Golosov
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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Quentmeier CC, Wehling A, Walla PJ. A Bioassay Based on the Ultrafast Response of a Reporter Molecule. ACTA ACUST UNITED AC 2007; 12:341-50. [PMID: 17307887 DOI: 10.1177/1087057106298635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The capability of using ultrafast detection technologies for a fast analysis of biomolecular reactions has been explored. As an example, the ultrafast response of tetramethylrhodamine (TMR)—labeled bovine serum albumin (BSA) as a function of different extents in proteolytic cleavage was investigated. The authors compared 4 samples of masses differing over several orders of magnitude: untreated, TMR-labeled BSA (66 kDa), TMR-labeled BSA treated with elastase (6-33 kDa) and with subtilisin (< 3 kDa), and the pure label TMR (0.4 kDa). A direct comparison with gel electrophoresis revealed that various ultrafast parameters give robust information about the progress of the proteolytic cleavage. The authors found the ratio of the transient absorption signal observed at 0 psec and 50 psec after excitation (λPump = 540 nm, λProbe = 570 nm) to be the most precise parameter for determining the cleavage. This parameter allowed determining the mass accurately within 1 sec (Z' factor of 0.83) or 600 msec (Z' factor of 0.64), measuring time per sample. This indicates that many of the known ultrafast detection technologies might be used for monitoring biochemical reactions, probably even without any labeling procedure. The authors also discuss briefly which ultrafast processes contribute to the signals and how they are affected by changes in the biomolecular environment. ( Journal of Biomolecular Screening 2007:341-350)
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Affiliation(s)
- Claudia C Quentmeier
- Technical University of Brunswick, Institute for Physical and Theoretical Chemistry, Department of Biophysical Chemistry, Braunschweig, Germany
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Nuernberger P, Vogt G, Brixner T, Gerber G. Femtosecond quantum control of molecular dynamics in the condensed phase. Phys Chem Chem Phys 2007; 9:2470-97. [PMID: 17508081 DOI: 10.1039/b618760a] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review the progress in controlling quantum dynamical processes in the condensed phase with femtosecond laser pulses. Due to its high particle density the condensed phase has both high relevance and appeal for chemical synthesis. Thus, in recent years different methods have been developed to manipulate the dynamics of condensed-phase systems by changing one or multiple laser pulse parameters. Single-parameter control is often achieved by variation of the excitation pulse's wavelength, its linear chirp or its temporal subpulse separation in case of pulse sequences. Multiparameter control schemes are more flexible and provide a much larger parameter space for an optimal solution. This is realized in adaptive femtosecond quantum control, in which the optimal solution is iteratively obtained through the combination of an experimental feedback signal and an automated learning algorithm. Several experiments are presented that illustrate the different control concepts and highlight their broad applicability. These fascinating achievements show the continuous progress on the way towards the control of complex quantum reactions in the condensed phase.
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Affiliation(s)
- Patrick Nuernberger
- Universität Würzburg, Physikalisches Institut, Am Hubland, 97074 Würzburg, Germany
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Shaw AK, Sarkar R, Banerjee D, Hintschich S, Monkman A, Pal SK. Direct observation of protein residue solvation dynamics. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2006.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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Mukherjee P, Haider M, Hargrove MS, Petrich JW. Characterization of the Interactions of Fluorescent Probes with Proteins: Coumarin 153 and 1,8-ANS in Complex with Holo- and Apomyoglobin. Photochem Photobiol 2006. [DOI: 10.1111/j.1751-1097.2006.tb09815.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Papagiannakis E, Vengris M, Larsen DS, van Stokkum IHM, Hiller RG, van Grondelle R. Use of ultrafast dispersed pump-dump-probe and pump-repump-probe spectroscopies to explore the light-induced dynamics of peridinin in solution. J Phys Chem B 2006; 110:512-21. [PMID: 16471563 DOI: 10.1021/jp053094d] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optical pump-induced dynamics of the highly asymmetric carotenoid peridinin in methanol was studied by dispersed pump-probe, pump-dump-probe, and pump-repump-probe transient absorption spectroscopy in the visible region. Dispersed pump-probe measurements show that the decay of the initially excited S2 state populates two excited states, the S1 and the intramolecular charge-transfer (ICT) state, at a ratio determined by the excitation wavelength. The ensuing spectral evolution occurs on the time scale of a few picoseconds and suggests the equilibration of these states. Dumping the stimulated emission of the ICT state with an additional 800-nm pulse after 400- and 530-nm excitation preferentially removes the ICT state contribution from the broad excited-state absorption, allowing for its spectral characterization. At the same time, an unrelaxed ground-state species, which has a subpicosecond lifetime, is populated. The application of the 800-nm pulse at early times, when the S2 state is still populated, led to direct generation of the peridinin cation, observed for the first time in a transient absorption experiment. The excited and ground electronic states manifold of peridinin has been reconstructed using target analysis; this approach combined with the measured multipulse spectroscopic data allows us to estimate the spectra and time scales of the corresponding transient states.
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Affiliation(s)
- Emmanouil Papagiannakis
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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Affiliation(s)
- Ninad Prabhu
- Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania
| | - Kim Sharp
- Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania
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49
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Tryptophan–water interaction in Monellin: Hydration patterns from molecular dynamics simulation. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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50
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Jaye AA, Stoner-Ma D, Matousek P, Towrie M, Tonge PJ, Meech SR. Time-Resolved Emission Spectra of Green Fluorescent Protein. Photochem Photobiol 2006. [DOI: 10.1562/2005-05-07-ra-518] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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