1
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Geometric description and electronic properties of the principal photosynthetic pigments of higher plants: a DFT study. J Mol Model 2015; 21:256. [PMID: 26369916 DOI: 10.1007/s00894-015-2796-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/24/2015] [Indexed: 10/23/2022]
Abstract
The geometric parameters, local and global chemical reactivity parameters (such as the ionization potential, electron affinity, electronegativity, hardness, softness, chemical potential, and electrophilicity index), as well as the energy levels (HOMO/LUMO) and HOMO-LUMO energy gaps have been determined for the principal carotenoids in higher plants. DFT calculations performed using the B3LYP functional in combination with the 6-31G(d,p) (for geometric parameters) and 6-31 + G(d,p) (for energy parameters) basis sets were carried out to study these structures. The HOMO-LUMO energy gaps obtained with the TPSSh functional were compared with the corresponding energy gaps obtained with B3LYP (when both functionals were used with the 6-31 + G(d,p) basis set). Upon analyzing all of the calculated parameters of the studied molecules, both carotenes were found to be the most reactive, followed by β-cryptoxanthin, zeaxanthin, lutein, violaxanthin, and finally neoxanthin, the least reactive molecule. The results reveal that all of the carotenoids show very high coplanarity in the photochemically active region, resulting in small HOMO-LUMO energy gaps. The calculated local and global chemical reactivity parameters indicate that all of the studied molecules may be classified as soft, as they are good electron donors/acceptors, making these molecules good candidates for use in artificial photosynthetic systems.
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2
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Blake HL, Robinson D. QM/MM studies of contemporary and novel membrane raft fluorescent probes. Molecules 2014; 19:10230-41. [PMID: 25029071 PMCID: PMC6271554 DOI: 10.3390/molecules190710230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 11/22/2022] Open
Abstract
We have studied a number of contemporary and novel membrane probes, selected for their structural similarity to membrane raft components, in order to properly anchor themselves within a sphingolipid/cholesterol rich region. A QM/MM approach was adopted in order to understand the structural and electrostatic influences of fluorescence emission shifts of the probes in different lipid and solvation environments. The proposed modifications to the membrane probes have shown encouraging data relating not only to emission shifts within the membrane, but also their ability to anchor within a membrane raft domain and the stability to internalization within a membrane system.
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Affiliation(s)
- Hannah L Blake
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - David Robinson
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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3
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Brezinski ME, Rupnick M. Can We Advance Macroscopic Quantum Systems Outside the Framework of Complex Decoherence Theory? JOURNAL OF COMPUTER SCIENCE AND SYSTEMS BIOLOGY 2014; 7:119-136. [PMID: 29200743 PMCID: PMC5710819 DOI: 10.4172/jcsb.1000147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Macroscopic quantum systems (MQS) are macroscopic systems driven by quantum rather than classical mechanics, a long studied area with minimal success till recently. Harnessing the benefits of quantum mechanics on a macroscopic level would revolutionize fields ranging from telecommunication to biology, the latter focused on here for reasons discussed. Contrary to misconceptions, there are no known physical laws that prevent the development of MQS. Instead, they are generally believed universally lost in complex systems from environmental entanglements (decoherence). But we argue success is achievable MQS with decoherence compensation developed, naturally or artificially, from top-down rather current reductionist approaches. This paper advances the MQS field by a complex systems approach to decoherence. First, why complex system decoherence approaches (top-down) are needed is discussed. Specifically, complex adaptive systems (CAS) are not amenable to reductionist models (and their master equations) because of emergent behaviour, approximation failures, not accounting for quantum compensatory mechanisms, ignoring path integrals, and the subentity problem. In addition, since MQS must exist within the context of the classical world, where rapid decoherence and prolonged coherence are both needed. Nature has already demonstrated this for quantum subsystems such as photosynthesis and magnetoreception. Second, we perform a preliminary study that illustrates a top-down approach to potential MQS. In summary, reductionist arguments against MQS are not justifiable. It is more likely they are not easily detectable in large intact classical systems or have been destroyed by reductionist experimental set-ups. This complex systems decoherence approach, using top down investigations, is critical to paradigm shifts in MQS research both in biological and non-biological systems.
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Affiliation(s)
- Mark E Brezinski
- Center for Optical Coherence Tomography and Modern Physics, Department of Orthopedic Surgery, Brigham and Women’s Hospital, 75 Francis Street, MRB-114, Boston, MA 02115, USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Rm 36-360, 50 Vassar St., Cambridge, MA 02139, USA
| | - Maria Rupnick
- Center for Optical Coherence Tomography and Modern Physics, Department of Orthopedic Surgery, Brigham and Women’s Hospital, 75 Francis Street, MRB-114, Boston, MA 02115, USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
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4
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Imhof P. Computational Study of Absorption Spectra of the Photoconvertible Fluorescent Protein EosFP in Different Protonation States. J Chem Theory Comput 2012; 8:4828-36. [DOI: 10.1021/ct300706r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Petra Imhof
- Computational Molecular Biophysics, Interdisciplinary
Center for Scientific Computing, University of Heidelberg, Speyererstrasse 6, 69115 Heidelberg, Germany
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5
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Robinson D, Besley NA, O’Shea P, Hirst JD. Di-8-ANEPPS Emission Spectra in Phospholipid/Cholesterol Membranes: A Theoretical Study. J Phys Chem B 2011; 115:4160-7. [DOI: 10.1021/jp1111372] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David Robinson
- School of Chemistry and ‡School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Nicholas A. Besley
- School of Chemistry and ‡School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Paul O’Shea
- School of Chemistry and ‡School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Jonathan D. Hirst
- School of Chemistry and ‡School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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6
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Olsen S. A Modified Resonance-Theoretic Framework for Structure−Property Relationships in a Halochromic Oxonol Dye. J Chem Theory Comput 2010. [DOI: 10.1021/ct100001b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Seth Olsen
- Centre for Organic Photonics and Electronics, School of Mathematics and Physics, The University of Queensland, Brisbane QLD 4072 Australia
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7
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Sun Q, Wang S, Zhang H, Li Z, Pifisterer C, Fischer S, Nanbu S, Smith SC. Structural and Relaxation Effects in Proton Wire Energetics: Model Studies of the Green Fluorescent Protein Photocycle. Aust J Chem 2010. [DOI: 10.1071/ch09509] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present the results of a systematic series of constrained minimum energy pathway calculations on ground state potential energy surfaces, for a cluster model of the proton chain transfer that mediates the photocycle of the green fluorescent protein, as well as for a model including the solvated protein environment. The calculations vary in terms of the types of modes that are assumed to be capable of relaxing in concert with the movement of the protons and the results demonstrate that the nature and extent of dynamical relaxation has a substantive impact on the activation energy for the proton transfer. We discuss the implications of this in terms of currently available dynamical models and chemical rate theories that might be brought to bear on the kinetics of this important example of proton chain transfer in a biological system.
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8
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Neugebauer J. Subsystem-Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies. Chemphyschem 2009; 10:3148-73. [DOI: 10.1002/cphc.200900538] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Li X, Chung LW, Mizuno H, Miyawaki A, Morokuma K. A Theoretical Study on the Nature of On- and Off-States of Reversibly Photoswitching Fluorescent Protein Dronpa: Absorption, Emission, Protonation, and Raman. J Phys Chem B 2009; 114:1114-26. [DOI: 10.1021/jp909947c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Lung Wa Chung
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Hideaki Mizuno
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Atsushi Miyawaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
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10
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Robinson D, Besley NA, Lunt EAM, O’Shea P, Hirst JD. Electronic Structure of 5-Hydroxyindole: From Gas Phase to Explicit Solvation. J Phys Chem B 2009; 113:2535-41. [DOI: 10.1021/jp808943d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- David Robinson
- School of Chemistry, and Cell Biophysics Group, School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Nicholas A. Besley
- School of Chemistry, and Cell Biophysics Group, School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Elizabeth A. M. Lunt
- School of Chemistry, and Cell Biophysics Group, School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Paul O’Shea
- School of Chemistry, and Cell Biophysics Group, School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D. Hirst
- School of Chemistry, and Cell Biophysics Group, School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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11
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Yampolsky IV, Kislukhin AA, Amatov TT, Shcherbo D, Potapov VK, Lukyanov S, Lukyanov KA. Synthesis and properties of the red chromophore of the green-to-red photoconvertible fluorescent protein Kaede and its analogs. Bioorg Chem 2008; 36:96-104. [PMID: 18262585 PMCID: PMC2323602 DOI: 10.1016/j.bioorg.2007.12.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 12/21/2007] [Accepted: 12/27/2007] [Indexed: 10/22/2022]
Abstract
Green fluorescent protein (GFP) and homologous proteins possess a unique pathway of chromophore formation based on autocatalytic modification of their own amino acid residues. Green-to-red photoconvertible fluorescent protein Kaede carries His-Tyr-Gly chromophore-forming triad. Here, we describe synthesis of Kaede red chromophore (2-[(1E)-2-(5-imidazolyl)ethenyl]-4-(p-hydroxybenzylidene)-5-imidazolone) and its analogs that can be potentially formed by natural amino acid residues. Chromophores corresponding to the following tripeptides were obtained: His-Tyr-Gly, Trp-Tyr-Gly, Phe-Trp-Gly, Tyr-Trp-Gly, Asn-Tyr-Gly, Phe-Tyr-Gly, and Tyr-Tyr-Gly. In basic conditions they fluoresced red with relatively high quantum yield (up to 0.017 for Trp-derived compounds). The most red-shifted absorption peak at 595nm was found for the chromophore Trp-Tyr-Gly in basic DMSO. Surprisingly, in basic DMF non-aromatic Asn-derived chromophore Asn-Tyr-Gly demonstrated the most red-shifted emission maximum at 642 nm. Thus, Asn residue may be a promising substituent, which can potentially diversify posttranslational chemistry in GFP-like proteins.
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Affiliation(s)
- Ilia V. Yampolsky
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | | | - Tynchtyk T. Amatov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Dmitry Shcherbo
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Victor K. Potapov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Sergey Lukyanov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
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12
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Chromophore protonation state controls photoswitching of the fluoroprotein asFP595. PLoS Comput Biol 2008; 4:e1000034. [PMID: 18369426 PMCID: PMC2274881 DOI: 10.1371/journal.pcbi.1000034] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Accepted: 02/12/2008] [Indexed: 11/19/2022] Open
Abstract
Fluorescent proteins have been widely used as genetically encodable fusion tags for biological imaging. Recently, a new class of fluorescent proteins was discovered that can be reversibly light-switched between a fluorescent and a non-fluorescent state. Such proteins can not only provide nanoscale resolution in far-field fluorescence optical microscopy much below the diffraction limit, but also hold promise for other nanotechnological applications, such as optical data storage. To systematically exploit the potential of such photoswitchable proteins and to enable rational improvements to their properties requires a detailed understanding of the molecular switching mechanism, which is currently unknown. Here, we have studied the photoswitching mechanism of the reversibly switchable fluoroprotein asFP595 at the atomic level by multiconfigurational ab initio (CASSCF) calculations and QM/MM excited state molecular dynamics simulations with explicit surface hopping. Our simulations explain measured quantum yields and excited state lifetimes, and also predict the structures of the hitherto unknown intermediates and of the irreversibly fluorescent state. Further, we find that the proton distribution in the active site of the asFP595 controls the photochemical conversion pathways of the chromophore in the protein matrix. Accordingly, changes in the protonation state of the chromophore and some proximal amino acids lead to different photochemical states, which all turn out to be essential for the photoswitching mechanism. These photochemical states are (i) a neutral chromophore, which can trans-cis photoisomerize, (ii) an anionic chromophore, which rapidly undergoes radiationless decay after excitation, and (iii) a putative fluorescent zwitterionic chromophore. The overall stability of the different protonation states is controlled by the isomeric state of the chromophore. We finally propose that radiation-induced decarboxylation of the glutamic acid Glu215 blocks the proton transfer pathways that enable the deactivation of the zwitterionic chromophore and thus leads to irreversible fluorescence. We have identified the tight coupling of trans-cis isomerization and proton transfers in photoswitchable proteins to be essential for their function and propose a detailed underlying mechanism, which provides a comprehensive picture that explains the available experimental data. The structural similarity between asFP595 and other fluoroproteins of interest for imaging suggests that this coupling is a quite general mechanism for photoswitchable proteins. These insights can guide the rational design and optimization of photoswitchable proteins. Proteins whose fluorescence can be reversibly switched on and off hold great promise for applications in high-resolution optical microscopy and nanotechnology. To systematically exploit the potential of such photoswitchable proteins and to enable rational improvements of their properties requires a detailed understanding of the molecular switching mechanism. Here, we have studied the photoswitching mechanism of the reversibly switchable fluoroprotein asFP595 by atomistic molecular dynamics simulations. Our simulations explain measured quantum yields and excited state lifetimes, and also predict the structures of the hitherto unknown intermediates and of the irreversibly fluorescent state. Further, we find that the proton distribution in the active site of the asFP595 controls the photochemical conversion pathways of the chromophore in the protein matrix. Our results show that a tight coupling between trans-cis isomerization of the chromophore and proton transfer is essential for the function of asFP595. The structural similarity between asFP595 and other fluoroproteins suggests that this coupling is a quite general mechanism for photoswitchable proteins. These insights can guide the rational design and optimization of photoswitchable proteins.
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13
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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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14
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Schäfer LV, Groenhof G, Klingen AR, Ullmann GM, Boggio-Pasqua M, Robb MA, Grubmüller H. Photoswitching of the fluorescent protein asFP595: mechanism, proton pathways, and absorption spectra. Angew Chem Int Ed Engl 2007; 46:530-6. [PMID: 17094157 DOI: 10.1002/anie.200602315] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lars V Schäfer
- Abteilung für theoretische und computergestützte Biophysik, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany
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15
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Schäfer L, Groenhof G, Klingen A, Ullmann G, Boggio-Pasqua M, Robb M, Grubmüller H. Photoswitching of the Fluorescent Protein asFP595: Mechanism, Proton Pathways, and Absorption Spectra. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200602315] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Wang S, Smith SC. Mechanistic aspects of proton chain transfer in the green fluorescent protein : Part II. A comparison of minimal quantum chemical models. Phys Chem Chem Phys 2007; 9:452-8. [PMID: 17216060 DOI: 10.1039/b612760f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper we report the results of extensive quantum chemical reaction pathway calculations for the electronic ground state of several different cluster models that mimic the proton chain transfer path within the green fluorescent protein (GFP). Our principal objective is to establish the robustness with respect to variations in the model of our recent mechanistic inferences for the ground state proton chain transfer [S. Wang and S. C. Smith, J. Phys. Chem. B, 2006, 110, 5084]. Additionally, comparison of our ground state results with the excited state proton transfer (ESPT) study by Vendrell et al. [O. Vendrell, R. Gelabert, M. Moreno and J. M. Lluch, J. Am. Chem. Soc., 2006, 128, 3564] leads to the conclusion that the mechanism of proton chain transfer may be expected to be analogous in ground and excited states, principally because in both cases the loss of the chromophore's phenolic proton contributes strongly to the reaction coordinate only late in the reaction path.
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Affiliation(s)
- Sufan Wang
- Centre for Computational Molecular Science, The University of Queensland, Brisbane, QLD 4072, Australia
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17
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Lammich L, Petersen MA, Nielsen MB, Andersen LH. The gas-phase absorption spectrum of a neutral GFP model chromophore. Biophys J 2006; 92:201-7. [PMID: 17040991 PMCID: PMC1697863 DOI: 10.1529/biophysj.106.093674] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have studied the gas-phase absorption properties of the green fluorescent protein (GFP) chromophore in its neutral (protonated) charge state in a heavy-ion storage ring. To accomplish this we synthesized a new molecular chromophore with a charged NH(3) group attached to a neutral model chromophore of GFP. The gas-phase absorption cross section of this chromophore molecule as a function of the wavelength is compared to the well-known absorption profile of GFP. The chromophore has a maximum absorption at 415 +/- 5 nm. When corrected for the presence of the charged group attached to the GFP model chromophore, the unperturbed neutral chromophore is predicted to have an absorption maximum at 399 nm in vacuum. This is very close to the corresponding absorption peak of the protein at 397 nm. Together with previous data obtained with an anionic GFP model chromophore, the present data show that the absorption of GFP is primarily determined by intrinsic chromophore properties. In other words, there is strong experimental evidence that, in terms of absorption, the conditions in the hydrophobic interior of this protein are very close to those in vacuum.
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Affiliation(s)
- L Lammich
- Department of Physics and Astronomy, University of Aarhus, Aarhus, Denmark
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18
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Wang S, Smith SC. Mechanistic Aspects of Proton Chain Transfer: A Computational Study for the Green Fluorescent Protein Chromophore. J Phys Chem B 2006; 110:5084-93. [PMID: 16526751 DOI: 10.1021/jp056966k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We explore several models for the ground-state proton chain transfer pathway between the green fluorescent protein chromophore and its surrounding protein matrix, with a view to elucidating mechanistic aspects of this process. We have computed quantum chemically the minimum energy pathways (MEPs) in the ground electronic state for one-, two-, and three-proton models of the chain transfer. There are no stable intermediates for our models, indicating that the proton chain transfer is likely to be a single, concerted kinetic step. However, despite the concerted nature of the overall energy profile, a more detailed analysis of the MEPs reveals clear evidence of sequential movement of protons in the chain. The ground-state proton chain transfer does not appear to be driven by the movement of the phenolic proton off the chromophore onto the neutral water bridge. Rather, this proton is the last of the three protons in the chain to move. We find that the first proton movement is from the bridging Ser205 moiety to the accepting Glu222 group. This is followed by the second proton moving from the bridging water to the Ser205--for our model this is where the barrier occurs. The phenolic proton on the chromophore is hence the last in the chain to move, transferring to a bridging "water" that already has substantial negative charge.
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Affiliation(s)
- Sufan Wang
- Centre for Computational Molecular Science, Chemistry Building #68, The University of Queensland, Brisbane, Queensland 4072, Australia
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19
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Bonsma S, Purchase R, Jezowski S, Gallus J, Könz F, Völker S. Green and red fluorescent proteins: photo- and thermally induced dynamics probed by site-selective spectroscopy and hole burning. Chemphyschem 2005; 6:838-49. [PMID: 15884066 DOI: 10.1002/cphc.200500005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Indexed: 11/12/2022]
Abstract
The cloning and expression of autofluorescent proteins in living matter, combined with modern imaging techniques, have thoroughly changed the world of bioscience. In particular, such proteins are widely used as genetically encoded labels to track the movement of proteins as reporters of cellular signals and to study protein-protein interactions by fluorescence resonance energy transfer (FRET). Their optical properties, however, are complex and it is important to understand these for the correct interpretation of imaging data and for the design of new fluorescent mutants. In this Minireview we start with a short survey of the field and then focus on the photo- and thermally induced dynamics of green and red fluorescent proteins. In particular, we show how fluorescence line narrowing and high-resolution spectral hole burning at low temperatures can be used to unravel the photophysics and photochemistry and shed light on the intricate electronic structure of these proteins.
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Affiliation(s)
- S Bonsma
- Huygens and Gorlaeus Laboratories, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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20
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Computation of Reaction Mechanisms and Dynamics in Photobiology. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1380-7323(05)80024-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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21
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Abstract
Computations are now an integrated part of structural biology and are used in data gathering, data processing, and data storage as well as in a full spectrum of theoretical pursuits. In this review, we focus on areas of great promise and call attention to important issues of internal consistency and error analysis.
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Affiliation(s)
- Irwin D Kuntz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-2440, USA
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22
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Menter DG. Cyclooxygenase 2 selective inhibitors in cancer treatment and prevention. Expert Opin Investig Drugs 2002; 11:1749-64. [PMID: 12457435 DOI: 10.1517/13543784.11.12.1749] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Prostaglandin synthesis by a number of enzymes is important at all stages during the genesis of cancer. The availability of prostaglandin H(2) as a substrate for prostaglandin production is a critical control point in its synthesis. Cyclooxygenase (COX) occurs in two forms (COX-1 and -2) and acts as the rate-limiting enzyme that generates prostaglandin H(2). COX-1 is produced as a steady-state enzyme, while COX-2 is heavily involved in inflammation and tumorigenesis. Differences in the catalytic sites of these enzymes are utilised to generate COX-2 selective inhibitors. Certain chemical characteristics of non-steroidal anti-inflammatory drugs and COX-2 selective inhibitors make some of these inhibitors more effective against COX-2 than others. Epidemiological, animal and preclinical data demonstrate the promise of non-steroidal anti-inflammatory drugs and COX-2 selective inhibitors as anticancer agents. Ongoing clinical trials are designed to determine the efficacy of non-steroidal anti-inflammatory drugs and COX-2 selective inhibitors in the prevention and treatment of many types of cancer.
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Affiliation(s)
- David G Menter
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Box 236, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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