1
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Moya R, Norris AC, Spangler LC, Scholes GD, Schlau-Cohen GS. Observation of conformational dynamics in single light-harvesting proteins from cryptophyte algae. J Chem Phys 2022; 157:035102. [PMID: 35868944 PMCID: PMC9894659 DOI: 10.1063/5.0095763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Photosynthetic organisms use pigment-protein complexes to capture the sunlight that powers most life on earth. Within these complexes, the position of the embedded pigments is all optimized for light harvesting. At the same time, the protein scaffold undergoes thermal fluctuations that vary the structure, and, thus, photophysics, of the complexes. While these variations are averaged out in ensemble measurements, single-molecule spectroscopy provides the ability to probe these conformational changes. We used single-molecule fluorescence spectroscopy to identify the photophysical substates reflective of distinct conformations and the associated conformational dynamics in phycoerythrin 545 (PE545), a pigment-protein complex from cryptophyte algae. Rapid switching between photophysical states was observed, indicating that ensemble measurements average over a conformational equilibrium. A highly quenched conformation was also identified, and its population increased under high light. This discovery establishes that PE545 has the characteristics to serve as a photoprotective site. Finally, unlike homologous proteins from the evolutionarily related cyanobacteria and red algae, quenching was not observed upon photobleaching, which may allow for robust photophysics without the need for rapid repair or replacement machinery. Collectively, these observations establish the presence of a rich and robust set of conformational states of PE545. Cryptophytes exhibit particularly diverse energetics owing to the variety of microenvironments in which they survive, and the conformational states and dynamics reported here may provide photophysical flexibility that contributes to their remarkable ability to flourish under diverse conditions.
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Affiliation(s)
- Raymundo Moya
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Audrey C. Norris
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Leah C. Spangler
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Gregory D. Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Gabriela S. Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA,Author to whom correspondence should be addressed:
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2
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van Heerden B, Vickers NA, Krüger TPJ, Andersson SB. Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107024. [PMID: 35758534 PMCID: PMC9308725 DOI: 10.1002/smll.202107024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 04/07/2022] [Indexed: 05/14/2023]
Abstract
Real-time feedback-driven single-particle tracking (RT-FD-SPT) is a class of techniques in the field of single-particle tracking that uses feedback control to keep a particle of interest in a detection volume. These methods provide high spatiotemporal resolution on particle dynamics and allow for concurrent spectroscopic measurements. This review article begins with a survey of existing techniques and of applications where RT-FD-SPT has played an important role. Each of the core components of RT-FD-SPT are systematically discussed in order to develop an understanding of the trade-offs that must be made in algorithm design and to create a clear picture of the important differences, advantages, and drawbacks of existing approaches. These components are feedback tracking and control, ranging from simple proportional-integral-derivative control to advanced nonlinear techniques, estimation to determine particle location from the measured data, including both online and offline algorithms, and techniques for calibrating and characterizing different RT-FD-SPT methods. Then a collection of metrics for RT-FD-SPT is introduced to help guide experimentalists in selecting a method for their particular application and to help reveal where there are gaps in the techniques that represent opportunities for further development. Finally, this review is concluded with a discussion on future perspectives in the field.
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Affiliation(s)
- Bertus van Heerden
- Department of Physics, University of Pretoria, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Nicholas A Vickers
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Sean B Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Systems Engineering, Boston University, Boston, MA, 02215, USA
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3
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Moya R, Norris AC, Kondo T, Schlau-Cohen GS. Observation of robust energy transfer in the photosynthetic protein allophycocyanin using single-molecule pump-probe spectroscopy. Nat Chem 2022; 14:153-159. [PMID: 34992285 PMCID: PMC9977402 DOI: 10.1038/s41557-021-00841-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/20/2021] [Indexed: 01/26/2023]
Abstract
Photosynthetic organisms convert sunlight to electricity with near unity quantum efficiency. Absorbed photoenergy transfers through a network of chromophores positioned within protein scaffolds, which fluctuate due to thermal motion. The resultant variation in the individual energy transfer steps has not yet been measured, and so how the efficiency is robust to this variation has not been determined. Here, we describe single-molecule pump-probe spectroscopy with facile spectral tuning and its application to the ultrafast dynamics of single allophycocyanin, a light-harvesting protein from cyanobacteria. We disentangled the energy transfer and energetic relaxation from nuclear motion using the spectral dependence of the dynamics. We observed an asymmetric distribution of timescales for energy transfer and a slower and more heterogeneous distribution of timescales for energetic relaxation, which was due to the impact of the protein environment. Collectively, these results suggest that energy transfer is robust to protein fluctuations, a prerequisite for efficient light harvesting.
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Affiliation(s)
- Raymundo Moya
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Audrey C. Norris
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Toru Kondo
- Department of Life Science and Technology, Tokyo Institute of Technology,PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Gabriela S. Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA,To whom correspondence should be addressed;
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4
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Squires A, Wang Q, Dahlberg P, Moerner WE. A bottom-up perspective on photodynamics and photoprotection in light-harvesting complexes using anti-Brownian trapping. J Chem Phys 2022; 156:070901. [DOI: 10.1063/5.0079042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Quan Wang
- Genomics, Princeton University, United States of America
| | | | - W. E. Moerner
- Department of Chemistry, Stanford University, United States of America
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5
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Navotnaya P, Sohoni S, Lloyd LT, Abdulhadi SM, Ting PC, Higgins JS, Engel GS. Annihilation of Excess Excitations along Phycocyanin Rods Precedes Downhill Flow to Allophycocyanin Cores in the Phycobilisome of Synechococcus elongatus PCC 7942. J Phys Chem B 2022; 126:23-29. [PMID: 34982932 PMCID: PMC8762654 DOI: 10.1021/acs.jpcb.1c06509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Cyanobacterial phycobilisome
complexes absorb visible sunlight
and funnel photogenerated excitons to the photosystems where charge
separation occurs. In the phycobilisome complex of Synechococcus
elongatus PCC 7942, phycocyanin protein rods that absorb
bluer wavelengths are assembled on allophycocyanin cores that absorb
redder wavelengths. This arrangement creates a natural energy gradient
toward the reaction centers of the photosystems. Here, we employ broadband
pump–probe spectroscopy to observe the fate of excess excitations
in the phycobilisome complex of this organism. We show that excess
excitons are quenched through exciton–exciton annihilation
along the phycocyanin rods prior to transfer to the allophycocyanin
cores. Our observations are especially relevant in comparison to other
antenna proteins, where exciton annihilation primarily occurs in the
lowest-energy chlorophylls. The observed effect could play a limited
photoprotective role in physiological light fluences. The exciton
decay dynamics is faster in the intact phycobilisome than in isolated
C-phycocyanin trimers studied in earlier work, confirming that this
effect is an emergent property of the complex assembly. Using the
obtained annihilation data, we calculate exciton hopping times of
2.2–6.4 ps in the phycocyanin rods. This value agrees with
earlier FRET calculations of exciton hopping times along phycocyanin
hexamers by Sauer and Scheer.
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Affiliation(s)
- Polina Navotnaya
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Siddhartha Sohoni
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lawson T Lloyd
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sami M Abdulhadi
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Po-Chieh Ting
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jacob S Higgins
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory S Engel
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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6
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Das A, Vishvakarma V, Dey A, Dey S, Gupta A, Das M, Vishwakarma KK, Roy DS, Yadav S, Kesarwani S, Venkatramani R, Maiti S. Biophysical properties of the isolated spike protein binding helix of human ACE2. Biophys J 2021; 120:2785-2792. [PMID: 34214538 PMCID: PMC8241576 DOI: 10.1016/j.bpj.2021.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/22/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
The entry of the severe acute respiratory syndrome coronavirus 2 virus in human cells is mediated by the binding of its surface spike protein to the human angiotensin-converting enzyme 2 (ACE2) receptor. A 23-residue long helical segment (SBP1) at the binding interface of human ACE2 interacts with viral spike protein and therefore has generated considerable interest as a recognition element for virus detection. Unfortunately, emerging reports indicate that the affinity of SBP1 to the receptor-binding domain of the spike protein is much lower than that of the ACE2 receptor itself. Here, we examine the biophysical properties of SBP1 to reveal factors leading to its low affinity for the spike protein. Whereas SBP1 shows good solubility (solubility > 0.8 mM), circular dichroism spectroscopy shows that it is mostly disordered with some antiparallel β-sheet content and no helicity. The helicity is substantial (>20%) only upon adding high concentrations (≥20% v/v) of 2,2,2-trifluoroethanol, a helix promoter. Fluorescence correlation spectroscopy and single-molecule photobleaching studies show that the peptide oligomerizes at concentrations >50 nM. We hypothesized that mutating the hydrophobic residues (F28, F32, and F40) of SBP1, which do not directly interact with the spike protein, to alanine would reduce peptide oligomerization without affecting its spike binding affinity. Whereas the mutant peptide (SBP1mod) shows substantially reduced oligomerization propensity, it does not show improved helicity. Our study shows that the failure of efforts, so far, to produce a short SBP1 mimic with a high affinity for the spike protein is not only due to the lack of helicity but is also due to the heretofore unrecognized problem of oligomerization.
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Affiliation(s)
- Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Vicky Vishvakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Simli Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Ankur Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Mitradip Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | | | - Debsankar Saha Roy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Swati Yadav
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Shubham Kesarwani
- Centre for Cardiovascular Biology and Disease, Institute of Stem Cell Science and Regenerative Medicine (inStem), Gandhi Krishi Vigyan Kendra Campus, Bangalore, Karnataka, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India.
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7
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Dey S, Das A, Dey A, Maiti S. Membrane affinity of individual toxic protein oligomers determined at the single-molecule level. Phys Chem Chem Phys 2020; 22:14613-14620. [PMID: 32483579 DOI: 10.1039/d0cp00450b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Oligomers are the key suspects in protein aggregation-linked diseases, such as Alzheimer's and Type II diabetes, and most likely exert their toxicity by interacting with lipid membranes. However, the "which oligomer" question remains an obstacle in understanding the disease mechanism, as the exact identity of the toxic oligomer(s) is not yet known. Oligomers exist as a mixture of species of different sizes (i.e. as different 'n-mers') in a physiological solution, making it difficult to determine the properties of individual species. Here we demonstrate a method based on single-molecule photo-bleaching (smPB) which can provide an answer to the "which oligomer" question, at least as far as membrane affinity is concerned. We calculate the ratio of the oligomer size distribution of human Islet Amyloid Polypeptide (IAPP) in the aqueous phase and that on a coexisting artificial lipid bilayer, and this measures the relative membrane affinity of individual oligomeric species. A problem with smPB measurements is that they can be very sensitive to pre-measurement bleaching. Here we correct for pre-bleaching using a covalently linked multimeric peptide as a bleaching standard. We find that the order of membrane affinity for IAPP n-mers is trimer > dimer > tetramer ≫ monomer. Our results agree well with the average membrane affinity values of oligomeric and monomeric solutions previously measured with Fluorescence Correlation Spectroscopy. The "which oligomer" question, in the context of membrane affinity, can therefore, be solved quantitatively for any membrane-active toxic protein aggregate.
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Affiliation(s)
- Simli Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
| | - Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
| | - Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
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8
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Wahadoszamen M, Krüger TPJ, Ara AM, van Grondelle R, Gwizdala M. Charge transfer states in phycobilisomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148187. [PMID: 32173383 DOI: 10.1016/j.bbabio.2020.148187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/17/2020] [Accepted: 03/09/2020] [Indexed: 10/24/2022]
Abstract
Phycobilisomes (PBs) absorb light and supply downstream photosynthetic processes with excitation energy in many cyanobacteria and algae. In response to a sudden increase in light intensity, excess excitation energy is photoprotectively dissipated in PBs by means of the orange carotenoid protein (OCP)-related mechanism or via a light-activated intrinsic decay channel. Recently, we have identified that both mechanisms are associated with far-red emission states. Here, we investigate the far-red states involved with the light-induced intrinsic mechanism by exploring the energy landscape and electro-optical properties of the pigments in PBs. While Stark spectroscopy showed that the far-red states in PBs exhibit a strong charge-transfer (CT) character at cryogenic temperatures, single molecule spectroscopy revealed that CT states should also be present at room temperature. Owing to the strong environmental sensitivity of CT states, the knowledge gained from this study may contribute to the design of a new generation of fluorescence markers.
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Affiliation(s)
- Md Wahadoszamen
- Department of Physics, University of Dhaka, Dhaka 1000, Bangladesh
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Pretoria 0023, South Africa
| | - Anjue Mane Ara
- Department of Physics, Jagannath University, Dhaka 1100, Bangladesh
| | - Rienk van Grondelle
- Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, the Netherlands
| | - Michal Gwizdala
- Department of Physics, University of Pretoria, Pretoria 0023, South Africa; Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, the Netherlands.
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9
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Dey S, Das A, Maiti S. Correction of Systematic Bias in Single Molecule Photobleaching Measurements. Biophys J 2020; 118:1101-1108. [PMID: 31972157 DOI: 10.1016/j.bpj.2019.12.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/02/2019] [Accepted: 12/30/2019] [Indexed: 10/25/2022] Open
Abstract
Single molecule photobleaching is a powerful technique to measure the number of fluorescent units in subresolution molecular complexes, such as in toxic protein oligomers associated with amyloid diseases. However, photobleaching can occur before the sample is appropriately placed and focused. Such "prebleaching" can introduce a strong systematic bias toward smaller oligomers. Quantitative correction of prebleaching is known to be an ill-posed problem, limiting the utility of the technique. Here, we provide an experimental solution to improve its reliability. We chemically construct multimeric standards to estimate the prebleaching probability, B. We show that B can be used as a constraint to reliably correct the statistics obtained from a known distribution of standard oligomers. Finally, we apply this method to the data obtained from a heterogeneous oligomeric solution of human islet amyloid polypeptide. Our results show that photobleaching can critically skew the estimation of oligomeric distributions, so that low abundance monomers display a much higher apparent abundance. In summary, any inference from photobleaching experiments with B > 0.1 is likely to be unreliable, but our method can be used to quantitatively correct possible errors.
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Affiliation(s)
- Simli Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra, India
| | - Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra, India.
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10
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Fleming GR. The contributions of 49ers to the measurements and models of ultrafast photosynthetic energy transfer. PHOTOSYNTHESIS RESEARCH 2018; 135:3-8. [PMID: 28247235 DOI: 10.1007/s11120-017-0360-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/21/2017] [Indexed: 06/06/2023]
Abstract
Progress in measuring and understanding the mechanism of the elementary energy transfer steps in photosynthetic light harvesting from roughly 1949 to the present is sketched with a focus on the group of scientists born in 1949 ± 1. Improvements in structural knowledge, laser spectroscopic methods, and quantum dynamical theories have led to the ability to record and calculate with reasonable accuracy the timescales of elementary energy transfer steps. The significance of delocalized excited states and of near-field Coulombic coupling is noted. The microscopic understanding enables consistent coarse graining and should enable a much-improved understanding of the regulation of photosynthetic light harvesting.
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Affiliation(s)
- Graham R Fleming
- Department of Chemistry and Kavli Energy NanoScience Institute, University of California Berkeley, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioengineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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11
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Löhner A, Cogdell R, Köhler J. Contribution of low-temperature single-molecule techniques to structural issues of pigment-protein complexes from photosynthetic purple bacteria. J R Soc Interface 2018; 15:rsif.2017.0680. [PMID: 29321265 DOI: 10.1098/rsif.2017.0680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/01/2017] [Indexed: 11/12/2022] Open
Abstract
As the electronic energies of the chromophores in a pigment-protein complex are imposed by the geometrical structure of the protein, this allows the spectral information obtained to be compared with predictions derived from structural models. Thereby, the single-molecule approach is particularly suited for the elucidation of specific, distinctive spectral features that are key for a particular model structure, and that would not be observable in ensemble-averaged spectra due to the heterogeneity of the biological objects. In this concise review, we illustrate with the example of the light-harvesting complexes from photosynthetic purple bacteria how results from low-temperature single-molecule spectroscopy can be used to discriminate between different structural models. Thereby the low-temperature approach provides two advantages: (i) owing to the negligible photobleaching, very long observation times become possible, and more importantly, (ii) at cryogenic temperatures, vibrational degrees of freedom are frozen out, leading to sharper spectral features and in turn to better resolved spectra.
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Affiliation(s)
- Alexander Löhner
- Spectroscopy of Soft Matter, University of Bayreuth, 95440 Bayreuth, Germany
| | - Richard Cogdell
- Institute of Molecular, Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Jürgen Köhler
- Spectroscopy of Soft Matter, University of Bayreuth, 95440 Bayreuth, Germany .,Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, 95440 Bayreuth, Germany
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12
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Zang H, Routh PK, Meng Q, Cotlet M. Electron transfer dynamics from single near infrared emitting lead sulfide-cadmium sulfide nanocrystals to titanium dioxide. NANOSCALE 2017; 9:14664-14671. [PMID: 28937699 DOI: 10.1039/c7nr03500d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this study we report the first successful demonstration of electron transfer between single near infrared emitting PbS/CdS nanocrystals and an external acceptor, titanium dioxide (TiO2). We demonstrate distance-dependent electron transfer from single nanocrystals to TiO2 and explore the effect of this process on the photoluminescence dynamics of these nanocrystals. Isolated PbS/CdS QDs are found to exhibit blinking dynamics similar to other nanocrystals like CdSe/ZnS; however, their photoluminescence follows a quasi two-state pattern with heterogeneous photoluminescence lifetimes which may be the result of their emission originating from different energy states. Electron transfer of these nanocrystals with an external acceptor inhibits their photoluminescence lifetime heterogeneity and biases their blinking dynamics in a manner similar to that observed for visible emitting CdSe/ZnS nanocrystals undergoing electron transfer with external acceptors. While the present study reconfirms the universality of quantum dot blinking among various types of nanocrystals, it also demonstrates that universality remains valid for the communication of various types of nanocrystals with the exterior world, here pictured as electron transfer with external acceptors.
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Affiliation(s)
- Huidong Zang
- Center for Functional Nanomaterials at Brookhaven National Laboratory, Upton, New York 11973, USA.
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13
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Eisenberg I, Caycedo-Soler F, Harris D, Yochelis S, Huelga SF, Plenio MB, Adir N, Keren N, Paltiel Y. Regulating the Energy Flow in a Cyanobacterial Light-Harvesting Antenna Complex. J Phys Chem B 2017; 121:1240-1247. [DOI: 10.1021/acs.jpcb.6b10590] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ido Eisenberg
- Applied
Physics Department and The Center for Nano-Science and Nano-Technology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Felipe Caycedo-Soler
- Institute
of Theoretical Physics, Ulm University, Albert Einstein Alle 11, 89069 Ulm, Germany
| | - Dvir Harris
- Schulich
Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Shira Yochelis
- Applied
Physics Department and The Center for Nano-Science and Nano-Technology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Susana F. Huelga
- Institute
of Theoretical Physics, Ulm University, Albert Einstein Alle 11, 89069 Ulm, Germany
| | - Martin B. Plenio
- Institute
of Theoretical Physics, Ulm University, Albert Einstein Alle 11, 89069 Ulm, Germany
| | - Noam Adir
- Schulich
Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Nir Keren
- Department
of Plant and Environmental Sciences, Alexander Silberman Institute
of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 9190401, Israel
| | - Yossi Paltiel
- Applied
Physics Department and The Center for Nano-Science and Nano-Technology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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14
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Kondo T, Chen WJ, Schlau-Cohen GS. Single-Molecule Fluorescence Spectroscopy of Photosynthetic Systems. Chem Rev 2017; 117:860-898. [DOI: 10.1021/acs.chemrev.6b00195] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Toru Kondo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
| | - Wei Jia Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
| | - Gabriela S. Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
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15
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Hontani Y, Shcherbakova DM, Baloban M, Zhu J, Verkhusha VV, Kennis JTM. Bright blue-shifted fluorescent proteins with Cys in the GAF domain engineered from bacterial phytochromes: fluorescence mechanisms and excited-state dynamics. Sci Rep 2016; 6:37362. [PMID: 27857208 PMCID: PMC5114657 DOI: 10.1038/srep37362] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/25/2016] [Indexed: 11/21/2022] Open
Abstract
Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes (BphPs) are of great interest for in vivo imaging. They utilize biliverdin (BV) as a chromophore, which is a heme degradation product, and therefore they are straightforward to use in mammalian tissues. Here, we report on fluorescence properties of NIR FPs with key alterations in their BV binding sites. BphP1-FP, iRFP670 and iRFP682 have Cys residues in both PAS and GAF domains, rather than in the PAS domain alone as in wild-type BphPs. We found that NIR FP variants with Cys in the GAF or with Cys in both PAS and GAF show blue-shifted emission with long fluorescence lifetimes. In contrast, mutants with Cys in the PAS only or no Cys residues at all exhibit red-shifted emission with shorter lifetimes. Combining these results with previous biochemical and BphP1-FP structural data, we conclude that BV adducts bound to Cys in the GAF are the origin of bright blue-shifted fluorescence. We propose that the long fluorescence lifetime follows from (i) a sterically more constrained thioether linkage, leaving less mobility for ring A than in canonical BphPs, and (ii) that π-electron conjugation does not extend on ring A, making excited-state deactivation less sensitive to ring A mobility.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Mikhail Baloban
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Jingyi Zhu
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - John T M Kennis
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
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16
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Dissecting pigment architecture of individual photosynthetic antenna complexes in solution. Proc Natl Acad Sci U S A 2015; 112:13880-5. [PMID: 26438850 DOI: 10.1073/pnas.1514027112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oligomerization plays a critical role in shaping the light-harvesting properties of many photosynthetic pigment-protein complexes, but a detailed understanding of this process at the level of individual pigments is still lacking. To study the effects of oligomerization, we designed a single-molecule approach to probe the photophysical properties of individual pigment sites as a function of protein assembly state. Our method, based on the principles of anti-Brownian electrokinetic trapping of single fluorescent proteins, step-wise photobleaching, and multiparameter spectroscopy, allows pigment-specific spectroscopic information on single multipigment antennae to be recorded in a nonperturbative aqueous environment with unprecedented detail. We focus on the monomer-to-trimer transformation of allophycocyanin (APC), an important antenna protein in cyanobacteria. Our data reveal that the two chemically identical pigments in APC have different roles. One (α) is the functional pigment that red-shifts its spectral properties upon trimer formation, whereas the other (β) is a "protective" pigment that persistently quenches the excited state of α in the prefunctional, monomer state of the protein. These results show how subtleties in pigment organization give rise to functionally important aspects of energy transfer and photoprotection in antenna complexes. The method developed here should find immediate application in understanding the emergent properties of other natural and artificial light-harvesting systems.
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17
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Long S, Zhou M, Tang K, Zeng XL, Niu Y, Guo Q, Zhao KH, Xia A. Single-molecule spectroscopy and femtosecond transient absorption studies on the excitation energy transfer process in ApcE(1–240) dimers. Phys Chem Chem Phys 2015; 17:13387-96. [DOI: 10.1039/c5cp01687h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The red-shifted absorption of ApcE dimers results from extending chromophore conformation, which does not depend on strong exction coupling.
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Affiliation(s)
- Saran Long
- Beijing National Laboratory for Molecular Sciences (BNLMS) and Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Meng Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS) and Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Kun Tang
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
- People's Republic of China
| | - Xiao-Li Zeng
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
- People's Republic of China
| | - Yingli Niu
- Beijing National Laboratory for Molecular Sciences (BNLMS) and Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Qianjin Guo
- Beijing National Laboratory for Molecular Sciences (BNLMS) and Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
- People's Republic of China
| | - Andong Xia
- Beijing National Laboratory for Molecular Sciences (BNLMS) and Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
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18
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De Mitri N, Prampolini G, Monti S, Barone V. Structural, dynamic and photophysical properties of a fluorescent dye incorporated in an amorphous hydrophobic polymer bundle. Phys Chem Chem Phys 2014; 16:16573-87. [PMID: 24988373 PMCID: PMC4618303 DOI: 10.1039/c4cp01828a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The properties of a low molecular weight organic dye, namely 4-naphthyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine, covalently bound to an apolar polyolefin were investigated by means of a multi-level approach, combining classical molecular dynamics simulations, based on purposely parameterized force fields, and quantum mechanical calculations based on density functional theory (DFT) and its time-dependent extension (TD-DFT). The structure and dynamics of the dye in its embedding medium were analyzed and discussed taking the entangling effect of the surrounding polymer into account, and also by comparing the results to those obtained for a different environment, i.e. toluene solution. Finally, the influence was investigated of long lived cages found in the polymeric embedding on photophysical properties, in terms of the slow and fast dye's internal dynamics, by comparing computed IR and UV spectra with their experimental counterparts.
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Affiliation(s)
- N De Mitri
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy
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19
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Krüger TPJ, Ilioaia C, Johnson MP, Belgio E, Horton P, Ruban AV, van Grondelle R. The specificity of controlled protein disorder in the photoprotection of plants. Biophys J 2014; 105:1018-26. [PMID: 23972853 DOI: 10.1016/j.bpj.2013.07.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 06/11/2013] [Accepted: 07/15/2013] [Indexed: 11/28/2022] Open
Abstract
Light-harvesting pigment-protein complexes of photosystem II of plants have a dual function: they efficiently use absorbed energy for photosynthesis at limiting sunlight intensity and dissipate the excess energy at saturating intensity for photoprotection. Recent single-molecule spectroscopy studies on the trimeric LHCII complex showed that environmental control of the intrinsic protein disorder could in principle explain the switch between their light-harvesting and photoprotective conformations in vivo. However, the validity of this proposal depends strongly on the specificity of the protein dynamics. Here, a similar study has been performed on the minor monomeric antenna complexes of photosystem II (CP29, CP26, and CP24). Despite their high structural homology, similar pigment content and organization compared to LHCII trimers, the environmental response of these proteins was found to be rather distinct. A much larger proportion of the minor antenna complexes were present in permanently weakly fluorescent states under most conditions used; however, unlike LHCII trimers the distribution of the single-molecule population between the strongly and weakly fluorescent states showed no significant sensitivity to low pH, zeaxanthin, or low detergent conditions. The results support a unique role for LHCII trimers in the regulation of light harvesting by controlled fluorescence blinking and suggest that any contribution of the minor antenna complexes to photoprotection would probably involve a distinct mechanism.
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Affiliation(s)
- Tjaart P J Krüger
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam, The Netherlands.
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20
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JØRGENSEN SUNEK, HATZAKIS NIKOSS. INSIGHTS IN ENZYME FUNCTIONAL DYNAMICS AND ACTIVITY REGULATION BY SINGLE MOLECULE STUDIES. ACTA ACUST UNITED AC 2014. [DOI: 10.1142/s1793048013300028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The advent of advanced single molecule measurements heralded the arrival of a wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways not deducible by conventional bulk assays. They offered the direct observation and quantification of the abundance and life time of multiple states and transient intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements, thus providing unprecedented insights into complex biological processes. Here we survey the current state of the art in single-molecule fluorescence microscopy methodology for studying the mechanism of enzymatic activity and the insights on protein functional dynamics. We will initially discuss the strategies employed to date, their limitations and possible ways to overcome them, and finally how single enzyme kinetics can advance our understanding on mechanisms underlying function and regulation of proteins. [Formula: see text]Special Issue Comment: This review focuses on functional dynamics of individual enzymes and is related to the review on ion channels by Lu,44 the reviews on mathematical treatment of Flomenbom45 and Sach et al.,46 and review on FRET by Ruedas-Rama et al.41
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Affiliation(s)
- SUNE K. JØRGENSEN
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center, Biomembranes in Nanomedicine University of Copenhagen, 2100 Copenhagen, Denmark
| | - NIKOS S. HATZAKIS
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center, Biomembranes in Nanomedicine University of Copenhagen, 2100 Copenhagen, Denmark
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21
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Schlau-Cohen GS, Bockenhauer S, Wang Q, Moerner WE. Single-molecule spectroscopy of photosynthetic proteins in solution: exploration of structure–function relationships. Chem Sci 2014. [DOI: 10.1039/c4sc00582a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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22
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Sultana T, Takagi H, Morimatsu M, Teramoto H, Li CB, Sako Y, Komatsuzaki T. Non-Markovian properties and multiscale hidden Markovian network buried in single molecule time series. J Chem Phys 2013; 139:245101. [DOI: 10.1063/1.4848719] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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23
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Böhm PS, Kunz R, Southall J, Cogdell RJ, Köhler J. Does the Reconstitution of RC-LH1 Complexes from Rhodopseudomonas acidophila Strain 10050 into a Phospholipid Bilayer Yield the Optimum Environment for Optical Spectroscopy? J Phys Chem B 2013; 117:15004-13. [DOI: 10.1021/jp409980k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Paul S. Böhm
- Experimental
Physics IV and Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, 95440 Bayreuth, Germany
| | - Ralf Kunz
- Experimental
Physics IV and Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, 95440 Bayreuth, Germany
| | - June Southall
- Institute of Molecular, Cell and Systems Biology, College
of Medical Veterinary and Life Sciences, Biomedical Research Building, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Richard J. Cogdell
- Institute of Molecular, Cell and Systems Biology, College
of Medical Veterinary and Life Sciences, Biomedical Research Building, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Jürgen Köhler
- Experimental
Physics IV and Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, 95440 Bayreuth, Germany
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24
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Kumazaki S, Akari M, Hasegawa M. Transformation of thylakoid membranes during differentiation from vegetative cell into heterocyst visualized by microscopic spectral imaging. PLANT PHYSIOLOGY 2013; 161:1321-33. [PMID: 23274239 PMCID: PMC3585599 DOI: 10.1104/pp.112.206680] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Some filamentous cyanobacteria carry out oxygenic photosynthesis in vegetative cells and nitrogen fixation in specialized cells known as heterocysts. Thylakoid membranes in vegetative cells contain photosystem I (PSI) and PSII, while those in heterocysts contain predominantly PSI. Therefore, the thylakoid membranes change drastically when differentiating from a vegetative cell into a heterocyst. The dynamics of these changes have not been sufficiently characterized in situ. Here, we used time-lapse fluorescence microspectroscopy to analyze cells of Anabaena variabilis under nitrogen deprivation at approximately 295 K. PSII degraded simultaneously with allophycocyanin, which forms the core of the light-harvesting phycobilisome. The other phycobilisome subunits that absorbed shorter wavelengths persisted for a few tens of hours in the heterocysts. The whole-thylakoid average concentration of PSI was similar in heterocysts and nearby vegetative cells. PSI was best quantified by selective excitation at a physiological temperature (approximately 295 K) under 785-nm continuous-wave laser irradiation, and detection of higher energy shifted fluorescence around 730 nm. Polar distribution of thylakoid membranes in the heterocyst was confirmed by PSI-rich fluorescence imaging. The findings and methodology used in this work increased our understanding of how photosynthetic molecular machinery is transformed to adapt to different nutrient environments and provided details of the energetic requirements for diazotrophic growth.
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Affiliation(s)
- Shigeichi Kumazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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25
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Tashyreva D, Elster J, Billi D. A novel staining protocol for multiparameter assessment of cell heterogeneity in Phormidium populations (cyanobacteria) employing fluorescent dyes. PLoS One 2013; 8:e55283. [PMID: 23437052 PMCID: PMC3577823 DOI: 10.1371/journal.pone.0055283] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 12/21/2012] [Indexed: 12/04/2022] Open
Abstract
Bacterial populations display high heterogeneity in viability and physiological activity at the single-cell level, especially under stressful conditions. We demonstrate a novel staining protocol for multiparameter assessment of individual cells in physiologically heterogeneous populations of cyanobacteria. The protocol employs fluorescent probes, i.e., redox dye 5-cyano-2,3-ditolyl tetrazolium chloride, ‘dead cell’ nucleic acid stain SYTOX Green, and DNA-specific fluorochrome 4′,6-diamidino-2-phenylindole, combined with microscopy image analysis. Our method allows simultaneous estimates of cellular respiration activity, membrane and nucleoid integrity, and allows the detection of photosynthetic pigments fluorescence along with morphological observations. The staining protocol has been adjusted for, both, laboratory and natural populations of the genus Phormidium (Oscillatoriales), and tested on 4 field-collected samples and 12 laboratory strains of cyanobacteria. Based on the mentioned cellular functions we suggest classification of cells in cyanobacterial populations into four categories: (i) active and intact; (ii) injured but active; (iii) metabolically inactive but intact; (iv) inactive and injured, or dead.
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Affiliation(s)
- Daria Tashyreva
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
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26
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Wang Q, Goldsmith RH, Jiang Y, Bockenhauer SD, Moerner W. Probing single biomolecules in solution using the anti-Brownian electrokinetic (ABEL) trap. Acc Chem Res 2012; 45:1955-64. [PMID: 22616716 DOI: 10.1021/ar200304t] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single-molecule fluorescence measurements allow researchers to study asynchronous dynamics and expose molecule-to-molecule structural and behavioral diversity, which contributes to the understanding of biological macromolecules. To provide measurements that are most consistent with the native environment of biomolecules, researchers would like to conduct these measurements in the solution phase if possible. However, diffusion typically limits the observation time to approximately 1 ms in many solution-phase single-molecule assays. Although surface immobilization is widely used to address this problem, this process can perturb the system being studied and contribute to the observed heterogeneity. Combining the technical capabilities of high-sensitivity single-molecule fluorescence microscopy, real-time feedback control and electrokinetic flow in a microfluidic chamber, we have developed a device called the anti-Brownian electrokinetic (ABEL) trap to significantly prolong the observation time of single biomolecules in solution. We have applied the ABEL trap method to explore the photodynamics and enzymatic properties of a variety of biomolecules in aqueous solution and present four examples: the photosynthetic antenna allophycocyanin, the chaperonin enzyme TRiC, a G protein-coupled receptor protein, and the blue nitrite reductase redox enzyme. These examples illustrate the breadth and depth of information which we can extract in studies of single biomolecules with the ABEL trap. When confined in the ABEL trap, the photosynthetic antenna protein allophycocyanin exhibits rich dynamics both in its emission brightness and its excited state lifetime. As each molecule discontinuously converts from one emission/lifetime level to another in a primarily correlated way, it undergoes a series of state changes. We studied the ATP binding stoichiometry of the multi-subunit chaperonin enzyme TRiC in the ABEL trap by counting the number of hydrolyzed Cy3-ATP using stepwise photobleaching. Unlike ensemble measurements, the observed ATP number distributions depart from the standard cooperativity models. Single copies of detergent-stabilized G protein-coupled receptor proteins labeled with a reporter fluorophore also show discontinuous changes in emission brightness and lifetime, but the various states visited by the single molecules are broadly distributed. As an agonist binds, the distributions shift slightly toward a more rigid conformation of the protein. By recording the emission of a reporter fluorophore which is quenched by reduction of a nearby type I Cu center, we probed the enzymatic cycle of the redox enzyme nitrate reductase. We determined the rate constants of a model of the underlying kinetics through an analysis of the dwell times of the high/low intensity levels of the fluorophore versus nitrite concentration.
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Affiliation(s)
- Quan Wang
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Randall H. Goldsmith
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Yan Jiang
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Samuel D. Bockenhauer
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - W.E. Moerner
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
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27
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Yoo H, Furumaki S, Yang J, Lee JE, Chung H, Oba T, Kobayashi H, Rybtchinski B, Wilson TM, Wasielewski MR, Vacha M, Kim D. Excitonic Coupling in Linear and Trefoil Trimer Perylenediimide Molecules Probed by Single-Molecule Spectroscopy. J Phys Chem B 2012; 116:12878-86. [DOI: 10.1021/jp307394x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Hyejin Yoo
- Department of Chemistry, Yonsei University, Seoul 120-749, Korea
| | - Shu Furumaki
- Department of Organic and Polymeric
Materials, Tokyo Institute of Technology, Ookayama 2-12-1-S8, Meguro-ku, Tokyo 152-8552, Japan
| | - Jaesung Yang
- Department of Chemistry, Yonsei University, Seoul 120-749, Korea
| | - Ji-Eun Lee
- Department of Chemistry, Yonsei University, Seoul 120-749, Korea
| | - Heejae Chung
- Department of Chemistry, Yonsei University, Seoul 120-749, Korea
| | - Tatsuya Oba
- Department of Organic and Polymeric
Materials, Tokyo Institute of Technology, Ookayama 2-12-1-S8, Meguro-ku, Tokyo 152-8552, Japan
| | - Hiroyuki Kobayashi
- Department of Organic and Polymeric
Materials, Tokyo Institute of Technology, Ookayama 2-12-1-S8, Meguro-ku, Tokyo 152-8552, Japan
| | - Boris Rybtchinski
- Department of Chemistry and Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Thea M. Wilson
- Department of Chemistry and Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Martin Vacha
- Department of Organic and Polymeric
Materials, Tokyo Institute of Technology, Ookayama 2-12-1-S8, Meguro-ku, Tokyo 152-8552, Japan
| | - Dongho Kim
- Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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28
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Chen H, Dang W, Xie J, Zhao J, Weng Y. Ultrafast energy transfer pathways in R-phycoerythrin from Polysiphonia urceolata. PHOTOSYNTHESIS RESEARCH 2012; 111:81-86. [PMID: 22083175 DOI: 10.1007/s11120-011-9708-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 10/31/2011] [Indexed: 05/31/2023]
Abstract
Energy transfer (ET) processes between chromophores in R-phycoerythrin (R-PE) from Polysiphonia urceolata were studied by use of ultrafast spectroscopic methods. Several primary ET pathways were elaborated. A fluorescence decay component with a time constant of several hundred picoseconds observed by streak camera is tentatively assigned to the reversible formation of exciton traps between α84 and β84 pigment pairs. In order to investigate much faster ET processes in R-PE, a noncollinear optical parametric amplifier based femtosecond time-resolved transient fluorescence spectrometer was employed. The results reveal that the ET between α84 and β84 pigment pair has a time constant of 1-2 ps; the energy migration between α84 and β84 pairs within the R-PE trimer has a time constant of 30-40 ps. We also demonstrated an ET process from phycourobilin to phycoerythrobilin with a time constant as fast as 2.5-3.0 ps, which was directly observed in fluorescence kinetics by selective excitation of the phycourobilin molecules acting as the energy donor.
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Affiliation(s)
- Hailong Chen
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijng, 100190, China
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29
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Observation of protein folding/unfolding dynamics of ubiquitin trapped in agarose gel by single-molecule FRET. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:189-98. [DOI: 10.1007/s00249-011-0772-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/13/2011] [Accepted: 10/24/2011] [Indexed: 11/27/2022]
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30
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Krüger TPJ, Ilioaia C, van Grondelle R. Fluorescence Intermittency from the Main Plant Light-Harvesting Complex: Resolving Shifts between Intensity Levels. J Phys Chem B 2011; 115:5071-82. [DOI: 10.1021/jp201609c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tjaart P. J. Krüger
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Cristian Ilioaia
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Rienk van Grondelle
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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31
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Krüger TPJ, Ilioaia C, Valkunas L, van Grondelle R. Fluorescence Intermittency from the Main Plant Light-Harvesting Complex: Sensitivity to the Local Environment. J Phys Chem B 2011; 115:5083-95. [DOI: 10.1021/jp109833x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Tjaart P. J. Krüger
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Cristian Ilioaia
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Leonas Valkunas
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231, LT-02300 Vilnius, Lithuania and Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9, LT-10222 Vilnius, Lithuania
| | - Rienk van Grondelle
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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32
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Goldsmith RH, Moerner WE. Watching conformational- and photo-dynamics of single fluorescent proteins in solution. Nat Chem 2011; 2:179-86. [PMID: 20625479 PMCID: PMC2899709 DOI: 10.1038/nchem.545] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Observing the dynamics of single biomolecules over prolonged time periods is difficult to achieve without significantly altering the molecule through immobilization. It can, however, be accomplished using the Anti-Brownian ELectrokinetic (ABEL) Trap, which allows extended investigation of solution-phase biomolecules - without immobilization -through real-time electrokinetic feedback. Here we apply the ABEL trap to study an important photosynthetic antenna protein, Allophycocyanin (APC). The technique allows the observation of single molecules of solution-phase APC for more than one second. We observe a complex relationship between fluorescence intensity and lifetime that cannot be explained by simple static kinetic models. Light-induced conformational changes are shown to occur and evidence is obtained for fluctuations in the spontaneous emission lifetime, which is typically assumed to be constant. Our methods provide a new window into the dynamics of fluorescent proteins and the observations are relevant for the interpretation of in vivo single-molecule imaging experiments, bacterial photosynthetic regulation, and biomaterials for solar energy harvesting.
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Johansson PG, Zhang Y, Abrahamsson M, Meyer GJ, Galoppini E. Slow excited state injection and charge recombination at star-shaped ruthenium polypyridyl compounds—TiO2 interfaces. Chem Commun (Camb) 2011; 47:6410-2. [DOI: 10.1039/c1cc11210d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Lenn T, Gkekas CN, Bernard L, Engl C, Jovanovic G, Buck M, Ying L. Measuring the stoichiometry of functional PspA complexes in living bacterial cells by single molecule photobleaching. Chem Commun (Camb) 2010; 47:400-2. [PMID: 20830338 DOI: 10.1039/c0cc01707h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a general method based on wide-field fluorescence imaging of single molecule photobleaching and the Chung-Kennedy algorithm to measure the stoichiometry of functional protein complexes in living bacterial cells.
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Affiliation(s)
- Tchern Lenn
- Division of Biology, Imperial College London, London, UK SW7 2AZ
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35
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36
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Womick JM, Moran AM. Exciton Coherence and Energy Transport in the Light-Harvesting Dimers of Allophycocyanin. J Phys Chem B 2009; 113:15747-59. [DOI: 10.1021/jp907644h] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jordan M. Womick
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Andrew M. Moran
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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37
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Burrows SM, Patel P, Pappas D. Light tolerance of R-phycoerythrin and a tandem conjugate observed by single molecule recrossing events. APPLIED SPECTROSCOPY 2009; 63:709-715. [PMID: 19531299 DOI: 10.1366/000370209788559737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The recrossing of single molecules in a probe volume was used to investigate light harvesting and energy transfer between R-phycoerythrin (R-PE) and a tandem conjugate dye. The normalized recrossing ratio, Nr/Nt, was defined as the number of molecules that reenter the probe volume (Nr) to the total number of molecules detected (Nt). The energy transfer process in phycobiliproteins was studied as a function of excitation irradiation and irradiation time. This was achieved by investigating the average baseline-subtracted fluorescence intensity, normalized molecular recrossing ratio (Nr/Nt), and the number of molecules detected per second. The photon saturation irradiance of the R-PE and the tandem conjugate were compared with each other, showing that energy transfer to the tandem dye significantly improves photostability and light tolerance of the phycobiliprotein. The Nr/Nt ratio was used to study the photophysical properties of R-phycoerythrin and the tandem conjugate Streptavidin R-Phycoerythrin-AlexaFluor-647 (PE-647). Normalized molecular recrossings showed that energy transfer to a tandem conjugate could reduce the formation of triplet states in R-phycoerythrin and extend the light tolerance of certain phycobiliproteins.
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Affiliation(s)
- Sean M Burrows
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
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Aumiler D, Wang S, Chen X, Xia A. Excited State Localization and Delocalization of Internal Charge Transfer in Branched Push−Pull Chromophores Studied by Single-Molecule Spectroscopy. J Am Chem Soc 2009; 131:5742-3. [DOI: 10.1021/ja901268h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Damir Aumiler
- The State Key Laboratory of Molecular Reaction Dynamics, and Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P. R. China, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China, and Institute of Physics, Bijenička cesta 46, 10000 Zagreb, Croatia
| | - Sufan Wang
- The State Key Laboratory of Molecular Reaction Dynamics, and Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P. R. China, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China, and Institute of Physics, Bijenička cesta 46, 10000 Zagreb, Croatia
| | - Xudong Chen
- The State Key Laboratory of Molecular Reaction Dynamics, and Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P. R. China, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China, and Institute of Physics, Bijenička cesta 46, 10000 Zagreb, Croatia
| | - Andong Xia
- The State Key Laboratory of Molecular Reaction Dynamics, and Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P. R. China, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China, and Institute of Physics, Bijenička cesta 46, 10000 Zagreb, Croatia
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Yoo H, Yang J, Nakamura Y, Aratani N, Osuka A, Kim D. Fluorescence Dynamics of Directly Meso−Meso Linked Porphyrin Rings Probed by Single Molecule Spectroscopy. J Am Chem Soc 2009; 131:1488-94. [DOI: 10.1021/ja807105n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hyejin Yoo
- Department of Chemistry and Center for Ultrafast Optical Characteristics Control, Yonsei University, Seoul 120-749, Korea, and Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jaesung Yang
- Department of Chemistry and Center for Ultrafast Optical Characteristics Control, Yonsei University, Seoul 120-749, Korea, and Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yasuyuki Nakamura
- Department of Chemistry and Center for Ultrafast Optical Characteristics Control, Yonsei University, Seoul 120-749, Korea, and Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Naoki Aratani
- Department of Chemistry and Center for Ultrafast Optical Characteristics Control, Yonsei University, Seoul 120-749, Korea, and Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Atsuhiro Osuka
- Department of Chemistry and Center for Ultrafast Optical Characteristics Control, Yonsei University, Seoul 120-749, Korea, and Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Dongho Kim
- Department of Chemistry and Center for Ultrafast Optical Characteristics Control, Yonsei University, Seoul 120-749, Korea, and Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Allophycocyanin trimer stability and functionality are primarily due to polar enhanced hydrophobicity of the phycocyanobilin binding pocket. J Mol Biol 2008; 384:406-21. [PMID: 18823993 DOI: 10.1016/j.jmb.2008.09.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2008] [Revised: 09/04/2008] [Accepted: 09/10/2008] [Indexed: 11/22/2022]
Abstract
Allophycocyanin (APC) is the primary pigment-protein component of the cores of the phycobilisome antenna complex. In addition to an extremely high degree of amino acid sequence conservation, the overall structures of APC from both mesophilic and thermophilic species are almost identical at all levels of assembly, yet APC from thermophilic organisms should have structural attributes that prevent thermally induced denaturation. We determined the structure of APC from the thermophilic cyanobacterium Thermosynechococcus vulcanus to 2.9 A, reaffirming the conservation of structural similarity with APC from mesophiles. We provide spectroscopic evidence that T. vulcanus APC is indeed more stable at elevated temperatures in vitro, when compared with the APC from mesophilic species. APC thermal and chemical stability levels are further enhanced when monitored in the presence of high concentrations of buffered phosphate, which increases the strength of hydrophobic interactions, and may mimic the effect of cytosolic crowding. Absorption spectroscopy, size-exclusion HPLC, and native gel electrophoresis also show that the thermally or chemically induced changes in the APC absorption spectra that result in the loss of the prominent 652-nm band in trimeric APC are not a result of physical monomerization. We propose that the bathochromic shift that occurs in APC upon trimerization is due to the coupling of the hydrophobicity of the alpha84 phycocyanobilin cofactor environment created by a deep cleft formed by the beta subunit with highly charged flanking regions. This arrangement also provides the additional stability required by thermophiles at elevated temperatures. The chemical environment that induces the bathochromic shift in APC trimers is different from the source of shifts in the absorption of monomers of the terminal energy acceptors APC(B) and L(CM), as visualized by the building of molecular models.
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Lu Y, Bowles RK, Paige MF. Dual-Polarization Imaging of a Dual-Fluorophore Ion Sensor: A Single-Molecule Study. Chemphyschem 2008; 9:1947-53. [DOI: 10.1002/cphc.200800337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Liu LN, Elmalk AT, Aartsma TJ, Thomas JC, Lamers GEM, Zhou BC, Zhang YZ. Light-induced energetic decoupling as a mechanism for phycobilisome-related energy dissipation in red algae: a single molecule study. PLoS One 2008; 3:e3134. [PMID: 18769542 PMCID: PMC2518951 DOI: 10.1371/journal.pone.0003134] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2008] [Accepted: 08/13/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Photosynthetic organisms have developed multiple protective mechanisms to prevent photodamage in vivo under high-light conditions. Cyanobacteria and red algae use phycobilisomes (PBsomes) as their major light-harvesting antennae complexes. The orange carotenoid protein in some cyanobacteria has been demonstrated to play roles in the photoprotective mechanism. The PBsome-itself-related energy dissipation mechanism is still unclear. METHODOLOGY/PRINCIPAL FINDINGS Here, single-molecule spectroscopy is applied for the first time on the PBsomes of red alga Porphyridium cruentum, to detect the fluorescence emissions of phycoerythrins (PE) and PBsome core complex simultaneously, and the real-time detection could greatly characterize the fluorescence dynamics of individual PBsomes in response to intense light. CONCLUSIONS/SIGNIFICANCE Our data revealed that strong green-light can induce the fluorescence decrease of PBsome, as well as the fluorescence increase of PE at the first stage of photobleaching. It strongly indicated an energetic decoupling occurring between PE and its neighbor. The fluorescence of PE was subsequently observed to be decreased, showing that PE was photobleached when energy transfer in the PBsomes was disrupted. In contrast, the energetic decoupling was not observed in either the PBsomes fixed with glutaraldehyde, or the mutant PBsomes lacking B-PE and remaining b-PE. It was concluded that the energetic decoupling of the PBsomes occurs at the specific association between B-PE and b-PE within the PBsome rod. Assuming that the same process occurs also at the much lower physiological light intensities, such a decoupling process is proposed to be a strategy corresponding to PBsomes to prevent photodamage of the photosynthetic reaction centers. Finally, a novel photoprotective role of gamma-subunit-containing PE in red algae was discussed.
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Affiliation(s)
- Lu-Ning Liu
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
- Biophysics Department, Huygens Laboratory, Leiden University, Leiden, The Netherlands
| | - Abdalmohsen T. Elmalk
- Biophysics Department, Huygens Laboratory, Leiden University, Leiden, The Netherlands
| | - Thijs J. Aartsma
- Biophysics Department, Huygens Laboratory, Leiden University, Leiden, The Netherlands
| | - Jean-Claude Thomas
- UMR 8186 CNRS & Ecole Normale Supérieure, Biologie Moléculaire des Organismes Photosynthétiques, Paris, France
| | | | - Bai-Cheng Zhou
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Yu-Zhong Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
- * E-mail:
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43
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Mackowski S, Wörmke S, Brotosudarmo THP, Jung C, Hiller RG, Scheer H, Bräuchle C. Energy transfer in reconstituted peridinin-chlorophyll-protein complexes: ensemble and single-molecule spectroscopy studies. Biophys J 2007; 93:3249-58. [PMID: 17675350 PMCID: PMC2025647 DOI: 10.1529/biophysj.107.112094] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We combine ensemble and single-molecule spectroscopy to gain insight into the energy transfer between chlorophylls (Chls) in peridinin-chlorophyll-protein (PCP) complexes reconstituted with Chl a, Chl b, as well as both Chl a and Chl b. The main focus is the heterochlorophyllous system (Chl a/b-N-PCP), and reference information essential to interpret experimental observations is obtained from homochlorophyllous complexes. Energy transfer between Chls in Chl a/b-N-PCP takes place from Chl b to Chl a and also from Chl a to Chl b with comparable Förster energy transfer rates of 0.0324 and 0.0215 ps(-1), respectively. Monte Carlo simulations yield the ratio of 39:61 for the excitation distribution between Chl a and Chl b, which is larger than the equilibrium distribution of 34:66. An average Chl a/Chl b fluorescence intensity ratio of 66:34 is measured, however, for single Chl a/b-N-PCP complexes excited into the peridinin (Per) absorption. This difference is attributed to almost three times more efficient energy transfer from Per to Chl a than to Chl b. The results indicate also that due to bilateral energy transfer, the Chl system equilibrates only partially during the excited state lifetimes.
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Affiliation(s)
- Sebastian Mackowski
- Department of Chemistry and Biochemistry and Center for Nanoscience, Ludwig Maximilian University, D-81377 Munich, Germany
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44
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Emory SR, Jensen RA, Wenda T, Han M, Nie S. Re-examining the origins of spectral blinking in single-molecule and single-nanoparticle SERS. Faraday Discuss 2007; 132:249-59; discussion 309-19. [PMID: 16833120 DOI: 10.1039/b509223j] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Single metal nanoparticles and nanoaggregates are known to emit intense bursts of surface-enhanced Raman scattering (SERS) in an intermittent on and off fashion. The characteristic "blinking" timescales range from milliseconds to seconds. Here we report detailed temperature dependence (both heating and cooling) and light-intensity studies to further examine the origins of this intriguing phenomenon. The results indicate that blinking SERS contains both a thermo-activated component and a light-induced component. Several lines of evidence suggest that the observed fluctuations are caused by thermally activated diffusion of individual molecules on the particle surface, coupled with photo-induced electron transfer and structural relaxation of surface active sites or atomic-scale roughness features.
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Affiliation(s)
- Steven R Emory
- Department of Chemistry, Western Washington University, Bellingham WA 98225, USA.
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45
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Sanda F, Mukamel S. Cooperative effects in photon statistics of molecular dimers with spectral diffusion. J Chem Phys 2007; 124:124103. [PMID: 16599658 DOI: 10.1063/1.2174001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The two-point fluorescence intensity correlation function g(2)t and the Mandel parameter Mt are calculated for a strongly pumped dimer of two-level molecules undergoing Gaussian-Markovian frequency fluctuations. The effects of detuning and saturation are examined. All fluctuation time scale regimes are explored using a continued fraction solution of the stochastic Liouville equation for the generating function. Bunching and antibunching are observed for slow and fast fluctuations, respectively. The short-time antibunching dip in g(2) and its variation with intermolecular coupling, the exciton annihilation rate, and laser detuning are studied.
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Affiliation(s)
- Frantisek Sanda
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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46
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Wörmke S, Mackowski S, Brotosudarmo THP, Jung C, Zumbusch A, Ehrl M, Scheer H, Hofmann E, Hiller RG, Bräuchle C. Monitoring fluorescence of individual chromophores in peridinin-chlorophyll-protein complex using single molecule spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:956-64. [PMID: 17572378 DOI: 10.1016/j.bbabio.2007.05.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 05/04/2007] [Accepted: 05/09/2007] [Indexed: 11/17/2022]
Abstract
Single molecule spectroscopy experiments are reported for native peridinin-chlorophyll a-protein (PCP) complexes, and three reconstituted light-harvesting systems, where an N-terminal construct of native PCP from Amphidinium carterae has been reconstituted with chlorophyll (Chl) mixtures: with Chl a, with Chl b and with both Chl a and Chl b. Using laser excitation into peridinin (Per) absorption band we take advantage of sub-picosecond energy transfer from Per to Chl that is order of magnitude faster than the Förster energy transfer between the Chl molecules to independently populate each Chl in the complex. The results indicate that reconstituted PCP complexes contain only two Chl molecules, so that they are spectroscopically equivalent to monomers of native-trimeric-PCP and do not aggregate further. Through removal of ensemble averaging we are able to observe for single reconstituted PCP complexes two clear steps in fluorescence intensity timetraces attributed to subsequent bleaching of the two Chl molecules. Importantly, the bleaching of the first Chl affects neither the energy nor the intensity of the emission of the second one. Since in strongly interacting systems Chl is a very efficient quencher of the fluorescence, this behavior implies that the two fluorescing Chls within a PCP monomer interact very weakly with each other which makes it possible to independently monitor the fluorescence of each individual chromophore in the complex. We apply this property, which distinguishes PCP from other light-harvesting systems, to measure the distribution of the energy splitting between two chemically identical Chl a molecules contained in the PCP monomer that reaches 280 cm(-1). In agreement with this interpretation, stepwise bleaching of fluorescence is also observed for native PCP complexes, which contain six Chls. Most PCP complexes reconstituted with both Chl a and Chl b show two emission lines, whose wavelengths correspond to the fluorescence of Chl a and Chl b. This is a clear proof that these two different chromophores are present in a single PCP monomer. Single molecule fluorescence studies of PCP complexes, both native and artificially reconstituted with chlorophyll mixtures, provide new and detailed information necessary to fully understand the energy transfer in this unique light-harvesting system.
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Affiliation(s)
- S Wörmke
- Department of Chemistry and Biochemistry and Center for Nanoscience, Ludwig-Maximilian-University, Butenandtstrasse 11, D-81377 Munich, Germany
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Horneffer V, Strupat K, Hillenkamp F. Localization of noncovalent complexes in MALDI-preparations by CLSM. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1599-1604. [PMID: 16905329 DOI: 10.1016/j.jasms.2006.06.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Revised: 06/11/2006] [Accepted: 06/27/2006] [Indexed: 05/11/2023]
Abstract
The unambiguous detection of noncovalent complexes (NCCs) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is still a far cry from being routine. For protein NCCs such as their quaternary structure it has been reported that signals of the intact complex are only obtained for the first or at most the first few laser exposures of a given sample area. This observation was called the first-shot phenomenon. In the present study, this first-shot phenomenon has been investigated for the hexameric protein complex allophycocyanine (APC) by two independent methods, MALDI-MS with a (nearly) pH-neutral matrix 6-aza-2-thiothymine (6-ATT) and by imaging the fluorescence of the complex in APC-6-ATT preparations by confocal laser scan microscopy (CLSM). The intact APC heterohexamer loses its visible fluorescence upon dissociation into its subunits. Both methods consistently show that intact APC complexes are precipitated at the matrix crystal surface, but dissociate upon incorporation into the matrix crystals.
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Affiliation(s)
- Verena Horneffer
- Institute for Medical Physics and Biophysics, University of Münster, Münster, Germany.
| | - Kerstin Strupat
- Institute for Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Franz Hillenkamp
- Institute for Medical Physics and Biophysics, University of Münster, Münster, Germany
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Fückel B, Hinze G, Diezemann G, Nolde F, Müllen K, Gauss J, Basché T. Flexibility of phenylene oligomers revealed by single molecule spectroscopy. J Chem Phys 2006; 125:144903. [PMID: 17042646 DOI: 10.1063/1.2355488] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rigidity of a p-phenylene oligomer (p-terphenyl) has been investigated by single molecule confocal fluorescence microscopy. Two different rylene diimide dyes attached to the terminal positions of the oligomer allowed for wavelength selective excitation of the two chromophores. In combination with polarization modulation the spatial orientation of the transition dipoles of both end groups could be determined independently. We have analyzed 597 single molecules in two different polymer hosts, polymethylmethacrylate and Zeonex. On average we find a 22 degrees deviation from the linear gas phase geometry (T = 0 K), indicating a rather high flexibility of the p-phenylene oligomer independent of the matrix. To substantiate our experimental results, we have performed quantum chemical calculations at the density functional theory level for the molecular geometry and the electronic excitations. Our findings are in agreement with former experiments on the persistence length of poly(p-phenylenes).
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Affiliation(s)
- Burkhard Fückel
- Institut für Physikalische Chemie, Universität Mainz, Jakob-Welderweg 11, D-55099 Mainz, Germany
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García-Parajó MF, Hernando J, Sanchez Mosteiro G, Hoogenboom JP, van Dijk EMHP, van Hulst NF. Energy transfer in single-molecule photonic wires. Chemphyschem 2006; 6:819-27. [PMID: 15884064 DOI: 10.1002/cphc.200400630] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular photonics is a new emerging field of research around the premise that it is possible to develop optical devices using single molecules as building blocks. Truly technological impact in the field requires focussed efforts on designing functional molecular devices as well as having access to their photonic properties on an individual basis. In this Minireview we discuss our approach towards the design and single-molecule investigation of one-dimensional multimolecular arrays intended to work as molecular photonic wires. Three different schemes have been explored: a) perylene-based dimer and trimer arrays displaying coherent exciton delocalisation at room temperature; b) DNA-based unidirectional molecular wires containing up to five different chromophores and exhibiting weak excitonic interactions between neighbouring dyes; and c) one-dimensional multichromophoric polymers based on perylene polyisocyanides showing excimerlike emission. As a whole, our single-molecule data show the importance of well-defined close packing of chromophores for obtaining optimal excitonic behaviour at room temperature. Further improvement on (bio)chemical synthesis, together with the use of single-molecule techniques, should lead in the near future to efficient and reliable photonic wires with true device functionality.
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Affiliation(s)
- María F García-Parajó
- Applied Optics Group, Faculty of Science & Technology, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
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50
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Ying L, Zhou D, Bruckbauer A. Comment on "trapping single molecules by dielectrophoresis". PHYSICAL REVIEW LETTERS 2006; 96:199801; author reply 199802. [PMID: 16803153 DOI: 10.1103/physrevlett.96.199801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Indexed: 05/10/2023]
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