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Pigment-protein Complexes of Photosynthetic Bacteria: Convex-Lens Induced Confinement Microscopy and Single Molecule Spectroscopy Simulations

Title:

Pigment-protein Complexes of Photosynthetic Bacteria: Convex-Lens Induced Confinement Microscopy and Single Molecule Spectroscopy Simulations

Eng-Michell, Brandon Ga Jing (2024) Pigment-protein Complexes of Photosynthetic Bacteria: Convex-Lens Induced Confinement Microscopy and Single Molecule Spectroscopy Simulations. Masters thesis, Concordia University.

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Abstract

This project involved studying photosynthetic pigment molecules and had two distinct
sections of the project: an experimental part and a computational part.
Throughout the experimental part of this project we explored several different
modifications to our experimental setup to overcome a lack of flatness and repeatability in
our sample. We realized that there may have been non-elastic properties to the gaskets we
were using, and we found that CLIC microscopy was not suitable for our purposes.
During the computational component, we generated a predictive model which more
than doubled the speed of generating appropriate energy landscapes for spectral hole burning
simulations for realistic values of md2
. We learned that an increase in md2
decreases the
spacing of the energy bands, and increasing the standard deviation of the wells increases the
spacing of energy levels within the same band. We developed a Markov chain Monte-Carlo
single molecule spectroscopy algorithm and implemented it into the larger program. We
observed several instances where the pigment molecules can oscillate between two wells very
quickly. This is a result of randomly generating landscapes where sometimes adjacent wells
with similar energy levels and low barriers are generated which creates exceptionally high
tunneling rates.
By comparing our histogram to the LH2 experimental results of Köhler’s group, we
were able to make a prediction of md2 =1.34*10-26 kg nm2
. This matches well with values
obtained for several other complexes.

Divisions:Concordia University > Faculty of Arts and Science > Physics
Item Type:Thesis (Masters)
Authors:Eng-Michell, Brandon Ga Jing
Institution:Concordia University
Degree Name:M. Sc.
Program:Physics
Date:21 March 2024
Thesis Supervisor(s):Zazubovits, Valter
ID Code:993617
Deposited By: Brandon Ga Jing Eng-Michell
Deposited On:05 Jun 2024 16:45
Last Modified:05 Jun 2024 16:45

References:

[1] Operamolla, A et al 2012. “Garnishing” the photosynthetic bacterial reaction center for bioelectronics, Journal of Materials Chemistry C.
[2] Jankowiak, R et al 2011. Site Selective and Single Complex Laser-Based Spectroscopies: A Window on Excited State Electronic Structure, Excitation Energy Transfer, and Electron-Phonon Coupling of Selected Photosynthetic Complexes, Chemical Reviews 2011[4] Baier J, Richter MF, Cogdell RJ, Oellerich S, Köhler J. Determination of the spectral diffusion kernel of a protein by single-molecule spectroscopy. Phys Rev Lett. 2008 Jan 11
[3] Xiche Hu et al 1998. Architecture and mechanism of the light-harvesting apparatus of purple bacteria, PNAS 95 (11) 5935-5941, 1998
[4] Baier J, Richter MF, Cogdell RJ, Oellerich S, Köhler J. Determination of the spectral diffusion kernel of a protein by single-molecule spectroscopy. Phys Rev Lett. 2008 Jan 11
[5] Papagiannakis, E et al 2001. An alternative carotenoid-to-bacteriochlorophyll energy transfer pathway in photosynthetic light harvesting. Proceedings of the National Academy of Sciences 2001
[6]: Vijayender Bhalla, Valter Zazubovitz. Self-assembly and sensor response of photosynthetic reaction centers on screen-printed electrodes, Anal Chim Acta, 2011
[7]: Vijayender Bhalla, Valter Zazubovitz. Detection of explosive compounds using Photosystem II-based biosensor, Journal of Electroanalytical Chemistry, 2011
[8] Daniel Modaferri, The Interaction of Tetryl, a Nitroaromatic Explosive, with Bacterial Reaction Centres, Concordia University Masters program
[9] Kasmi, Asma El et al 2001. Adsorptive immobilization of cytochrome c on indium/tin oxide (ITO): electrochemical evidence for electron transfer-induced conformational changes
[10] Lebedev, Nikolai et al 2006. Conductive Wiring of Immobilized Photosynthetic Reaction Center to Electrode by Cytochrome c. J. AM. CHEM. SOC Vol. 128, NO 37, 2006
[11] Szabó Tibor et al 2012. Photosynthetic Reaction Centers/ITO Hybrid Nanostructure. Materials Science and Engineering C, 2012
[12] Leslie, Sabrina et al 2010, Convex Lens-Induced Confinement for Imaging Single Molecules, Anal. Chem. 2010
[13] Berard, J et al 2014. Convex lens induced nanoscale templating, Proceedings of the National Academy of Sciences.
[14] Candide Champion. 2016 Honors research Project. Concordia University
[15] Voigtländer, B. 2019. Atomic Force Microscopy, Springer Cham, 2019
[16] Protein Data Bank from Research Collaboratory for Structural Bioinformatics https://www.rcsb.org/
[17] AlphaFold by Google Deepmind https://deepmind.google/technologies/alphafold/
[18] Zwanzig, R et al. 1991, Levinthal’s Paradox, Proc. Natl. Acad. Sci. USA Vol. 89, pp. 20-22, January 1992 Biophysics
[19] Christopher M. Dobson. 2002. Protein Misfolding and Disease. Nature Publishing Group
[20] Najafi, M et al. 2015. Conformational Changes in Pigment-Protein Complexes at Low Temperatures-Spectral Memory and a Possibility of Cooperative Effects. Journal of Physical Chemistry B. 2015
[21] Montana State University website: https://physics.montana.edu/arebane/research/tutorials/hole_burning/index.html
[22] Hofmann, C et al. 2003 Direct Observation of Tiers in the Energy Landscape of a Chromoprotein: A Single-molecule study. PNAS 2003
[23] Dand, Nhan et al. 2008. The CP43 Proximal Antenna Complex of Higher Plant Photosystem II Revisited: Modeling and Hole Burning Study. J. Phys. Chem B 2008, 112, 32, 9921-9933
[24] Hofmann, C 2004. Spectral dynamics in the B800 band of LH2 from Rhodospirillum molischianum: a single-molecule study. New Journal of Physics 2004
[25] Trempe, A et al 2021. Effects of Chlorophyll Triplet States on the Kinetics of Spectral Hole Growth, Journal of Physical Chemistry 2021.
[26] Levenberg, A et al. 2017 Probing Energy Landscapes of Cytochrome b6f with Spectral HoleBurning: Effects of Solvent Deuteration and Detergent, Journal of Physical Chemistry B 121 (2017) 9848-9858
[27] Levenberg, A et al. Simultaneous Spectral Hole Burning Involving Two Tiers of the Protein Energy Landscape in Cytochrome b6f. Journal of Physical Chemistry B 123 (2019) 10930-10938
[28] Shafiei, G et al. 2019. Evidence of Simultaneous Spectral Hole Burning Involving Two Tiers of the Protein Energy Landscape in Cytochrome b6f
[29] Najafi, M. PHD thesis 2013. Modeling and Characterization of Protein Energy Landscape at Low Temperature using Spectral Hole Burning Spectroscopy.
[30] Najafi. M, Zazubovich, V. Monte-Carlo Modeling of Spectral Diffusion Employing Multi-Well Protein Energy Landscapes: Application to Pigment-Protein Complexes Involved in Photosynthesis, J. Phys. Chem. B 119 (2015) 7911-7921.
[31] Garashchuk, S.; Gu, B.; Mazzuca, J. Calculation of the Quantum-Mechanical Tunneling in Bound Potentials. J. Theor. Chem. 2014, 2014, 240491.
[32] D. T. Colbert and W. H. Miller, A novel discrete variable representation for quantum mechanical reactive scattering via the S-matrix Kohn method. J. Chem. Phys. 1992, 96 1982-1991.
[33] Mai, M. Masters project. Molecular Dynamics Simulations of the Water-Soluble Chlorophyll-binding Protein: Identifying Structural Features Responsible for Spectral Dynamics. Concordia University 2024.
[34] Pirson, A and Zimmermann, M.H. 1977. Photosynthesis I: Photosynthetic Electron Transport and Photophosphorylation, Encyclopedia of Plant Physiology New Series Volume 5. 1977,
[35] Krasilnikov, P et al. Relaxation Mechanism of Molecular Systems Containing Hydrogen Bonds and Free Energy Temperature Dependence of Reaction of Charges Recombination within Rhdobacter sphaeroids RC. Photochem. Photobiol. Sci., 2009, 8, 181-195.
[36] Friebe, V et al 2017. Cytochrome c Provides an Electron-Funneling Anetenna for Efficient Photocurrent Generation in a Reaction Center Biophotocathode, ACS Applied Materials and Interfaces 2017
[37] Carey, A et al 2016. Photocurrent Generation by Photosynthetic Purple Bacterial Reaction Centers Interfaced with a Porous Antimony-Doped Tin Oxide (ATO) Electrode, ACS Applied Materials and Interfaces 2016.
[38]. H. H. van Amerongen, R.van Grondelle, and L. Valkunas, Photosynthetic Excitons, World Scientific Publishing, 2000.
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