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Open Access Publications from the University of California

Scholarly Works (6 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2011)

Experiments using two-dimensional (2D) electronic spectroscopy to investigate the structure-function relationships that give rise to photosynthetic energy transfer within pigment protein complexes are presented and discussed in this dissertation. 2D electronic spectroscopy using ultrafast laser pulses throughout the visible regime was applied to study excitation energy transfer in the major light harvesting complex of photosystem II (LHCII) and the reaction center from purple bacteria. These experiments elucidated information about the excited state structure and the energy transfer timescales within these complexes. All-parallel 2D spectroscopy was used to monitor the energy transfer dynamics in LHCII and reveals previously unobserved sub-100 fs energy transfer between the chlorophyll-b (Chl-b) and chlorophyll-a (Chl-a) bands and within the Chl-a band. Reproducing these results with simulations led to improvements in the values of the uncoupled transition energies of the chlorophyll in the working Hamiltonian of LHCII. The delocalized excited states observed in the experimental and theoretical results were found to increase the range of optimal angles for energy transfer from LHCII to neighboring pigment-protein complexes, as opposed to the case of a single, isolated donor excited state. Polarized 2D spectroscopy experiments reported here identified previously unresolved excitation energy transfer steps in LHCII. These results were used to determine the angle between

transition dipole moments of the donor and acceptor. A new method was developed to use the angle between transition dipole moments to find the uncoupled transition energies of the chlorophyll, previously the major unknown for an accurate electronic Hamiltonian. This method was applied to LHCII. Quantum coherence, or a long-lived superposition of excited states, was observed in LHCII using a second polarization sequence. The observable timescales of coherence was determined to be 700-900 fs, which illustrates that quantum coherence lasts longer than many energy transfer steps. The potential contribution of coherence to the robustness of photosynthetic energy transfer to the rugged energy landscape and to temperature variations is discussed. Experiments on the B band of the bacterial reaction center were able to isolate the previously inseparable two peaks and observe energy transfer between these two excited states. A new extension of 2D spectroscopy, two-color 2D spectroscopy, was demonstrated for

examining the interactions between two spectrally separate chromophores. Using this approach, energy was found to transfer from the carotenoid to the bacteriochlorophyll both via S1 and via Qx in the bacterial reaction center in an approximately 2:1 ratio, and within about 750 fs.

    Cover page: Multidimensional Spectroscopy of Photosynthetic Complexes
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2019)
    The epidermal growth factor receptor (EGFR) is critical to normal cellular signaling pathways. Moreover, it has been implicated in a range of pathologies, including cancer. As a result, it is the primary target of many anticancer drugs. One limitation to the design and development of these drugs has been the lack of molecular-level information about the interactions and conformational dynamics of EGFR. To overcome this limitation, this work reports the construction and characterization of functional, fluorescently labeled, and full-length EGFR in model membrane nanolipoprotein particles (NLPs) for in vitro fluorescence studies. To demonstrate the utility of the system, we investigate ATP-EGFR interactions. We observe that ATP binds at the catalytic site providing a means to measure a range of distances between the catalytic site and the C-terminus via Förster resonance energy transfer (FRET). These ATP-based experiments suggest a range of conformations of the C-terminus that may be a function of the phosphorylation state for EGFR. This work is a proof-of-principle demonstration of single-molecule studies as a noncrystallographic assay for EGFR interactions in real-time and under near-physiological conditions. The diverse nature of EGFR interactions means that new tools at the molecular level have the potential to significantly enhance our understanding of receptor pathology and are of utmost importance for cancer-related drug discovery.
      Cover page: Single-Molecule Fluorescence Detection of the Epidermal Growth Factor Receptor in Membrane Discs
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2014)
      Carotenoids play an essential role in photoprotection, interacting with other pigments to safely dissipate excess absorbed energy as heat. In cyanobacteria, the short time scale photoprotective mechanisms involve the photoactive orange carotenoid protein (OCP), which binds a single carbonyl carotenoid. Blue-green light induces the photoswitching of OCP from its ground state form (OCPO) to a metastable photoproduct (OCPR). OCPR can bind to the phycobilisome antenna and induce fluorescence quenching. The photoswitching is accompanied by structural and functional changes at the level of the protein and of the bound carotenoid. Here, we use broadband two-dimensional electronic spectroscopy to study the differences in excited state dynamics of the carotenoid in the two forms of OCP. Our results provide insight into the origin of the pronounced vibrational lineshape and oscillatory dynamics observed in linear absorption and 2D electronic spectroscopy of OCPO and the large inhomogeneous broadening in OCPR, with consequences for the chemical function of the two forms.
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2023)
        Photosynthesis is generally assumed to be initiated by a single photon1-3 from the Sun, which, as a weak light source, delivers at most a few tens of photons per nanometre squared per second within a chlorophyll absorption band1. Yet much experimental and theoretical work over the past 40 years has explored the events during photosynthesis subsequent to absorption of light from intense, ultrashort laser pulses2-15. Here, we use single photons to excite under ambient conditions the light-harvesting 2 (LH2) complex of the purple bacterium Rhodobacter sphaeroides, comprising B800 and B850 rings that contain 9 and 18 bacteriochlorophyll molecules, respectively. Excitation of the B800 ring leads to electronic energy transfer to the B850 ring in approximately 0.7 ps, followed by rapid B850-to-B850 energy transfer on an approximately 100-fs timescale and light emission at 850-875 nm (refs. 16-19). Using a heralded single-photon source20,21 along with coincidence counting, we establish time correlation functions for B800 excitation and B850 fluorescence emission and demonstrate that both events involve single photons. We also find that the probability distribution of the number of heralds per detected fluorescence photon supports the view that a single photon can upon absorption drive the subsequent energy transfer and fluorescence emission and hence, by extension, the primary charge separation of photosynthesis. An analytical stochastic model and a Monte Carlo numerical model capture the data, further confirming that absorption of single photons is correlated with emission of single photons in a natural light-harvesting complex.
          Cover page: Single-photon absorption and emission from a natural photosynthetic complex
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2022)
          Single pass cell surface receptors regulate cellular processes by transmitting ligand-encoded signals across the plasma membrane via changes to their extracellular and intracellular conformations. This transmembrane signaling is generally initiated by ligand binding to the receptors in their monomeric form. While subsequent receptor-receptor interactions are established as key aspects of transmembrane signaling, the contribution of monomeric receptors has been challenging to isolate due to the complexity and ligand-dependence of these interactions. By combining membrane nanodiscs produced with cell-free expression, single-molecule Förster Resonance Energy Transfer measurements, and molecular dynamics simulations, we report that ligand binding induces intracellular conformational changes within monomeric, full-length epidermal growth factor receptor (EGFR). Our observations establish the existence of extracellular/intracellular conformational coupling within a single receptor molecule. We implicate a series of electrostatic interactions in the conformational coupling and find the coupling is inhibited by targeted therapeutics and mutations that also inhibit phosphorylation in cells. Collectively, these results introduce a facile mechanism to link the extracellular and intracellular regions through the single transmembrane helix of monomeric EGFR, and raise the possibility that intramolecular transmembrane conformational changes upon ligand binding are common to single-pass membrane proteins.
            Cover page: Ligand-induced transmembrane conformational coupling in monomeric EGFR
            • Article
            • Peer Reviewed
            LBL Publications (2024)
            Photosynthesis-the conversion of energy from sunlight into chemical energy-is essential for life on Earth. Yet there is much we do not understand about photosynthetic energy conversion on a fundamental level: how it evolved and the extent of its diversity, its dynamics, and all the components and connections involved in its regulation. In this commentary, researchers working on fundamental aspects of photosynthesis including the light-dependent reactions, photorespiration, and C4 photosynthetic metabolism pose and discuss what they view as the most compelling open questions in their areas of research.
              Cover page: Lighting the way: Compelling open questions in photosynthesis research.
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