Honors & Awards

  • Panofsky Fellow, SLAC National Accelerator Laboratory (11/2017-)
  • NIH Ruth Kirschstein Postoctoral Fellow, Lawrence Berkeley National Laboratory (09/2015-09/2017)


  • Stochastic Spectroscopy, SLAC National Accelerator Laboratory (November 1, 2017 - Present)

    X-rays are used to probe molecules with element-specificity and atomic locality owing to the core-level electrons that they excite. This makes X-rays extremely attractive for the study of chemical systems that have a few unique atoms, like many transition metal catalysts, as it allows one to probe the catalytic site directly. X-rays have been used in this capacity for decades, with a gamut of single-photon or linear techniques ranging from scattering to absorption to fluorescence. Most linear methods are poorly sensitive to interesting chemical properties like bond type, which has motivated the study of weaker, more sensitive signals like valence to core emission at XFELs and synchrotrons. Non-linear X-ray methods, or multi-photon methods, are a different avenue uniquely enabled by the short pulse duration of XFELs to obtaining improved chemical sensitivity. Multi-photon interactions probe a much wider space of electronic configurations than single-photon interactions, which both expands the information they can reveal and makes them more complex to study. Following the creation of a single core-hole by the first photon interaction, the system can relax via a cascade of inner-shell transitions and/or auger decay, which will ultimately alter the chemical configuration of the material. When X-ray interactions are nearly simultaneous the explosion of intermediate states is limited, and the initial state of matter can be non-trivially related to subsequent photon interactions. It is in this ultrafast, early time period of X-ray non-linear interactions where chemical systems study stands to benefit from multi-photon interactions.

    Despite the difficulty associated with even seeing non-linear X-ray effects, it is possible at LCLS and other XFEL facilities. In this proposal we aim to develop multidimensional spectroscopy to study ultrafast multi-photon processes in chemical systems using natural fluctuations of the SASE source. Using SASE fluctuations are central to the project, because at present we have few other reliable pulse control options. We focus on double core-hole ionization as a tractable multi-photon signal that offers improved chemical contrast. Double core holes are created by two photon interactions and can reside on either a single atom or two separate atoms. The challenge that double core-hole (DCH) signals present, in common with other non-linear signals, is that they are difficult to disentangle from signals produced by other processes, namely single core hole fluorescence. Inferring the signal’s dependence on the exciting field in multiple dimensions (multidimensional spectroscopy) is our strategy to isolate the DCH signal, segregating it from single core-hole signals by its unique dependence on both photon energies.

    The majority of this project is centered around development of Gaussian Process based regression tools to extract the multi-dimensional signals. The code for our projects are hosted on github:

    RIXS Spectroscopy

    Nonlinear Spectroscopy

    Publications of Note:
    Communications Chemistry (2021) https://doi.org/10.1038/s42004-021-00512-3


    Menlo Park, CA,USA

  • Sample Delivery for Time Resolved XRD at XFELs, SLAC National Accelerator Laboratory (May 2014 - Present)

    X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality.

    This project is centered around a hybrid combination of "fixed target" and "continuous sample delivery" in order to deliver controlled sample amounts on demand. Presently, we use acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. We have studied a variety of systems with this approach ranging from photosystem II, phytochromes, ribonucleotide reductace, hydrogenases, and other enzymes which use oxygen as a substrate. The approach is best used to study reactions on the millisecond to second scale, but permits high rep-rate acquisition even for second-scale delays after activation.

    Publications of note:
    Nature Methods (2017). https://doi.org/10.1038/nmeth.4195
    Nature (2018). https://doi.org/10.1038/s41586-018-0681-2
    PNAS (2019) https://doi.org/10.1073/pnas.1912041116


    Menlo Park, CA,USA


    • Junko Yano, Senior Staff Scientist, Lawrence Berkeley National Laboratory
    • Jan Kern, Staff Scientist, Lawrence Berkeley National Laboratory
    • Vittal Yachandra, Senior Staff Scientist, Lawrence Berkeley National Laboratory

All Publications

  • Resonant X-ray Emission spectroscopy from broadband stochastic pulses at an X-ray free electron laser Communications Chemistry Fuller, F. D., Loukianov, A., et al 2021
  • High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Srinivas, V., Banerjee, R., Lebrette, H., Jones, J. C., Aurelius, O., Kim, I., Pham, C. C., Gul, S., Sutherlin, K. D., Bhowmick, A., John, J., Bozkurt, E., Fransson, T., Aller, P., Butryn, A., Bogacz, I., Simon, P., Keable, S., Britz, A., Tono, K., Kim, K., Park, S., Lee, S., Park, J., Alonso-Mori, R., Fuller, F. D., Batyuk, A., Brewster, A. S., Bergmann, U., Sauter, N. K., Orville, A. M., Yachandra, V. K., Yano, J., Lipscomb, J. D., Kern, J., Hogbom, M. 2020; 142 (33): 14249–66


    Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. This study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.

    View details for DOI 10.1021/jacs.0c05613

    View details for Web of Science ID 000563079000029

    View details for PubMedID 32683863

    View details for PubMedCentralID PMC7457426

  • Observation of Seeded Mn K beta Stimulated X-Ray Emission Using Two-Color X-Ray Free-Electron Laser Pulses PHYSICAL REVIEW LETTERS Kroll, T., Weninger, C., Fuller, F. D., Guetg, M. W., Benediktovitch, A., Zhang, Y., Marinelli, A., Alonso-Mori, R., Aquila, A., Liang, M., Koglin, J. E., Koralek, J., Sokaras, D., Zhu, D., Kern, J., Yano, J., Yachandra, V. K., Rohringer, N., Lutman, A., Bergmann, U. 2020; 125 (3)
  • Untangling the sequence of events during the S2 S3 transition in photosystem II and implications for the water oxidation mechanism. Proceedings of the National Academy of Sciences of the United States of America Ibrahim, M., Fransson, T., Chatterjee, R., Cheah, M. H., Hussein, R., Lassalle, L., Sutherlin, K. D., Young, I. D., Fuller, F. D., Gul, S., Kim, I., Simon, P. S., de Lichtenberg, C., Chernev, P., Bogacz, I., Pham, C. C., Orville, A. M., Saichek, N., Northen, T., Batyuk, A., Carbajo, S., Alonso-Mori, R., Tono, K., Owada, S., Bhowmick, A., Bolotovsky, R., Mendez, D., Moriarty, N. W., Holton, J. M., Dobbek, H., Brewster, A. S., Adams, P. D., Sauter, N. K., Bergmann, U., Zouni, A., Messinger, J., Kern, J., Yachandra, V. K., Yano, J. 2020


    In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 s after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (tau of 350 s) during the S2 S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

    View details for DOI 10.1073/pnas.2000529117

    View details for PubMedID 32434915

  • Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases INORGANIC CHEMISTRY Miller, K. R., Paretsky, J. D., Follmer, A. H., Heinisch, T., Mittra, K., Gul, S., Kim, I., Fuller, F. D., Batyuk, A., Sutherlin, K. D., Brewster, A. S., Bhowmick, A., Sauter, N. K., Kern, J., Yano, J., Green, M. T., Ward, T. R., Borovik, A. S. 2020; 59 (9): 6000–6009


    An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. We have utilized biotin-streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S112E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic FeII complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S112E. Two aqua ligands complete the primary coordination sphere of the FeII center with both involved in hydrogen bond networks within Sav. The corresponding FeIII protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The FeIII protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.

    View details for DOI 10.1021/acs.inorgchem.9b03791

    View details for Web of Science ID 000530668400025

    View details for PubMedID 32309932

    View details for PubMedCentralID PMC7219546

  • Photoreversible interconversion of a phytochrome photosensory module in the crystalline state. Proceedings of the National Academy of Sciences of the United States of America Burgie, E. S., Clinger, J. A., Miller, M. D., Brewster, A. S., Aller, P., Butryn, A., Fuller, F. D., Gul, S., Young, I. D., Pham, C. C., Kim, I., Bhowmick, A., O'Riordan, L. J., Sutherlin, K. D., Heinemann, J. V., Batyuk, A., Alonso-Mori, R., Hunter, M. S., Koglin, J. E., Yano, J., Yachandra, V. K., Sauter, N. K., Cohen, A. E., Kern, J., Orville, A. M., Phillips, G. N., Vierstra, R. D. 2019


    A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within the crystal lattice. Here, we describe a crystalline form of the cyclic GMP phosphodiesterases/adenylyl cyclase/FhlA (GAF) domain from the cyanobacteriochrome PixJ in Thermosynechococcus elongatus assembled with phycocyanobilin that permits reversible photoconversion between the blue light-absorbing Pb and green light-absorbing Pg states, as well as thermal reversion of Pg back to Pb. The X-ray crystallographic structure of Pb matches previous models, including autocatalytic conversion of phycocyanobilin to phycoviolobilin upon binding and its tandem thioether linkage to the GAF domain. Cryocrystallography at 150 K, which compared diffraction data from a single crystal as Pb or after irradiation with blue light, detected photoconversion product(s) based on Fobs - Fobs difference maps that were consistent with rotation of the bonds connecting pyrrole rings C and D. Further spectroscopic analyses showed that phycoviolobilin is susceptible to X-ray radiation damage, especially as Pg, during single-crystal X-ray diffraction analyses, which could complicate fine mapping of the various intermediate states. Fortunately, we found that PixJ crystals are amenable to serial femtosecond crystallography (SFX) analyses using X-ray free-electron lasers (XFELs). As proof of principle, we solved by room temperature SFX the GAF domain structure of Pb to 1.55-A resolution, which was strongly congruent with synchrotron-based models. Analysis of these crystals by SFX should now enable structural characterization of the early events that drive phytochrome photoconversion.

    View details for DOI 10.1073/pnas.1912041116

    View details for PubMedID 31852825

  • XANES and EXAFS of dilute solutions of transition metals at XFELs. Journal of synchrotron radiation Chatterjee, R., Weninger, C., Loukianov, A., Gul, S., Fuller, F. D., Cheah, M. H., Fransson, T., Pham, C. C., Nelson, S., Song, S., Britz, A., Messinger, J., Bergmann, U., Alonso-Mori, R., Yachandra, V. K., Kern, J., Yano, J. 2019; 26 (Pt 5): 1716–24


    This work has demonstrated that X-ray absorption spectroscopy (XAS), both Mn XANES and EXAFS, of solutions with millimolar concentrations of metal is possible using the femtosecond X-ray pulses from XFELs. Mn XAS data were collected using two different sample delivery methods, a Rayleigh jet and a drop-on-demand setup, with varying concentrations of Mn. Here, a new method for normalization of XAS spectra based on solvent scattering that is compatible with data collection from a highly variable pulsed source is described. The measured XANES and EXAFS spectra of such dilute solution samples are in good agreement with data collected at synchrotron sources using traditional scanning protocols. The procedures described here will enable XFEL-based XAS on dilute biological samples, especially metalloproteins, with low sample consumption. Details of the experimental setup and data analysis methods used in this XANES and EXAFS study are presented. This method will also benefit XAS performed at high-repetition-rate XFELs such as the European XFEL, LCLS-II and LCLS-II-HE.

    View details for DOI 10.1107/S1600577519007550

    View details for PubMedID 31490163

  • The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source JOURNAL OF SYNCHROTRON RADIATION Sierra, R. G., Batyuk, A., Sun, Z., Aquila, A., Hunter, M. S., Lane, T. J., Liang, M., Yoon, C., Alonso-Mori, R., Armenta, R., Castagna, J., Hollenbeck, M., Osier, T. O., Hayes, M., Aldrich, J., Curtis, R., Koglin, J. E., Rendahl, T., Rodriguez, E., Carbajo, S., Guillet, S., Paul, R., Hart, P., Nakahara, K., Carini, G., DeMirci, H., Dao, E., Hayes, B. M., Rao, Y. P., Chollet, M., Feng, Y., Fuller, F. D., Kupitz, C., Sato, T., Seaberg, M. H., Song, S., van Driel, T. B., Yavas, H., Zhu, D., Cohen, A. E., Wakatsuki, S., Boutet, S. 2019; 26: 346–57
  • Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature Kern, J., Chatterjee, R., Young, I. D., Fuller, F. D., Lassalle, L., Ibrahim, M., Gul, S., Fransson, T., Brewster, A. S., Alonso-Mori, R., Hussein, R., Zhang, M., Douthit, L., de Lichtenberg, C., Cheah, M. H., Shevela, D., Wersig, J., Seuffert, I., Sokaras, D., Pastor, E., Weninger, C., Kroll, T., Sierra, R. G., Aller, P., Butryn, A., Orville, A. M., Liang, M., Batyuk, A., Koglin, J. E., Carbajo, S., Boutet, S., Moriarty, N. W., Holton, J. M., Dobbek, H., Adams, P. D., Bergmann, U., Sauter, N. K., Zouni, A., Messinger, J., Yano, J., Yachandra, V. K. 2018


    Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's S-state clock or cycle1,2. The model comprises four (meta)stable intermediates (S0, S1, S2 and S3) and one transient S4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn4CaO5) cluster in the oxygen-evolving complex3-7. This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone QB at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok's cycle as high-resolution structures (2.04-2.08A). In addition, we report structures of two transient states at 150 and 400s, revealing notable structural changes including the binding of one additional 'water', Ox, during the S2S3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 supports O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. Thus, our results exclude peroxo-bond formation in the S3 state, and the nucleophilic attack of W3 onto W2 is unlikely.

    View details for DOI 10.1038/s41586-018-0681-2

    View details for PubMedID 30405241

  • X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser. Biochemistry Fransson, T., Chatterjee, R., Fuller, F. D., Gul, S., Weninger, C., Sokaras, D., Kroll, T., Alonso-Mori, R., Bergmann, U., Kern, J., Yachandra, V. K., Yano, J. 2018


    Serial femtosecond crystallography (SFX) using the ultrashort X-ray pulses from a X-ray free-electron laser (XFEL) provides a new way of collecting structural data at room temperature that allows for following the reaction in real time after initiation. XFEL experiments are conducted in a shot-by-shot mode as the sample is destroyed and replenished after each X-ray pulse, and therefore, monitoring and controlling the data quality by using in situ diagnostic tools is critical. To study metalloenzymes, we developed the use of simultaneous collection of X-ray diffraction of crystals along with X-ray emission spectroscopy (XES) data that is used as a diagnostic tool for crystallography, by monitoring the chemical state of the metal catalytic center. We have optimized data analysis methods and sample delivery techniques for fast and active feedback to ensure the quality of each batch of samples and the turnover of the catalytic reaction caused by reaction triggering methods. Here, we describe this active in situ feedback system using Photosystem II as an example that catalyzes the oxidation of H2O to O2 at the Mn4CaO5 active site. We used the first moments of the Mn Kbeta1,3 emission spectra, which are sensitive to the oxidation state of Mn, as the primary diagnostics. This approach is applicable to different metalloproteins to determine the integrity of samples and follow changes in the chemical states of the reaction that can be initiated by light or activated by substrates and offers a metric for determining the diffraction images that are used for the final data sets.

    View details for DOI 10.1021/acs.biochem.8b00325

    View details for PubMedID 29906115

  • Stimulated X-Ray Emission Spectroscopy in Transition Metal Complexes PHYSICAL REVIEW LETTERS Kroll, T., Weninger, C., Alonso-Mori, R., Sokaras, D., Zhu, D., Mercadier, L., Majety, V. P., Marinelli, A., Lutman, A., Guetg, M. W., Decker, F., Boutet, S., Aquila, A., Koglin, J., Koralek, J., DePonte, D. P., Kern, J., Fuller, F. D., Pastor, E., Fransson, T., Zhang, Y., Yano, J., Yachandra, V. K., Rohringer, N., Bergmann, U. 2018; 120 (13): 133203


    We report the observation and analysis of the gain curve of amplified Kα x-ray emission from solutions of Mn(II) and Mn(VII) complexes using an x-ray free electron laser to create the 1s core-hole population inversion. We find spectra at amplification levels extending over 4 orders of magnitude until saturation. We observe bandwidths below the Mn 1s core-hole lifetime broadening in the onset of the stimulated emission. In the exponential amplification regime the resolution corrected spectral width of ∼1.7  eV FWHM is constant over 3 orders of magnitude, pointing to the buildup of transform limited pulses of ∼1  fs duration. Driving the amplification into saturation leads to broadening and a shift of the line. Importantly, the chemical sensitivity of the stimulated x-ray emission to the Mn oxidation state is preserved at power densities of ∼10^{20}  W/cm^{2} for the incoming x-ray pulses. Differences in signal sensitivity and spectral information compared to conventional (spontaneous) x-ray emission spectroscopy are discussed. Our findings build a baseline for nonlinear x-ray spectroscopy for a wide range of transition metal complexes in inorganic chemistry, catalysis, and materials science.

    View details for DOI 10.1103/PhysRevLett.120.133203

    View details for Web of Science ID 000428394800008

    View details for PubMedID 29694162

  • Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers STRUCTURAL DYNAMICS Kubin, M., Kern, J., Gul, S., Kroll, T., Chatterjee, R., Loechel, H., Fuller, F. D., Sierra, R. G., Quevedo, W., Weniger, C., Rehanek, J., Firsov, A., Laksmono, H., Weninger, C., Alonso-Mori, R., Nordlund, D. L., Lassalle-Kaiser, B., Glownia, J. M., Krzywinski, J., Moeller, S., Turner, J. J., Minitti, M. P., Dakovski, G. L., Koroidov, S., Kawde, A., Kanady, J. S., Tsui, E. Y., Suseno, S., Han, Z., Hill, E., Taguchi, T., Borovik, A. S., Agapie, T., Messinger, J., Erko, A., Foehlisch, A., Bergmann, U., Mitzner, R., Yachandra, V. K., Yano, J., Wernet, P. 2017; 4 (5): 054307


    X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn ∼ 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn4CaO5) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions.

    View details for PubMedID 28944255

  • Structure of photosystem II and substrate binding at room temperature NATURE Young, I. D., Ibrahim, M., Chatterjee, R., Gul, S., Fuller, F. D., Koroidov, S., Brewster, A. S., Tran, R., Alonso-Mori, R., Kroll, T., Michels-Clark, T., Laksmono, H., Sierra, R. G., Stan, C. A., Hussein, R., Zhang, M., Douthit, L., Kubin, M., de Lichtenberg, C., Long Vo Pham, L. V., Nilsson, H., Cheah, M. H., Shevela, D., Saracini, C., Bean, M. A., Seuffert, I., Sokaras, D., Weng, T., Pastor, E., Weninger, C., Fransson, T., Lassalle, L., Braeuer, P., Aller, P., Docker, P. T., Andi, B., Orville, A. M., Glownia, J. M., Nelson, S., Sikorski, M., Zhu, D., Hunter, M. S., Lane, T. J., Aquila, A., Koglin, J. E., Robinson, J., Liang, M., Boutet, S., Lyubimov, A. Y., Uervirojnangkoorn, M., Moriarty, N. W., Liebschner, D., Afonine, P. V., Waterman, D. G., Evans, G., Wernet, P., Dobbek, H., Weis, W. I., Brunger, A. T., Zwart, P. H., Adams, P. D., Zouni, A., Messinger, J., Bergmann, U., Sauter, N. K., Kern, J., Yachandra, V. K., Yano, J. 2016; 540 (7633): 453-?


    Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

    View details for DOI 10.1038/nature20161

    View details for Web of Science ID 000389716800046

    View details for PubMedID 27871088

    View details for PubMedCentralID PMC5201176

  • X-ray absorption spectroscopy using a self-seeded soft X-ray free-electron laser OPTICS EXPRESS Kroll, T., Kern, J., Kubin, M., Ratner, D., Gul, S., Fuller, F. D., Loechel, H., Krzywinski, J., Lutman, A., Ding, Y., Dakovski, G. L., Moeller, S., Turner, J. J., Alonso-Mori, R., Nordlund, D. L., Rehanek, J., Weniger, C., Firsov, A., Brzhezinskaya, M., Chatterjee, R., Lassalle-Kaiser, B., Sierra, R. G., Laksmono, H., Hill, E., Borovik, A., Erko, A., Foehlisch, A., Mitzner, R., Yachandra, V. K., Yano, J., Wernet, P., Bergmann, U. 2016; 24 (20): 22469-22480


    X-ray free electron lasers (XFELs) enable unprecedented new ways to study the electronic structure and dynamics of transition metal systems. L-edge absorption spectroscopy is a powerful technique for such studies and the feasibility of this method at XFELs for solutions and solids has been demonstrated. However, the required x-ray bandwidth is an order of magnitude narrower than that of self-amplified spontaneous emission (SASE), and additional monochromatization is needed. Here we compare L-edge x-ray absorption spectroscopy (XAS) of a prototypical transition metal system based on monochromatizing the SASE radiation of the linac coherent light source (LCLS) with a new technique based on self-seeding of LCLS. We demonstrate how L-edge XAS can be performed using the self-seeding scheme without the need of an additional beam line monochromator. We show how the spectral shape and pulse energy depend on the undulator setup and how this affects the x-ray spectroscopy measurements.

    View details for DOI 10.1364/OE.24.022469

    View details for Web of Science ID 000387543000016

    View details for PubMedID 27828320

    View details for PubMedCentralID PMC5234502

  • Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II NATURE METHODS Sierra, R. G., Gati, C., Laksmono, H., Dao, E. H., Gul, S., Fuller, F., Kern, J., Chatterjee, R., Ibrahim, M., Brewster, A. S., Young, I. D., Michels-Clark, T., Aquila, A., Liang, M., Hunter, M. S., Koglin, J. E., Boutet, S., Junco, E. A., Hayes, B., Bogan, M. J., Hampton, C. Y., Puglisi, E. V., Sauter, N. K., Stan, C. A., Zouni, A., Yano, J., Yachandra, V. K., Soltis, S. M., Puglisi, J. D., DeMirci, H. 2016; 13 (1): 59-?


    We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).

    View details for DOI 10.1038/NMETH.3667

    View details for Web of Science ID 000367463600028

    View details for PubMedCentralID PMC4890631

  • Experimental Implementations of Two-Dimensional Fourier Transform Electronic Spectroscopy ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 66 Fuller, F. D., Ogilvie, J. P., Johnson, M. A., Martinez, T. J. 2015; 66: 667–90


    Two-dimensional electronic spectroscopy (2DES) reveals connections between an optical excitation at a given frequency and the signals it creates over a wide range of frequencies. These connections, manifested as cross-peak locations and their lineshapes, reflect the underlying electronic and vibrational structure of the system under study. How these spectroscopic signatures evolve in time reveals the system dynamics and provides a detailed picture of coherent and incoherent processes. 2DES is rapidly maturing and has already found numerous applications, including studies of photosynthetic energy transfer and photochemical reactions and many-body interactions in nanostructured materials. Many systems of interest contain electronic transitions spanning the ultraviolet to the near infrared and beyond. Most 2DES measurements to date have explored a relatively small frequency range. We discuss the challenges of implementing 2DES and compare and contrast different approaches in terms of their information content, ease of implementation, and potential for broadband measurements.

    View details for DOI 10.1146/annurev-physchem-040513-103623

    View details for Web of Science ID 000352259800029

    View details for PubMedID 25664841

  • Vibronic coherence in oxygenic photosynthesis NATURE CHEMISTRY Fuller, F. D., Pan, J., Gelzinis, A., Butkus, V., Senlik, S., Wilcox, D. E., Yocum, C. F., Valkunas, L., Abramavicius, D., Ogilvie, J. P. 2014; 6 (8): 706–11


    Photosynthesis powers life on our planet. The basic photosynthetic architecture consists of antenna complexes that harvest solar energy and reaction centres that convert the energy into stable separated charge. In oxygenic photosynthesis, the initial charge separation occurs in the photosystem II reaction centre, the only known natural enzyme that uses solar energy to split water. Both energy transfer and charge separation in photosynthesis are rapid events with high quantum efficiencies. In recent nonlinear spectroscopic experiments, long-lived coherences have been observed in photosynthetic antenna complexes, and theoretical work suggests that they reflect underlying electronic-vibrational resonances, which may play a functional role in enhancing energy transfer. Here, we report the observation of coherent dynamics persisting on a picosecond timescale at 77 K in the photosystem II reaction centre using two-dimensional electronic spectroscopy. Supporting simulations suggest that the coherences are of a mixed electronic-vibrational (vibronic) nature and may enhance the rate of charge separation in oxygenic photosynthesis.

    View details for DOI 10.1038/NCHEM.2005

    View details for Web of Science ID 000341371100014

    View details for PubMedID 25054941

  • Pulse shaping based two-dimensional electronic spectroscopy in a background free geometry OPTICS EXPRESS Fuller, F. D., Wilcox, D. E., Ogilvie, J. P. 2014; 22 (1): 1018–27


    We demonstrate a "drop-in" modification of the pulse-shaped pump-probe geometry two-dimensional Fourier transform spectrometer that significantly improves its performance by making the measurement background-free. The modification uses a hybrid diffractive optic/pulse-shaping approach that combines the advantages of background-free detection with the precise timing and phase-cycling capabilities enabled by pulse-shaping. In addition, we present a simple new method for accurate phasing of optically heterodyned two-dimensional spectra. We demonstrate the high quality of data obtainable with this approach by reporting two-dimensional Fourier transform electronic spectra of chlorophyll a in glycerol/water at 77 K.

    View details for DOI 10.1364/OE.22.001018

    View details for Web of Science ID 000330579300123

    View details for PubMedID 24515061

  • Fast second-harmonic generation frequency-resolved optical gating using only a pulse shaper OPTICS LETTERS Wilcox, D. E., Fuller, F. D., Ogilvie, J. P. 2013; 38 (16): 2980–83


    In many ultrafast contexts, a collinear pulse-shaping frequency-resolved optical gating (FROG) technique is desired. Some applicable techniques already exist, but they suffer from one of two issues: either they require many time points to allow for Fourier filtering, or they do not yield a traditional FROG trace. To overcome these issues, we propose and demonstrate a fast new phase-cycled FROG technique using a pulse shaper.

    View details for DOI 10.1364/OL.38.002980

    View details for Web of Science ID 000323204500013

    View details for PubMedID 24104626

  • Tight-binding model of the photosystem II reaction center: application to two-dimensional electronic spectroscopy NEW JOURNAL OF PHYSICS Gelzinis, A., Valkunas, L., Fuller, F. D., Ogilvie, J. P., Mukamel, S., Abramavicius, D. 2013; 15
  • Simulations of the Two-Dimensional Electronic Spectroscopy of the Photosystem II Reaction Center JOURNAL OF PHYSICAL CHEMISTRY A Lewis, K. M., Fuller, F. D., Myers, J. A., Yocum, C. F., Mukamel, S., Abramavicius, D., Ogilvie, J. P. 2013; 117 (1): 34–41


    We report simulations of the two-dimensional electronic spectroscopy of the Q(y) band of the D1-D2-Cyt b559 photosystem II reaction center at 77 K. We base the simulations on an existing Hamiltonian that was derived by simultaneous fitting to a wide range of linear spectroscopic measurements and described within modified Redfield theory. The model obtains reasonable agreement with most aspects of the two-dimensional spectra, including the overall peak shapes and excited state absorption features. It does not reproduce the rapid equilibration from high energy to low energy excitonic states evident by a strong cross-peak below the diagonal. We explore modifications to the model to incorporate new structural data and improve agreement with the two-dimensional spectra. We find that strengthening the system-bath coupling and lowering the degree of disorder significantly improves agreement with the cross-peak feature, while lessening agreement with the relative diagonal/antidiagonal width of the 2D spectra. We conclude that two-dimensional electronic spectroscopy provides a sensitive test of excitonic models of the photosystem II reaction center and discuss avenues for further refinement of such models.

    View details for DOI 10.1021/jp3081707

    View details for Web of Science ID 000313220400006

    View details for PubMedID 23210463

    View details for PubMedCentralID PMC3702820

  • Continuum probe two-dimensional electronic spectroscopy of the photosystem II reaction center Fuller, F. D., Ogilvie, J. P., Chergui, M., Taylor, A., Cundiff, S., DeVivieRiedle, R., Yamagouchi, K. E D P SCIENCES. 2013
  • Effects of chirp on two-dimensional Fourier transform electronic spectra OPTICS EXPRESS Tekavec, P. F., Myers, J. A., Lewis, K. M., Fuller, F. D., Ogilvie, J. P. 2010; 18 (11): 11015–24


    We examine the effect that pulse chirp has on the shape of two- dimensional electronic spectra through calculations and experiments. For the calculations we use a model two electronic level system with a solvent interaction represented by a simple Gaussian correlation function and compare the resulting spectra to experiments carried out on an organic dye molecule (Rhodamine 800). Both calculations and experiments show that distortions due to chirp are most significant when the pulses used in the experiment have different amounts of chirp, introducing peak shape asymmetry that could be interpreted as spectrally dependent relaxation. When all pulses have similar chirp the distortions are reduced but still affect the anti-diagonal symmetry of the peak shapes and introduce negative features that could be interpreted as excited state absorption.

    View details for DOI 10.1364/OE.18.011015

    View details for Web of Science ID 000278512300011

    View details for PubMedID 20588957

  • Conformational dynamics of single pre-mRNA molecules during in vitro splicing NATURE STRUCTURAL & MOLECULAR BIOLOGY Abelson, J., Blanco, M., Ditzler, M. A., Fuller, F., Aravamudhan, P., Wood, M., Villa, T., Ryan, D. E., Pleiss, J. A., Maeder, C., Guthrie, C., Walter, N. G. 2010; 17 (4): 504–U156


    The spliceosome is a complex small nuclear RNA (snRNA)-protein machine that removes introns from pre-mRNAs via two successive phosphoryl transfer reactions. The chemical steps are isoenergetic, yet splicing requires at least eight RNA-dependent ATPases responsible for substantial conformational rearrangements. To comprehensively monitor pre-mRNA conformational dynamics, we developed a strategy for single-molecule FRET (smFRET) that uses a small, efficiently spliced yeast pre-mRNA, Ubc4, in which donor and acceptor fluorophores are placed in the exons adjacent to the 5' and 3' splice sites. During splicing in vitro, we observed a multitude of generally reversible time- and ATP-dependent conformational transitions of individual pre-mRNAs. The conformational dynamics of branchpoint and 3'-splice site mutants differ from one another and from wild type. Because all transitions are reversible, spliceosome assembly appears to be occurring close to thermal equilibrium.

    View details for DOI 10.1038/nsmb.1767

    View details for Web of Science ID 000276416800021

    View details for PubMedID 20305654

    View details for PubMedCentralID PMC2881217