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Du DX, Simjanoska M, Fitzpatrick AWP. Four-dimensional microED of conformational dynamics in protein microcrystals on the femto-to-microsecond timescales. J Struct Biol 2023; 215:107941. [PMID: 36773734 DOI: 10.1016/j.jsb.2023.107941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
As structural determination of protein complexes approaches atomic resolution, there is an increasing focus on conformational dynamics. Here we conceptualize the combination of two techniques which have become established in recent years: microcrystal electron diffraction and ultrafast electron microscopy. We show that the extremely low dose of pulsed photoemission still enables microED due to the strength of the electron bunching from diffraction of the protein crystals. Indeed, ultrafast electron diffraction experiments on protein crystals have already been demonstrated to be effective in measuring intermolecular forces in protein microcrystals. We discuss difficulties that may arise in the acquisition and processing of data and the overall feasibility of the experiment, paying specific attention to dose and signal-to-noise ratio. In doing so, we outline a detailed workflow that may be effective in minimizing the dose on the specimen. A series of model systems that would be good candidates for initial experiments is provided.
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Affiliation(s)
- Daniel X Du
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Marija Simjanoska
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Anthony W P Fitzpatrick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA.
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Giovagnetti V, Ruban AV. The mechanism of regulation of photosystem I cross-section in the pennate diatom Phaeodactylum tricornutum. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:561-575. [PMID: 33068431 DOI: 10.1093/jxb/eraa478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Photosystems possess distinct fluorescence emissions at low (77K) temperature. PSI emits in the long-wavelength region at ~710-740 nm. In diatoms, a successful clade of marine primary producers, the contribution of PSI-associated emission (710-717 nm) has been shown to be relatively small. However, in the pennate diatom Phaeodactylum tricornutum, the source of the long-wavelength emission at ~710 nm (F710) remains controversial. Here, we addressed the origin and modulation of F710 fluorescence in this alga grown under continuous and intermittent light. The latter condition led to a strong enhancement in F710. Biochemical and spectral properties of the photosynthetic complexes isolated from thylakoid membranes were investigated for both culture conditions. F710 emission appeared to be associated with PSI regardless of light acclimation. To further assess whether PSII could also contribute to this emission, we decreased the concentration of PSII reaction centres and core antenna by growing cells with lincomycin, a chloroplast protein synthesis inhibitor. The treatment did not diminish F710 fluorescence. Our data suggest that F710 emission originates from PSI under the conditions tested and is enhanced in intermittent light-grown cells due to increased energy flow from the FCP antenna to PSI.
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Affiliation(s)
- Vasco Giovagnetti
- Department of Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Alexander V Ruban
- Department of Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Basic pH-induced modification of excitation-energy dynamics in fucoxanthin chlorophyll a/c-binding proteins isolated from a pinguiophyte, Glossomastix chrysoplasta. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148306. [PMID: 32926861 DOI: 10.1016/j.bbabio.2020.148306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/03/2020] [Accepted: 09/09/2020] [Indexed: 11/20/2022]
Abstract
Photosynthetic organisms have diversified light-harvesting complexes (LHCs) to collect solar energy efficiently, leading to an acquisition of their ecological niches. Herein we report on biochemical and spectroscopic characterizations of fucoxanthin chlorophyll a/c-binding protein (FCP) complexes isolated from a marine pinguiophyte Glossomastix chrysoplasta. The pinguiophyte FCP showed one subunit band in SDS-PAGE and one protein-complex band with a molecular weight at around 66 kDa in clear-native PAGE. By HPLC analysis, the FCP possesses chlorophylls a and c, fucoxanthin, and violaxanthin. To clarify excitation-energy-relaxation processes in the FCP, we measured time-resolved fluorescence spectra at 77 K of the FCP adapted to pH 5.0, 6.5, and 8.0. Fluorescence curves measured at pH 5.0 and 8.0 showed shorter lifetime components compared with those at pH 6.5. The rapid decay components at pH 5.0 and 8.0 are unveiled by fluorescence decay-associated (FDA) spectra; fluorescence decays occur in the 270 and 160-ps FDA spectra only at pH 5.0 and 8.0, respectively. In addition, energy-transfer pathways with time constants of tens of picoseconds are altered under the basic pH condition but not the acidic pH condition. These findings provide novel insights into pH-dependent energy-transfer and energy-quenching machinery in not only FCP family but also photosynthetic LHCs.
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Nagao R, Kagatani K, Ueno Y, Shen JR, Akimoto S. Ultrafast Excitation Energy Dynamics in a Diatom Photosystem I-Antenna Complex: A Femtosecond Fluorescence Upconversion Study. J Phys Chem B 2019; 123:2673-2678. [DOI: 10.1021/acs.jpcb.8b12086] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ryo Nagao
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Kohei Kagatani
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Yoshifumi Ueno
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Seiji Akimoto
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
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High photochemical trapping efficiency in Photosystem I from the red clade algae Chromera velia and Phaeodactylum tricornutum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:56-63. [DOI: 10.1016/j.bbabio.2016.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 11/23/2022]
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Litvín R, Bína D, Herbstová M, Gardian Z. Architecture of the light-harvesting apparatus of the eustigmatophyte alga Nannochloropsis oceanica. PHOTOSYNTHESIS RESEARCH 2016; 130:137-150. [PMID: 26913864 DOI: 10.1007/s11120-016-0234-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/12/2016] [Indexed: 05/10/2023]
Abstract
We present proteomic, spectroscopic, and phylogenetic analysis of light-harvesting protein (Lhc) function in oleaginous Nannochloropsis oceanica (Eustigmatophyta, Stramenopila). N. oceanica utilizes Lhcs of multiple classes: Lhcr-type proteins (related to red algae LHCI), Lhcv (VCP) proteins (violaxanthin-containing Lhcs related to Lhcf/FCP proteins of diatoms), Lhcx proteins (related to Lhcx/LhcSR of diatoms and green algae), and Lhc proteins related to Red-CLH of Chromera velia. Altogether, 17 Lhc-type proteins of the 21 known from genomic data were found in our proteomic analyses. Besides Lhcr-type antennas, a RedCAP protein and a member of the Lhcx protein subfamily were found in association with Photosystem I. The free antenna fraction is formed by trimers of a mixture of Lhcs of varied origins (Lhcv, Lhcr, Lhcx, and relatives of Red-CLH). Despite possessing several proteins of the Red-CLH-type Lhc clade, N. oceanica is not capable of chromatic adaptation under the same conditions as the diatom Phaeodactylum tricornutum or C. velia. In addition, a naming scheme of Nannochloropsis Lhcs is proposed to facilitate further work.
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Affiliation(s)
- Radek Litvín
- Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic.
| | - David Bína
- Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Miroslava Herbstová
- Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Zdenko Gardian
- Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
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Herbstová M, Bína D, Koník P, Gardian Z, Vácha F, Litvín R. Molecular basis of chromatic adaptation in pennate diatom Phaeodactylum tricornutum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:534-43. [DOI: 10.1016/j.bbabio.2015.02.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/25/2015] [Accepted: 02/27/2015] [Indexed: 12/17/2022]
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Chukhutsina VU, Büchel C, van Amerongen H. Disentangling two non-photochemical quenching processes in Cyclotella meneghiniana by spectrally-resolved picosecond fluorescence at 77K. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:899-907. [PMID: 24582663 DOI: 10.1016/j.bbabio.2014.02.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 11/24/2022]
Abstract
Diatoms, which are primary producers in the oceans, can rapidly switch on/off efficient photoprotection to respond to fast light-intensity changes in moving waters. The corresponding thermal dissipation of excess-absorbed-light energy can be observed as non-photochemical quenching (NPQ) of chlorophyll a fluorescence. Fluorescence-induction measurements on Cyclotella meneghiniana diatoms show two NPQ processes: qE1 relaxes rapidly in the dark while qE2 remains present upon switching to darkness and is related to the presence of the xanthophyll-cycle pigment diatoxanthin (Dtx). We performed picosecond fluorescence measurements on cells locked in different (quenching) states, revealing the following sequence of events during full development of NPQ. At first, trimers of light-harvesting complexes (fucoxanthin-chlorophyll a/c proteins), or FCPa, become quenched, while being part of photosystem II (PSII), due to the induced pH gradient across the thylakoid membrane. This is followed by (partial) detachment of FCPa from PSII after which quenching persists. The pH gradient also causes the formation of Dtx which leads to further quenching of isolated PSII cores and some aggregated FCPa. In subsequent darkness, the pH gradient disappears but Dtx remains present and quenching partly pertains. Only in the presence of some light the system completely recovers to the unquenched state.
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Affiliation(s)
- Volha U Chukhutsina
- Laboratory of Biophysics, Wageningen University, 6703HA Wageningen, The Netherlands; BioSolar Cells, P.O. Box 98, 6700 AB Wageningen, The Netherlands
| | - Claudia Büchel
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, 60438 Frankfurt am Main, Germany
| | - Herbert van Amerongen
- Laboratory of Biophysics, Wageningen University, 6703HA Wageningen, The Netherlands; BioSolar Cells, P.O. Box 98, 6700 AB Wageningen, The Netherlands; MicroSpectroscopy Centre, Wageningen University, 6703HA Wageningen, The Netherlands.
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Shibata Y, Nishi S, Kawakami K, Shen JR, Renger T. Photosystem II does not possess a simple excitation energy funnel: time-resolved fluorescence spectroscopy meets theory. J Am Chem Soc 2013; 135:6903-14. [PMID: 23537277 PMCID: PMC3650659 DOI: 10.1021/ja312586p] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The experimentally
obtained time-resolved fluorescence spectra
of photosystem II (PS II) core complexes, purified from a thermophilic
cyanobacterium Thermosynechococcus vulcanus, at 5–180 K are compared with simulations. Dynamic localization
effects of excitons are treated implicitly by introducing exciton
domains of strongly coupled pigments. Exciton relaxations within a
domain and exciton transfers between domains are treated on the basis
of Redfield theory and generalized Förster theory, respectively.
The excitonic couplings between the pigments are calculated by a quantum
chemical/electrostatic method (Poisson-TrEsp). Starting with previously
published values, a refined set of site energies of the pigments is
obtained through optimization cycles of the fits of stationary optical
spectra of PS II. Satisfactorily agreement between the experimental
and simulated spectra is obtained for the absorption spectrum including
its temperature dependence and the linear dichroism spectrum of PS
II core complexes (PS II-CC). Furthermore, the refined site energies
well reproduce the temperature dependence of the time-resolved fluorescence
spectrum of PS II-CC, which is characterized by the emergence of a
695 nm fluorescence peak upon cooling down to 77 K and the decrease
of its relative intensity upon further cooling below 77 K. The blue
shift of the fluorescence band upon cooling below 77 K is explained
by the existence of two red-shifted chlorophyll pools emitting at
around 685 and 695 nm. The former pool is assigned to Chl45 or Chl43
in CP43 (Chl numbering according to the nomenclature of Loll et al. Nature2005, 438, 1040) while
the latter is assigned to Chl29 in CP47. The 695 nm emitting chlorophyll
is suggested to attract excitations from the peripheral light-harvesting
complexes and might also be involved in photoprotection.
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Affiliation(s)
- Yutaka Shibata
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya, Japan.
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Lavaud J, Lepetit B. An explanation for the inter-species variability of the photoprotective non-photochemical chlorophyll fluorescence quenching in diatoms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013. [DOI: 10.1016/j.bbabio.2012.11.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ikeda Y, Yamagishi A, Komura M, Suzuki T, Dohmae N, Shibata Y, Itoh S, Koike H, Satoh K. Two types of fucoxanthin-chlorophyll-binding proteins I tightly bound to the photosystem I core complex in marine centric diatoms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:529-39. [PMID: 23416844 DOI: 10.1016/j.bbabio.2013.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 01/31/2013] [Accepted: 02/06/2013] [Indexed: 12/30/2022]
Abstract
Intact fucoxanthin (Fucox)-chlorophyll (Chl)-binding protein I-photosystem I supercomplexes (FCPI-PSIs) were prepared by a newly developed simple fast procedure from centric diatoms Chaetoceros gracilis and Thalassiosira pseudonana to study the mechanism of their efficient solar energy accumulation. FCPI-PSI purified from C. gracilis contained 252 Chl a, 23 Chl c, 56 Fucox, 34 diadinoxanthin+diatoxanthin, 1 violaxanthin, 21 ß-carotene, and 2 menaquinone-4 per P700. The complex showed a high electron transfer activity at 185,000μmolmg Chl a(-1)·h(-1) to reduce methyl viologen from added cytochrome c6. We identified 14 and 21 FCP proteins in FCPI-PSI of C. gracilis and T. pseudonana, respectively, determined by N-terminal and internal amino acid sequences and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. PsaO and a red lineage Chla/b-binding-like protein (RedCAP), Thaps3:270215, were also identified. Severe detergent treatment of FCPI-PSI released FCPI-1 first, leaving the FCPI-2-PSI-core complex. FCPI-1 contained more Chl c and showed Chl a fluorescence at a shorter wavelength than FCPI-2, suggesting an excitation-energy transfer from FCPI-1 to FCPI-2 and then to the PSI core. Fluorescence emission spectra at 17K in FCPI-2 varied depending on the excitation wavelength, suggesting two independent energy transfer routes. We formulated a model of FCPI-PSI based on the biochemical assay results.
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Affiliation(s)
- Yohei Ikeda
- Graduate School of Life Science, University of Hyogo, Harima Science Garden City, Hyogo 678-1297, Japan.
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Juhas M, Büchel C. Properties of photosystem I antenna protein complexes of the diatom Cyclotella meneghiniana. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:3673-81. [PMID: 22442408 PMCID: PMC3388839 DOI: 10.1093/jxb/ers049] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Analysis of photosystem I (PSI) complexes from Cyclotella meneghiniana cultured under different growth conditions led to the identification of three groups of antenna proteins, having molecular weights of around 19, 18, and 17 kDa. The 19-kDa proteins have earlier been demonstrated to be more peripherally bound to PSI, and their amount in the PSI complexes was significantly reduced when the iron supply in the growth medium was lowered. This polypeptide was almost missing, and thus the total amount of fucoxanthin-chlorophyll proteins (Fcps) bound to PSI was reduced as well. When treating cells with high light in addition, no further changes in antenna polypeptide composition were detected. Xanthophyll cycle pigments were found to be bound to all Fcps of PSI. However, PSI of high light cultures had a significantly higher diatoxanthin to diadinoxanthin ratio, which is assumed to protect against a surplus of excitation energy. PSI complexes from the double-stressed cultures (high light plus reduced iron supply) were slightly more sensitive against destruction by the detergent treatment. This could be seen as a higher 674-nm emission at 77 K in comparison to the PSI complexes isolated from other growth conditions. Two major emission bands of the Fcps bound to PSI at 77 K could be identified, whereby chlorophyll a fluorescing at 697 nm was more strongly coupled to the PSI core than those fluorescing at 685 nm. Thus, the build up of the PSI antenna of several Fcp components enables variable reactions to several stress factors commonly experienced by the diatoms in vivo, in particular diatoxanthin enrichment under high light and reduction of antenna size under reduced iron conditions.
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Miyake H, Komura M, Itoh S, Kosugi M, Kashino Y, Satoh K, Shibata Y. Multiple dissipation components of excess light energy in dry lichen revealed by ultrafast fluorescence study at 5 K. PHOTOSYNTHESIS RESEARCH 2011; 110:39-48. [PMID: 21986932 DOI: 10.1007/s11120-011-9691-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 09/21/2011] [Indexed: 05/31/2023]
Abstract
A time-resolved fluorescence study of living lichen thalli at 5 K was conducted to clarify the dynamics and mechanism of the effective dissipation of excess light energy taking place in lichen under extreme drought conditions. The decay-associated spectra obtained from the experiment at 5 K were characterized by a drastically sharpened spectral band which could not be resolved by experiments at higher temperatures. The present results indicated the existence of two distinct dissipation components of excess light energy in desiccated lichen; one is characterized as rapid fluorescence decay with a time constant of 27 ps in the far-red region that was absent in wet lichen thalli, and the other is recognized as accelerated fluorescence decay in the 685-700 nm spectral region. The former energy-dissipation component with extremely high quenching efficiency is most probably ascribed to the emergence of a rapid quenching state in the peripheral-antenna system of photosystem II (PS II) on desiccation. This is an extremely effective protection mechanism of PS II under desiccation, which lichens have developed to survive in the severely desiccated environments. The latter, which is less efficient at 5 K, might have a supplementary role and take place either in the core antenna of PS II or aggregated peripheral antenna of PS II.
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Affiliation(s)
- Hirohisa Miyake
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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