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Article ; Online: Regulation of light energy conversion between linear and cyclic electron flow within photosystem II controlled by the plastoquinone/quinol redox poise.

Gates, Colin / Ananyev, Gennady / Roy-Chowdhury, Shatabdi / Fromme, Petra / Dismukes, G Charles

2022 Volume 156, Issue 1, Page(s) 113–128

Abstract: Ultrapurified Photosystem II complexes crystalize as uniform microcrystals (PSIIX) of unprecedented homogeneity that allow observation of details previously unachievable, including the longest sustained oscillations of flash-induced ... ...

Abstract	Ultrapurified Photosystem II complexes crystalize as uniform microcrystals (PSIIX) of unprecedented homogeneity that allow observation of details previously unachievable, including the longest sustained oscillations of flash-induced O
MeSH term(s)	Photosystem II Protein Complex/metabolism ; Electron Transport ; Plastoquinone/metabolism ; Electrons ; Protons ; Photosynthesis/physiology ; Hydroquinones ; Oxidation-Reduction ; Water/chemistry
Chemical Substances	Photosystem II Protein Complex ; Plastoquinone (OAC30J69CN) ; Protons ; hydroquinone (XV74C1N1AE) ; Hydroquinones ; Water (059QF0KO0R)
Language	English
Publishing date	2022-11-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1475688-2
ISSN	1573-5079 ; 0166-8595
ISSN (online)	1573-5079
ISSN	0166-8595
DOI	10.1007/s11120-022-00985-w
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Article: Why Did Nature Choose Manganese over Cobalt to Make Oxygen Photosynthetically on the Earth?

Gates, Colin / Ananyev, Gennady / Roy-Chowdhury, Shatabdi / Cullinane, Brendan / Miller, Mathias / Fromme, Petra / Dismukes, G. Charles

Journal of physical chemistry. 2022 Apr. 21, v. 126, no. 17

2022

Abstract: All contemporary oxygenic phototrophs─from primitive cyanobacteria to complex multicellular plants─split water using a single invariant cluster comprising Mn₄CaO₅ (the water oxidation catalyst) as the catalyst within photosystem II, the universal ... ...

Abstract	All contemporary oxygenic phototrophs─from primitive cyanobacteria to complex multicellular plants─split water using a single invariant cluster comprising Mn₄CaO₅ (the water oxidation catalyst) as the catalyst within photosystem II, the universal oxygenic reaction center of natural photosynthesis. This cluster is unstable outside of PSII and can be reconstituted, both in vivo and in vitro, using elemental aqueous ions and light, via photoassembly. Here, we demonstrate the first functional substitution of manganese in any oxygenic reaction center by in vitro photoassembly. Following complete removal of inorganic cofactors from cyanobacterial photosystem II microcrystal (PSIIX), photoassembly with free cobalt (Co²⁺), calcium (Ca²⁺), and water (OH–) restores O₂ evolution activity. Photoassembly occurs at least threefold faster using Co²⁺ versus Mn²⁺ due to a higher quantum yield for PSIIX-mediated charge separation (P): Co²⁺ → P → Co³⁺QA–. However, this kinetic preference for Co²⁺ over native Mn²⁺ during photoassembly is offset by significantly poorer catalytic activity (∼25% of the activity with Mn²⁺) and ∼3- to 30-fold faster photoinactivation rate. The resulting reconstituted Co-PSIIX oxidizes water by the standard four-flash photocycle, although they produce 4-fold less O₂ per PSII, suggested to arise from faster charge recombination (Co³⁺QA ← Co⁴⁺QA–) in the catalytic cycle. The faster photoinactivation of reconstituted Co-PSIIX occurs under anaerobic conditions during the catalytic cycle, suggesting direct photodamage without the involvement of O₂. Manganese offers two advantages for oxygenic phototrophs, which may explain its exclusive retention throughout Darwinian evolution: significantly slower charge recombination (Mn³⁺QA ← Mn⁴⁺QA–) permits more water oxidation at low and fluctuating solar irradiation (greater net energy conversion) and much greater tolerance to photodamage at high light intensities (Mn⁴⁺ is less oxidizing than Co⁴⁺). Future work to identify the chemical nature of the intermediates will be needed for further interpretation.
Keywords	Cyanobacteria ; autotrophs ; calcium ; catalysts ; catalytic activity ; cobalt ; energy conversion ; manganese ; oxidation ; oxygen ; photosystem II ; physical chemistry ; solar radiation
Language	English
Dates of publication	2022-0421
Size	p. 3257-3268.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.2c00749
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Article ; Online: Why Did Nature Choose Manganese over Cobalt to Make Oxygen Photosynthetically on the Earth?

Gates, Colin / Ananyev, Gennady / Roy-Chowdhury, Shatabdi / Cullinane, Brendan / Miller, Mathias / Fromme, Petra / Dismukes, G Charles

The journal of physical chemistry. B

2022 Volume 126, Issue 17, Page(s) 3257–3268

Abstract: All contemporary oxygenic phototrophs─from primitive cyanobacteria to complex multicellular plants─split water using a single invariant cluster comprising ... ...

Abstract	All contemporary oxygenic phototrophs─from primitive cyanobacteria to complex multicellular plants─split water using a single invariant cluster comprising Mn
MeSH term(s)	Cobalt ; Cyanobacteria/metabolism ; Manganese/chemistry ; Oxidation-Reduction ; Oxygen/chemistry ; Photosystem II Protein Complex/chemistry ; Water/chemistry
Chemical Substances	Photosystem II Protein Complex ; Water (059QF0KO0R) ; Cobalt (3G0H8C9362) ; Manganese (42Z2K6ZL8P) ; Oxygen (S88TT14065)
Language	English
Publishing date	2022-04-21
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.2c00749
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Article ; Online: Serial macromolecular crystallography at ALBA Synchrotron Light Source. Erratum.

Martin-Garcia, Jose M / Botha, Sabine / Hu, Hao / Jernigan, Rebecca / Castellví, Albert / Lisova, Stella / Gil, Fernando / Calisto, Barbara / Crespo, Isidro / Roy-Chowdhury, Shatabdi / Grieco, Alice / Ketawala, Gihan / Weierstall, Uwe / Spence, John / Fromme, Petra / Zatsepin, Nadia / Boer, Dirk Roeland / Carpena, Xavi

Journal of synchrotron radiation

2022 Volume 29, Issue Pt 4, Page(s) 1130

Abstract: A revised version of Table 2 of Martin-Garcia et al. [J. Synchrotron Rad. (2022). 29, 896-907] is provided. ...

Abstract	A revised version of Table 2 of Martin-Garcia et al. [J. Synchrotron Rad. (2022). 29, 896-907] is provided.
Language	English
Publishing date	2022-05-16
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2021413-3
ISSN	1600-5775 ; 0909-0495
ISSN (online)	1600-5775
ISSN	0909-0495
DOI	10.1107/S1600577522005185
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Article ; Online: Serial macromolecular crystallography at ALBA Synchrotron Light Source.

Journal of synchrotron radiation

2022 Volume 29, Issue Pt 3, Page(s) 896–907

Abstract: The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In ...

Abstract	The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In this work, we report the first SSX experiments with viscous jets conducted at ALBA beamline BL13-XALOC. Small crystals (15-30 µm) of five soluble proteins (lysozyme, proteinase K, phycocyanin, insulin and α-spectrin-SH3 domain) were suspended in lipidic cubic phase (LCP) and delivered to the X-ray beam with a high-viscosity injector developed at Arizona State University. Complete data sets were collected from all proteins and their high-resolution structures determined. The high quality of the diffraction data collected from all five samples, and the lack of specific radiation damage in the structures obtained in this study, confirm that the current capabilities at the beamline enables atomic resolution determination of protein structures from microcrystals as small as 15 µm using viscous jets at room temperature. Thus, BL13-XALOC can provide a feasible alternative to X-ray free-electron lasers when determining snapshots of macromolecular structures.
MeSH term(s)	Crystallography, X-Ray ; Humans ; Lasers ; Macromolecular Substances ; Proteins ; Synchrotrons ; Viscosity
Chemical Substances	Macromolecular Substances ; Proteins
Language	English
Publishing date	2022-04-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2021413-3
ISSN	1600-5775 ; 0909-0495
ISSN (online)	1600-5775
ISSN	0909-0495
DOI	10.1107/S1600577522002508
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Article ; Online: Serial femtosecond crystallography: A revolution in structural biology.

Martin-Garcia, Jose M / Conrad, Chelsie E / Coe, Jesse / Roy-Chowdhury, Shatabdi / Fromme, Petra

Archives of biochemistry and biophysics

2016 Volume 602, Page(s) 32–47

Abstract: Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of ... ...

Abstract	Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein.
MeSH term(s)	Computer Simulation ; Crystallization/methods ; Crystallization/trends ; Models, Molecular ; Protein Conformation ; Proteins/chemical synthesis ; Proteins/ultrastructure ; X-Ray Diffraction/methods ; X-Ray Diffraction/trends
Chemical Substances	Proteins
Language	English
Publishing date	2016-07-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	523-x
ISSN	1096-0384 ; 0003-9861
ISSN (online)	1096-0384
ISSN	0003-9861
DOI	10.1016/j.abb.2016.03.036
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Article: Protein Crystallization in an Actuated Microfluidic Nanowell Device.

Abdallah, Bahige G / Roy-Chowdhury, Shatabdi / Fromme, Raimund / Fromme, Petra / Ros, Alexandra

Crystal growth & design

2016 Volume 16, Issue 4, Page(s) 2074–2082

Abstract: Protein crystallization is a major bottleneck of structure determination by X-ray crystallography, hampering the process by years in some cases. Numerous matrix screening trials using significant amounts of protein are often applied, while a systematic ... ...

Abstract	Protein crystallization is a major bottleneck of structure determination by X-ray crystallography, hampering the process by years in some cases. Numerous matrix screening trials using significant amounts of protein are often applied, while a systematic approach with phase diagram determination is prohibited for many proteins that can only be expressed in small amounts. Here, we demonstrate a microfluidic nanowell device implementing protein crystallization and phase diagram screening using nanoscale volumes of protein solution per trial. The device is made with cost-effective materials and is completely automated for efficient and economical experimentation. In the developed device, 170 trials can be realized with unique concentrations of protein and precipitant established by gradient generation and isolated by elastomeric valving for crystallization incubation. Moreover, this device can be further downscaled to smaller nanowell volumes and larger scale integration. The device was calibrated using a fluorescent dye and compared to a numerical model where concentrations of each trial can be quantified to establish crystallization phase diagrams. Using this device, we successfully crystallized lysozyme and C-phycocyanin, as visualized by compatible crystal imaging techniques such as bright-field microscopy, UV fluorescence, and second-order nonlinear imaging of chiral crystals. Concentrations yielding observed crystal formation were quantified and used to determine regions of the crystallization phase space for both proteins. Low sample consumption and compatibility with a variety of proteins and imaging techniques make this device a powerful tool for systematic crystallization studies.
Language	English
Publishing date	2016-02-25
Publishing country	United States
Document type	Journal Article
ISSN	1528-7483
ISSN	1528-7483
DOI	10.1021/acs.cgd.5b01748
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Article: High Throughput Protein Nanocrystal Fractionation in a Microfluidic Sorter

Abdallah, Bahige G / Coe Jesse / Fromme Petra / Ros Alexandra / Roy-Chowdhury Shatabdi

Analytical chemistry. 2015 Apr. 21, v. 87, no. 8

2015

Abstract: Protein crystallography is transitioning into a new generation with the introduction of the X-ray free electron laser, which can be used to solve the structures of complex proteins via serial femtosecond crystallography. Sample characteristics play a ... ...

Abstract	Protein crystallography is transitioning into a new generation with the introduction of the X-ray free electron laser, which can be used to solve the structures of complex proteins via serial femtosecond crystallography. Sample characteristics play a critical role in successful implementation of this new technology, whereby a small, narrow protein crystal size distribution is desired to provide high quality diffraction data. To provide such a sample, we developed a microfluidic device that facilitates dielectrophoretic sorting of heterogeneous particle mixtures into various size fractions. The first generation device demonstrated great potential and success toward this endeavor; thus, in this work, we present a comprehensive optimization study to improve throughput and control over sorting outcomes. First, device geometry was designed considering a variety of criteria, and applied potentials were modeled to determine the scheme achieving the largest sorting efficiency for isolating nanoparticles from microparticles. Further, to investigate sorting efficiency within the nanoparticle regime, critical geometrical dimensions and input parameters were optimized to achieve high sorting efficiencies. Experiments revealed fractionation of nanobeads from microbeads in the optimized device with high sorting efficiencies, and protein crystals were sorted into submicrometer size fractions as desired for future serial femtosecond crystallography experiments.
Keywords	crystal proteins ; crystallography ; dielectrophoresis ; fractionation ; geometry ; nanocrystals ; nanoparticles ; X-radiation
Language	English
Dates of publication	2015-0421
Size	p. 4159-4167.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021%2Facs.analchem.5b00589
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Article ; Online: High throughput protein nanocrystal fractionation in a microfluidic sorter.

Abdallah, Bahige G / Roy-Chowdhury, Shatabdi / Coe, Jesse / Fromme, Petra / Ros, Alexandra

Analytical chemistry

2015 Volume 87, Issue 8, Page(s) 4159–4167

Abstract	Protein crystallography is transitioning into a new generation with the introduction of the X-ray free electron laser, which can be used to solve the structures of complex proteins via serial femtosecond crystallography. Sample characteristics play a critical role in successful implementation of this new technology, whereby a small, narrow protein crystal size distribution is desired to provide high quality diffraction data. To provide such a sample, we developed a microfluidic device that facilitates dielectrophoretic sorting of heterogeneous particle mixtures into various size fractions. The first generation device demonstrated great potential and success toward this endeavor; thus, in this work, we present a comprehensive optimization study to improve throughput and control over sorting outcomes. First, device geometry was designed considering a variety of criteria, and applied potentials were modeled to determine the scheme achieving the largest sorting efficiency for isolating nanoparticles from microparticles. Further, to investigate sorting efficiency within the nanoparticle regime, critical geometrical dimensions and input parameters were optimized to achieve high sorting efficiencies. Experiments revealed fractionation of nanobeads from microbeads in the optimized device with high sorting efficiencies, and protein crystals were sorted into submicrometer size fractions as desired for future serial femtosecond crystallography experiments.
MeSH term(s)	Crystallography ; High-Throughput Screening Assays ; Microfluidic Analytical Techniques ; Photosystem I Protein Complex/chemistry ; Photosystem I Protein Complex/metabolism
Chemical Substances	Photosystem I Protein Complex
Language	English
Publishing date	2015-04-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.5b00589
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Article ; Online: Microcrystallization techniques for serial femtosecond crystallography using photosystem II from Thermosynechococcus elongatus as a model system.

Kupitz, Christopher / Grotjohann, Ingo / Conrad, Chelsie E / Roy-Chowdhury, Shatabdi / Fromme, Raimund / Fromme, Petra

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2014 Volume 369, Issue 1647, Page(s) 20130316

Abstract: Serial femtosecond crystallography (SFX) is a new emerging method, where X-ray diffraction data are collected from a fully hydrated stream of nano- or microcrystals of biomolecules in their mother liquor using high-energy, X-ray free-electron lasers. The ...

Abstract	Serial femtosecond crystallography (SFX) is a new emerging method, where X-ray diffraction data are collected from a fully hydrated stream of nano- or microcrystals of biomolecules in their mother liquor using high-energy, X-ray free-electron lasers. The success of SFX experiments strongly depends on the ability to grow large amounts of well-ordered nano/microcrystals of homogeneous size distribution. While methods to grow large single crystals have been extensively explored in the past, method developments to grow nano/microcrystals in sufficient amounts for SFX experiments are still in their infancy. Here, we describe and compare three methods (batch, free interface diffusion (FID) and FID centrifugation) for growth of nano/microcrystals for time-resolved SFX experiments using the large membrane protein complex photosystem II as a model system.
MeSH term(s)	Crystallization/methods ; Crystallography, X-Ray/methods ; Cyanobacteria ; Electrons ; Lasers ; Nanoparticles/chemistry ; Photosystem II Protein Complex/chemistry ; Protein Conformation ; X-Ray Diffraction/methods
Chemical Substances	Photosystem II Protein Complex
Language	English
Publishing date	2014-06-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2013.0316
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