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Article ; Online: Structural biology in the age of X-ray free-electron lasers and exascale computing.

Mous, Sandra / Poitevin, Frédéric / Hunter, Mark S / Asthagiri, Dilipkumar N / Beck, Thomas L

2024 Volume 86, Page(s) 102808

Abstract: Serial femtosecond X-ray crystallography has emerged as a powerful method for investigating biomolecular structure and dynamics. With the new generation of X-ray free-electron lasers, which generate ultrabright X-ray pulses at megahertz repetition rates, ...

Abstract	Serial femtosecond X-ray crystallography has emerged as a powerful method for investigating biomolecular structure and dynamics. With the new generation of X-ray free-electron lasers, which generate ultrabright X-ray pulses at megahertz repetition rates, we can now rapidly probe ultrafast conformational changes and charge movement in biomolecules. Over the last year, another innovation has been the deployment of Frontier, the world's first exascale supercomputer. Synergizing extremely high repetition rate X-ray light sources and exascale computing has the potential to accelerate discovery in biomolecular sciences. Here we outline our perspective on each of these remarkable innovations individually, and the opportunities and challenges in yoking them within an integrated research infrastructure.
Language	English
Publishing date	2024-03-27
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2024.102808
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Article: RNA structures and dynamics with Å resolution revealed by x-ray free electron lasers.

Zielinski, Kara A / Sui, Shuo / Pabit, Suzette A / Rivera, Daniel A / Wang, Tong / Hu, Qingyue / Kashipathy, Maithri M / Lisova, Stella / Schaffer, Chris B / Mariani, Valerio / Hunter, Mark S / Kupitz, Christopher / Moss, Frank R / Poitevin, Frédéric P / Grant, Thomas D / Pollack, Lois

bioRxiv : the preprint server for biology

2023

Abstract: RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We ... ...

Abstract	RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free electron laser sources to reveal the formation and ready identification of Å scale features in structured and unstructured RNAs. New structural signatures of RNA secondary and tertiary structures are identified through wide angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base paired intermediate to assume a triple helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. In addition to understanding how RNA triplexes form and thereby function as dynamic signaling elements, this new method can vastly increase the rate of structure determination for these biologically essential, but mostly uncharacterized macromolecules.
Language	English
Publishing date	2023-05-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.24.541763
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers.

Science advances

2023 Volume 9, Issue 39, Page(s) eadj3509

Abstract	RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free-electron laser sources to reveal the formation and ready identification of angstrom-scale features in structured and unstructured RNAs. Previously unrecognized structural signatures of RNA secondary and tertiary structures are identified through wide-angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base-paired intermediate to assume a triple-helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. This method may help to rapidly characterize and identify structural elements in nucleic acids in both equilibrium and time-resolved experiments.
MeSH term(s)	RNA ; Electrons ; Nucleic Acids ; Lasers
Chemical Substances	RNA (63231-63-0) ; Nucleic Acids
Language	English
Publishing date	2023-09-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adj3509
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Detection of a geminate photoproduct of bovine cytochrome c oxidase by time-resolved serial femtosecond crystallography.

Ishigami, Izumi / Carbajo, Sergio / Zatsepin, Nadia / Hikita, Masahide / Conrad, Chelsie E / Nelson, Garrett / Coe, Jesse / Basu, Shibom / Grant, Thomas / Seaberg, Matthew H / Sierra, Raymond G / Hunter, Mark S / Fromme, Petra / Fromme, Raimund / Rousseau, Denis L / Yeh, Syun-Ru

bioRxiv : the preprint server for biology

2023

Abstract: ... ...

Abstract	Cytochrome
Language	English
Publishing date	2023-05-10
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.08.539888
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Article ; Online: Detection of a Geminate Photoproduct of Bovine Cytochrome

Journal of the American Chemical Society

2023 Volume 145, Issue 41, Page(s) 22305–22309

Abstract: ... ...

Abstract	Cytochrome
MeSH term(s)	Cattle ; Animals ; Electron Transport Complex IV/chemistry ; Oxidation-Reduction ; Copper/chemistry ; Ligands ; Oxygen/chemistry ; Crystallography, X-Ray ; Iron/chemistry ; Water/metabolism
Chemical Substances	Electron Transport Complex IV (EC 1.9.3.1) ; Copper (789U1901C5) ; Ligands ; Oxygen (S88TT14065) ; Iron (E1UOL152H7) ; Water (059QF0KO0R)
Language	English
Publishing date	2023-09-11
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c07803
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Article ; Online: Toward structure determination using membrane-protein nanocrystals and microcrystals.

Hunter, Mark S / Fromme, Petra

Methods (San Diego, Calif.)

2011 Volume 55, Issue 4, Page(s) 387–404

Abstract: Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been ... ...

Abstract	Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only 100 unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet brought fully-hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses (∼70fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. During the initial experiments at the AMO beamline using 6.9-Å wavelength, Bragg peaks were recorded to 8.5-Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage [94]. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.
MeSH term(s)	Algorithms ; Crystallization ; Crystallography, X-Ray/instrumentation ; Crystallography, X-Ray/methods ; Humans ; Membrane Proteins/chemistry ; Membrane Proteins/radiation effects ; Models, Molecular ; Nanoparticles ; Photosystem I Protein Complex/chemistry ; Photosystem I Protein Complex/isolation & purification ; Powder Diffraction ; Protein Conformation ; X-Ray Diffraction
Chemical Substances	Membrane Proteins ; Photosystem I Protein Complex
Language	English
Publishing date	2011-12-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2011.12.006
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Article: Toward structure determination using membrane–protein nanocrystals and microcrystals

Hunter, Mark S / Fromme, Petra

Methods. 2011 Dec., v. 55, no. 4

2011

Abstract	Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only 100unit cells with sizes of less than 200nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet brought fully-hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses (∼70fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. During the initial experiments at the AMO beamline using 6.9-Å wavelength, Bragg peaks were recorded to 8.5-Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage [94]. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.
Keywords	X-radiation ; X-ray diffraction ; crystallites ; membrane proteins ; nanocrystals ; photosystem I ; signal transduction ; wavelengths
Language	English
Dates of publication	2011-12
Size	p. 387-404.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2011.12.006
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography.

Smith, Nathan / Dasgupta, Medhanjali / Wych, David C / Dolamore, Cole / Sierra, Raymond G / Lisova, Stella / Marchany-Rivera, Darya / Cohen, Aina E / Boutet, Sébastien / Hunter, Mark S / Kupitz, Christopher / Poitevin, Frédéric / Moss, Frank R / Mittan-Moreau, David W / Brewster, Aaron S / Sauter, Nicholas K / Young, Iris D / Wolff, Alexander M / Tiwari, Virendra K /

Kumar, Nivesh / Berkowitz, David B / Hadt, Ryan G / Thompson, Michael C / Follmer, Alec H / Wall, Michael E / Wilson, Mark A

Science advances

2024 Volume 10, Issue 13, Page(s) eadk7201

Abstract: Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant ... ...

Abstract	Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp
MeSH term(s)	Crystallography, X-Ray ; Proteins/chemistry ; Catalysis ; Molecular Dynamics Simulation ; Protein Conformation ; Hydrolases
Chemical Substances	Proteins ; Hydrolases (EC 3.-)
Language	English
Publishing date	2024-03-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adk7201
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Article: Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase.

Lee, Ming-Yue / Geiger, James / Ishchenko, Andrii / Han, Gye Won / Barty, Anton / White, Thomas A / Gati, Cornelius / Batyuk, Alexander / Hunter, Mark S / Aquila, Andrew / Boutet, Sébastien / Weierstall, Uwe / Cherezov, Vadim / Liu, Wei

IUCrJ

2020 Volume 7, Issue Pt 6, Page(s) 976–984

Abstract: Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has ... ...

Abstract	Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A
Language	English
Publishing date	2020-10-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2754953-7
ISSN	2052-2525
ISSN	2052-2525
DOI	10.1107/S2052252520012701
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Article: Intersubunit Coupling Enables Fast CO

DeMirci, Hasan / Rao, Yashas / Stoffel, Gabriele M / Vögeli, Bastian / Schell, Kristina / Gomez, Aharon / Batyuk, Alexander / Gati, Cornelius / Sierra, Raymond G / Hunter, Mark S / Dao, E Han / Ciftci, Halil I / Hayes, Brandon / Poitevin, Fredric / Li, Po-Nan / Kaur, Manat / Tono, Kensuke / Saez, David Adrian / Deutsch, Samuel /

Yoshikuni, Yasuo / Grubmüller, Helmut / Erb, Tobias J / Vöhringer-Martinez, Esteban / Wakatsuki, Soichi

ACS central science

2022 Volume 8, Issue 8, Page(s) 1091–1101

Abstract: Enoyl-CoA carboxylases/reductases (ECRs) are some of the most efficient ... ...

Abstract	Enoyl-CoA carboxylases/reductases (ECRs) are some of the most efficient CO
Language	English
Publishing date	2022-04-25
Publishing country	United States
Document type	Journal Article
ISSN	2374-7943
ISSN	2374-7943
DOI	10.1021/acscentsci.2c00057
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