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Article ; Online: Intermolecular correlations are necessary to explain diffuse scattering from protein crystals

Ariana Peck / Frédéric Poitevin / Thomas J. Lane

IUCrJ, Vol 5, Iss 2, Pp 211-

2018 Volume 222

Abstract: Conformational changes drive protein function, including catalysis, allostery and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our ... ...

Abstract	Conformational changes drive protein function, including catalysis, allostery and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work has challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid-body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid-body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.
Keywords	diffuse scattering ; intermolecular correlations ; Science ; Q
Subject code	612
Language	English
Publishing date	2018-03-01T00:00:00Z
Publisher	International Union of Crystallography
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Inferring the rate-length law of protein folding.

Thomas J Lane / Vijay S Pande

PLoS ONE, Vol 8, Iss 12, p e

2013 Volume 78606

Abstract: We investigate the rate-length scaling law of protein folding, a key undetermined scaling law in the analytical theory of protein folding. Available data yield statistically significant evidence for the existence of a rate-length law capable of ... ...

Abstract	We investigate the rate-length scaling law of protein folding, a key undetermined scaling law in the analytical theory of protein folding. Available data yield statistically significant evidence for the existence of a rate-length law capable of predicting folding times to within about two orders of magnitude (over 9 decades of variation). Unambiguous determination of the functional form of such a law could provide key mechanistic insight into folding. Four proposed laws from literature (power law, exponential, and two stretched exponentials) are tested against one another, and it is found that the power law best explains the data by a modest margin. We conclude that more data is necessary to unequivocally infer the rate-length law. Such data could be obtained through a small number of protein folding experiments on large protein domains.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Liquid-liquid phase separation in supercooled water from ultrafast heating of low-density amorphous ice

Katrin Amann-Winkel / Kyung Hwan Kim / Nicolas Giovambattista / Marjorie Ladd-Parada / Alexander Späh / Fivos Perakis / Harshad Pathak / Cheolhee Yang / Tobias Eklund / Thomas J. Lane / Seonju You / Sangmin Jeong / Jae Hyuk Lee / Intae Eom / Minseok Kim / Jaeku Park / Sae Hwan Chun / Peter H. Poole / Anders Nilsson

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 8

Abstract: Obtaining experimental evidence of a liquid-liquid phase transition in supercooled water is challenging due to the rapid crystallization. Here the authors drive low-density amorphous ice to the conditions of liquid-liquid coexistence using ultrafast ... ...

Abstract	Obtaining experimental evidence of a liquid-liquid phase transition in supercooled water is challenging due to the rapid crystallization. Here the authors drive low-density amorphous ice to the conditions of liquid-liquid coexistence using ultrafast laser heating and observe the liquid-liquid phase transition with femtosecond x-ray laser pulses.
Keywords	Science ; Q
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Observation of site-selective chemical bond changes via ultrafast chemical shifts

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 7

Abstract: X-ray photoelectron spectroscopy probes the chemical environment in a molecule at a specific atomic site. Here the authors extend this concept with a site selective trigger to follow chemical bond changes as they occur on the femtosecond time scale. ...

Abstract	X-ray photoelectron spectroscopy probes the chemical environment in a molecule at a specific atomic site. Here the authors extend this concept with a site selective trigger to follow chemical bond changes as they occur on the femtosecond time scale.
Keywords	Science ; Q
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet

Marie Luise Grünbein / Alexander Gorel / Lutz Foucar / Sergio Carbajo / William Colocho / Sasha Gilevich / Elisabeth Hartmann / Mario Hilpert / Mark Hunter / Marco Kloos / Jason E. Koglin / Thomas J. Lane / Jim Lewandowski / Alberto Lutman / Karol Nass / Gabriela Nass Kovacs / Christopher M. Roome / John Sheppard / Robert L. Shoeman /

Miriam Stricker / Tim van Driel / Sharon Vetter / R. Bruce Doak / Sébastien Boutet / Andrew Aquila / Franz Josef Decker / Thomas R. M. Barends / Claudiu Andrei Stan / Ilme Schlichting

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 11

Abstract: X-ray fee-electron lasers (XFELs) enable time-resolved crystallography experiments and the structure determination of proteins with little or no radiation damage. However currently it is unknown whether the designated 4.5 MHz maximum pulse rate for the ... ...

Abstract	X-ray fee-electron lasers (XFELs) enable time-resolved crystallography experiments and the structure determination of proteins with little or no radiation damage. However currently it is unknown whether the designated 4.5 MHz maximum pulse rate for the European XFEL could lead to sample damage caused by shock waves from preceding pulses. Here, the authors address this question by performing a X-ray pump X-ray probe experiment on haemoglobin microcrystals at the Stanford XFEL facility that mimics the 4.5 MHz data collection mode and observe structural changes and a drop in diffraction data quality of the crystals.
Keywords	Science ; Q
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

Derek Mendez / Herschel Watkins / Shenglan Qiao / Kevin S. Raines / Thomas J. Lane / Gundolf Schenk / Garrett Nelson / Ganesh Subramanian / Kensuke Tono / Yasumasa Joti / Makina Yabashi / Daniel Ratner / Sebastian Doniach

IUCrJ, Vol 3, Iss 6, Pp 420-

2016 Volume 429

Abstract: During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the ... ...

Abstract	During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlined for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. It is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.
Keywords	angular photon correlations ; solution diffraction ; XFELs ; correlated X-ray scattering ; gold nanoparticles ; Science ; Q
Subject code	541
Language	English
Publishing date	2016-11-01T00:00:00Z
Publisher	International Union of Crystallography
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies

IUCrJ, Vol 6, Iss 4, Pp 714-

2019 Volume 728

Abstract: Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data ...

Abstract	Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data collection times owing to higher hit rates. Here, a new method of on-chip crystallization is reported which allows the efficient and reproducible growth of large numbers of protein crystals directly on micro-patterned silicon chips for in-situ serial crystallography experiments. Crystals are grown by sitting-drop vapor diffusion and previously established crystallization conditions can be directly applied. By reducing the number of crystal-handling steps, the method is particularly well suited for sensitive crystal systems. Excessive mother liquor can be efficiently removed from the crystals by blotting, and no sealing of the fixed-target sample holders is required to prevent the crystals from dehydrating. As a consequence, `naked' crystals are obtained on the chip, resulting in very low background scattering levels and making the crystals highly accessible for external manipulation such as the application of ligand solutions. Serial diffraction experiments carried out at cryogenic temperatures at a synchrotron and at room temperature at an X-ray free-electron laser yielded high-quality X-ray structures of the human membrane protein aquaporin 2 and two new ligand-bound structures of thermolysin and the human kinase DRAK2. The results highlight the applicability of the method for future high-throughput on-chip screening of pharmaceutical compounds.
Keywords	serial crystallography ; silicon chip ; fixed-target crystallography ; in-situ diffraction ; vapor diffusion ; ligand binding ; ligand soaking ; drug discovery ; protein structure ; X-ray crystallography ; Science ; Q
Subject code	500
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	International Union of Crystallography
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease

Vasundara Srinivasan / Hévila Brognaro / Prince R. Prabhu / Edmarcia Elisa de Souza / Sebastian Günther / Patrick Y. A. Reinke / Thomas J. Lane / Helen Ginn / Huijong Han / Wiebke Ewert / Janina Sprenger / Faisal H. M. Koua / Sven Falke / Nadine Werner / Hina Andaleeb / Najeeb Ullah / Bruno Alves Franca / Mengying Wang / Angélica Luana C. Barra /

Markus Perbandt / Martin Schwinzer / Christina Schmidt / Lea Brings / Kristina Lorenzen / Robin Schubert / Rafael Rahal Guaragna Machado / Erika Donizette Candido / Danielle Bruna Leal Oliveira / Edison Luiz Durigon / Stephan Niebling / Angelica Struve Garcia / Oleksandr Yefanov / Julia Lieske / Luca Gelisio / Martin Domaracky / Philipp Middendorf / Michael Groessler / Fabian Trost / Marina Galchenkova / Aida Rahmani Mashhour / Sofiane Saouane / Johanna Hakanpää / Markus Wolf / Maria Garcia Alai / Dusan Turk / Arwen R. Pearson / Henry N. Chapman / Winfried Hinrichs / Carsten Wrenger / Alke Meents

Communications Biology, Vol 5, Iss 1, Pp 1-

2022 Volume 12

Abstract: Three natural phenolic compounds are found to bind to an allosteric site in SARS-CoV-2 papain-like protease and exhibit antiviral activity in vitro, showing potential as starting scaffolds for drug design. ...

Abstract	Three natural phenolic compounds are found to bind to an allosteric site in SARS-CoV-2 papain-like protease and exhibit antiviral activity in vitro, showing potential as starting scaffolds for drug design.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser

Nature Communications, Vol 7, Iss 1, Pp 1-

2016 Volume 5

Abstract: X-ray free electron lasers are increasingly available for use in macromolecular structure determination. Here, the authors describe the successful use of selenium single-wavelength anomalous diffraction data to calculate experimentally derived phases. ...

Abstract	X-ray free electron lasers are increasingly available for use in macromolecular structure determination. Here, the authors describe the successful use of selenium single-wavelength anomalous diffraction data to calculate experimentally derived phases.
Keywords	Science ; Q
Language	English
Publishing date	2016-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Coherent X-rays reveal the influence of cage effects on ultrafast water dynamics

Fivos Perakis / Gaia Camisasca / Thomas J. Lane / Alexander Späh / Kjartan Thor Wikfeldt / Jonas A. Sellberg / Felix Lehmkühler / Harshad Pathak / Kyung Hwan Kim / Katrin Amann-Winkel / Simon Schreck / Sanghoon Song / Takahiro Sato / Marcin Sikorski / Andre Eilert / Trevor McQueen / Hirohito Ogasawara / Dennis Nordlund / Wojciech Roseker /

Jake Koralek / Silke Nelson / Philip Hart / Roberto Alonso-Mori / Yiping Feng / Diling Zhu / Aymeric Robert / Gerhard Grübel / Lars G. M. Pettersson / Anders Nilsson

Nature Communications, Vol 9, Iss 1, Pp 1-

2018 Volume 10

Abstract: The dynamics of liquid water is rich due to its complex, highly disordered hydrogen-bond network, which hasn’t been fully understood. Perakis et al. measure water dynamics at sub-100 fs and show that it cannot be described by simple thermal motion due to ...

Abstract	The dynamics of liquid water is rich due to its complex, highly disordered hydrogen-bond network, which hasn’t been fully understood. Perakis et al. measure water dynamics at sub-100 fs and show that it cannot be described by simple thermal motion due to the build-up of tetrahedral structures upon supercooling.
Keywords	Science ; Q
Language	English
Publishing date	2018-05-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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