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  • 1
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    Serial femtosecond crystallography of soluble proteins in lipidic cubic phase (2015)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2015-08-06
    Description: Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is demonstrated that LCP can also be used as a suitable carrier medium for microcrystals of soluble proteins, enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals delivered by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.
    Keywords: serial femtosecond crystallographyX-ray free-electron laserlipidic cubic phasesoluble protein
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 2
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    An exceptional series of phase transitions in hydrophobic amino acids with linear side chains (2016)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2016-08-10
    Description: The solid-state phase transitions and intermediate structures of S-2-aminobutanoic acid (l-2-aminobutyric acid), S-2-aminopentanoic acid (l-norvaline), S-2-aminohexanoic acid (l-norleucine) and l-methionine between 100 and 470 K, identified by differential scanning calorimetry, have been characterized in a comprehensive single-crystal X-ray diffraction investigation. Unlike other enantiomeric amino acids investigated until now, this group featuring linear side chains displays up to five distinct phases. The multiple transitions between them involve a number of different processes: alteration of the hydrogen-bond pattern, to our knowledge the first example of this observed for an amino acid, sliding of molecular bilayers, seen previously only for racemates and quasiracemates, concerted side-chain rearrangements and abrupt as well as gradual modifications of the side-chain disorder. Ordering of l-norleucine upon cooling even proceeds via an incommensurately modulated structure. l-Methionine has previously been described as being fully ordered at room temperature. An accurate refinement now reveals extensive disorder for both molecules in the asymmetric unit, while two previously unknown phases occur above room temperature.
    Keywords: amino acidsdisorderhydrogen bondingmodulated phasesphase transitionsside-chain stackingpolymorphismmolecular crystals
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 3
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    Committee machine that votes for similarity between materials (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-10-30
    Description: A method has been developed to measure the similarity between materials, focusing on specific physical properties. The information obtained can be utilized to understand the underlying mechanisms and support the prediction of the physical properties of materials. The method consists of three steps: variable evaluation based on nonlinear regression, regression-based clustering, and similarity measurement with a committee machine constructed from the clustering results. Three data sets of well characterized crystalline materials represented by critical atomic predicting variables are used as test beds. Herein, the focus is on the formation energy, lattice parameter and Curie temperature of the examined materials. Based on the information obtained on the similarities between the materials, a hierarchical clustering technique is applied to learn the cluster structures of the materials that facilitate interpretation of the mechanism, and an improvement in the regression models is introduced to predict the physical properties of the materials. The experiments show that rational and meaningful group structures can be obtained and that the prediction accuracy of the materials' physical properties can be significantly increased, confirming the rationality of the proposed similarity measure.
    Keywords: data miningmaterials informaticsfirst-principles calculationsphysical properties of materialsmachine learningsimilarity
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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