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CRYSTALLOGRAPHY (23 journals)

Showing 1 - 20 of 20 Journals sorted alphabetically
Acta Crystallographica Section A: Foundations and Advances     Hybrid Journal   (Followers: 8)
Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials     Hybrid Journal   (Followers: 6)
Acta Crystallographica Section C: Structural Chemistry     Hybrid Journal   (Followers: 4)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 7)
Acta Crystallographica Section E : Crystallographic Communications     Open Access   (Followers: 3)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 8)
Crystal Growth & Design     Hybrid Journal   (Followers: 13)
Crystal Research and Technology     Hybrid Journal   (Followers: 6)
Crystallography Reports     Hybrid Journal   (Followers: 2)
Crystallography Reviews     Hybrid Journal   (Followers: 3)
IUCrJ     Open Access  
Journal of Applied Crystallography     Hybrid Journal   (Followers: 7)
Journal of Chemical Crystallography     Hybrid Journal   (Followers: 2)
Journal of Crystal Growth     Hybrid Journal   (Followers: 6)
Liquid Crystals     Hybrid Journal   (Followers: 1)
Liquid Crystals Today     Hybrid Journal   (Followers: 1)
Materials and Devices     Open Access  
Molecular Crystals and Liquid Crystals     Hybrid Journal   (Followers: 1)
Polymer crystallization     Hybrid Journal  
Progress in Crystal Growth and Characterization of Materials     Full-text available via subscription   (Followers: 8)
Similar Journals
Journal Cover
Acta Crystallographica Section D : Biological Crystallography
Number of Followers: 7  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1399-0047 - ISSN (Online) 2059-7983
Published by IUCr Homepage  [10 journals]
  • Implications of AlphaFold2 for crystallographic phasing by molecular
           replacement

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      Authors: McCoy; A.J., Sammito, M.D., Read, R.J.
      Pages: 1 - 13
      Abstract: The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether or not the protein is related to known structures through high-coverage sequence similarity. As highly accurate models become available, generated by harnessing the power of correlated mutations and deep learning, one of the aspects of structural biology to be impacted will be methods of phasing in crystallography. Here, the data from CASP14 are used to explore the prospects for changes in phasing methods, and in particular to explore the prospects for molecular-replacement phasing using in silico models.
      Keywords: protein structure prediction; crystallographic phase problem; molecular replacement; AlphaFold2
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321012122
      Issue No: Vol. 78, No. 1 (2022)
       
  • Best practices for time-resolved serial synchrotron crystallography

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      Authors: Schulz; E.C., Yorke, B.A., Pearson, A.R., Mehrabi, P.
      Pages: 14 - 29
      Abstract: With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resolved structural study are outlined, with a particular focus on synchrotron-based experiments.
      Keywords: time-resolved crystallography; serial crystallography; SSX; structural enzymology; mechanistic structural biology
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321011621
      Issue No: Vol. 78, No. 1 (2022)
       
  • X-ray diffraction and in vivo studies reveal the quinary structure of
           Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical
           oligomer structure

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      Authors: Gomez Barroso; J.A., Miranda, M.R., Pereira, C.A., Garratt, R.C., Aguilar, C.F.
      Pages: 30 - 42
      Abstract: Trypanosoma cruzi is a flagellated protozoan parasite that causes Chagas disease, which represents a serious health problem in the Americas. Nucleoside diphosphate kinases (NDPKs) are key enzymes that are implicated in cellular energy management. TcNDPK1 is the canonical isoform in the T. cruzi parasite. TcNDPK1 has a cytosolic, perinuclear and nuclear distribution. It is also found in non-membrane-bound filaments adjacent to the nucleus. In the present work, X-ray diffraction and in vivo studies of TcNDPK1 are described. The structure reveals a novel, multi-hexameric, left-handed helical oligomer structure. The results of directed mutagenesis studies led to the conclusion that the microscopic TcNDPK1 granules observed in vivo in T. cruzi parasites are made up by the association of TcNDPK1 oligomers. In the absence of experimental data, analysis of the interactions in the X-ray structure of the TcNDPK1 oligomer suggests the probable assembly and disassembly steps: dimerization, assembly of the hexamer as a trimer of dimers, hexamer association to generate the left-handed helical oligomer structure and finally oligomer association in a parallel manner to form the microscopic TcNDPK1 filaments that are observed in vivo in T. cruzi parasites. Oligomer disassembly takes place on the binding of substrate in the active site of TcNDPK1, leading to dissociation of the hexamers. This study constitutes the first report of such a protein arrangement, which has never previously been seen for any protein or NDPK. Further studies are needed to determine its physiological role. However, it may suggest a paradigm for protein storage reflecting the complex mechanism of action of TcNDPK1.
      Keywords: quinary multi-hexameric X-ray structure; Trypanosoma cruzi; nucleoside diphosphate kinases; in vivo protein granules
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321011219
      Issue No: Vol. 78, No. 1 (2022)
       
  • A radical approach to radicals

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      Authors: Liu; Y., Biczysko, M., Moriarty, N.W.
      Pages: 43 - 51
      Abstract: Nitroxide radicals are characterized by a long-lived spin-unpaired electronic ground state and are strongly sensitive to their chemical surroundings. Combined with electron paramagnetic resonance spectroscopy, these electronic features have led to the widespread application of nitroxide derivatives as spin labels for use in studying protein structure and dynamics. Site-directed spin labelling requires the incorporation of nitroxides into the protein structure, leading to a new protein–ligand molecular model. However, in protein crystallographic refinement nitroxides are highly unusual molecules with an atypical chemical composition. Because macromolecular crystallography is almost entirely agnostic to chemical radicals, their structural information is generally less accurate or even erroneous. In this work, proteins that contain an example of a radical compound (Chemical Component Dictionary ID MTN) from the nitroxide family were re-refined by defining its ideal structural parameters based on quantum-chemical calculations. The refinement results show that this procedure improves the MTN ligand geometries, while at the same time retaining higher agreement with experimental data.
      Keywords: ligand restraints; macromolecular refinement; quantum chemistry; spin labelling; nitroxides; chemical radicals
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321010809
      Issue No: Vol. 78, No. 1 (2022)
       
  • Two states of a light-sensitive membrane protein captured at room
           temperature using thin-film sample mounts

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      Authors: Axford; D., Judge, P.J., Bada Juarez, J.F., Kwan, T.O.C., Birch, J., Vinals, J., Watts, A., Moraes, I.
      Pages: 52 - 58
      Abstract: Room-temperature diffraction methods are highly desirable for dynamic studies of biological macromolecules, since they allow high-resolution structural data to be collected as proteins undergo conformational changes. For crystals grown in lipidic cubic phase (LCP), an extruder is commonly used to pass a stream of microcrystals through the X-ray beam; however, the sample quantities required for this method may be difficult to produce for many membrane proteins. A more sample-efficient environment was created using two layers of low X-ray transmittance polymer films to mount crystals of the archaerhodopsin-3 (AR3) photoreceptor and room-temperature diffraction data were acquired. By using transparent and opaque polymer films, two structures, one corresponding to the desensitized, dark-adapted (DA) state and the other to the ground or light-adapted (LA) state, were solved to better than 1.9 Å resolution. All of the key structural features of AR3 were resolved, including the retinal chromophore, which is present as the 13-cis isomer in the DA state and as the all-trans isomer in the LA state. The film-sandwich sample environment enables diffraction data to be recorded at room temperature in both illuminated and dark conditions, which more closely approximate those in vivo. This simple approach is applicable to a wide range of membrane proteins crystallized in LCP and light-sensitive samples in general at synchrotron and laboratory X-ray sources.
      Keywords: membrane proteins; microbial rhodopsin; archaerhodopsin; retinal; LCP; room temperature; synchrotron; proton transport; thin-film sample; photoreceptors; polymer films; lipidic cubic phase
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321011220
      Issue No: Vol. 78, No. 1 (2022)
       
  • Molecular basis of transcriptional repression of anti-CRISPR by
           anti-CRISPR-associated 2

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      Authors: Lee; S.Y., Kim, G.E., Park, H.H.
      Pages: 59 - 68
      Abstract: CRISPR–Cas systems are well known host defense mechanisms that are conserved in bacteria and archaea. To counteract CRISPR–Cas systems, phages and viruses have evolved to possess multiple anti-CRISPR (Acr) proteins that can inhibit the host CRISPR–Cas system via different strategies. The expression of acr genes is controlled by anti-CRISPR-associated (Aca) proteins that bind to an upstream promoter and regulate the expression of acr genes during transcription. Although the role of Aca as a transcriptional repressor has been demonstrated, the mechanism of action of Aca has not been determined. Here, the molecular mechanism underlying the Aca2-mediated transcriptional control of acr genes was elucidated by determining the crystal structure of Aca2 from Oceanimonas smirnovii at a high resolution of 1.92 Å. Aca2 forms a dimer in solution, and dimerization of Aca2 is critical for specific promoter binding. The promoter-binding strategy of dimeric Aca2 was also revealed by performing mutagenesis studies. The atomic structure of the Aca family shown in this study provides insights into the fine regulation of host defense and immune-escape mechanisms and also demonstrates the conserved working mechanism of the Aca family.
      Keywords: Aca2; adaptive immunity; anti-CRISPR-associated 2; anti-CRISPR; CRISPR–Cas; Oceanimonas smirnovii; crystal structure
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321011670
      Issue No: Vol. 78, No. 1 (2022)
       
  • B-factor accuracy in protein crystal structures

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      Authors: Carugo O.
      Pages: 69 - 74
      Abstract: The accuracy of B factors in protein crystal structures has been determined by comparing the same atoms in numerous, independent crystal structures of Gallus gallus lysozyme. Both B-factor absolute differences and normal probability plots indicate that the estimated B-factor errors are quite large, close to 9 Å2 in ambient-temperature structures and to 6 Å2 in low-temperature structures, and surprisingly are comparable to values estimated two decades ago. It is well known that B factors are not due to local movements only but reflect several, additional factors from crystal defects, large-scale disorder, diffraction data quality etc. It therefore remains essential to normalize B factors when comparing different crystal structures, although it has clearly been shown that they provide useful information about protein dynamics. Improved, quantitative analyses of raw B factors require novel experimental and computational tools that are able to disaggregate local movements from other features and properties that affect B factors.
      Keywords: accuracy; B factors; normal probability plot; validation; protein crystal structures
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321011736
      Issue No: Vol. 78, No. 1 (2022)
       
  • Identification and characterization of two drug-like fragments that bind
           to the same cryptic binding pocket of Burkholderia pseudomallei DsbA

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      Authors: Petit; G.A., Mohanty, B., McMahon, R.M., Nebl, S., Hilko, D.H., Wilde, K.L., Scanlon, M.J., Martin, J.L., Halili, M.A.
      Pages: 75 - 90
      Abstract: Disulfide-bond-forming proteins (Dsbs) play a crucial role in the pathogenicity of many Gram-negative bacteria. Disulfide-bond-forming protein A (DsbA) catalyzes the formation of the disulfide bonds necessary for the activity and stability of multiple substrate proteins, including many virulence factors. Hence, DsbA is an attractive target for the development of new drugs to combat bacterial infections. Here, two fragments, bromophenoxy propanamide (1) and 4-methoxy-N-phenylbenzenesulfonamide (2), were identified that bind to DsbA from the pathogenic bacterium Burkholderia pseudomallei, the causative agent of melioidosis. The crystal structures of oxidized B. pseudomallei DsbA (termed BpsDsbA) co-crystallized with 1 or 2 show that both fragments bind to a hydrophobic pocket that is formed by a change in the side-chain orientation of Tyr110. This conformational change opens a `cryptic' pocket that is not evident in the apoprotein structure. This binding location was supported by 2D-NMR studies, which identified a chemical shift perturbation of the Tyr110 backbone amide resonance of more than 0.05 p.p.m. upon the addition of 2 mM fragment 1 and of more than 0.04 p.p.m. upon the addition of 1 mM fragment 2. Although binding was detected by both X-ray crystallography and NMR, the binding affinity (Kd) for both fragments was low (above 2 mM), suggesting weak interactions with BpsDsbA. This conclusion is also supported by the crystal structure models, which ascribe partial occupancy to the ligands in the cryptic binding pocket. Small fragments such as 1 and 2 are not expected to have a high energetic binding affinity due to their relatively small surface area and the few functional groups that are available for intermolecular interactions. However, their simplicity makes them ideal for functionalization and optimization. The identification of the binding sites of 1 and 2 to BpsDsbA could provide a starting point for the development of more potent novel antimicrobial compounds that target DsbA and bacterial virulence.
      Keywords: DsbA; fragments; cryptic pocket; Burkholderia pseudomallei; NMR; X-ray crystallography
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321011475
      Issue No: Vol. 78, No. 1 (2022)
       
  • Catalytically active holo Homo sapiens adenosine deaminase I adopts a
           closed conformation

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      Authors: Ma; M.T., Jennings, M.R., Blazeck, J., Lieberman, R.L.
      Pages: 91 - 103
      Abstract: Homo sapiens adenosine deaminase 1 (HsADA1; UniProt P00813) is an immunologically relevant enzyme with roles in T-cell activation and modulation of adenosine metabolism and signaling. Patients with genetic deficiency in HsADA1 suffer from severe combined immunodeficiency, and HsADA1 is a therapeutic target in hairy cell leukemias. Historically, insights into the catalytic mechanism and the structural attributes of HsADA1 have been derived from studies of its homologs from Bos taurus (BtADA) and Mus musculus (MmADA). Here, the structure of holo HsADA1 is presented, as well as biochemical characterization that confirms its high activity and shows that it is active across a broad pH range. Structurally, holo HsADA1 adopts a closed conformation distinct from the open conformation of holo BtADA. Comparison of holo HsADA1 and MmADA reveals that MmADA also adopts a closed conformation. These findings challenge previous assumptions gleaned from BtADA regarding the conformation of HsADA1 that may be relevant to its immunological interactions, particularly its ability to bind adenosine receptors. From a broader perspective, the structural analysis of HsADA1 presents a cautionary tale for reliance on homologs to make structural inferences relevant to applications such as protein engineering or drug development.
      Keywords: adenosine deaminase 1; closed conformation; homologs; structural inference
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321011785
      Issue No: Vol. 78, No. 1 (2022)
       
  • Structure of the plant growth-promoting factor YxaL from the
           rhizobacterium Bacillus velezensis and its application to protein
           engineering

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      Authors: Kim; J., Pham, H., Baek, Y., Jo, I., Kim, Y.-H., Ha, N.-C.
      Pages: 104 - 112
      Abstract: The YxaL protein was isolated from the soil bacterium Bacillus velezensis and has been shown to promote the root growth of symbiotic plants. YxaL has further been suggested to act as an exogenous signaling protein to induce the growth and branching of plant roots. Amino acid sequence analysis predicted YxaL to exhibit an eight-bladed β-propeller fold stabilized by six tryptophan-docking motifs and two modified motifs. Protein engineering to improve its structural stability is needed to increase the utility of YxaL as a plant growth-promoting factor. Here, the crystal structure of YxaL from B. velezensis was determined at 1.8 Å resolution to explore its structural features for structure-based protein engineering. The structure showed the typical eight-bladed β-propeller fold with structural variations in the third and fourth blades, which may decrease the stability of the β-propeller fold. Engineered proteins targeting the modified motifs were subsequently created. Crystal structures of the engineered YxaL proteins showed that the typical tryptophan-docking interaction was restored in the third and fourth blades, with increased structural stability, resulting in improved root growth-promoting activity in Arabidopsis seeds. The work is an example of structure-based protein engineering to improve the structural stability of β-propellor fold proteins.
      Keywords: plant growth-promoting factors; YxaL; β-propellers; structure-based protein engineering; Bacillus velezensis
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321011724
      Issue No: Vol. 78, No. 1 (2022)
       
  • CryoEM analysis of small plant biocatalysts at sub-2 Å
           resolution

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      Authors: Dimos; N., Helmer, C.P.O., Chánique, A.M., Wahl, M.C., Kourist, R., Hilal, T., Loll, B.
      Pages: 113 - 123
      Abstract: Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse pools of biosynthetic enzymes that facilitate complex reactions, such as the formation of intricate terpene carbon skeletons, with exquisite specificity. High-resolution structural analysis of these enzymes is crucial in order to understand their mechanisms and modulate their properties by targeted engineering. Although cryo-electron microscopy (cryoEM) has revolutionized structural biology, its applicability to high-resolution structural analysis of comparatively small enzymes has so far been largely unexplored. Here, it is shown that cryoEM can reveal the structures of plant borneol dehydrogenases of ∼120 kDa at or below 2 Å resolution, paving the way for the rapid development of new biocatalysts that can provide access to bioactive terpenes and terpenoids.
      Keywords: cryo-electron microscopy; camphor; terpenes; borneol dehydrogenases; high resolution; green chemistry; plant biocatalysts
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S205979832101216X
      Issue No: Vol. 78, No. 1 (2022)
       
  • A case for glycerol as an acceptable additive for single-particle cryoEM
           samples

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      Authors: Basanta; B., Hirschi, M.M., Grotjahn, D.A., Lander, G.C.
      Pages: 124 - 135
      Abstract: Buffer-composition and sample-preparation guidelines for cryo-electron microscopy are geared towards maximizing imaging contrast and reducing electron-beam-induced motion. These pursuits often involve the minimization or the complete removal of additives that are commonly used to facilitate proper protein folding and minimize aggregation. Among these admonished additives is glycerol, a widely used osmolyte that aids protein stability. In this work, it is shown that the inclusion of glycerol does not preclude high-resolution structure determination by cryoEM, as demonstrated by an ∼2.3 Å resolution reconstruction of mouse apoferritin (∼500 kDa) and an ∼3.3 Å resolution reconstruction of rabbit muscle aldolase (∼160 kDa) in the presence of 20%(v/v) glycerol. While it was found that generating thin ice that is amenable to high-resolution imaging requires long blot times, the addition of glycerol did not result in increased beam-induced motion or an inability to pick particles. Overall, these findings indicate that glycerol should not be discounted as a cryoEM sample-buffer additive, particularly for large, fragile complexes that are prone to disassembly or aggregation upon its removal.
      Keywords: cryoEM; glycerol; sample buffer; apoferritin; aldolase
      Citation: urn:issn:2059-7983
      PubDate: 2022-01-01
      DOI: 10.1107/S2059798321012110
      Issue No: Vol. 78, No. 1 (2022)
       
 
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