Publisher: IUCr   (Total: 10 journals)   [Sort alphabetically]

Showing 1 - 10 of 10 Journals sorted by number of followers
Acta Crystallographica Section A: Foundations and Advances     Hybrid Journal   (Followers: 8, SJR: 5.99, CiteScore: 13)
Acta Crystallographica Section C: Structural Chemistry     Hybrid Journal   (Followers: 8, SJR: 0.834, CiteScore: 3)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 8, SJR: 0.592, CiteScore: 1)
J. of Applied Crystallography     Hybrid Journal   (Followers: 7, SJR: 1.635, CiteScore: 3)
Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials     Hybrid Journal   (Followers: 6, SJR: 1.654, CiteScore: 5)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 5)
Acta Crystallographica Section E : Crystallographic Communications     Open Access   (Followers: 3, SJR: 0.153, CiteScore: 0)
J. of Synchrotron Radiation     Open Access   (Followers: 3, SJR: 1.65, CiteScore: 3)
IUCrData     Open Access   (Followers: 1)
IUCrJ     Open Access   (SJR: 3.212, CiteScore: 5)
Similar Journals
Journal Cover
IUCrJ
Journal Prestige (SJR): 3.212
Citation Impact (citeScore): 5
Number of Followers: 0  

  This is an Open Access Journal Open Access journal
ISSN (Online) 2052-2525
Published by IUCr Homepage  [10 journals]
  • In situ serial crystallography facilitates 96-well plate structural
           analysis at low symmetry

    • Authors: Foos; N., Florial, J.-B., Eymery, M., Sinoir, J., Felisaz, F., Oscarsson, M., Beteva, A., Bowler, M.W., Nurizzo, D., Papp, G., Soler-Lopez, M., Nanao, M., Basu, S., McCarthy, A.A.
      Abstract: The advent of serial crystallography has rejuvenated and popularized room-temperature X-ray crystal structure determination. Structures determined at physiological temperature reveal protein flexibility and dynamics. In addition, challenging samples (e.g. large complexes, membrane proteins and viruses) form fragile crystals that are often difficult to harvest for cryo-crystallography. Moreover, a typical serial crystallography experiment requires a large number of microcrystals, mainly achievable through batch crystallization. Many medically relevant samples are expressed in mammalian cell lines, producing a meager quantity of protein that is incompatible with batch crystallization. This can limit the scope of serial crystallography approaches. Direct in situ data collection from a 96-well crystallization plate enables not only the identification of the best diffracting crystallization condition but also the possibility for structure determination under ambient conditions. Here, we describe an in situ serial crystallography (iSX) approach, facilitating direct measurement from crystallization plates mounted on a rapidly exchangeable universal plate holder deployed at a microfocus beamline, ID23-2, at the European Synchrotron Radiation Facility. We applied our iSX approach on a challenging project, autotaxin, a therapeutic target expressed in a stable human cell line, to determine the structure in the lowest-symmetry P1 space group at 3.0 Å resolution. Our in situ data collection strategy provided a complete dataset for structure determination while screening various crystallization conditions. Our data analysis reveals that the iSX approach is highly efficient at a microfocus beamline, improving throughput and demonstrating how crystallization plates can be routinely used as an alternative method of presenting samples for serial crystallography experiments at synchrotrons.
      Keywords: in situ serial crystallography; room-temperature structures; crystallization plates; conformational flexibility; plate holders; triclinic symmetry; macromolecular crystallography; autotaxin
      Citation: urn:issn:2052-2525
      PubDate: 2024-07-15
      DOI: 10.1107/S2052252524005785
      Issue No: Vol. 11, No. 5 (2024)
       
  • Benchmarking predictive methods for small-angle X-ray scattering from
           atomic coordinates of proteins using maximum likelihood consensus data

    • Authors: Trewhella; J., Vachette, P., Larsen, A.H.
      Abstract: Stimulated by informal conversations at the XVII International Small Angle Scattering (SAS) conference (Traverse City, 2017), an international team of experts undertook a round-robin exercise to produce a large dataset from proteins under standard solution conditions. These data were used to generate consensus SAS profiles for xylose isomerase, urate oxidase, xylanase, lysozyme and ribonuclease A. Here, we apply a new protocol using maximum likelihood with a larger number of the contributed datasets to generate improved consensus profiles. We investigate the fits of these profiles to predicted profiles from atomic coordinates that incorporate different models to account for the contribution to the scattering of water molecules of hydration surrounding proteins in solution. Programs using an implicit, shell-type hydration layer generally optimize fits to experimental data with the aid of two parameters that adjust the volume of the bulk solvent excluded by the protein and the contrast of the hydration layer. For these models, we found the error-weighted residual differences between the model and the experiment generally reflected the subsidiary maxima and minima in the consensus profiles that are determined by the size of the protein plus the hydration layer. By comparison, all-atom solute and solvent molecular dynamics (MD) simulations are without the benefit of adjustable parameters and, nonetheless, they yielded at least equally good fits with residual differences that are less reflective of the structure in the consensus profile. Further, where MD simulations accounted for the precise solvent composition of the experiment, specifically the inclusion of ions, the modelled radius of gyration values were significantly closer to the experiment. The power of adjustable parameters to mask real differences between a model and the structure present in solution is demonstrated by the results for the conformationally dynamic ribonuclease A and calculations with pseudo-experimental data. This study shows that, while methods invoking an implicit hydration layer have the unequivocal advantage of speed, care is needed to understand the influence of the adjustable parameters. All-atom solute and solvent MD simulations are slower but are less susceptible to false positives, and can account for thermal fluctuations in atomic positions, and more accurately represent the water molecules of hydration that contribute to the scattering profile.
      Keywords: biomolecular small-angle scattering; SAXS; SAXS profile modelling; hydration layer; waters of hydration; consensus data; benchmarking; molecular dynamics; simulation; maximum likelihood
      Citation: urn:issn:2052-2525
      PubDate: 2024-07-10
      DOI: 10.1107/S205225252400486X
      Issue No: Vol. 11, No. 5 (2024)
       
  • Fixed-target pump–probe SFX: eliminating the scourge of light
           contamination

    • Authors: Gotthard; G., Flores-Ibarra, A., Carrillo, M., Kepa, M.W., Mason, T.J., Stegmann, D.P., Olasz, B., Pachota, M., Dworkowski, F., Ozerov, D., Pedrini, B.F., Padeste, C., Beale, J.H., Nogly, P.
      Abstract: X-ray free-electron laser (XFEL) light sources have enabled the rapid growth of time-resolved structural experiments, which provide crucial information on the function of macromolecules and their mechanisms. Here, the aim was to commission the SwissMX fixed-target sample-delivery system at the SwissFEL Cristallina experimental station using the PSI-developed micro-structured polymer (MISP) chip for pump–probe time-resolved experiments. To characterize the system, crystals of the light-sensitive protein light–oxygen–voltage domain 1 (LOV1) from Chlamydomonas reinhardtii were used. Using different experimental settings, the accidental illumination, referred to as light contamination, of crystals mounted in wells adjacent to those illuminated by the pump laser was examined. It was crucial to control the light scattering from and through the solid supports otherwise significant contamination occurred. However, the results here show that the opaque MISP chips are suitable for defined pump–probe studies of a light-sensitive protein. The experiment also probed the sub-millisecond structural dynamics of LOV1 and indicated that at Δt = 10 µs a covalent thioether bond is established between reactive Cys57 and its flavin mononucleotide cofactor. This experiment validates the crystals to be suitable for in-depth follow-up studies of this still poorly understood signal-transduction mechanism. Importantly, the fixed-target delivery system also permitted a tenfold reduction in protein sample consumption compared with the more common high-viscosity extrusion-based delivery system. This development creates the prospect of an increase in XFEL project throughput for the field.
      Keywords: time-resolved crystallography; fixed targets; X-ray free-electron lasers; room-temperature crystallography; pump–probe; photoreceptor light–oxygen–voltage domains; serial femtosecond crystallography; light contamination; sample consumpti
      Citation: urn:issn:2052-2525
      PubDate: 2024-07-09
      DOI: 10.1107/S2052252524005591
      Issue No: Vol. 11, No. 5 (2024)
       
  • Many locks to one key: N-acetylneuraminic acid binding to proteins

    • Authors: Dhanabalan; K., Cheng, Y., Thach, T., Subramanian, R.
      Abstract: Sialic acids play crucial roles in cell surface glycans of both eukaryotic and prokaryotic organisms, mediating various biological processes, including cell–cell interactions, development, immune response, oncogenesis and host–pathogen interactions. This review focuses on the β-anomeric form of N-acetylneuraminic acid (Neu5Ac), particularly its binding affinity towards various proteins, as elucidated by solved protein structures. Specifically, we delve into the binding mechanisms of Neu5Ac to proteins involved in sequestering and transporting Neu5Ac in Gram-negative bacteria, with implications for drug design targeting these proteins as antimicrobial agents. Unlike the initial assumptions, structural analyses revealed significant variability in the Neu5Ac binding pockets among proteins, indicating diverse evolutionary origins and binding modes. By comparing these findings with existing structures from other systems, we can effectively highlight the intricate relationship between protein structure and Neu5Ac recognition, emphasizing the need for tailored drug design strategies to inhibit Neu5Ac-binding proteins across bacterial species.
      Keywords: sialic acids; N-acetyl neuraminic acid; Neu5Ac; Gram-negative bacteria; binding sites; drug discovery; protein structures; molecular recognition
      Citation: urn:issn:2052-2525
      PubDate: 2024-07-04
      DOI: 10.1107/S2052252524005360
      Issue No: Vol. 11, No. 5 (2024)
       
  • Structure of Aquifex aeolicus lumazine synthase by cryo-electron
           microscopy to 1.42 Å resolution

    • Authors: Savva; C.G., Sobhy, M.A., De Biasio, A., Hamdan, S.M.
      Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become an essential structural determination technique with recent hardware developments making it possible to reach atomic resolution, at which individual atoms, including hydrogen atoms, can be resolved. In this study, we used the enzyme involved in the penultimate step of riboflavin biosynthesis as a test specimen to benchmark a recently installed microscope and determine if other protein complexes could reach a resolution of 1.5 Å or better, which so far has only been achieved for the iron carrier ferritin. Using state-of-the-art microscope and detector hardware as well as the latest software techniques to overcome microscope and sample limitations, a 1.42 Å map of Aquifex aeolicus lumazine synthase (AaLS) was obtained from a 48 h microscope session. In addition to water molecules and ligands involved in the function of AaLS, we can observe positive density for ∼50% of the hydrogen atoms. A small improvement in the resolution was achieved by Ewald sphere correction which was expected to limit the resolution to ∼1.5 Å for a molecule of this diameter. Our study confirms that other protein complexes can be solved to near-atomic resolution. Future improvements in specimen preparation and protein complex stabilization may allow more flexible macromolecules to reach this level of resolution and should become a priority of study in the field.
      Keywords: cryo-EM; atomic resolution; Aquifex aeolicus; lumazine synthase; single-particle analysis
      Citation: urn:issn:2052-2525
      PubDate: 2024-07-04
      DOI: 10.1107/S2052252524005530
      Issue No: Vol. 11, No. 5 (2024)
       
 
JournalTOCs
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Email: journaltocs@hw.ac.uk
Tel: +00 44 (0)131 4513762
 


Your IP address: 3.235.182.206
 
Home (Search)
API
About JournalTOCs
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-
JournalTOCs
 
 

Publisher: IUCr   (Total: 10 journals)   [Sort alphabetically]

Showing 1 - 10 of 10 Journals sorted by number of followers
Acta Crystallographica Section A: Foundations and Advances     Hybrid Journal   (Followers: 8, SJR: 5.99, CiteScore: 13)
Acta Crystallographica Section C: Structural Chemistry     Hybrid Journal   (Followers: 8, SJR: 0.834, CiteScore: 3)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 8, SJR: 0.592, CiteScore: 1)
J. of Applied Crystallography     Hybrid Journal   (Followers: 7, SJR: 1.635, CiteScore: 3)
Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials     Hybrid Journal   (Followers: 6, SJR: 1.654, CiteScore: 5)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 5)
Acta Crystallographica Section E : Crystallographic Communications     Open Access   (Followers: 3, SJR: 0.153, CiteScore: 0)
J. of Synchrotron Radiation     Open Access   (Followers: 3, SJR: 1.65, CiteScore: 3)
IUCrData     Open Access   (Followers: 1)
IUCrJ     Open Access   (SJR: 3.212, CiteScore: 5)
Similar Journals
Similar Journals
A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z  All
HOME > Browse the 3359 Publishers covered by JournalTOCs 4 5 6 7 8 9 10 11  
PublisherTotal Journals
4 5 6 7 8 9 10 11  
 
JournalTOCs
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Email: journaltocs@hw.ac.uk
Tel: +00 44 (0)131 4513762
 


Your IP address: 3.235.182.206
 
Home (Search)
API
About JournalTOCs
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-