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JOURNAL ARTICLE
Francois J F Jacobs, John R Helliwell, Alice Brink
Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein...
May 1, 2024: IUCrJ
#2
JOURNAL ARTICLE
B Dittrich, L E Connor, F P A Fabbiani, P Piechon
Categorization underlies understanding. Conceptualizing solid-state structures of organic molecules with `archetype crystal structures' bridges established categories of disorder, polymorphism and solid solutions and is herein extended to special position and high-Z' structures. The concept was developed in the context of disorder modelling [Dittrich, B. (2021). IUCrJ, 8, 305-318] and relies on adding quantum chemical energy differences between disorder components to other criteria as an explanation as to why disorder - and disappearing disorder - occurs in an average structure...
May 1, 2024: IUCrJ
#3
JOURNAL ARTICLE
Ruwini S K Ekanayake, Victor A Streltsov, Stephen P Best, Christopher T Chantler
An X-ray absorption spectroscopy (XAS) electrochemical cell was used to collect high-quality XAS measurements of N-truncated Cu:amyloid-β (Cu:Aβ) samples under near-physiological conditions. N-truncated Cu:Aβ peptide complexes contribute to oxidative stress and neurotoxicity in Alzheimer's patients' brains. However, the redox properties of copper in different Aβ peptide sequences are inconsistent. Therefore, the geometry of binding sites for the copper binding in Aβ4-8/12/16 was determined using novel advanced extended X-ray absorption fine structure (EXAFS) analysis...
May 1, 2024: IUCrJ
#4
JOURNAL ARTICLE
Stephen K Burley, Dennis W Piehl, Brinda Vallat, Christine Zardecki
The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules (e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic...
May 1, 2024: IUCrJ
#5
JOURNAL ARTICLE
Jason N Busby, Sarah Trevelyan, Cassandra L Pegg, Edward D Kerr, Benjamin L Schulz, Irene Chassagnon, Michael J Landsberg, Mitchell K Weston, Mark R H Hurst, J Shaun Lott
Bacterial ABC toxin complexes (Tcs) comprise three core proteins: TcA, TcB and TcC. The TcA protein forms a pentameric assembly that attaches to the surface of target cells and penetrates the cell membrane. The TcB and TcC proteins assemble as a heterodimeric TcB-TcC subcomplex that makes a hollow shell. This TcB-TcC subcomplex self-cleaves and encapsulates within the shell a cytotoxic `cargo' encoded by the C-terminal region of the TcC protein. Here, we describe the structure of a previously uncharacterized TcC protein from Yersinia entomophaga, encoded by a gene at a distant genomic location from the genes encoding the rest of the toxin complex, in complex with the TcB protein...
May 1, 2024: IUCrJ
#6
JOURNAL ARTICLE
Barbara Olech, Petr Brázda, Lukas Palatinus, Paulina Maria Dominiak
Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al...
May 1, 2024: IUCrJ
#7
JOURNAL ARTICLE
Elizabeth Blackburn
Small-angle X-ray scattering has revealed how magnetic Janus particles pair up in solutions in small and large magnetic fields.
March 1, 2024: IUCrJ
#8
JOURNAL ARTICLE
Muhammad Shahbaz, Saba Farooq, M Iqbal Choudhary, Sammer Yousuf
Leishmaniasis is a neglected parasitic tropical disease with numerous clinical manifestations. One of the causative agents of cutaneous leishmaniasis (CL) is Leishmania tropica (L. tropica) known for causing ulcerative lesions on the skin. The adverse effects of the recommended available drugs, such as amphotericin B and pentavalent antimonial, and the emergence of drug resistance in parasites, mean the search for new safe and effective anti-leishmanial agents is crucial. Miltefosine (MIL) was the first recommended oral medication, but its use is now limited because of the rapid emergence of resistance...
March 1, 2024: IUCrJ
#9
JOURNAL ARTICLE
María Menéndez-Herrero, Ángel Martín Pendás
Evidence that the electronic structure of atoms persists in molecules to a much greater extent than has been usually admitted is presented. This is achieved by resorting to N-electron real-space descriptors instead of one- or at most two-particle projections like the electron or exchange-correlation densities. Here, the 3N-dimensional maxima of the square of the wavefunction, the so-called Born maxima, are used. Since this technique is relatively unknown to the crystallographic community, a case-based approach is taken, revisiting first the Born maxima of atoms in their ground state and then some of their excited states...
March 1, 2024: IUCrJ
#10
JOURNAL ARTICLE
Linshuo Guo, Shitao Wu, Zhengyang Zhou, Yanhang Ma
As an important characterization method, pair distribution function (PDF) has been extensively used in structural analysis of nanomaterials, providing key insights into the degree of crystallinity, atomic structure, local disorder etc. The collection of scattering signals with good statistics is necessary for a reliable structural analysis. However, current conventional electron diffraction experiments using PDF (ePDF) are limited in their ability to acquire continuous diffraction rings for large nanoparticles...
March 1, 2024: IUCrJ
#11
JOURNAL ARTICLE
Gerard J Kleywegt, Paul D Adams, Sarah J Butcher, Catherine L Lawson, Alexis Rohou, Peter B Rosenthal, Sriram Subramaniam, Maya Topf, Sanja Abbott, Philip R Baldwin, John M Berrisford, Gérard Bricogne, Preeti Choudhary, Tristan I Croll, Radostin Danev, Sai J Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J Bernard Heymann, Juha T Huiskonen, Andrei Istrate, Takayuki Kato, Gabriel C Lander, Shee Mei Lok, Steven J Ludtke, Garib N Murshudov, Ryan Pye, Grigore D Pintilie, Jane S Richardson, Carsten Sachse, Osman Salih, Sjors H W Scheres, Gunnar F Schroeder, Carlos Oscar S Sorzano, Scott M Stagg, Zhe Wang, Rangana Warshamanage, John D Westbrook, Martyn D Winn, Jasmine Y Young, Stephen K Burley, Jeffrey C Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations...
March 1, 2024: IUCrJ
#12
JOURNAL ARTICLE
Marina Galchenkova, Alexandra Tolstikova, Bjarne Klopprogge, Janina Sprenger, Dominik Oberthuer, Wolfgang Brehm, Thomas A White, Anton Barty, Henry N Chapman, Oleksandr Yefanov
Serial crystallography (SX) has become an established technique for protein structure determination, especially when dealing with small or radiation-sensitive crystals and investigating fast or irreversible protein dynamics. The advent of newly developed multi-megapixel X-ray area detectors, capable of capturing over 1000 images per second, has brought about substantial benefits. However, this advancement also entails a notable increase in the volume of collected data. Today, up to 2 PB of data per experiment could be easily obtained under efficient operating conditions...
March 1, 2024: IUCrJ
#13
JOURNAL ARTICLE
Yuji Takiguchi, Daisuke Nakane, Takashiro Akitsu
This paper uses deep learning to present a proof-of-concept for data-driven chemistry in single-molecule magnets (SMMs). Previous discussions within SMM research have proposed links between molecular structures (crystal structures) and single-molecule magnetic properties; however, these have only interpreted the results. Therefore, this study introduces a data-driven approach to predict the properties of SMM structures using deep learning. The deep-learning model learns the structural features of the SMM molecules by extracting the single-molecule magnetic properties from the 3D coordinates presented in this paper...
March 1, 2024: IUCrJ
#14
JOURNAL ARTICLE
Jee Hoon Park, Rachel E Reviello, Patrick J Loll
Vancomycin is a glycopeptide antibiotic that for decades has been a mainstay of treatment for persistent bacterial infections. However, the spread of antibiotic resistance threatens its continued utility. In particular, vancomycin-resistant enterococci (VRE) have become a pressing clinical challenge. Vancomycin acts by binding and sequestering the intermediate Lipid II in cell-wall biosynthesis, specifically recognizing a D-alanine-D-alanine dipeptide motif within the Lipid II molecule. VRE achieve resistance by remodeling this motif to either D-alanine-D-lactate or D-alanine-D-serine; the former substitution essentially abolishes recognition by vancomycin of Lipid II, whereas the latter reduces the affinity of the antibiotic by roughly one order of magnitude...
March 1, 2024: IUCrJ
#15
JOURNAL ARTICLE
Ewa Patyk-Kaźmierczak, Fernando Izquierdo-Ruiz, Alvaro Lobato, Michał Kaźmierczak, Ida Moszczyńska, Anna Olejniczak, J Manuel Recio
In the search for new active pharmaceutical ingredients, the precise control of the chemistry of cocrystals becomes essential. One crucial step within this chemistry is proton migration between cocrystal coformers to form a salt, usually anticipated by the empirical ΔpKa rule. Due to the effective role it plays in modifying intermolecular distances and interactions, pressure adds a new dimension to the ΔpKa rule. Still, this variable has been scarcely applied to induce proton-transfer reactions within these systems...
March 1, 2024: IUCrJ
#16
JOURNAL ARTICLE
Zengru Li, Haifu Fan, Wei Ding
Highly accurate protein structure prediction can generate accurate models of protein and protein-protein complexes in X-ray crystallography. However, the question of how to make more effective use of predicted models for completing structure analysis, and which strategies should be employed for the more challenging cases such as multi-helical structures, multimeric structures and extremely large structures, both in the model preparation and in the completion steps, remains open for discussion. In this paper, a new strategy is proposed based on the framework of direct methods and dual-space iteration, which can greatly simplify the pre-processing steps of predicted models both in normal and in challenging cases...
March 1, 2024: IUCrJ
#17
JOURNAL ARTICLE
Badri S Rajagopal, Nick Yates, Jake Smith, Alessandro Paradisi, Catherine Tétard-Jones, William G T Willats, Susan Marcus, J Paul Knox, Mohd Firdaus-Raih, Bernard Henrissat, Gideon J Davies, Paul H Walton, Alison Parkin, Glyn R Hemsworth
The discovery of lytic polysaccharide monooxygenases (LPMOs), a family of copper-dependent enzymes that play a major role in polysaccharide degradation, has revealed the importance of oxidoreductases in the biological utilization of biomass. In fungi, a range of redox proteins have been implicated as working in harness with LPMOs to bring about polysaccharide oxidation. In bacteria, less is known about the interplay between redox proteins and LPMOs, or how the interaction between the two contributes to polysaccharide degradation...
March 1, 2024: IUCrJ
#18
JOURNAL ARTICLE
Michał Chodkiewicz, Leonid Patrikeev, Sylwia Pawlędzio, Krzysztof Woźniak
Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen-Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested...
March 1, 2024: IUCrJ
#19
JOURNAL ARTICLE
Jack Stubbs, Theo Hornsey, Niall Hanrahan, Luis Blay Esteban, Rachel Bolton, Martin Malý, Shibom Basu, Julien Orlans, Daniele de Sanctis, Jung Uk Shim, Patrick D Shaw Stewart, Allen M Orville, Ivo Tews, Jonathan West
Serial crystallography requires large numbers of microcrystals and robust strategies to rapidly apply substrates to initiate reactions in time-resolved studies. Here, we report the use of droplet miniaturization for the controlled production of uniform crystals, providing an avenue for controlled substrate addition and synchronous reaction initiation. The approach was evaluated using two enzymatic systems, yielding 3 µm crystals of lysozyme and 2 µm crystals of Pdx1, an Arabidopsis enzyme involved in vitamin B6 biosynthesis...
March 1, 2024: IUCrJ
#20
JOURNAL ARTICLE
Edward N Baker
Researchers have long sought to `see' proteins and other macromolecules in motion, to better understand their functions. Technological developments, notably advances in serial crystallography, are now making these dreams a reality, heralding a new era of kinetic crystallography.
March 1, 2024: IUCrJ
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