Review
Biochemistry & Molecular Biology
Robbie P. Joosten, Robert A. Nicholls, Jon Agirre
Summary: Macromolecular restrained refinement is a commonly used method to improve the agreement between an atomic structural model and experimental data. This study discusses the functional differences between restraint generators and the process of achieving consistent results. Practical considerations and recommendations for generating new restraint dictionaries are provided.
CURRENT MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Linghan Kong, Richard A. Bryce
Summary: This research evaluates the ability of machine learning potentials and semiempirical quantum chemical methods to model ring pucker conformers of carbohydrates. The results show that the machine learning method ANI-1ccx accurately reproduces the ring pucker energy landscape and provides the most accurate estimate of the energetics. The study also finds that all three models reproduce chair more accurately than non-chair geometries.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Organic
Joseph R. Romeo, Jon D. Lucera, Drew Jensen, Luke M. Davis, Clay S. Bennett
Summary: The direct coupling of shelf-stable TCNHPI glycosyl donors with alkylzinc reagents is achieved through a redox catalysis process. This method allows for the formation of alkyl C-glycosides without the need for photocatalytic activation or additional reductants. Furthermore, the coupling of TCNHPI donors with stereodefined alpha-alkoxy furan-containing alkylzinc halides enables the synthesis of methylene-linked exo-C-disaccharides via an Achmatowicz rearrangement.
Article
Chemistry, Multidisciplinary
Yen Vo, Brett D. Schwartz, Hideki Onagi, Jas S. Ward, Michael G. Gardiner, Martin G. Banwell, Keats Nelms, Lara R. Malins
Summary: This study describes the synthesis of the largest homogeneous persulfated xylooligomers, up to eight xylose residues, as standards for biological studies. Near quantitative sulfation was achieved using a mild and simple protocol, allowing definitive identification of impurities in a commercially prepared Pentosan drug.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Organic
Yves Bleriot
Summary: This account focuses on the design of glycomimetics targeting carbohydrate processing enzymes and the use of glycosyl cations for studying glycosylation reactions. These efforts have provided important data on this key ionic species and innovative strategies for accessing iminosugars of interest.
SYNTHESIS-STUTTGART
(2021)
Article
Chemistry, Multidisciplinary
Thomas M. McGuire, Jessica Bowles, Edward Deane, Elliot H. E. Farrar, Matthew N. Grayson, Antoine Buchard
Summary: Manipulating the stereochemistry of polymers can alter their physical properties, with crystalline polyethers derived from d- and l-xylose showing enhanced thermal properties compared to enantiopure polymers. In contrast, atactic polymers from racemic mixtures of monomers are amorphous, and the polymer hydroxyl groups are amenable to post-polymerisation functionalization.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Anja Kostelac, Leander Sutzl, Jolanta Puc, Valentina Furlanetto, Christina Divne, Dietmar Haltrich
Summary: This study reports the biochemical characterization of a pyranose oxidase (ScPOx) from Streptomyces canus. The results showed that ScPOx oxidizes monosaccharides and various C- and O-glycosides, and belongs to the same sequence space as the recently discovered FAD-dependent C-glycoside 3-oxidase.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Chemistry, Multidisciplinary
Kevin J. Naidoo, Tomas Bruce-Chwatt, Tharindu Senapathi, Malcolm Hillebrand
Summary: Enzyme reactions, especially glycoenzymes, are complex to accurately simulate due to the need for rigorous sampling of protein frame, carbohydrate substrate conformational space, and unbiased treatment of electron dynamics. Two computational methods, FEARCF and QSL, are demonstrated as effective tools for multidimensional sampling and accelerating quantum dynamics in enzyme catalysis simulations. The combination of these methods allows for in-depth exploration of carbohydrate catalyzed reactions and discovery of experimentally inaccessible molecular and electronic mechanisms.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Chemistry, Organic
Xiaoxiao Liaoejoc, Kai Yuan, David Crichejoc
Summary: In this study, two interesting intramolecular displacement reactions involving thiolate sulfur and thiirane sulfur were discovered during the synthesis of 3,5-dithio-glucofuranose. The use of a 5-S,6-O-isopropylidene protecting group successfully solved the intramolecular displacement problem, leading to the synthesis of 3,5-dithio-glucofuranose with a 9% overall yield.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Polymer Science
Giulia Amici, Michele Caraglio, Enzo Orlandini, Cristian Micheletti
Summary: In this study, catenated ring polymers confined inside channels and slits were investigated using Langevin dynamics simulations. It was found that catenation constraints generate a drag that couples the contour motion of the interlocked regions. The strength of this coupling decreases as the interlocking becomes tighter and shorter due to confinement, with the results having implications for linked biomolecules in experimental or biological confining conditions.
Review
Biochemistry & Molecular Biology
Marian Vincenzi, Flavia Anna Mercurio, Marilisa Leone
Summary: This review focuses on using NMR tools to study the 3D structures of small unlabeled peptides, emphasizing the experimental methods and key steps involved. It highlights the importance of NMR in revealing peptide conformational preferences and discusses the recent advancements in NMR spectroscopy for studying large systems and overcoming molecular weight limits.
CURRENT MEDICINAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Bohdan Schneider, Blake Alexander Sweeney, Alex Bateman, Jiri Cerny, Tomasz Zok, Marta Szachniuk
Summary: Due to limited data and quality issues, it is challenging to predict the 3D structure of RNA using deep learning methods like AlphaFold in the short term. However, by addressing data quality and volume issues, utilizing more data, and developing new machine learning methods, an accurate RNA structure prediction method can be created.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Organic
Yan Liang, Adrien G. Laporte, Anne Bodlenner, Philippe Compain
Summary: A convenient method for accessing glycosyl cyanides is presented, involving TMSCN ring opening of 1,6-anhydro sugars mediated by TMSOTf with stereocontrol in D-gluco, D-galacto, and D-manno series. The reaction shows tolerance towards various functional groups including free alcohols, alkenes, and terminal alkynes. The synthesis of a constrained analogue of 1-cyano-D-glucal with a 3,6-anhydro sugar framework illustrates the significance of the TMSCN ring-opening reaction.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Physical
Xiaojun Li, Shuna Li, Jun Lu, Hongjiang Ren, Mengqi Zhang, Wangdi Zhang
Summary: In this study, the chemical stabilities, bonding character, electronic properties, and electronic transitions of perfluorocubane were systematically explored using density functional theory calculations. The results showed that the C8F8 molecule has high chemical stability and a special electronic structure, capable of generating a radical anion with an electron hosted inside the cubane frame. The induced ring currents revealed that perfluorocubane exhibits an overall small diamagnetic current supported by anisotropy of the current-induced density and gauge-including magnetically induced currents. Furthermore, the main electronic transitions of perfluorocubane were found to come from the surface of the cubic frame to its inner structure. Therefore, perfluorocubane can be recognized as a small electron acceptor material with special electron-carrying capacity, which will promote further applications of novel conducting and semiconducting materials.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Organic
Jun Cao, Stephane P. Vincent
Summary: This review article focuses on recent advancements in the synthesis of spirocyclopropyl carbohydrates and nucleosides. The versatile cyclopropyl moiety has been shown to facilitate the preparation of various value-added compounds, including b-C-glycosyl amino acids, spiroketals, and dioxaspirolactones. Additionally, the review highlights the use of spirocyclopropyl carbohydrates as glycomimetic inhibitors of biologically relevant enzymes such as glycosidases, protein methyltransferase, kinase, and viral polymerases. ©2023 Elsevier Ltd. All rights reserved.
Article
Biochemical Research Methods
Bart van Beusekom, George Damaskos, Maarten L. Hekkelman, Fernando Salgado-Polo, Yoshitaka Hiruma, Anastassis Perrakis, Robbie P. Joosten
Summary: Comparison of homologous structure models is crucial in protein structure analysis. LAHMA website allows comparison of any structure model with all close homologs from the PDB-REDO databank, visualizing structural features and facilitating identification of differences for further analysis. LAHMA also provides easy comparison of structure-quality plots and in-browser structural visualization of 3D models.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Robert A. Nicholls, Robbie P. Joosten, Fei Long, Marcin Wojdyr, Andrey Lebedev, Eugene Krissinel, Lucrezia Catapano, Marcus Fischer, Paul Emsley, Garib N. Murshudov
Summary: This article discusses the protocols and tools for modelling covalent linkages within the CCP4 suite, including the generation of link dictionaries and the use of various tools for covalent linkage modelling. These integrated solutions streamline the workflow and aim to improve the quality of future modelled covalent linkages.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Robbie P. Joosten, Robert A. Nicholls, Jon Agirre
Summary: Macromolecular restrained refinement is a commonly used method to improve the agreement between an atomic structural model and experimental data. This study discusses the functional differences between restraint generators and the process of achieving consistent results. Practical considerations and recommendations for generating new restraint dictionaries are provided.
CURRENT MEDICINAL CHEMISTRY
(2022)
Article
Biology
Chloe R. Koulouris, Sian E. Gardiner, Tessa K. Harris, Karen T. Elvers, S. Mark Roe, Jason A. Gillespie, Simon E. Ward, Olivera Grubisha, Robert A. Nicholls, John R. Atack, Benjamin D. Bax
Summary: Human serine racemase (hSR) catalyzes the conversion of L-serine to D-serine and plays a role in the activation of NMDA receptors. The positioning of Tyr121 appears to be crucial in regulating the activity of hSR.
COMMUNICATIONS BIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Jon Agirre, Robbie P. Joosten, Alan Roseman
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Maarten L. Hekkelman, Ida de Vries, Robbie P. Joosten, Anastassis Perrakis
Summary: Artificial intelligence-based protein structure prediction has greatly impacted biomolecular sciences. However, the predicted protein models in the AlphaFold database lack coordinates for small molecules and ions necessary for structure and function. The AlphaFill algorithm addresses this issue by transplanting missing small molecules and ions from experimentally determined structures to predicted protein models.
Article
Biochemical Research Methods
Jordan S. Dialpuri, Haroldas Bagdonas, Mihaela Atanasova, Lucy C. Schofield, Maarten L. Hekkelman, Robbie P. Joosten, Jon Agirre
Summary: The oligosaccharides in N-glycosylation play a crucial role in the structure and function of glycoproteins, which is dependent on the composition and conformation of the glycans. The Privateer software enables structural biologists to assess and enhance the atomic structures of carbohydrates, including N-glycans; it has recently been updated to analyze glycan composition using glycomics data. This study presents an expanded analysis of the overall conformation of N-glycans using a curated set of glycoprotein models and their glycosidic linkage torsional preferences.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Keitaro Yamashita, Marcin Wojdyr, Fei Long, Robert A. Nicholls, Garib N. Murshudov
Summary: Macromolecular refinement uses experimental data and prior chemical knowledge to fit an atomic structural model into the data, while ensuring chemical plausibility. In CCP4 suite, the Monomer Library stores the chemical knowledge in restraint dictionaries. Recently, this part of CCP4 has been overhauled, allowing for increased flexibility and easier experimentation.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Jon Agirre, Mihaela Atanasova, Haroldas Bagdonas, Charles B. Ballard, Arnaud Basle, James Beilsten-Edmands, Rafael J. Borges, David G. Brown, J. Javier Burgos-Marmol, John M. Berrisford, Paul S. Bond, Iracema Caballero, Lucrezia Catapano, Grzegorz Chojnowski, Atlanta G. Cook, Kevin D. Cowtan, Tristan I. Croll, Judit E. Debreczeni, Nicholas E. Devenish, Eleanor J. Dodson, Tarik R. Drevon, Paul Emsley, Gwyndaf Evans, Phil R. Evans, Maria Fando, James Foadi, Luis Fuentes-Montero, Elspeth F. Garman, Markus Gerstel, Richard J. Gildea, Kaushik Hatti, Maarten L. Hekkelman, Philipp Heuser, Soon Wen Hoh, Michael A. Hough, Huw T. Jenkins, Elisabet Jimenez, Robbie P. Joosten, Ronan M. Keegan, Nicholas Keep, Eugene B. Krissinel, Petr Kolenko, Oleg Kovalevskiy, Victor S. Lamzin, David M. Lawson, Andrey A. Lebedev, Andrew G. W. Leslie, Bernhard Lohkamp, Fei Long, Martin Maly, Airlie J. McCoy, Stuart J. McNicholas, Ana Medina, Claudia Millan, James W. Murray, Garib N. Murshudov, Robert A. Nicholls, Martin E. M. Noble, Robert Oeffner, Navraj S. Pannu, James M. Parkhurst, Nicholas Pearce, Joana Pereira, Anastassis Perrakis, Harold R. Powell, Randy J. Read, Daniel J. Rigden, William Rochira, Massimo Sammito, Filomeno Sanchez Rodriguez, George M. Sheldrick, Kathryn L. Shelley, Felix Simkovic, Adam J. Simpkin, Pavol Skubak, Egor Sobolev, Roberto A. Steiner, Kyle Stevenson, Ivo Tews, Jens M. H. Thomas, Andrea Thorn, Josep Trivino Valls, Ville Uski, Isabel Uson, Alexei Vagin, Sameer Velankar, Melanie Vollmar, Helen Walden, David Waterman, Keith S. Wilson, Martyn D. Winn, Graeme Winter, Marcin Wojdyr, Keitaro Yamashita
Summary: The Collaborative Computational Project No. 4 (CCP4) is an international collective led by the UK, dedicated to the development, testing, distribution, and promotion of software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs, unified by familiar execution routines, common libraries, and graphical interfaces. This article serves as a general literature citation for the use of the CCP4 software suite, providing an overview of its recent changes, new features, and future developments, while also highlighting the individual programs within the suite and providing up-to-date references for crystallographers worldwide.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biology
Ida de Vries, Danique Ammerlaan, Tatjana Heidebrecht, Patrick H. N. Celie, Daan P. Geerke, Robbie P. Joosten, Anastassis Perrakis
Summary: Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). This study presents a crystal structure of the JDBD and proposes recognition models for JDBD binding to J-DNA, which were confirmed by mutagenesis experiments. The findings provide insights into the molecular mechanism of base-J replication.
LIFE SCIENCE ALLIANCE
(2023)
