Article
Instruments & Instrumentation
Leonard M. G. Chavas, Patrick Gourhant, Beatriz G. Guimaraes, Tatiana Isabet, Pierre Legrand, Robin Lener, Pierre Montaville, Serena Sirigu, Andrew Thompson
Summary: The PROXIMA-1 undulator beamline at Synchrotron SOLEIL is dedicated to biomolecular crystallography experiments and has a layout designed to favor anomalous data recording and studies of crystals with large cell dimensions. Over 12 years, it has accommodated a large number of shifts and visitors, resulting in numerous published scientific papers and coordinates deposited in the Protein Data Bank. The beamline is equipped with advanced beam-shaping equipment, a three-axis goniometer, an X-ray detector, and a sample exchange robot, allowing for standard experimental schemes as well as remote or `mail-in' access.
JOURNAL OF SYNCHROTRON RADIATION
(2021)
Article
Polymer Science
Marina G. Guenza
Summary: The study investigates the short-time anomalous behaviors in macromolecular liquids, focusing on a melt of short homopolymer chains. By analyzing molecular dynamics simulation trajectories, the research sheds light on the microscopic molecular mechanisms responsible for the observed anomalous behavior. The relevance of the correlation hole, unique to polymer liquids, in relation to the observed subdiffusive dynamics naturally emerges from the analysis of the van Hove distribution functions and other properties.
Article
Crystallography
Ki Hyun Nam
Summary: Cryocrystallography is a widely used method for determining the crystal structure of macromolecules. This study introduces a method for processing multicrystal diffraction data using a serial crystallography program, which allows for the integration of diffraction patterns from multiple crystals in a single image.
Review
Multidisciplinary Sciences
Gisela Branden, Richard Neutze
Summary: Conformational changes within biological macromolecules regulate chemical reactions in living cells. Time-resolved crystallography can reveal these changes in detail, while serial crystallography approaches are now being routinely used for studying macromolecules. Recent progress includes visualizing ultrafast and slower time-scale structural changes in proteins like bacteriorhodopsin and photosystem II.
Article
Biochemistry & Molecular Biology
Stavros Azinas, Marta Carroni
Summary: Cryo-EM is a major tool for determining protein structures, while AlphaFold2 enables high-confidence atomic models for polypeptide chains. Cryo-EM retains unique characteristics for determining structures of macromolecular complexes, allowing for near-atomic structures and exploring conformational panoramas. It also has the potential to develop a structural proteomic approach using ex vivo specimens.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Max T. B. Clabbers, Hongyi Xu
Summary: Microcrystal electron diffraction (MicroED) has emerged as a promising method for macromolecular structure determination in structural biology, showing capabilities in revealing atomic structures, solving new protein structures, visualizing ligand-binding interactions, and determining membrane-protein structures. Further development and optimization are needed to make MicroED experiments more accurate and accessible, but it is anticipated to become a robust method complementing existing methods in structural biology.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Wladek Minor, Mariusz Jaskolski, Seamus J. Martin, Zbigniew Dauter
Summary: This tribute honors Alexander Wlodawer for his contributions to the community of structural biology researchers, focusing on his dedication to crystallography and structural science, as well as his outstanding contributions to the success of the FEBS Journal.
Article
Chemistry, Multidisciplinary
Jue Liu, Zhijia Du, Xuelong Wang, Sha Tan, Xianyang Wu, Linxiao Geng, Bohang Song, Po-Hsiu Chien, S. Michelle Everett, Enyuan Hu
Summary: Ni-rich cathodes undergo a four-stage structural evolution during the initial cycle, with a universal structural transition occurring at around 75% delithiation. This transition, marked by an anomalous increase in average TM-O bond lengths, is induced by the direct oxidation of lattice oxygen ions. The onset of this transition correlates well with the release of oxygen gas and decline in capacity retention, highlighting its crucial role in the degradation process.
ENERGY & ENVIRONMENTAL SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Bharath Srinivasan
Summary: The rise of macromolecular crystallography has greatly impacted various scientific fields, including molecular pharmacology, drug discovery, and biotechnology, by allowing atomic resolution visualization of protein structures. However, the teaching of this subject in universities worldwide has been suboptimal due to its interdisciplinary nature and the complex concepts and terminology involved. Additionally, the use of robotics and advanced software algorithms has diminished the incentive for students to understand the foundational concepts of macromolecular crystallography. This article proposes a comprehensive framework for teaching and learning this subject, advocating for interdisciplinary approaches, visual tools, computational resources, and historical context to make it more accessible and relatable to students.
Article
Instruments & Instrumentation
Gloria E. O. Borgstahl, William B. O'Dell, Martin Egli, Jan F. Kern, Andrey Kovalevsky, Jiao Y. Y. Lin, Dean Myles, Mark A. Wilson, Wen Zhang, Petrus Zwart, Leighton Coates
Summary: Neutron macromolecular crystallography (NMC) is crucial for revealing the positions of all atoms in large macromolecules due to its sensitive and gentle probing capabilities. The new design of EWALD will overcome the crystal volume barrier and enable new types of experiments, study of grand challenge systems, and more routine use of NMC in biology.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2022)
Review
Biochemistry & Molecular Biology
Sachiko Toma-Fukai, Toshiyuki Shimizu
Summary: Post-translational modifications of proteins play a critical role in regulating biological processes and their dysfunction can be linked to diseases. Ubiquitination, a type of post-translational modification, involves a complex reaction requiring three enzymes. Recent studies have focused on the structural understanding of E3 ligases, with advancements such as the characterization of PCAF_N, a newly categorized E3 ligase.
Article
Chemistry, Multidisciplinary
Christopher D. M. Hutchison, James M. Baxter, Ann Fitzpatrick, Gabriel Dorlhiac, Alisia Fadini, Samuel Perrett, Karim Maghlaoui, Salome Bodet Lefevre, Violeta Cordon-Preciado, Josie L. Ferreira, Volha U. Chukhutsina, Douglas Garratt, Jonathan Barnard, Gediminas Galinis, Flo Glencross, Rhodri M. Morgan, Sian Stockton, Ben Taylor, Letong Yuan, Matthew G. Romei, Chi-Yun Lin, Jon P. Marangos, Marius Schmidt, Viktoria Chatrchyan, Tiago Buckup, Dmitry Morozov, Jaehyun Park, Sehan Park, Intae Eom, Minseok Kim, Dogeun Jang, Hyeongi Choi, HyoJung Hyun, Gisu Park, Eriko Nango, Rie Tanaka, Shigeki Owada, Kensuke Tono, Daniel P. DePonte, Sergio Carbajo, Matt Seaberg, Andrew Aquila, Sebastien Boutet, Anton Barty, So Iwata, Steven G. Boxer, Gerrit Groenhof, Jasper J. van Thor
Summary: The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. High-resolution pump-probe X-ray crystallography reveals complex sub-angstrom, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. The measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state.
Review
Crystallography
Melanie Vollmar, Gwyndaf Evans
Summary: After over 50 years of development, machine learning and artificial intelligence are now experiencing a significant surge in applications in various commercial and research sectors. In the context of X-ray crystallography and structural biology, machine learning is being integrated into expert and automated systems to predict experimental outcomes, analyze data, forecast crystal growth, and even generate macromolecular structures. This review offers a historical overview of AI and machine learning, discusses their application in crystallography, and presents current examples of their impact on macromolecular crystallography.
CRYSTALLOGRAPHY REVIEWS
(2021)
Article
Materials Science, Multidisciplinary
Peter Schoderboeck, Kevin Ploner
Summary: The production of molybdenum from MoO3 in industrial scale was compared with laboratory scale reduction. Different process conditions and scales resulted in kinetically controlled and thermodynamically controlled reductions. Similar intermediates were formed in both processes with different crystallographic structures, which were identified using crystallographic methods.
INTERNATIONAL JOURNAL OF REFRACTORY METALS & HARD MATERIALS
(2023)
Review
Biochemistry & Molecular Biology
Karolina Michalska, Andrzej Joachimiak
Summary: Structural Genomics emerged over the last three decades to bridge the gap between microbial genomic, functional, and structural data. The field has developed structure-determination pipelines and applied them to uncharacterized proteins, leading to rapid progress in molecular and structural biology. The Protein Data Bank played a central role in coordinating efforts and maintaining high quality of structural data.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Virology
Sharmin Afroz, Robert Brownlie, Michel Fodje, Sylvia van Drunen Littel-van den Hurk
JOURNAL OF VIROLOGY
(2016)
Article
Biochemical Research Methods
Naheda Sahtout, Jijin R. A. Kuttiyatveetil, Michel Fodje, David A. R. Sanders
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2016)
Article
Instruments & Instrumentation
Pawel Grochulski, Michel Fodje, Shaun Labiuk, Tomasz W. Wysokinski, George Belev, Malgorzata Korbas, Scott M. Rosendahl
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS
(2017)
Article
Virology
Sharmin Afroz, Ravendra Garg, Michel Fodje, Sylvia van Drunen Littel-van den Hurk
JOURNAL OF VIROLOGY
(2018)
Article
Crystallography
Gabriele Schatte, Shaunivan Labiuk, Bonnie Li, Peta-Gaye Burnett, Martin Reaney, Pawel Grochulski, Michel Fodje, Jian Yang, Ramaswami Sammynaiken
ACTA CRYSTALLOGRAPHICA SECTION-E STRUCTURE REPORTS ONLINE
(2012)
Article
Crystallography
Pramodkumar Jadhav, Gabriele Schatte, Shaunivan Labiuk, Peta-Gaye Burnett, Bonnie Li, Denis Okinyo-Owiti, Martin Reaney, Pawel Grochulski, Michel Fodje, Ramaswami Sammynaiken
ACTA CRYSTALLOGRAPHICA SECTION-E STRUCTURE REPORTS ONLINE
(2011)
Article
Physics, Multidisciplinary
P. Grochulski, M. N. Fodje, G. George
ACTA PHYSICA POLONICA A
(2012)
Article
Biochemistry & Molecular Biology
Jais R. Bjelke, Ole H. Olsen, Michel Fodje, L. Anders Svensson, Susanne Bang, Gert Bolt, Birthe B. Kragelund, Egon Persson
JOURNAL OF BIOLOGICAL CHEMISTRY
(2008)
Article
Instruments & Instrumentation
Pawel Grochulski, Michel N. Fodje, James Gorin, Shaunivan L. Labiuk, Russ Berg
JOURNAL OF SYNCHROTRON RADIATION
(2011)
Article
Instruments & Instrumentation
Julien J. H. Cotelesage, Pawel Grochulski, Ingrid J. Pickering, Graham N. George, Michel N. Fodje
JOURNAL OF SYNCHROTRON RADIATION
(2012)
Software Review
Instruments & Instrumentation
Michel Fodje, Kathryn Janzen, Russ Berg, Gillian Black, Shaunivan Labiuk, James Gorin, Pawel Grochulski
JOURNAL OF SYNCHROTRON RADIATION
(2012)
Article
Virology
Sharmin Afroz, Robert Brownlie, Michel Fodje, Sylvia van Drunen Littel-van den Hurk
Article
Biochemical Research Methods
Michel Fodje, Kiran Mundboth, Shaunivan Labiuk, Kathryn Janzen, James Gorin, Denis Spasyuk, Scott Colville, Pawel Grochulski
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2020)
Proceedings Paper
Instruments & Instrumentation
James Gorin, Ingvar Blomqvist, Michael Sigrist, Tasha Summers, Michel Fodje, Pawel Grochulski
11TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION (SRI 2012)
(2013)
