Article
Multidisciplinary Sciences
Elyse A. Schriber, Daniel W. Paley, Robert Bolotovsky, Daniel J. Rosenberg, Raymond G. Sierra, Andrew Aquila, Derek Mendez, Frederic Poitevin, Johannes P. Blaschke, Asmit Bhowmick, Ryan P. Kelly, Mark Hunter, Brandon Hayes, Derek C. Popple, Matthew Yeung, Carina Pareja-Rivera, Stella Lisova, Kensuke Tono, Michihiro Sugahara, Shigeki Owada, Tevye Kuykendall, Kaiyuan Yao, P. James Schuck, Diego Solis-Ibarra, Nicholas K. Sauter, Aaron S. Brewster, J. Nathan Hohman
Summary: The increase in inorganic-organic hybrid materials has led to a bottleneck in their characterization, which can be addressed using small-molecule serial femtosecond X-ray crystallography as a solution for determining their crystal structures.
Article
Multidisciplinary Sciences
P. Mehrabi, R. Buecker, G. Bourenkov, H. M. Ginn, D. von Stetten, H. M. Mueller-Werkmeister, A. Kuo, T. Morizumi, B. T. Eger, W-L Ou, S. Oghbaey, A. Sarracini, J. E. Besaw, O. Pare-Labrosse, S. Meier, H. Schikora, F. Tellkamp, A. Marx, D. A. Sherrell, D. Axford, R. L. Owen, O. P. Ernst, E. F. Pai, E. C. Schulz, R. J. D. Miller
Summary: This study systematically compared crystallographic diffraction data collected by SFX and SSX methods for myoglobin and fluoroacetate dehalogenase, finding that approximately 5000 room-temperature diffraction images are sufficient for reasonable data statistics regardless of the radiation source. The data suggest that the quality of diffraction data obtained from these samples is more related to the properties of the crystals rather than the radiation source.
Article
Biology
Kazumasa Oda, Takashi Nomura, Takanori Nakane, Keitaro Yamashita, Keiichi Inoue, Shota Ito, Johannes Vierock, Kunio Hirata, Andres D. Maturana, Kota Katayama, Tatsuya Ikuta, Itsuki Ishigami, Tamaki Izume, Rie Umeda, Ryuun Eguma, Satomi Oishi, Go Kasuya, Takafumi Kato, Tsukasa Kusakizako, Wataru Shihoya, Hiroto Shimada, Tomoyuki Takatsuji, Mizuki Takemoto, Reiya Taniguchi, Atsuhiro Tomita, Ryoki Nakamura, Masahiro Fukuda, Hirotake Miyauchi, Yongchan Lee, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Michihiro Sugahara, Tetsunari Kimura, Tatsuro Shimamura, Takaaki Fujiwara, Yasuaki Yamanaka, Shigeki Owada, Yasumasa Joti, Kensuke Tono, Ryuichiro Ishitani, Shigehiko Hayashi, Hideki Kandori, Peter Hegemann, So Iwata, Minoru Kubo, Tomohiro Nishizawa, Osamu Nureki
Summary: Channelrhodopsins (ChRs) are microbial light-gated ion channels used in optogenetics for controlling neural activity with light. Time-resolved crystallographic analyses revealed conformational changes in ChR following photoactivation, suggesting early changes in the pore-forming helices trigger the opening of the ion conducting pore.
Article
Multidisciplinary Sciences
Max T. B. Clabbers, Susannah Holmes, Timothy W. Muusse, Parimala R. Vajjhala, Sara J. Thygesen, Alpeshkumar K. Malde, Dominic J. B. Hunter, Tristan Croll, Leonie Flueckiger, Jeffrey D. Nanson, Md Habibur Rahaman, Andrew Aquila, Mark S. Hunter, Mengning Liang, Chun Hong Yoon, Jingjing Zhao, Nadia A. Zatsepin, Brian Abbey, Emma Sierecki, Yann Gambin, Katryn J. Stacey, Connie Darmanin, Bostjan Kobe, Hongyi Xu, Thomas Ve
Summary: MyD88 and MAL are TLR adaptors that induce pro-inflammatory cytokine production, with the TIR domain of MAL forming filaments in vitro that nucleate the assembly of crystalline arrays of the MyD88 TIR domain. The structures of these assemblies were determined using MicroED and SFX techniques, showing the importance of the MyD88 interface residues for TLR4 signaling in vivo. The study provides insight into TLR signal transduction and compares the MicroED and SFX techniques.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Thomas R. M. Barends, Benjamin Stauch, Vadim Cherezov, Ilme Schlichting
Summary: This article introduces the basic principles of X-ray free-electron lasers and serial crystallography, providing assistance for structural biology groups in planning and conducting SFX experiments. The main content includes microcrystal growth and characterization, sample delivery and data processing techniques, experimental preparation and operation at different stages, as well as the possibilities of SFX in various application areas.
NATURE REVIEWS METHODS PRIMERS
(2022)
Article
Biochemistry & Molecular Biology
Jonathan A. R. Worrall, Michael A. Hough
Summary: Enzymes with iron-containing active sites are crucial for aerobic organisms, but their structural studies are challenging due to radiation-induced chemistry. Novel light source technologies have overcome this issue and allow for time-resolved structural analysis.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Physical
Cecilia M. Casadei, Ahmad Hosseinizadeh, Spencer Bliven, Tobias Weinert, Jorg Standfuss, Russell Fung, Gebhard F. X. Schertler, Robin Santra
Summary: Low-pass spectral analysis (LPSA) is an effective algorithm for retrieving dynamics in model data affected by incompleteness and weighting errors. In this study, LPSA is applied to experimental time-resolved crystallography data and the parametric sensitivity is analyzed. The presence of high-frequency contamination in dynamical modes is investigated using synthetic data with various uncertainties and errors. A method is proposed to handle missing observations and improved dynamics retrieval is achieved.
STRUCTURAL DYNAMICS-US
(2023)
Review
Biochemistry & Molecular Biology
Sabine Botha, Petra Fromme
Summary: Serial femtosecond crystallography (SFX) is a revolutionary method that allows the collection of X-ray diffraction data from tiny crystals at room temperature, enabling high temporal resolution studies of macromolecules. The global COVID-19 pandemic in 2020 had a significant impact on SFX research, leading to a shift in focus towards studying the SARS-CoV-2 virus.
Article
Biochemical Research Methods
Kunio Nakata, Tatsuki Kashiwagi, Naoki Kunishima, Hisashi Naitow, Yoshinori Matsuura, Hiroshi Miyano, Toshimi Mizukoshi, Kensuke Tono, Makina Yabashi, Eriko Nango, So Iwata
Summary: Phosphoketolase and transketolase are important enzymes in the primary metabolism of bifidobacteria. They catalyze the cleavage of xylulose 5-phosphate or fructose 6-phosphate in the first reaction step and have different substrate specificity in the second reaction step. The structures of these enzymes have been determined using crystallography and X-ray free-electron laser.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Izumi Ishigami, Sergio Carbajo, Nadia Zatsepin, Masahide Hikita, Chelsie E. Conrad, Garrett Nelson, Jesse Coe, Shibom Basu, Thomas Grant, Matthew H. Seaberg, Raymond G. Sierra, Mark S. Hunter, Petra Fromme, Raimund Fromme, Denis L. Rousseau, Syun-Ru Yeh
Summary: Cytochrome c oxidase (CcO) is a hemeprotein that reduces dioxygen to water. It has a unique structure with a binuclear center composed of a copper atom and a heme iron. In the CO complex of CcO, the CO molecule dissociates from the heme iron and moves to a temporary binding site between the copper atom and the heme iron. This new structure provides insight into the ligand dissociation trajectory and protein dynamics.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Analytical
Tao Liu, Jiucheng Wu, Amane Suzuki, Ryo Sato, Hiraku Matsukuma, Wei Gao
Summary: Two algorithms are proposed to shorten the unmeasurable dead-zone close to the zero-position of measurement in a dispersive interferometer using a femtosecond laser. The spectral fringe algorithm and the combined algorithm are presented, and simulation results demonstrate their high accuracy in shortening the dead-zone. Experimental results show that the dead-zone using the proposed algorithms can be half of that using the conventional algorithm, with further improvement in measurement accuracy using the combined algorithm.
Article
Construction & Building Technology
Fatima-Zahra Abir, Youssef El Hafiane, Agnes Smith, Yoshinobu Kondo, Yusuke Sakai, Toru Asaka, Koichiro Fukuda, Mohamed Mesnaoui, Younes Abouliatim, Lhabib Nibou
Summary: Pure powders of ye'elimite Ca4Al6-2xFe2xSO16 particles containing iron were synthesized by chemical route for the first time. The increase in iron content in the reaction system leads to an increase in the amount of iron-stabilized cubic phase and a decrease in the orthorhombic phase until a concentration of x = 1.13 where only the cubic phase is detected. The presence of iron also causes the formation of ferritic phases, and a chemical treatment with sodium dithionite was proposed to eliminate them.
CEMENT AND CONCRETE RESEARCH
(2023)
Article
Materials Science, Ceramics
Jinping Cui, Zhenyuan Gong, Pinggen Rao, Kang Guan, Qingfen Zeng
Summary: The femtosecond laser was utilized in this study to process ultra-sharp defects on test bars, with results showing consistent stress intensity factor ratios for different defect conditions. This method demonstrates high accuracy and operability for fracture toughness testing of structural ceramics.
JOURNAL OF THE AMERICAN CERAMIC SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Chuanxu Ma, Zhongcan Xiao, Peter Bonnesen, Liangbo Liang, Alexander A. Puretzky, Jingsong Huang, Marek Kolmer, Bobby G. Sumpter, Wenchang Lu, Kunlun Hong, Jerzy Bernholc, An-Ping Li
Summary: This study investigates the cyclodehydrogenation reaction mechanism in the on-surface synthesis of graphene nanoribbons using isotopic labeling. A reaction pathway involving conrotatory electrocyclization and a [1,9]-sigmatropic D shift, followed by H/D eliminations, is identified and substantiated by experiments and simulations. The research not only helps clarify the reaction process in GNR synthesis, but also presents a rational strategy for designing precise hydrogen/deuterium isotope labeling patterns in on-surface reactions.
Article
Biochemistry & Molecular Biology
Shanli Chen, Cai Yuan, Longguang Jiang, Zhipu Luo, Mingdong Huang
Summary: Metallodrugs play a significant role in anticancer treatments, mainly by binding to human serum albumin (HSA) and affecting their pharmacokinetics and anticancer efficacy. This study used X-ray crystallography to identify the binding sites of cisplatin, a widely used metallodrug, in HSA in the presence or absence of a representative fatty acid (myristate). The results revealed new binding sites and the mechanism of cisplatin-induced HSA aggregation.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Graeme Winter, James Beilsten-Edmands, Nicholas Devenish, Markus Gerstel, Richard J. Gildea, David McDonagh, Elena Pascal, David G. Waterman, Benjamin H. Williams, Gwyndaf Evans
Summary: The DIALS software is introduced as a toolkit for processing X-ray diffraction data, emphasizing its usage as a toolkit for data processing, with support for automated systems and command-line usage, and the ability to write new tools using the API for bespoke analysis. In addition to macromolecular X-ray crystallography, DIALS can also be applied to techniques outside of this field.
Article
Biochemistry & Molecular Biology
Matthew Herdman, Andriko von Kugelgen, Danguole Kureisaite-Ciziene, Ramona Duman, Kamel El Omari, Elspeth F. Garman, Andreas Kjaer, Dimitrios Kolokouris, Jan Lowe, Armin Wagner, Phillip J. Stansfeld, Tanmay A. M. Bharat
Summary: In this study, the role of metal ions in the formation of Caulobacter crescentus S-layer was investigated. It was found that calcium ions facilitate S-layer lattice formation and cell-surface binding, and that bound metal ions are crucial for the S-layer lattice. The positions of metal ions in the S-layer were also mapped using advanced imaging techniques. These findings contribute to the understanding of S-layer formation and have implications for synthetic biology.
Article
Biochemistry & Molecular Biology
Matthew J. Rodrigues, Nitai Giri, Antoine Royant, Yang Zhang, Rachel Bolton, Gwyndaf Evans, Steve E. Ealick, Tadhg Begley, Ivo Tews
Summary: The Pdx1 enzyme catalyzes the formation of pyridoxal 5-phosphate (PLP) through an imine relay mechanism, involving stereoselective deprotonation and substrate-assisted phosphate elimination. The I-333 intermediate, characterized by structural, UV-vis absorption spectroscopy and mass spectrometry analyses, plays a central role in PLP biosynthesis.
RSC CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Paola Lanzoni-Mangutchi, Oishik Banerji, Jason Wilson, Anna Barwinska-Sendra, Joseph A. Kirk, Filipa Vaz, Shauna O'Beirne, Arnaud Basle, Kamel El Omari, Armin Wagner, Neil F. Fairweather, Gillian R. Douce, Per A. Bullough, Robert P. Fagan, Paula S. Salgado
Summary: S-layers are two-dimensional protein arrays that cover the surface of bacteria and archaea, playing important roles in cell physiology. In this study, the crystal structure of the main S-layer protein SIpA from the bacterial pathogen Clostridioides difficile was determined, and the organization and assembly mechanism of the S-layer was studied using electron microscopy. The compact and tightly-packed array of triangular prisms in the crystal lattice mimics the assembly of the S-layer in the cell, and the flexible ridges on the surface of the array were found to be dispensable for overall structure and assembly.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Richard J. Gildea, James Beilsten-Edmands, Danny Axford, Sam Horrell, Pierre Aller, James Sandy, Juan Sanchez-Weatherby, C. David Owen, Petra Lukacik, Claire Strain-Damerell, Robin L. Owen, Martin A. Walsh, Graeme Winter
Summary: In macromolecular crystallography, data collection from a single crystal is limited by radiation damage. Thus, merging data sets from multiple crystals is necessary. A new program called xia2.multiplex has been developed to facilitate the scaling and merging of multi-crystal data sets, including symmetry analysis and analysis of factors affecting data quality.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Abudureyimu Abula, Tingting Yang, Yingxin Zhang, Tinghan Li, Xiaoyun Ji
Summary: This study found that EcR exhibits higher cytosine sensitivity when degrading RNA, especially when the 1-nt upstream of C is A, U, or G. The substitution of glycine with proline in EcR enhances its cytosine sensitivity. The EcR G273P mutant has the potential to detect and analyze various RNA species in biological and clinical samples.
MOLECULAR BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
V. U. Chukhutsina, J. M. Baxter, A. Fadini, R. M. Morgan, M. A. Pope, K. Maghlaoui, C. M. Orr, A. Wagner, J. J. van Thor
Summary: This study provides insights into the photo-sensing mechanism of Orange Carotenoid protein (OCP), revealing the involvement of single bond isomerization and structural changes. The findings contribute to a better understanding of OCP's role in light-harvesting.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sarah A. E. Barwell, Ramona Duman, Armin Wagner, Todd Holyoak
Summary: Phosphoenolpyruvate carboxykinase (PEPCK) is an enzyme involved in glucose metabolism, catalyzing a key step in gluconeogenesis. The preferential synthesis of phosphoenolpyruvate (PEP) from oxaloacetic acid (OAA) catalyzed by PEPCK in vivo is facilitated by anion-mediated enzyme inhibition. The binding of ubiquitous anions like chloride restricts the enzyme to function in the direction of PEP synthesis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Michael W. W. Martynowycz, Anna Shiriaeva, Max T. B. Clabbers, William J. J. Nicolas, Sara J. J. Weaver, Johan Hattne, Tamir Gonen
Summary: In this study, the authors demonstrate a method for milling vitrified biological material and collecting MicroED data for the adenosine receptor. They use an integrated fluorescence light microscope inside a focused ion beam and scanning electron microscope to identify and mill fluorescently labeled GPCR crystals. Plasma ion-beam milling is shown to be a powerful tool for preparing biological lamellae.
NATURE COMMUNICATIONS
(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
Biochemical Research Methods
Jack D. Whitehead, Jonathan M. Grimes, Jeremy R. Keown
Summary: Bornaviruses are RNA viruses that infect a wide range of hosts including mammals, reptiles, and birds. This study presents the structure of the oligomerization domain of the phosphoprotein, which is an important component of the bornavirus replication complex. The findings provide valuable insights into the assembly process of the phosphoprotein and its role in viral replication.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
James M. Parkhurst, Adam D. Crawshaw, C. Alistair Siebert, Maud Dumoux, C. David Owen, Pedro Nunes, David Waterman, Thomas Glen, David I. Stuart, James H. Naismith, Gwyndaf Evans
Summary: Three-dimensional electron diffraction from nanocrystals of biological macromolecules requires the use of very small crystals, typically less than 300 nm-thick. Focused-ion-beam milling has been used to prepare thin samples for this purpose, but little work has been done to quantify the damage caused to delicate biological samples. This study analyzed the effect of plasma FIB milling on lysozyme crystals and compared argon and xenon plasmas with a gallium source. The results showed an upper bound and a lower bound for the depth of the milling damage layer.
Article
Multidisciplinary Sciences
Jeremy R. R. Keown, Adam D. D. Crawshaw, Jose Trincao, Loic Carrique, Richard J. J. Gildea, Sam Horrell, Anna J. J. Warren, Danny Axford, Robin Owen, Gwyndaf Evans, Annie Bezier, Peter Metcalf, Jonathan M. M. Grimes
Summary: Infectious protein crystals called occlusion bodies or polyhedra are crucial for the viral lifecycle of certain insect viruses. A study reveals the structure of a polyhedrin from the Nudiviridae family, which was previously thought to lack occlusion bodies. The findings show that the nudivirus occlusion body has a distinct protein structure but shares common principles with occlusion bodies from other viruses.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Max T. B. Clabbers, Michael W. Martynowycz, Johan Hattne, Tamir Gonen
Summary: Microcrystal electron diffraction (MicroED) is a powerful technique for protein structure determination. Recent studies have shown that with high-resolution MicroED data, it is possible to accurately identify over a third of hydrogen atom positions and visualize hydrogen bonding interactions and the charged states of residues.
JOURNAL OF STRUCTURAL BIOLOGY-X
(2022)
