Review
Biochemistry & Molecular Biology
Miguel Ricardo Leung, Tzviya Zeev-Ben-Mordehai
Summary: The different oligomeric forms of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) have defined cellular and subcellular distributions. While crystal structures of AChE and BChE have been available for many years, structures of the physiologically relevant cholinesterase tetramer were only recently solved by cryo-electron microscopy (cryo-EM). The next frontier in cholinesterase structural biology is to image membrane-anchored ChE oligomers directly in their native environment - the cell.
JOURNAL OF NEUROCHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Axel T. Brunger, Jeremy Leitz
Summary: Synaptic neurotransmitter release involves a complex interplay of presynaptic proteins, including SNAREs, synaptotagmin, complexin, and other factors. This review focuses on the interactions between the SNARE complex and synaptotagmin, particularly the validated primary interface. The study also discusses other potential interfaces and presents new data on the tripartite interface and an inhibitor of the primary interface in a reconstituted system of synaptic vesicle fusion.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Review
Biology
Kendra E. Leigh, Yorgo Modis
Summary: The global impact of the SARS-CoV-2 pandemic has highlighted the importance of scientific research, which has been facilitated by advancements in various scientific fields. Technological improvements in cryo-electron microscopy have allowed for a quicker and more detailed visualization of the virus, aiding in the accelerated development of vaccines and therapeutics.
Article
Microbiology
Cristina Jimenez-Ortigosa, Jennifer Jiang, Muyuan Chen, Xuyuan Kuang, Kelley R. Healey, Paul Castellano, Nikpreet Boparai, Steven J. Ludtke, David S. Perlin, Wei Dai
Summary: Echinocandin drugs have become a front-line therapy against Candida spp. infections, but the rising resistance to these drugs by Candida species is a concern. By using cryo-ET and subtomogram analysis, researchers have provided a preliminary structure of the putative C. glabrata GS complex, laying the foundation for future studies on this elusive protein complex.
Article
Biochemistry & Molecular Biology
Noemi Zimmermann, Akira Noga, Jagan Mohan Obbineni, Takashi Ishikawa
Summary: Using in situ cryo-electron tomography, subtomogram averaging, and classification, we analyzed three states of the axonemal outer dynein arm (ODA) during the power stroke cycle, which include the prepower stroke, postpower stroke, and intermediate state conformations. Our analysis revealed differences in the orientation and position of the dynein head compared to published in vitro atomic structures. Additionally, we found that in the absence of ATP, dynein linkers interact with the AAA3/AAA4 domains, suggesting that they are directed by interactions with the adjacent microtubule doublet B-tubule. Our findings provide insight into the conformational changes of ODA during force generation.
Article
Biochemistry & Molecular Biology
Mohammed Kaplan, Qing Yao, Grant J. Jensen
Summary: This study utilized cryo-electron tomography and subtomogram averaging to investigate the structure of the flagellar motor of Proteus mirabilis. It was found that the motor of P. mirabilis is structurally similar to those of E. coli and S. enterica, lacking the periplasmic elaborations found in other specialized gammaproteobacterial motors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Joseph George Beton, Jim Monistrol, Anne Wentink, Erin C. Johnston, Anthony John Roberts, Bernd Gerhard Bukau, Bart W. Hoogenboom, Helen R. Saibil
Summary: Specific combinations of molecular chaperones in the human body can disassemble protein aggregates, which is important for combating disease-related fiber formation. This study reveals the mechanism of this disassembly process and the localization and activity of molecular chaperones on the fibers using techniques such as atomic force microscopy.
Article
Biochemistry & Molecular Biology
Darja Bozic, Matej Hocevar, Matic Kisovec, Manca Pajnic, Ljubisa Paden, Marko Jeran, Apolonija Bedina Zavec, Marjetka Podobnik, Ksenija Kogej, Ales Iglic, Veronika Kralj-Iglic
Summary: EVs have potential in diagnostics and therapy, but poor reproducibility in studies hinders practical application. Study on hbEVs stability reveals consistent morphology under specific conditions, making them suitable as EV reference material.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Domenica Farci, Patrycja Haniewicz, Dario Piano
Summary: The study found that the S-layer in Deinococcus radiodurans has crystalline regularity in all layers of the cell envelope, indicating its importance as a structural and functional scaffold.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Miguel Ricardo Leung, Marc C. Roelofs, Ravi Teja Ravi, Paula Maitan, Heiko Henning, Min Zhang, Elizabeth G. Bromfield, Stuart C. Howes, Bart M. Gadella, Hermes Bloomfield-Gadelha, Tzviya Zeev-Ben-Mordehai
Summary: This study utilized advanced cryo-imaging techniques to analyze the internal structures of sperm flagella from three mammalian species, revealing novel ways in which microtubule inner proteins are connected. The importance of the base structure for flagellar beating, as well as the coupling of outer dense fibers to microtubules, was demonstrated. Mammalian sperm flagella are decorated at multiple scales, with key structures at the nano- and micrometer levels.
Article
Multidisciplinary Sciences
Meijing Li, Ishita Tripathi-Giesgen, Brenda A. Schulman, Wolfgang Baumeister, Florian Wilfling
Summary: Selective macroautophagy is a process in which cytosolic material is enclosed in a double membrane organelle and transported to a lytic compartment for degradation. This study used cryo-electron tomography to observe the formation of phagophores around damaged Salmonella-containing vacuoles (SCVs). Host cells generated multiple phagophores at the site of SCVs and established contact with the endoplasmic reticulum for membrane formation and expansion.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Dou Wu, Jingying Huang, Hao Zhu, Zhe Chen, Yongping Chai, Jingyi Ke, Kexin Lei, Zhao Peng, Ranhao Zhang, Xueming Li, Kaiyao Huang, Wei Li, Chengtian Zhao, Guangshuo Ou
Summary: The formation and regeneration of cilia require new protein synthesis. The study found that flagellar genes are transcriptionally activated early but translationally repressed late in the process. Additionally, sphingolipid metabolism enzymes were identified as essential regulators for ciliogenesis, and their interaction with the ciliary membrane and axoneme was suggested to be crucial for cilium formation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Linhua Tai, Guoliang Yin, Fei Sun, Yun Zhu
Summary: The nuclear pore complex (NPC) is a large protein assembly that penetrates the nuclear membrane. Recent breakthroughs in cryo-EM and artificial intelligence-based modeling have allowed for improved understanding of the complex structure of the NPC. This review article summarizes the history and latest advancements in studying the architecture of the NPC, as well as future directions for research.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Shuxin Wang, Mikaila I. Sass, Yujin Kwon, W. Grant Ludlam, Theresa M. Smith, Ethan J. Carter, Nathan E. Gladden, Margot Riggi, Janet H. Iwasa, Barry M. Willardson, Peter S. Shen
Summary: This study determined the structures of human CCT in complex with its accessory co-chaperone PhLP1 during the folding process of G05 protein, and revealed the mechanism by which CCT facilitates G05 folding.
Article
Biochemistry & Molecular Biology
Amin Guo, Bo He, Angdi Li, Huaidong Jiang
Summary: This study investigated the location and distribution of insulin vesicles in pancreatic beta cells using electron microscopy. The content of Zn2+ and Ca2+ in vesicles was analyzed, and a proportional relationship between Zn2+ content and vesicle size was observed. The three-dimensional structure of insulin vesicles was obtained using TEM tomography.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Endocrinology & Metabolism
Montgomery Blencowe, Allison Furterer, Qing Wang, Fuying Gao, Madeline Rosenberger, Lina Pei, Hiroshi Nomoto, Alex M. Mawla, Mark O. Huising, Giovanni Coppola, Xia Yang, Peter C. Butler, Tatyana Gurlo
Summary: The study found that the islet transcriptomes in individuals with prediabetes and type 2 diabetes are remarkably similar. Overexpression of human IAPP induced islet inflammation present in prediabetes and type 2 diabetes.
Review
Biochemistry & Molecular Biology
Naveen Vankadari, Doulin C. Shepherd, Stephen D. Carter, Debnath Ghosal
Summary: Enveloped viruses require a host cell to replicate and cause various diseases. Cryo-electron tomography is a well-suited tool for studying the complex structures of enveloped viruses at a high resolution, and this review explores the latest insights it has provided on the architectures, mechanisms, and processes of these viruses during infection.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Valentina Loconte, Jitin Singla, Angdi Li, Jian-Hua Chen, Axel Ekman, Gerry McDermott, Andrej Sali, Mark Le Gros, Kate L. White, Carolyn A. Larabell
Summary: This study demonstrates the use of soft X-ray tomography to map the ultrastructural reorganization and inter-organelle interactions in cells, specifically the co-localization and interaction between insulin vesicles and mitochondria. These findings are important for understanding cell reorganization processes.
Article
Biochemistry & Molecular Biology
Jitin Singla, Kylie Burdsall, Brian Cantrell, Jordan R. Halsey, Alex McDowell, Colleen McGregor, Sanraj Mittal, Raymond C. Stevens, Shaoyu Su, Alexandra Thomopoulos, Theotime Vaillant, Kate L. White, Bryan Zhang, Helen M. Berman
Summary: As part of a project, a spatiotemporal model of the pancreatic b-cell is being built and an immersive experience called World in a Cell is being created for integrating and generating new educational tools. A new visual design language using tetrahedral building blocks has been developed to represent the structural features of biological molecules and organelles in crowded cellular environments, enabling more efficient animation and user interaction in the immersive environment.
Article
Biology
Jamie S. Depelteau, Ludovic Renault, Nynke Althof, C. Keith Cassidy, Luiza M. Mendonca, Grant J. Jensen, Guenter P. Resch, Ariane Briegel
Summary: Depelteau et al. present a new method to inactivate cryo-EM samples from pathogenic organisms using ultraviolet-C radiation in cryogenic conditions, with no discernable structural impact. This research demonstrates the effectiveness and cost-effectiveness of UVC treatment in cryo-EM sample preparation, which is important for studying the structure and function of pathogens.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Mohammed Kaplan, Catherine M. Oikonomou, Cecily R. Wood, Georges Chreifi, Poorna Subramanian, Davi R. Ortega, Yi-Wei Chang, Morgan Beeby, Carrie L. Shaffer, Grant J. Jensen
Summary: The assembly of flagellar motors is not a simple accumulation of components, but a dynamic process in which accessory components interact transiently to help build the complex nanomachine. Novel cytoplasmic rings were discovered in high-torque motors of Beta-, Gamma-, and Epsilon-proteobacteria, which interact with the cytoplasmic torque ring formed by FliG and are essential for the assembly of stator ring.
Article
Biochemistry & Molecular Biology
Ariana Peck, Stephen D. Carter, Huanghao Mai, Songye Chen, Alister Burt, Grant J. Jensen
Summary: Cryo-electron tomography provides detailed views of macromolecules in situ. However, imaging a large field of view with high magnification restricts the resolution. To overcome this trade-off, we have developed a montage data collection scheme that utilizes overlapping circular tiles to construct tomograms with small pixel size and large field of view. When applied to HeLa cells, this method successfully detected small Thon rings and observed diverse cellular features.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Angdi Li, Xiangyi Zhang, Jitin Singla, Kate White, Valentina Loconte, Chuanyang Hu, Chuyu Zhang, Shuailin Li, Weimin Li, John Paul Francis, Chenxi Wang, Andrej Sali, Liping Sun, Xuming He, Raymond C. Stevens
Summary: This study presents a pipeline for automated segmentation and systematic analysis of SXT tomograms to investigate organelle organization under different treatments. The impact of glucose stimulation on insulin vesicles and mitochondria was revealed through the analysis of INS-1E pancreatic beta cells.
Article
Multidisciplinary Sciences
Angdi Li, Shuning Zhang, Valentina Loconte, Yan Liu, Axel Ekman, Garth J. Thompson, Andrej Sali, Raymond C. Stevens, Kate White, Jitin Singla, Liping Sun
Summary: Investigating the 3D structures and rearrangements of organelles within a single cell is critical for better characterizing cellular function. Here, researchers propose an intensity-based post-processing tool to identify and separate organelle instances more accurately, validating its efficacy using synthetic and experimental tomograms.
Article
Multidisciplinary Sciences
Lauren Ann Metskas, Davi Ortega, Luke M. Oltrogge, Cecilia Blikstad, Derik R. Lovejoy, Thomas G. Laughlin, David F. Savage, Grant J. Jensen
Summary: The authors investigated the position, orientation, and structure of Rubisco in autotrophic bacteria and found that it polymerizes and forms a lattice inside alpha-carboxysomes. This study provides insight into the organization and spatial arrangement of microcompartments in prokaryotic biology and bioengineering.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Daan B. Boltje, Jacob P. Hoogenboom, Arjen J. Jakobi, Grant J. Jensen, Caspar T. H. Jonker, Max J. Kaag, Abraham J. Koster, Mart G. F. Last, Cecilia de Agrela Pinto, Juergen M. Plitzko, Stefan Raunser, Sebastian Tacke, Zhexin Wang, Ernest B. van der Wee, Roger Wepf, Sander den Hoedt, Suzanne R. Pfeffer
Summary: Cryo-ET combined with subtomogram averaging is a powerful technique for visualizing and determining the structure of macromolecular complexes. However, standard cryo-FIB fabrication used for sample preparation is blind to the precise location of structures or proteins of interest. In this study, a fluorescence microscopy-guided FIB fabrication method was developed to address this issue. By retrofitting a cryogenic microcooler and a fluorescence microscope onto an existing FIB scanning electron microscope, precise targeting at every milling step in the lamella fabrication process was achieved, resulting in improved success rate and throughput for high-resolution imaging.
Article
Biochemistry & Molecular Biology
Tatyana Gurlo, Thazha P. Prakash, Zhongying Wang, Maani Archang, Lina Pei, Madeline Rosenberger, Elaine Pirie, Richard G. Lee, Peter C. Butler
Summary: Insulin resistance is a major risk factor for Type 2 diabetes, causing a progressive loss of insulin secretion and islet pathology. Excessive expression of IAPP contributes to beta cell failure and compromises the autophagy lysosomal pathway. Suppression of IAPP expression through an antisense oligonucleotide shows potential as a disease modifying therapy for Type 2 diabetes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Mohammed Kaplan, Qing Yao, Grant J. Jensen
Summary: This study utilized cryo-electron tomography and subtomogram averaging to investigate the structure of the flagellar motor of Proteus mirabilis. It was found that the motor of P. mirabilis is structurally similar to those of E. coli and S. enterica, lacking the periplasmic elaborations found in other specialized gammaproteobacterial motors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Meeting Abstract
Biophysics
Valentina Loconte, Jitin Singla, Angdi Li, Jian-Hua Chen, Axel Ekman, Gerry McDermott, Andrej Sali, Kate L. White, Carolyn Larabell
BIOPHYSICAL JOURNAL
(2022)
