Article
Multidisciplinary Sciences
Dominik Hrebik, Tibor Fuzik, Maria Gondova, Lenka Smerdova, Athanassios Adamopoulos, Ondrej Sedo, Zbynek Zdrahal, Pavel Plevka
Summary: This study elucidated the structure of the rhinovirus 14 complex with ICAM-1, showing how this complex is crucial for virus activation and genome release. The binding of ICAM-1 induces conformational changes in the capsid of rhinovirus 14, priming it for activation and genome release under acidic pH conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
James C. V. Stacey, Aaron Tan, John M. Lu, Leo C. James, Robert A. Dick, John A. G. Briggs
Summary: Using single-particle cryoEM, researchers have determined the structure of the mature HIV-1 CA pentamer and hexamer from conical CA-IP6 polyhedra. Comparison of these structures revealed that the conical HIV-1 capsid has different host-protein binding properties at different positions on its surface, which may facilitate cell entry and represent an evolutionary advantage of conical morphology.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Qinfen Zhang, Yuanzhu Gao, Matthew L. L. Baker, Shanshan Liu, Xudong Jia, Haidong Xu, Jianguo He, Jason T. T. Kaelber, Shaoping Weng, Wen Jiang
Summary: This study reports the structure of mud crab reovirus (MCRV) and reveals its important components and arrangement, as well as its infectivity, genome packaging, and RdRp organization in hosts.
Article
Virology
Michaela Prochazkova, Tibor Fuzik, Danyil Grybchuk, Francesco Luca Falginella, Lucie Podesvova, Vyacheslav Yurchenko, Robert Vacha, Pavel Plevka
Summary: Leishmania parasites carrying Leishmania RNA virus 1 (LRV1) are more likely to cause severe disease, and the structure of the LRV1 capsid provides insights for developing new treatments.
JOURNAL OF VIROLOGY
(2021)
Article
Virology
Naoyuki Miyazaki, Chihong Song, Tomoichiro Oka, Motohiro Miki, Kosuke Murakami, Kenji Iwasaki, Kazuhiko Katayama, Kazuyoshi Murata
Summary: SaV and norovirus are common causes of acute gastroenteritis in humans and animals, posing public health problems worldwide. The genetically diverse HuSaV has hindered the development of vaccines and therapeutics due to the lack of viral replication system and structural information. This study successfully produced a virus-like particle from HuSaV and determined its atomic structure, providing important insights for medical treatment and vaccine development.
JOURNAL OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jennifer M. Podgorski, Krista Freeman, Sophia Gosselin, Alexis Huet, James F. Conway, Mary Bird, John Grecco, Shreya Patel, Deborah Jacobs-Sera, Graham Hatfull, Johann Peter Gogarten, Janne Ravantti, Simon J. White
Summary: Many double-stranded DNA viruses, including tailed bacteriophages and herpesviruses, use the HK97-fold in their major capsid protein. The evolution of capsid structural stability within the actinobacteriophages has been investigated using cryo-EM structure determination, structural comparisons, phylogenetic analyses, and AlphaFold predictions. The actinobacteriophage major capsid proteins can be classified into 15 groups based on their HK97-fold.
Article
Chemistry, Multidisciplinary
Lukas Sukenik, Liya Mukhamedova, Michaela Prochazkova, Karel Skubnik, Pavel Plevka, Robert Vacha
Summary: Virus-like nanoparticles and wild-type viruses share similar protein shells and aims of delivering genes into cells, but the mechanism of gene release differs. Interactions between capsid subunits and compactness of genes affect the speed and pathways of release, providing insights for drug delivery design.
Article
Multidisciplinary Sciences
Baldeep Khare, Thomas Klose, Qianglin Fang, Michael G. Rossmann, Richard J. Kuhn
Summary: Usutu virus (USUV) is an emerging arbovirus in Europe that causes neuroinvasive human disease. There are currently no treatment or prevention options available due to a lack of understanding of USUV pathogenesis. Research on the mature USUV virus structure may lead to the development of therapeutics and expand knowledge on flavivirus biology.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Nathaniel Talledge, Huixin Yang, Ke Shi, Raffaele Coray, Guichuan Yu, William G. Arndt, Shuyu Meng, Gloria C. Baxter, Luiza M. Mendonca, Daniel Castano-Diez, Hideki Aihara, Louis M. Mansky, Wei Zhang
Summary: The morphology of HIV-2 immature particles consists of a distinct and extensive Gag lattice structure. Using cryo-electron microscopy, the 3D organization of the HIV-2 Gag lattice was determined, revealing a stable wineglass-shaped structure. Cryo-electron tomography showed nearly complete ordered Gag lattice structures in HIV-2 immature particles. Additionally, the crystal structure of the carboxyl-terminal domain of the HIV-2 capsid protein identified a structured helix 12, which plays a critical role in particle release and infectivity.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Karel Skubnik, Lukas Sukenik, David Buchta, Tibor Fuzik, Michaela Prochazkova, Jana Moravcova, Lenka Smerdova, Antonin Pridal, Robert Vacha, Pavel Plevka
Summary: The Iflaviridae family consists of economically important viruses affecting western honeybees. These viruses induce genome release through conformational changes triggered by acidic pH, with different mechanisms for releasing genomes from their capsids.
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)
Article
Biology
Danyil Grybchuk, Michaela Prochazkova, Tibor Fuzik, Aleksandras Konovalovas, Saulius Serva, Vyacheslav Yurchenko, Pavel Plevka
Summary: This study determined the structure and assembly mechanism of the L-BC virus using cryo-electron microscopy. The L-BC capsid has an icosahedral symmetry and the capsid proteins are stabilized by domain swapping. Additionally, some L-BC virus particles were found to be open and lacked one decamer of capsid proteins.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Mathilde Briday, Francois Halle, Lauriane Lecoq, Sylvie Radix, Juliette Martin, Roland Montserret, Marie Dujardin, Marie-Laure Fogeron, Michael Nassal, Beat H. Meier, Thierry Lomberget, Anja Bockmann
Summary: Hepatitis B virus (HBV) is a significant human pathogen and its capsid-forming core protein (Cp) plays a key role in envelopment. Recent studies have found that Triton X-100, a detergent used in Cp purification, strongly binds to the hydrophobic pocket of Cp. The aromatic moiety is crucial for binding, while the aliphatic chain affects binding affinity. Moreover, the hydrophilic tail shows high tolerance to changes in length and type.
Article
Biotechnology & Applied Microbiology
Anshu Nain, Mohit Kumar, Manidipa Banerjee
Summary: This study successfully generated recombinant VP1 oligomers from Hepatitis A Virus in the E. coli expression system. Purification of the protein from inclusion bodies and refolding resulted in correctly folded VP1 oligomers with similar structure to other picornaviruses. These VP1 oligomers could be utilized for understanding the molecular pathway of HAV capsid assembly and have potential biomedical applications in prevention and diagnostics of HAV infections.
MICROBIAL CELL FACTORIES
(2022)
Article
Biochemistry & Molecular Biology
Hyeongseop Jeong, Youngmin Park, Sooji Song, Kyungmin Min, Jae-Sung Woo, Young-Ho Lee, Eun-Ju Sohn, Sangmin Lee
Summary: Research indicates that VLPs, as a safe drug/vehicle candidate, have great potential in the fields of preventive medicine and therapeutics. Scientists propose that rAMV-CP VLP, based on efficient VLP production process and high-resolution structure analysis, can serve as a useful platform for the development of various new drugs.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
J. Bernard Heymann, Roberto Marabini, Mohsen Kazemi, Carlos Oscar S. Sorzano, Maya Holmdahl, Joshua H. Mendez, Scott M. Stagg, Slavica Jonic, Eugene Palovcak, Jean-Paul Armache, Jianhua Zhao, Yifan Cheng, Grigore Pintilie, Wah Chiu, Ardan Patwardhan, Jose-Maria Carazo
JOURNAL OF STRUCTURAL BIOLOGY
(2018)
Article
Cell Biology
J. Bernard Heymann, Camasamudra Vijayasarathy, Rick K. Huang, Altaira D. Dearborn, Paul A. Sieving, Alasdair C. Steven
JOURNAL OF CELL BIOLOGY
(2019)
Article
Biochemical Research Methods
J. Bernard Heymann
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2019)
Meeting Abstract
Biophysics
Bernard Heymann, Christopher K. E. Bleck, Robert N. Fariss, Alexandr Smirnov, Dennis C. Winkler, Camasamudram Vijayasarathy, Rick Huang, Altaira D. Dearborn, Paul A. Sieving, Alasdair C. Steven
BIOPHYSICAL JOURNAL
(2019)
Article
Microbiology
Ambroise Desfosses, Hariprasad Venugopal, Tapan Joshi, Jan Felix, Matthew Jessop, Hyengseop Jeong, Jaekyung Hyun, J. Bernard Heymann, Mark R. H. Hurst, Irina Gutsche, Alok K. Mitra
NATURE MICROBIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
J. Bernard Heymann
Summary: Bsoft offers tools for processing tomographic tilt series and interpreting tomograms. The field has advanced significantly in the past two decades, requiring refinement of old algorithms and development of new ones. Direct detectors now allow more efficient data collection and progress towards automation.
Article
Virology
J. Bernard Heymann, Bing Wang, William W. Newcomb, Weimin Wu, Dennis C. Winkler, Naiqian Cheng, Erin R. Reilly, Ru-Ching Hsia, Julie A. Thomas, Alasdair C. Steven
Article
Multidisciplinary Sciences
Erney Ramirez-Aportela, David Maluenda, Yunior C. Fonseca, Pablo Conesa, Roberto Marabini, J. Bernard Heymann, Jose Maria Carazo, Carlos Oscar S. Sorzano
Summary: This article introduces a method for local analysis of map-to-model fit in cryoEM, using a comparison of two local resolution maps and introducing FSC-Q as a quantitative estimation of how much of the model is supported by the signal content of the map.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Michael H. C. Buch, William W. Newcomb, Dennis C. Winkler, Alasdair C. Steven, J. Bernard Heymann
Summary: The portal protein of Herpes simplex virus 1 plays a crucial role in packaging its genome and maturation process, forming a complex with scaffold proteins. As the capsid angularizes during maturation, the portal protein moves outward and strengthens its contacts with the capsid shell. Most capsids contain a single portal protein supporting the assembly of procapsids.
Article
Computer Science, Interdisciplinary Applications
J. Bernard Heymann
Summary: This study aims to assess and improve the quality of cryoEM reconstructions by calculating the spectral SNR (SSNR) and radiation damage. Through alignment and calculation of several test cases of movie frames, it was found that alignment compensated for global movement, the effect on SSNR was negligible, and the subset SSNR confirmed residual movement. The progressive SSNR reflected radiation damage and signal accumulation decrease. The results contribute to the assessment of micrograph quality and progression of radiation damage.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Review
Ophthalmology
J. Bernard Heymann, Camasamudram Vijayasarathy, Robert N. Fariss, Paul A. Sieving
Summary: Retinoschisin (RS1) is crucial for maintaining retinal integrity, but mutations in RS1 cause X-linked retinoschisis (XLRS) and vision loss. The formation of cysts and schisis in the retina disrupts synaptic transmission. Gene augmentation therapy using AAV vectors is being evaluated as a potential treatment for XLRS. Understanding the secretion and molecular function of RS1 is essential for improving therapeutic strategies.
PROGRESS IN RETINAL AND EYE RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
J. Bernard Heymann
Summary: In cryoEM, it is essential to consider the Ewald sphere/focus gradient and its implications for high resolution and handedness information recovery. Different approaches have been proposed, but the correct one remains uncertain. The traditional projection approximation breaks down at high acceleration voltages, but correct reconstruction along the Ewald spheres can avoid its limitations and reach resolutions to the Nyquist frequency.
JOURNAL OF STRUCTURAL BIOLOGY-X
(2023)
Article
Biology
J. Bernard Heymann
Summary: Bsoft is a software package developed for processing electron micrographs. It has over 150 programs for manipulating and understanding images. The primary aim is to provide powerful capabilities for processing large numbers of images.
Article
Biology
J. Bernard Heymann
Article
Biology
Evan S. Krystofiak, J. Bernard Heymann, Bechara Kachar
COMMUNICATIONS BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)