Article
Multidisciplinary Sciences
Carolyn M. Highland, Aaron Tan, Clifton L. Ricana, John A. G. Briggs, Robert A. Dick
Summary: In this study, the authors used cryoelectron tomography and single particle analysis to reveal detailed structural information of the HIV-1 capsid lattice, including both hexamers and pentamers. They also discovered the critical role of inositol hexakisphosphate in pentamer formation and determined the structure of the capsid lattice bound to the antiretroviral drug GS-6207. The combination of lattice templating and single particle analysis proved to be a robust strategy for studying retroviral capsid structure and interactions with host proteins and antiviral compounds.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Yan Zhang, Xiaoyun Pang, Jian Li, Jiashu Xu, Victor W. Hsu, Fei Sun
Summary: By using cryoelectron microscopy, researchers have revealed the protein lattice formed by SNX1, which helps to understand how it functions in generating transport carriers. Comparing the structure of SNX1 with that of an endosomal coat complex formed by retromer coupled to a SNX provides insights into the molecular organization of SNX and the intermediary stages of assembly leading to the formation of the complex on the membrane.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Jiahua He, Sheng-You Huang
Summary: The study presents a semi-automatic de novo structure determination method named DeepMM that can build atomic-accuracy all-atom models from cryo-EM maps at near-atomic resolution. It uses Densely Connected Convolutional Networks to predict main-chain, Ca positions, amino acid, and secondary structure types in the EM map. DeepMM showed significant improvement in accuracy and coverage in building full-length protein structures on various test sets compared to existing methods like RosettaES, MAINMAST, and Phenix.
Article
Multidisciplinary Sciences
Jonathan L. Torres, Gabriel Ozorowski, Emanuele Andreano, Hejun Liu, Jeffrey Copps, Giulia Piccini, Lorena Donnici, Matteo Conti, Cyril Planchais, Delphine Planas, Noemi Manganaro, Elisa Pantano, Ida Paciello, Piero Pileri, Timothee Bruel, Emanuele Montomoli, Hugo Mouquet, Olivier Schwartz, Claudia Sala, Raffaele De Francesco, Ian A. Wilson, Rino Rappuoli, Andrew B. Ward
Summary: As the COVID-19 pandemic continues, highly potent monoclonal antibodies are needed to combat SARS-CoV-2 variants of concern. This study evaluates the efficacy of mAb J08 against these variants and investigates the binding details using cryo-EM and X-ray crystallography. The results demonstrate that mAb J08 has strong affinity against most variants and binds at a specific location on the receptor binding domain, away from the mutation sites. These findings further support the use of mAb J08 as a monoclonal therapy in ongoing clinical trials.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Philip Schmiege, Michael Fine, Xiaochun Li
Summary: TRPML1 regulates lysosomal calcium signaling, lipid trafficking, and autophagy-related processes. Small molecules like ML-SI3 have been shown to modulate channel activity by targeting the TRPML family. The cryo-EM structure of TRPML1 with ML-SI3 provides insights into how these molecules and native lipids regulate TRPML1 activity.
Article
Multidisciplinary Sciences
Muchen Pan, Ana L. Alvarez-Cabrera, Joon S. Kang, Lihua Wang, Chunhai Fan, Z. Hong Zhou
Summary: The authors presented a 3.3 angstrom cryo-EM asymmetric reconstruction of transcribing MRV, revealing molecular interactions among virion proteins and genomic and messenger RNA. The study helps to understand the molecular mechanisms involved in virus assembly and RNA transcription by elucidating different interactions among molecules.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Songwon Kim, Sang Soo Lee, Jun Gyou Park, Ji Won Kim, Seulgi Ju, Seung Hun Choi, Subin Kim, Na Jin Kim, Semi Hong, Jin Young Kang, Mi Sun Jin
Summary: The cryo-EM structures of human ABCB6 with its substrates CPIII and hemin were reported. The study revealed that ABCB6 utilizes different mechanisms to regulate substrate specificity and transport efficiency.
MOLECULES AND CELLS
(2022)
Article
Multidisciplinary Sciences
Lei Yang, Binglin Xing, Fen Li, Li Kui Wang, Linlin Yuan, Amosi Leonard Mbuji, Zhengqiang Peng, Farag Malhat, Shaoying Wu
Summary: This study used PacBio single-molecule real-time (SMRT) sequencing to uncover the full-length transcriptome profiling of fall armyworm larval brain, identifying a large number of detoxification genes and providing crucial data support for understanding the insecticide resistance mechanisms in fall armyworm.
Article
Biochemistry & Molecular Biology
Ling Zheng, Yiwu Zhao, Yifeng Gan, Hao Li, Shiqi Luo, Xiang Liu, Yuanyuan Li, Qun Shao, Hui Zhang, Yanxiu Zhao, Changle Ma
Summary: Quinoa demonstrates a wide stress response to cold temperature, especially in regulating osmoregulation and ROS homeostasis. The cold-resistant variety CRQ64 shows more extensive stress response compared to the cold-sensitive variety CSQ5.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Zelin Liu, Changyu Tao, Shiwei Li, Minghao Du, Yongtai Bai, Xueyan Hu, Yu Li, Jian Chen, Ence Yang
Summary: circFL-seq is a novel method for full-length circRNA sequencing, allowing accurate identification and quantification of complete circRNA sequences with significant advantages at the isoform level. This method enables large-scale screening of functional circRNAs.
Review
Biochemistry & Molecular Biology
Hisham Mazal, Franz -Ferdinand Wieser, Vahid Sandoghdar
Summary: In the last two decades, fluorescence microscopy has seen many innovations, but the resolution is still limited by sample motion. Cryogenic light microscopy offers a solution with higher resolution and more photons at low temperatures, making it useful for studying the structure of proteins and protein complexes.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Plant Sciences
Beibei Chen, Tingting Liu, Zhuanying Yang, Shaoxia Yang, Jinhui Chen
Summary: This study analyzed the molecular mechanism of salt stress response in Sonneratia apetala leaves using Iso-seq and RNA-seq technologies. The results showed significant changes in growth and physiological indexes under salt stress. Additionally, several genes related to salt stress response were identified.
Article
Environmental Sciences
Xiaolin Guo, Xixi Li, Feng Zhao, Danwen Liu, Zujing Yang, Moli Li, Yajuan Li, Huilan Wei, Hao Wang, Zhenkui Qin, Zhifeng Zhang, Zhenmin Bao
Summary: This study generated a comprehensive transcriptome for M. lateralis at different developmental stages and investigated the mechanisms of larval shell formation in molluscs at the molecular level. Key genes involved in shell formation were identified. This research is valuable for understanding the mechanisms of larval shell formation and other developmental processes in molluscs.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Xuedi Du, Weiwei Zhang, Jiali Wu, Congyuan You, Xiaojing Dong
Summary: In this study, hybrid transcriptome sequencing was used to analyze the gene expression profiles of Celestial-Eye (CE) and Ryukin (RK) goldfish embryos. Thousands of alternative splicing and alternative polyadenylation events were identified, most of which were breed-specific. RNA-seq analysis revealed extensive differences in gene expression between CE and RK goldfish at each embryonic stage, indicating that artificial selection has had far-reaching effects on goldfish gene expression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Physiology
Mariah R. R. Pierce, James L. L. Hougland
Summary: Acylation modifications in biological processes and their association with various health conditions have attracted much research interest. The membrane bound O-acyltransferase (MBOAT) family of enzymes play a crucial role in these modifications. Recent advancements in solubilization approaches and structural characterization techniques have provided a wealth of information on the structure and function of MBOATs, enabling a better understanding of their catalytic activity and potential therapeutic applications.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alexander Krah, Roland G. Huber, Ulrich Zachariae, Peter J. Bond
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2020)
Article
Biochemistry & Molecular Biology
Jitka Petrlova, Ganna Petruk, Roland G. Huber, Eilish W. McBurnie, Mariena J. A. van der Plas, Peter J. Bond, Manoj Puthia, Artur Schmidtchen
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Kwok-Fong Chan, Chinh Tran-To Su, Alexander Krah, Ser-Xian Phua, Joshua Yi Yeo, Wei-Li Ling, Peter J. Bond, Samuel Ken-En Gan
Article
Biochemistry & Molecular Biology
Ganna Petruk, Jitka Petrlova, Firdaus Samsudin, Rita Del Giudice, Peter J. Bond, Artur Schmidtchen
Article
Biochemistry & Molecular Biology
Wanwisa Dejnirattisai, Daming Zhou, Helen M. Ginn, Helen M. E. Duyvesteyn, Piyada Supasa, James Brett Case, Yuguang Zhao, Thomas S. Walter, Alexander J. Mentzer, Chang Liu, Beibei Wang, Guido C. Paesen, Jose Slon-Campos, Cesar Lopez-Camacho, Natasha M. Kafai, Adam L. Bailey, Rita E. Chen, Baoling Ying, Craig Thompson, Jai Bolton, Alex Fyfe, Sunetra Gupta, Tiong Kit Tan, Javier Gilbert-Jaramillo, William James, Michael Knight, Miles W. Carroll, Donal Skelly, Christina Dold, Yanchun Peng, Robert Levin, Tao Dong, Andrew J. Pollard, Julian C. Knight, Paul Klenerman, Nigel Temperton, David R. Hall, Mark A. Williams, Neil G. Paterson, Felicity K. R. Bertram, C. Alistair Siebert, Daniel K. Clare, Andrew Howe, Julika Radecke, Yun Song, Alain R. Townsend, Kuan-Ying A. Huang, Elizabeth E. Fry, Juthathip Mongkolsapaya, Michael S. Diamond, Jingshan Ren, David Stuart, Gavin R. Screaton
Summary: Antibodies play a crucial role in immune protection against SARS-CoV-2, with some being used as therapeutics. A study identified 377 human monoclonal antibodies, focusing on 80 that bind the virus spike, and found that most highly inhibitory antibodies can block the virus-receptor interaction. Novel binding modes of potent inhibitory antibodies were discovered, showing potential for prophylactic or therapeutic use in animal models.
Article
Multidisciplinary Sciences
Joshua B. R. White, Daniel P. Maskell, Andrew Howe, Martin Harrow, Daniel K. Clare, C. Alistair Siebert, Emma L. Hesketh, Rebecca F. Thompson
Summary: Cryo-electron microscopy is a powerful technique for structure determination of macromolecular complexes through single particle analysis, involving vitrification, specimen screening, data collection, and image processing, with options for user modification and common troubleshooting. Variations on imaging protocols to assist users in efficient operation and imaging when physical access to the microscope is limited are being developed due to remote microscope operation becoming standard.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemistry & Molecular Biology
James M. Parkhurst, Maud Dumoux, Mark Basham, Daniel Clare, C. Alistair Siebert, Trond Varslot, Angus Kirkland, James H. Naismith, Gwyndaf Evans
Summary: Parakeet is a digital twin software for assessing the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions, and optimizing the performance and utilization of physical instruments for in silico optimization of sample geometries, data acquisition schemes, and instrument parameters.
Article
Multidisciplinary Sciences
Pu Qian, Alastair T. Gardiner, Ivana Simova, Katerina Naydenova, Tristan Croll, Philip J. Jackson, Nupur, Miroslav Kloz, Petra Cubakova, Marek Kuzma, Yonghui Zeng, Pablo Castro-Hartmann, Bart van Knippenberg, Kenneth N. Goldie, David Kaftan, Pavel Hrouzek, Jan Hajek, Jon Agirre, C. Alistair Siebert, David Bina, Kasim Sader, Henning Stahlberg, Roman Sobotka, Christopher J. Russo, Tomas Polivka, C. Neil Hunter, Michal Koblizek
Summary: Phototrophic Gemmatimonadetes have evolved the ability to use solar energy through horizontal gene transfer. The study reveals the unique solar energy harvesting and trapping architecture of Gemmatimonas phototrophica, as well as the flow of energy within the complex.
Article
Biochemistry & Molecular Biology
Matthew S. Proctor, Lorna A. Malone, David A. Farmer, David J. K. Swainsbury, Frederick R. Hawkings, Federica Pastorelli, Thomas Z. Emrich-Mills, C. Alistair Siebert, C. Neil Hunter, Matthew P. Johnson, Andrew Hitchcock
Summary: In this study, the structure of the Synechocystis sp. PCC 6803 cytb(6)f complex in the presence and absence of PetP was determined using cryogenic electron microscopy. The results revealed that PetP interacts with cytb(6)f, affecting the structure and function of the complex, and thereby regulating the electron transfer process in photosynthesis.
BIOCHEMICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Manoj Puthia, Jan K. Marzinek, Ganna Petruk, Gizem Erturk Bergdahl, Peter J. Bond, Jitka Petrlova
Summary: This study demonstrates that APOE has anti-bacterial activity against several Gram-negative bacterial strains and exhibits significant binding affinity for lipopolysaccharide and heparin. Molecular dynamics simulations reveal the binding region in helix 4 of APOE as a primary site for interaction with these molecules through electrostatic interactions.
Article
Biology
Maud Dumoux, Thomas Glen, Jake L. R. Smith, Elaine M. L. Ho, Luis M. A. Perdigao, Avery Pennington, Sven Klumpe, Neville B. Y. Yee, David Andrew Farmer, Pui Y. A. Lai, William Bowles, Ron Kelley, Juergen M. Plitzko, Liang Wu, Mark Basham, Daniel K. Clare, C. Alistair Siebert, Michele C. Darrow, James H. Naismith, Michael Grange, Giulia Zanetti
Summary: Cryogenic plasma FIB/SEM overcomes challenges in imaging non-stained biological samples, producing high-quality images with automated workflows. This technique allows for three-dimensional imaging of bacteria, human cells, and tissue with resolutions typically ranging from 20-50 nm.
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
Biochemistry & Molecular Biology
Priscilla L. S. Boon, Ana S. Martins, Xin Ni Lim, Francisco J. Enguita, Nuno C. Santos, Peter J. Bond, Yue Wan, Ivo C. Martins, Roland G. Huber
Summary: Dengue virus is a significant health risk in tropical and subtropical regions. The structure of the packaged genome in complex with C proteins remains elusive. This study investigates the interactions of C proteins with viral RNA and shows their role in coordinating key interactions for proper packaging of viral RNA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Yuewen Sheng, Peter J. Harrison, Vinod Vogirala, Zhengyi Yang, Claire Strain-Damerell, Thomas Frosio, Benjamin A. Himes, C. Alistair Siebert, Peijun Zhang, Daniel K. Clare
Summary: Developments in cryo-electron tomography and sub-tomogram averaging show exciting potential in achieving near-atomic resolution structures in protein determination. The application of super-resolution mode in single particle analysis and cryo-ET STA data collection yield different resolution benefits, with considerations needed for specific experimental conditions.
FARADAY DISCUSSIONS
(2022)
Article
Chemistry, Multidisciplinary
Firdaus Samsudin, Joshua Yi Yeo, Samuel Ken-En Gan, Peter J. Bond
