Article
Chemistry, Multidisciplinary
Shinji Kishimoto, Ayumi Minami, Yoshimitsu Aoki, Yuya Matsubara, Shogo Watanabe, Kenji Watanabe
Summary: Pathogenic fungi of Aspergillus section Fumigati are capable of producing various secondary metabolites. This study reports the isolation of fumimycin and a new compound named lentofuranine from A. lentulus. These compounds were found to be assembled through a nonenzymatic condensation involving a polyketide intermediate from the terrein biosynthetic pathway and a highly reactive azlactone intermediate. The formation of an unusual carbon skeleton is attributed to the reactivity of azlactone.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Engineering, Mechanical
Wenhui Shen, Zihan Tang, Xuwei Wu, Liang Pan, Yuan Cheng, Bo Huo, Jizhou Song, Weiqiu Chen, Baohua Ji, Dechang Li
Summary: This study constructed an atomistic silk protein network model and investigated the structure evolution and stress distribution of silk protein under external loading. The study found that a pre-stretching treatment during the spinning process can improve the strength of silk protein by enhancing the properties of the silk protein network.
ACTA MECHANICA SINICA
(2022)
Article
Biochemistry & Molecular Biology
Francesca Malagrino, Giuliana Fusco, Valeria Pennacchietti, Angelo Toto, Caterina Nardella, Livia Pagano, Alfonso de Simone, Stefano Gianni
Summary: PDZ domains are common protein-protein interaction modules in the human proteome, often present in multiple repeats. PDZD2 is a protein with six PDZ domains, which undergoes proteolytic cleavage to produce sPDZD2, consisting of a tandem of two PDZ domains, namely PDZ5 and PDZ6. The folding pathway of sPDZD2 involves a transient folding intermediate that may be formed from the denaturation of both PDZ5 and PDZ6 domains. Importantly, this intermediate shows increased affinity for the physiological ligand of sPDZD2 compared to the native state. These findings provide an interesting example of a functionally competent misfolded intermediate.
Article
Biochemical Research Methods
Truc Lam Pham, Michael Kovermann, Franziska Thomas
Summary: This study presents a monomeric beta-sheet peptide that can switch between a molten globule and folded state through Zn(II) binding, with specific recognition of Zn(II) compared to other divalent metal ions. The peptide is pH-switchable, surviving multiple cycles of acidification and neutralization. Structural characterization was achieved through circular dichroism and multinuclear NMR spectroscopy, indicating a viable approach for a globular beta-sheet Zn(II) mini-receptor prototype.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Computer Science, Information Systems
Yixing Niu, Wansheng Cheng, Yushan Lai, Hongzhi Zhang, Mingrui Cao, Kang Cao, Song Fan
Summary: This study proposes a high-quality integration domain framework for pedestrian recognition. Super-resolution algorithms and a generative framework are used to generate high-quality intermediate domains, and a multi-source domain fusion scheme is proposed to improve the framework's quality. A anchor-free center and scale prediction model is used for pedestrian detection. Experimental results show that the framework performs well in cross-domain pedestrian detection.
Editorial Material
Biochemistry & Molecular Biology
Hao Xu
Summary: The study revealed that the transmembrane domains of syntaxin6 and syntaxin8 could be used for tau release, providing a new insight into the mechanism of tau secretion. This has significant implications for research on neurodegenerative diseases.
BIOCHEMICAL JOURNAL
(2021)
Article
Biology
Priyanka Baloni, Matthias Arnold, Luna Buitrago, Kwangsik Nho, Herman Moreno, Kevin Huynh, Barbara Brauner, Gregory Louie, Alexandra Kueider-Paisley, Karsten Suhre, Andrew J. Saykin, Kim Ekroos, Peter J. Meikle, Leroy Hood, Nathan D. Price, P. Murali Doraiswamy, Cory C. Funk, A. Ivan Hernandez, Gabi Kastenmueller, Rebecca Baillie, Xianlin Han, Rima Kaddurah-Daouk
Summary: This study investigates the role of sphingomyelin and ceramide metabolism in Alzheimer's disease through multi-omics analyses and imaging features. The findings suggest potential therapeutic targets in the sphingomyelin pathway and demonstrate the efficacy of modulators of S1P metabolism in treating Alzheimer's disease, as validated in mouse models.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jason Y. C. Tam, Tim Lorsbach, Sebastian Schmidt, Joerg S. Wicker
Summary: The prediction of metabolism and biotransformation pathways of xenobiotics is important in various fields. Existing prediction systems may not account for specific challenges like missing transformation products in low concentrations or evaluate performance solely based on defined rules. A new evaluation framework is introduced in this paper to address these challenges and improve performance metrics.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Engineering, Environmental
Reshmi John, Charuvila T. Aravindakumar, Usha K. Aravind
Summary: The molecular basis of protein unfolding in response to the herbicide Glyphosate and its metabolite aminomethylphosphonic acid, as well as the commercial formulation Roundup, has been investigated using human and bovine serum albumins. It was found that Glyphosate led to the formation of fibrils in bovine serum albumin, while aminomethylphosphonic acid resulted in the formation of oligomer networks in serum albumins. Roundup triggered the formation of amorphous aggregates in serum albumins.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Multidisciplinary Sciences
Mithu Baidya, Madhu Chaturvedi, Hemlata Dwivedi-Agnihotri, Ashutosh Ranjan, Dominic Devost, Yoon Namkung, Tomasz Maciej Stepniewski, Shubhi Pandey, Minakshi Baruah, Bhanupriya Panigrahi, Parishmita Sarma, Manish K. Yadav, Jagannath Maharana, Ramanuj Banerjee, Kouki Kawakami, Asuka Inoue, Jana Selent, Stephane A. Laporte, Terence E. Hebert, Arun K. Shukla
Summary: This study reveals that synthetic antibodies can be used to modulate GPCR trafficking and signaling in live cells.
NATURE COMMUNICATIONS
(2022)
Article
Biophysics
Hanne Hollas, Juan Ramirez, Yves Nomine, Camille Kostmann, Angelo Toto, Stefano Gianni, Gilles Trave, Anni Vedeler
Summary: Annexins are a family of proteins that can bind and aggregate lipid vesicles in the presence of calcium. This study found that specific regions of AnxA2 and interactions between certain residues are crucial for its folding and stability. However, the folding of the full-length protein is robust and may involve intermediate steps. Mutations in specific amino acids of AnxA2 can affect its cooperative folding and stability. These findings are important for designing anticancer drugs targeting AnxA2.
BIOPHYSICAL JOURNAL
(2022)
Article
Microbiology
Philip Ruelens, J. Arjan G. M. de Visser
Summary: The study found that at low cefotaxime concentrations, the R164S mutation, which confers relatively low resistance, is competitively superior to the G238S mutation, conferring higher resistance. This highlights the critical influence of antibiotic concentration on long-term resistance evolution.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Review
Biochemistry & Molecular Biology
Anna Kozell, Aleksei Solomonov, Ulyana Shimanovich
Summary: In the past, ultrasound and protein complexes were considered unrelated topics. However, recent studies have focused on the ability of ultrasound to induce chemical modifications on proteins, leading to changes in protein-protein interactions and self-assembly. Despite limited understanding of these phenomena, this review provides a comprehensive analysis of the role of ultrasound in protein complexation, with a specific focus on amyloid self-assembly relevant to neurodegenerative disorders.
Article
Engineering, Industrial
Xuelei Zhao, Hengan Ou
Summary: This research introduces a new flexible multi-point incremental sheet forming process with multi-layer sheets (F-MPIF-MLS). The novelty of this process lies in the development of a new flexible multi-point die system and the use of multi-layer sheets, which overcome the limitations of excessive sheet thinning and poor surface finish in the conventional MPIF process. Experimental testing and FE simulation are conducted to compare the new F-MPIF-MLS with the conventional MPIF processes, showing a reduction in wrinkling and a more uniform thickness distribution in the formed part using the new flexible multi-point die system with multi-layer sheets.
JOURNAL OF MATERIALS PROCESSING TECHNOLOGY
(2023)
Article
Chemistry, Physical
Matthew T. O. Okenyi, Laura E. Ratcliff, Aron Walsh
Summary: This study explores proton tautomerism in the molecular ferroelectric croconic acid and provides insights into constructing effective Hamiltonians to describe proton transfer ferroelectrics, by approximating the minimum energy path between structural ground states and analyzing the potential energy curve along this path.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Ki-Young Lee, Zhenhao Fang, Masahiro Enomoto, Genevieve Gasmi-Seabrook, Le Zheng, Shohei Koide, Mitsuhiko Ikura, Christopher B. Marshall
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Review
Biochemistry & Molecular Biology
Oliver Hantschel, Matthew Biancalana, Shohei Koide
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2020)
Article
Immunology
Carmine Fedele, Shuai Li, Kai Wen Teng, Connor J. R. Foster, David Peng, Hao Ran, Paolo Mita, Mitchell J. Geer, Takamitsu Hattori, Akiko Koide, Yubao Wang, Kwan Ho Tang, Joshua Leinwand, Wei Wang, Brian Diskin, Jiehui Deng, Ting Chen, Igor Dolgalev, Ugur Ozerdem, George Miller, Shohei Koide, Kwok-Kin Wong, Benjamin G. Neel
Summary: The combination of SHP2 inhibitor and KRAS (G12C) inhibitor shows significant survival benefits in PDAC and NSCLC, inducing favorable changes in the tumor microenvironment by reducing myeloid suppressor cells, increasing CD8(+) T cells, and enhancing sensitivity to PD-1 blockade.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Biochemical Research Methods
Takamitsu Hattori, Akiko Koide, Tatyana Panchenko, Larizbeth A. Romero, Kai Wen Teng, Alexis D. Corrado, Shohei Koide
Summary: Accurate quantification of protein-ligand interactions is crucial in biology and medicine, and multiplex bead binding assays (MBBAs) provide a powerful method for analyzing multiple interactions simultaneously. This research introduces a cost-effective MBBA method using the irreversible biotin-streptavidin interaction, offering a way to improve throughput and reduce antigen consumption in characterization assays.
JOURNAL OF IMMUNOLOGICAL METHODS
(2021)
Article
Biochemistry & Molecular Biology
Takamitsu Hattori, Akiko Koide, Maria G. Noval, Tatyana Panchenko, Larizbeth A. Romero, Kai Wen Teng, Takuya Tada, Nathaniel R. Landau, Kenneth A. Stapleford, Shohei Koide
Summary: The experimentation revealed that only a small fraction of antibodies targeted the ACE2-interacting surface of the spike protein, while other regions of the virus were more immunogenic. This has significant implications for the treatment and vaccine development for COVID-19.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Maria G. Noval, Maria E. Kaczmarek, Akiko Koide, Bruno A. Rodriguez-Rodriguez, Ping Louie, Takuya Tada, Takamitsu Hattori, Tatyana Panchenko, Larizbeth A. Romero, Kai Wen Teng, Andrew Bazley, Maren de Vries, Marie Samanovic, Jeffrey N. Weiser, Ioannis Aifantis, Joan Cangiarella, Mark J. Mulligan, Ludovic Desvignes, Meike Dittmann, Nathaniel R. Landau, Maria Aguero-Rosenfeld, Shohei Koide, Kenneth A. Stapleford
Summary: Studies have shown that a majority of recovered healthcare workers produce antibodies with low neutralization capacity against SARS-CoV-2, with only a small percentage showing high neutralizing titers. Higher neutralizing sera are correlated with detection of a broader range of antibodies, while individuals with only IgG antibodies exhibit poor neutralization response.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Sarah E. Garnish, Yanxiang Meng, Akiko Koide, Jarrod J. Sandow, Eric Denbaum, Annette V. Jacobsen, Wayland Yeung, Andre L. Samson, Christopher R. Horne, Cheree Fitzgibbon, Samuel N. Young, Phoebe P. C. Smith, Andrew I. Webb, Emma J. Petrie, Joanne M. Hildebrand, Natarajan Kannan, Peter E. Czabotar, Shohei Koide, James M. Murphy
Summary: Phosphorylation of MLKL by RIPK3 kinase leads to MLKL oligomerization, translocation, and membrane permeabilization to induce cell death. Monobodies can bind to the MLKL pseudokinase domain, revealing distinct conformations during activation and disengagement from RIPK3, a key regulatory step in necroptosis. These structural and functional studies shed light on the mechanism of MLKL activation and regulation in necroptosis.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Kai Wen Teng, Steven T. Tsai, Takamitsu Hattori, Carmine Fedele, Akiko Koide, Chao Yang, Xuben Hou, Yingkai Zhang, Benjamin G. Neel, John P. O'Bryan, Shohei Koide
Summary: A monobody named 12VC1 that can selectively recognize and bind to the active state of KRAS mutants has been discovered in this study, showing great potential in inhibiting the proliferation of RAS-driven cancer cell lines. This finding suggests a new strategy for treating oncogenic RAS mutants through inhibition and degradation.
NATURE COMMUNICATIONS
(2021)
Article
Physiology
Maria Lopez-Redondo, Shujie Fan, Akiko Koide, Shohei Koide, Oliver Beckstein, David L. Stokes
Summary: The study reveals unique Zn2+ binding sites and conformational changes of YiiP and Znt8 through structural analysis. Results show that YiiP adopts an inward-facing conformation in the presence of Zn2+ and exhibits a novel, intermediate conformation between inward and outward states after removal of Zn2+.
JOURNAL OF GENERAL PHYSIOLOGY
(2021)
Article
Multidisciplinary Sciences
Julien Oury, Wei Zhang, Nadia Leloup, Akiko Koide, Alexis D. Corrado, Gayatri Ketavarapu, Takamitsu Hattori, Shohei Koide, Steven J. Burden
Summary: Congenital myasthenia is a devastating neuromuscular disease caused by mutations in DOK7 gene, which is crucial for neuromuscular synapse formation. The most common disease-causing mutation truncates DOK7, leading to loss of phosphorylated tyrosine residues essential for acetylcholine receptor anchoring. Studies on mouse models identified a severe deficiency in muscle-specific kinase activation as the cause of deficits, and antibody treatment against MUSK showed potential therapy for CM.
Article
Microbiology
Imran Sulaiman, Matthew Chung, Luis Angel, Jun-Chieh J. Tsay, Benjamin G. Wu, Stephen T. Yeung, Kelsey Krolikowski, Yonghua Li, Ralf Duerr, Rosemary Schluger, Sara A. Thannickal, Akiko Koide, Samaan Rafeq, Clea Barnett, Radu Postelnicu, Chang Wang, Stephanie Banakis, Lizzette Perez-Perez, Guomiao Shen, George Jour, Peter Meyn, Joseph Carpenito, Xiuxiu Liu, Kun Ji, Destiny Collazo, Anthony Labarbiera, Nancy Amoroso, Shari Brosnahan, Vikramjit Mukherjee, David Kaufman, Jan Bakker, Anthony Lubinsky, Deepak Pradhan, Daniel H. Sterman, Michael Weiden, Adriana Hegu, Laura Evans, Timothy M. Uyeki, Jose C. Clemente, Emmie de Wit, Ann Marie Schmidt, Bo Shopsin, Ludovic Desvignes, Chan Wang, Huilin Li, Bin Zhang, Christian Forst, Shohei Koide, Kenneth A. Stapleford, Kamal M. Khanna, Elodie Ghedin, Leopoldo N. Segal
Summary: Analysis of lower respiratory tract microbiome of mechanically ventilated COVID-19 patients rules out a role for secondary respiratory infections as drivers of increased mortality. Mortality is more likely associated with viral replication levels, host immune response, and enrichment of specific microbes.
NATURE MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Lauren Wallon, Imran Khan, Kai Wen Teng, Akiko Koide, Mariyam Zuberi, Jianping Li, Gayatri Ketavarapu, Nathaniel J. Traaseth, John P. O'Bryan, Shohei Koide
Summary: A new class of tool biologics called JAM20, which can bind to all RAS isoforms, has been developed and shown to inhibit RAS-mediated signaling and tumorigenesis in vivo.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Oncology
Takamitsu Hattori, Lorenzo Maso, Kiyomi Y. Araki, Akiko Koide, James Hayman, Padma Akkapeddi, Injin Bang, Benjamin G. Neel, Shohei Koide
Summary: The study establishes a platform technology that creates distinct neoantigens using hapten-peptide conjugates generated by covalent inhibitors, effectively marking cancer cells. HapImmune antibodies, developed using FDA-approved covalent inhibitors sotorasib and osimertinib, selectively bind to drug-peptide conjugate/MHC complexes but not to free drugs. A HapImmune-based bispecific T-cell engager is capable of selectively and potently killing sotorasib-resistant lung cancer cells. This strategy creates targetable neoantigens by design, combining targeted and immune therapies.
Article
Chemistry, Analytical
Jessica R. Chapman, Max Paukner, Micheal Leser, Kai Wen Teng, Shohei Koide, Marlene Holder, Karim-Jean Armache, Chris Becker, Beatrix Ueberheide, Michael Brenowitz
Summary: Correlating the structure and dynamics of proteins with biological function is critical for understanding cellular mechanisms. A quantitative method using common equipment for protein oxidative footprinting is described. The method allows dose-dependent oxidation of protein samples to be observed and quantitated by mass spectrometry, with high resolution. The method's efficacy is demonstrated by mapping protein interfaces.
ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Padma Akkapeddi, Kai Wen Teng, Shohei Koide
Summary: Despite increased investment and technological advancement, new drug approvals have not proportionally increased, mainly due to insufficient target validation at early stages. Therefore, there is still a strong demand for effective target validation techniques. Monobodies, as tools for drug target validation, can be rapidly developed against challenging targets using protein engineering technologies and can serve as targeting ligands for bio-PROTACs.
RSC MEDICINAL CHEMISTRY
(2021)