Review
Virology
Andreas Kuhn, Julie A. Thomas
Summary: Viruses are biochemically complex structures made up of folded proteins containing nucleic acids. The molecular details of assembly processes in bacteriophage T4 have been studied, revealing the dynamics of protein folding and structural interactions in assembled complexes.
Article
Multidisciplinary Sciences
Taehwan Kim, Jaewoong Lee, Jin-Pyo Lee, Bit-Na Kim, Yang-Hoon Kim, Youn-Sik Lee, Jiho Min
Summary: This study applied a novel method for the detection of VDBP-Complex in the blood, and identified a phage with the highest binding affinity to VDBP-Complex, which has a sequence of SFTKTSTFTWRD (called M3). The significant decrease of VDBP-Complex was confirmed through the removal test using magnetic beads conjugated with M3 peptide. It is expected that the M3 peptide may be used to determine the vitamin D levels in the blood.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Multidisciplinary
Tammy R. Johnson, Taylor E. Andrzejak, Himanshu S. Raje
Summary: Biofilms are collections of microorganisms that adhere to a surface and pose a potential hazard to human health. This study found that both T4 and MS2 coliphages can desorb natural biofilms, and nutrient deprivation has a similar effect on biofilm desorption as the bacteriophages.
APPLIED SCIENCES-BASEL
(2022)
Article
Chemistry, Multidisciplinary
Minh-Tram T. Nguyen, Yu-Chien Shih, Meng-Hsuan Lin, Steve R. Roffler, Chiao-Yu Hsiao, Tian-Lu Cheng, Wen-Wei Lin, En-Chi Lin, Yuh-Jyh Jong, Chin-Yuan Chang, Yu-Cheng Su
Summary: Covalent attachment of methoxy poly(ethylene) glycol (mPEG) to therapeutic molecules is commonly used to enhance their systemic circulation time and efficacy, but it can also induce anti-PEG antibodies that negatively affect drug therapeutic effects. In this study, the researchers determined the co-crystal structure of the humanized 15-2b anti-mPEG antibody with mPEG, providing insights into understanding the binding specificity and antigenicity of anti-mPEG antibodies.
COMMUNICATIONS CHEMISTRY
(2022)
Article
Virology
Do-Won Park, Jong-Hyun Park
Summary: BECP10, a novel bacteriophage targeting E. coli O157 strains, shows strong antibacterial activity and can effectively reduce the pathogen levels in contaminated food matrices over a long period of time, making it a promising biocontrol agent.
Article
Virology
Xinyi Chen, Qi Tang, Xue Li, Xiangkuan Zheng, Pei Li, Min Li, Fei Wu, Zhengjun Xu, Renfei Lu, Wei Zhang
Summary: In this study, a phage P929 specifically infecting Klebsiella pneumoniae was isolated. The phage showed stable antibacterial activity and significantly reduced biofilm formation. Therefore, phage P929 may play an important role in the clinical treatment of carbapenem-resistant and biofilm-forming K. pneumoniae.
Article
Multidisciplinary Sciences
Jingen Zhu, Himanshu Batra, Neeti Ananthaswamy, Marthandan Mahalingam, Pan Tao, Xiaorong Wu, Wenzheng Guo, Andrei Fokine, Venigalla B. Rao
Summary: This study describes the development of artificial viral vectors (AVVs) by modifying the structural components of bacteriophage T4. These AVVs have the potential to deliver genes and perform molecular repairs, making them valuable for gene therapy and personalized medicine.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Benedict G. Tan, Christian D. Mutti, Yonghong Shi, Xie Xie, Xuefeng Zhu, Pedro Silva-Pinheiro, Katja E. Menger, Hector Diaz-Maldonado, Wei Wei, Thomas J. Nicholls, Patrick F. Chinnery, Michal Minczuk, Maria Falkenberg, Claes M. Gustafsson
Summary: The discovery of a second light strand promoter (LSP2) in the human mitochondrial genome expands our understanding of mitochondrial gene expression by allowing replication and gene expression to be orchestrated from two distinct sites.
Article
Biology
Fengwei Zheng, Roxana Georgescu, Nina Y. Yao, Huilin Li, Michael E. O'Donnell
Summary: The RFC complex has been shown to have a second DNA binding site, located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. This 5' DNA site exhibits ideal binding to a 7-nt gap and shows enhanced binding to 5 and 10 nt gaps. It is proposed that the 5' site facilitates RFC's PCNA loading activity at DNA damage-induced gaps and plays a potential role in lagging strand DNA synthesis.
Article
Immunology
Jisu Hong, Youngjin Choi, Yoonjoo Choi, Jiwoo Lee, Hyo Jeong Hong
Summary: By conducting experiments and structural analysis, it was found that 1A8 can effectively block HBV infection of different genotypes, making it a promising candidate for the prevention and treatment of HBV infection.
Article
Immunology
Mohammed Zghaebi, Maria Byazrova, Sabine Flicker, Sergio Villazala-Merino, Nicholas J. Campion, Victoria Stanek, Aldine Tu, Heimo Breiteneder, Alexander Filatov, Musa Khaitov, Verena Niederberger-Leppin, Julia Eckl-Dorna, Rudolf Valenta
Summary: A new sequential gating strategy was developed to detect cells bearing the IgE BCR on their surface, using a monoclonal anti-IgE antibody. This strategy allowed for the clear identification of allergen-specific IgE(+) memory B cells and plasma cells in human PBMCs, offering new insights into allergic responses.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Chemistry, Analytical
Bingzhi Li, Bin Zhou, Yue Chen, Xing Zhang, He Huang
Summary: In this study, a new strategy was proposed to sensitively detect transcription factors using T4 DNA ligase protection assay and rolling circle amplification. By preventing the ligation reaction through the binding of T4 DNA ligase to the nick region of dsDNA, the undesired dissociation of TF-DNA complexes was effectively avoided, improving the accuracy of the assay. Through sequence engineering, multiple transcription factors can be detected at low picomolar levels.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Review
Chemistry, Medicinal
Susie L. Brown, Samantha Kendrick
Summary: The i-motif is a dynamic secondary DNA structure rich in cytosine, with potential as a molecular switch for gene expression control. It may play a role in facilitating or hindering expansion of DNA elements in genomic areas with repetitive nucleotide sequences. Recent discoveries, including the identification of a specific i-motif antibody, are advancing the field of i-motif research.
Article
Genetics & Heredity
Omar Rawashdeh, Rabeah Y. Rawashdeh, Temesgen Kebede, David Kapp, Anca Ralescu
Summary: The study revealed the specific positioning of PAM sequences in the transcriptional regulatory regions of bacteriophage genomes, with certain PAMs preferentially located at the core of promoters and being more prevalent in essential genes. Analysis showed that amino acids translated from certain PAMs tend to prefer protein surfaces, suggesting their role in protein-protein interactions.
Article
Biochemistry & Molecular Biology
Guoxing Yu, Kangkang Niu, Yuling Peng, Zhenming Liu, Qisheng Song, Qili Feng
Summary: In this study, a large-scale screening of binding compounds targeting the i-motif structure of BmPOUM2 was conducted using surface plasmon resonance imaging (SPRi), resulting in the identification of several compounds with binding affinity to the i-motif structure. These compounds have potential applications in gene transcription regulation and functional analysis of i-motif structure.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Alice Boulanger, Kyung Moon, Kimberly B. Decker, Qing Chen, Leslie Knipling, Scott Stibitz, Deborah M. Hinton
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Multidisciplinary Sciences
Maxime G. Cuypers, Sax A. Mason, Estelle Mossou, Michael Haertlein, V. Trevor Forsyth, Edward P. Mitchell
SCIENTIFIC REPORTS
(2016)
Article
Biochemistry & Molecular Biology
Sandra P. Santos, Maxime G. Cuypers, Adam Round, Stephanie Finet, Theyencheri Narayanan, Edward P. Mitchell, Celia V. Romao
JOURNAL OF MOLECULAR BIOLOGY
(2017)
Article
Virology
Jennifer Patterson-West, Tamara D. James, Llorenc Fernandez-Coll, James R. Iben, Kyung Moon, Leslie Knipling, Michael Cashel, Deborah M. Hinton
Article
Virology
Jennifer Patterson-West, Melissa Arroyo-Mendoza, Meng-Lun Hsieh, Danielle Harrison, Morgan M. Walker, Leslie Knipling, Deborah M. Hinton
Meeting Abstract
Chemistry, Multidisciplinary
F. Romoli, E. Mossou, M. Cuypers, P. Carpentier, P. Van der Linden, S. Mason, D. De Sanctis, S. Mc Sweeney, T. Forsyth
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2014)
Article
Biochemistry & Molecular Biology
Maxime G. Cuypers, Chitra Subramanian, Jessica M. Gullett, Matthew W. Frank, Stephen W. White, Charles O. Rock
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Jessica M. Gullett, Maxime G. Cuypers, Matthew W. Frank, Stephen W. White, Charles O. Rock
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Gyanendra Kumar, Maxime Cuypers, Richard R. Webby, Thomas R. Webb, Stephen W. White
Summary: The endonuclease activity within the influenza virus cap-snatching process is a proven therapeutic target. Baloxavir, an anti-influenza drug, is effective but linked to resistance mutations. By studying complexes of PA(N) with RNA and DNA oligonucleotides, insights are gained on specificity and structural basis of baloxavir resistance mutations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Jessica M. Gullett, Maxime G. Cuypers, Christy R. Grace, Shashank Pant, Chitra Subramanian, Emad Tajkhorshid, Charles O. Rock, Stephen W. White
Summary: This study reveals the conformational change and mechanism of action of fatty acid transfer proteins in cell membranes, providing a theoretical basis for how fatty acid exchange occurs through the cell membrane.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Chitra Subramanian, Maxime G. Cuypers, Christopher D. Radka, Stephen W. White, Charles O. Rock
Summary: Fatty acid kinase (Fak) is an enzyme that generates acyl-phosphate for phospholipid synthesis. It consists of FakA and FakB components, with FakA containing three separate domains and FakB having specific binding properties. The study reveals the importance of FakA's structure and function in substrate binding and catalysis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Peter J. Slavish, Maxime G. Cuypers, Mary Ashley Rimmer, Alireza Abdolvahabi, Trushar Jeevan, Gyanendra Kumar, Jamie A. Jarusiewicz, Sivaraja Vaithiyalingam, Jeremy C. Jones, John J. Bowling, Jeanine E. Price, Rebecca M. DuBois, Jaeki Min, Richard J. Webby, Zoran Rankovic, Stephen W. White
Summary: Influenza is a major cause of disease-related deaths globally. Strategies to inhibit influenza virus replication have resulted in the emergence of resistant strains. Baloxavir marboxil, a recently approved compound, is significantly less effective due to a mutation in the active site of the target enzyme. Raltegravir, an HIV inhibitor, shows moderate activity against the enzyme. In this study, researchers used structure-guided approaches to design molecules that effectively target the enzyme's active site and successfully developed potent inhibitors for both wild-type and baloxavir-resistant forms.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biology
Meng-Lun Hsieh, Alice Boulanger, Leslie G. Knipling, Deborah M. Hinton