Article
Biochemical Research Methods
Xiaofeng Zhang, Yue Chen, Sung Yun Jung, Xianju Li, Fanjie Meng, Bowen Zhong, Jun Qin, Yi Wang
Summary: In this study, the dynamic interaction network of EGFR wildtype and mutant NSCLC cell lines was characterized. It was found that while the core signaling modules and downstream pathways were maintained in the mutant cell line, receptor internalization and intracellular trafficking were delayed. Additionally, mutant EGFR-associated proteins that could affect EGFR functions in lung adenocarcinoma were identified.
JOURNAL OF PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Alexey S. Kazakov, Evgenia Deryusheva, Maria E. Permyakova, Andrey S. Sokolov, Victoria A. Rastrygina, Vladimir N. Uversky, Eugene A. Permyakov, Sergei E. Permyakov
Summary: S100 proteins are versatile calcium-binding proteins that interact with four-helical cytokines, potentially serving as inhibitors of their action.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Lucia Sanjurjo, Esmee C. Broekhuizen, Rory R. Koenen, Victor L. J. L. Thijssen
Summary: Galectins, a family of glycan-binding proteins, play a role in shaping the immune microenvironment by directly affecting immune cell activity and survival, as well as indirectly affecting immune response through binding to cytokines. Galectin-cytokine heterodimers, known as galectokines, add complexity to immune homeostasis regulation. This article summarizes current knowledge on galectokine formation and function, describes mechanisms by which galectokines shape the immune microenvironment, and discusses outstanding questions and challenges for future research on the role of galectokines in immunomodulation.
Article
Biotechnology & Applied Microbiology
Xinguo Lu, Fang Liu, Qiumai Miao, Ping Liu, Yan Gao, Keren He
Summary: Our study aimed to reveal functional overlapping patterns in gene modules to elucidate regulatory relationships between overlapping genes and communities, as well as explore cancer formation and progression. We analyzed six cancer datasets and identified three types of gene functional modules for each cancer, with our method outperforming others in terms of identifying distinguishing communities and survival prognostics for patients. In conclusion, overlapping genes play a crucial role in constructing comprehensive carcinogenesis by establishing communication bridges between different specific functional groups.
Article
Biology
Prithvi Singh, Arpita Rai, Amit Kumar Verma, Mohammed A. Alsahli, Arshad Husain Rahmani, Saleh A. Almatroodi, Faris Alrumaihi, Kapil Dev, Anuradha Sinha, Shweta Sankhwar, Ravins Dohare
Summary: In this study, four OSCC-specific hub genes were identified through high-throughput RNA-Seq data analysis, and a weighted PPI network was constructed. Pathway enrichment analysis of the significant module genes may provide clinical utility for early diagnosis and precision therapy.
Article
Multidisciplinary Sciences
Xiaoli Yang, Zhanyu Ding, Lisi Peng, Qiuyue Song, Deyu Zhang, Fang Cui, Chuanchao Xia, Keliang Li, Hua Yin, Shiyu Li, Zhaoshen Li, Haojie Huang
Summary: This study provides structural insights into the rearrangements of EP surface-loops and heavy chain dynamics in the EP catalytic cycle, advancing our understanding of EP-associated pancreatitis.
NATURE COMMUNICATIONS
(2022)
Article
Fisheries
Chang Min Kim, Hyunseok Jang, Eunmi Hong, Jun Hyuck Lee, Hyun Ho Park
Summary: In this study, the TRAF4 gene was cloned and purified from the Antarctic yellowbelly rockcod. The crystal structure of teleost fish TRAF4 was determined, and the mechanisms of cold adaptiveness of signaling molecules were elucidated. The interaction between the platelet receptor GPIb beta homolog and ncTRAF4 was also identified, indicating the role of ncTRAF4 in mediating cellular signaling. These findings provide new insights into TRAF4-mediated immune cell and platelet signaling in fish and the cold adaptiveness of signaling molecules.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Plant Sciences
Xiaoyu Liang, Zhan Ma, Yuhang Ke, Jiali Wang, Lifeng Wang, Bi Qin, Chaorong Tang, Mingyang Liu, Xuemei Xian, Ye Yang, Meng Wang, Yu Zhang
Summary: This study characterized the transcriptomes in Hevea leaves during early powdery mildew infection using single-cell RNA sequencing. The gene expression patterns of different cell clusters, especially the epidermal cells, were significantly altered under powdery mildew infection. The HbCNL2 gene was found to positively modulate the defence response of rubber leaves against powdery mildew.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Biology
Sofiyah Shaibullah, Nurshahirah Shuhaimi, De-Sheng Ker, Nurhikmah Mohd-Sharif, Kok Lian Ho, Aik-Hong Teh, Jitka Waterman, Thean-Hock Tang, Rui-Rui Wong, Sheila Nathan, Rahmah Mohamed, Min Jia Ng, Shin-Yee Fung, Mohd Anuar Jonet, Mohd Firdaus-Raih, Chyan Leong Ng
Summary: BPSL1038 is a hypothetical protein found in Burkholderia pseudomallei with nuclease activity. Its structure is similar to known Cas2 nucleases, suggesting a common ancestor.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Madhuranayaki Thulasingam, Laura Orellana, Emmanuel Nji, Shabbir Ahmad, Agnes Rinaldo-Matthis, Jesper Z. Haeggstrom
Summary: Through analysis of the crystal structures of human MGST2, it was discovered that the enzyme employs a unique mechanism involving local unfolding and global conformational changes to regulate catalysis and optimize reaction conditions at the active site. The synchronized changes in the central pore also play a role in modulating hydrophobicity and controlling solvent influx. These insights may have implications for other structurally related drug targets.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Mingming Du, Kun Zhou, Runze Yu, Yufeng Zhai, Gang Chen, Qiangbin Wang
Summary: This study utilized an anisotropic building block RhuA and introduced histidine residues to achieve the construction of highly ordered protein superstructures through pi-pi stacking interactions, shedding light on the structural and dynamic aspects of protein assembly.
Article
Cell Biology
Jingyi Chen, Wenjing Wu, Zhiqian Wang, Chuannan Zhai, Baocheng Deng, Mohammad Alzogool, Yan Wang
Summary: The study found differential protein expression in corneal stroma tissues between subjects with low and high myopia, involving catalytic activity, molecular function regulator, and transporter activity, as well as metabolic processes, biological regulation, and response to stimulus. Pathway enrichment analysis revealed activation of mineral absorption, ferroptosis, and HIF-1 signaling pathways in the cornea of myopic individuals. Iron metabolic proteins may play a crucial role in the pathogenesis of myopia, indicating disturbances in iron metabolism and corneal oxidative stress in more myopic eyes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Immunology
Kang Tang, Jing Tang, Jinfeng Zeng, Wei Shen, Min Zou, Chi Zhang, Qianru Sun, Xiaoyan Ye, Chunwei Li, Caijun Sun, Siyang Liu, Guozhi Jiang, Xiangjun Du
Summary: The HUMPPI-2022 network provides insights into the network topology and functional characteristics of immune-related genes and virus-human interactions, shedding light on their roles in the human immune system and viral pathogenesis.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Zhexin Wang, Michael Grange, Sabrina Pospich, Thorsten Wagner, Ay Lin Kho, Mathias Gautel, Stefan Raunser
Summary: This study reveals the structure of nebulin bound to thin filaments and demonstrates its stabilizing role. It also highlights the different interactions of nebulin with actin and myosin, as well as its interaction with a troponin T linker, explaining its regulatory function.
Article
Multidisciplinary Sciences
Yu-Chen Yen, Christopher T. Schafer, Martin Gustaysson, Stefanie A. Eberle, Pawel K. Dominik, Dawid Deneka, Penglie Zhang, Thomas J. Schall, Anthony A. Kossiakoff, John J. G. Tesmer, Tracy M. Handel
Summary: This study presents cryo-EM structures of ACKR3 in complex with CXCL12, a more potent CXCL12 variant, and a small-molecule agonist. The binding poses of these chemokines are different from those established for CXCR4 and observed in other receptor-chemokine complexes. These structures, together with functional studies, provide insights into the ligand-binding promiscuity of ACKR3, its inability to couple to G proteins, and its bias towards beta-arrestin, laying the foundation for understanding the physiological interplay of ACKR3 with other GPCRs.
Article
Chemistry, Medicinal
Bernhard C. Lechtenberg, Peter D. Mace, E. Hampton Sessions, Robert Williamson, Romain Stalder, Yann Wallez, Gregory P. Roth, Stefan J. Ried, Elena B. Pasquale
ACS MEDICINAL CHEMISTRY LETTERS
(2017)
Article
Oncology
Siang-Boon Koh, Yann Wallez, Charles R. Dunlop, Sandra Bernaldo de Quiros Fernandez, Tashinga E. Bapiro, Frances M. Richards, Duncan I. Jodrell
Article
Multidisciplinary Sciences
Yann Wallez, Stephanie Bouillot, Emmanuelle Soleilhac, Philippe Huber, Ina Attree, Eric Faudry
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Sam A. Jamieson, Zheng Ruan, Abigail E. Burgess, Jack R. Curry, Hamish D. Mcmilan, Jodi L. Brewster, Anita K. Dunbier, Alison D. Axtman, Natarajan Kannan, Peter D. Mace
Article
Multidisciplinary Sciences
Martina Foglizzo, Adam J. Middleton, Abigail E. Burgess, Jennifer M. Crowther, Renwick C. J. Dobson, James M. Murphy, Catherine L. Day, Peter D. Mace
NATURE COMMUNICATIONS
(2018)
Article
Chemistry, Medicinal
Rinu Shrestha, Emma V. Petley, Kathryn J. Farrand, Sam A. Jamieson, Wanting Jiao, Paul H. Teesdale-Spittle, Peter D. Mace, Ian F. Hermans, Phillip M. Rendle
Article
Biochemistry & Molecular Biology
Sarah J. Trevelyan, Jodi L. Brewster, Abigail E. Burgess, Jennifer M. Crowther, Antonia L. Cadell, Benjamin L. Parker, David R. Croucher, Renwick C. J. Dobson, James M. Murphy, Peter D. Mace
Review
Biochemistry & Molecular Biology
Cameron J. Reddington, Matthias Fellner, Abigail E. Burgess, Peter D. Mace
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Multidisciplinary Sciences
Pavel Filipcik, Sharissa L. Latham, Antonia L. Cadell, Catherine L. Day, David R. Croucher, Peter D. Mace
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Anubrita Das, Adam J. Middleton, Prasanth Padala, Elizabeth C. Ledgerwood, Peter D. Mace, Catherine L. Day
Summary: Members of the TRAF family share a common domain architecture but play distinct physiological roles in cell signaling. The RING domain of TRAF6 forms homodimers and heterodimers with TRAF3 and TRAF2, promoting ubiquitin chain assembly. Both homo- and hetero-dimers of TRAF have the potential to modulate TRAF-mediated signaling by interacting with nearby TRAF trimers.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Oncology
Hamish D. McMillan, Karen Keeshan, Anita K. Dunbier, Peter D. Mace
Summary: TRIB1, a member of the Tribbles protein family, plays significant roles in various cancer types, particularly in acute myeloid leukemia. Its structural characteristics and potential as a target for small-molecule inhibitors make it a promising biomarker for treatment response in diverse cancers. Further research is needed to fully understand its role in solid tumors and to explore its potential as a therapeutic target.
Article
Multidisciplinary Sciences
Andrej Paluda, Adam J. Middleton, Claudia Rossig, Peter D. Mace, Catherine L. Day
Summary: This study reveals the mechanism of enzymatic activity regulation by elucidating the structure of Ark2C bound to both regulatory ubiquitin and activated E2-ubiquitin conjugate. It also identifies the charged loop that enhances activity and the mechanism of ubiquitin chain assembly.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sam A. Jamieson, Michael Pudjihartono, Christopher R. Horne, Juan Salamanca Viloria, Jessica L. Dunlop, Hamish D. McMillan, Robert C. Day, Karen Keeshan, James M. Murphy, Peter D. Mace
Summary: This study reports the identification of nanobodies that bind the TRIB2 pseudokinase domain and stabilize a TRIB2 pseudokinase domain dimer. The nanobodies specifically recognize TRIB2 in an activated conformation. These findings provide insights for the development of TRIB2 inhibitors and nanobody tools for future research.
Article
Biology
Christopher Hakkaart, John F. Pearson, Louise Marquart, Joe Dennis, George A. R. Wiggins, Daniel R. Barnes, Bridget A. Robinson, Peter D. Mace, Kristiina Aittomaki, Irene L. Andrulis, Banu K. Arun, Jacopo Azzollini, Judith Balmana, Rosa B. Barkardottir, Sami Belhadj, Lieke Berger, Marinus J. Blok, Susanne E. Boonen, Julika Borde, Angela R. Bradbury, Joan Brunet, Saundra S. Buys, Maria A. Caligo, Ian Campbell, Wendy K. Chung, Kathleen B. M. Claes, Marie-Agnes Collonge-Rame, Jackie Cook, Casey Cosgrove, Fergus J. Couch, Mary B. Daly, Sita Dandiker, Rosemarie Davidson, Miguel de la Hoya, Robin de Putter, Capucine Delnatte, Mallika Dhawan, Orland Diez, Yuan Chun Ding, Susan M. Domchek, Alan Donaldson, Jacqueline Eason, Douglas F. Easton, Hans Ehrencrona, Christoph Engel, D. Gareth Evans, Ulrike Faust, Lidia Feliubadalo, Florentia Fostira, Eitan Friedman, Megan Frone, Debra Frost, Judy Garber, Simon A. Gayther, Andrea Gehrig, Paul Gesta, Andrew K. Godwin, David E. Goldgar, Mark H. Greene, Eric Hahnen, Christopher R. Hake, Ute Hamann, Thomas V. O. Hansen, Jan Hauke, Julia Hentschel, Natalie Herold, Ellen Honisch, Peter J. Hulick, Evgeny N. Imyanitov, Claudine Isaacs, Louise Izatt, Angel Izquierdo, Anna Jakubowska, Paul A. James, Ramunas Janavicius, Esther M. John, Vijai Joseph, Beth Y. Karlan, Zoe Kemp, Judy Kirk, Irene Konstantopoulou, Marco Koudijs, Ava Kwong, Yael Laitman, Fiona Lalloo, Christine Lasset, Charlotte Lautrup, Conxi Lazaro, Clementine Legrand, Goska Leslie, Fabienne Lesueur, Phuong L. Mai, Siranoush Manoukian, Veronique Mari, John W. M. Martens, Lesley McGuffog, Noura Mebirouk, Alfons Meindl, Austin Miller, Marco Montagna, Lidia Moserle, Emmanuelle Mouret-Fourme, Hannah Musgrave, Sophie Nambot, Katherine L. Nathanson, Susan L. Neuhausen, Heli Nevanlinna, Joanne Ngeow Yuen Yie, Tu Nguyen-Dumont, Liene Nikitina-Zake, Kenneth Offit, Edith Olah, Olufunmilayo I. Olopade, Ana Osorio, Claus-Eric Ott, Sue K. Park, Michael T. Parsons, Inge Sokilde Pedersen, Ana Peixoto, Pedro Perez-Segura, Paolo Peterlongo, Timea Pocza, Paolo Radice, Juliane Ramser, Johanna Rantala, Gustavo C. Rodriguez, Karina Ronlund, Efraim H. Rosenberg, Maria Rossing, Rita K. Schmutzler, Payal D. Shah, Saba Sharif, Priyanka Sharma, Lucy E. Side, Jacques Simard, Christian F. Singer, Katie Snape, Doris Steinemann, Dominique Stoppa-Lyonnet, Christian Sutter, Yen Yen Tan, Manuel R. Teixeira, Soo Hwang Teo, Mads Thomassen, Darcy L. Thull, Marc Tischkowitz, Amanda E. Toland, Alison H. Trainer, Vishakha Tripathi, Nadine Tung, Klaartje van Engelen, Elizabeth J. van Rensburg, Ana Vega, Alessandra Viel, Lisa Walker, Jeffrey N. Weitzel, Marike R. Wevers, Georgia Chenevix-Trench, Amanda B. Spurdle, Antonis C. Antoniou, Logan C. Walker
Summary: The risk of germline copy number variants (CNVs) in BRCA1 and BRCA2 pathogenic variant carriers in breast cancer is assessed. CNVs overlapping SULT1A1 decrease breast cancer risk in BRCA1 carriers. Functional analyses show that reduced SULT1A1 expression is associated with reduced cellular proliferation and DNA damage.
COMMUNICATIONS BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Peter D. Mace, James M. Murphy
Summary: Protein kinases are known for their catalytic functions in cellular signaling, but recent research has shown that they also have noncatalytic roles. These noncatalytic activities, such as allosteric modulation and scaffolding, highlight the versatility of protein kinases as protein-protein interaction modules. Despite the challenges, targeting the noncatalytic functions of protein kinases with small molecules has significant potential in health and disease.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
