Article
Multidisciplinary Sciences
Stephanie Schumacher, Dirk Dedden, Roberto Vazquez Nunez, Kyoko Matoba, Junichi Takagi, Christian Biertuempfel, Naoko Mizuno
Summary: The interaction mechanism between Integrin alpha(5)beta(1) and fibronectin was studied, revealing significant conformational changes upon complex formation. Additionally, the resting state of the integrin adopts an incompletely bent conformation, challenging the existing model.
Review
Urology & Nephrology
Nicola M. Tomas, Simon A. Mortensen, Matthias Wilmanns, Tobias B. Huber
Summary: In recent decades, structural biology methods like X-ray crystallography and cryo-electron microscopy have been increasingly utilized to study protein functions, molecular interactions, physiological processes, and disease mechanisms. This review discusses how these methods have contributed to a deeper understanding of life processes and how they can be applied to investigate kidney molecules' functions and pathogenic mechanisms of renal diseases.
KIDNEY INTERNATIONAL
(2021)
Article
Immunology
Chuanxin Shi, Shuli Wang, Jincheng Han, Li Xi, Min Li, Zhiqiang Li, Hui Zhang
Summary: The ArsR family transcription factors play a crucial role in regulating the adaptation of Brucella to environmental changes and their virulence. This study identified the direct targets of the ArsR6 transcriptional regulator in Brucella and demonstrated its importance in survival and inflammatory response modulation in macrophages.
MICROBIAL PATHOGENESIS
(2022)
Article
Chemistry, Physical
Qingyue Cui, Shengzhong Frank Liu, Kui Zhao
Summary: In the past three years, metal-free perovskites have gained significant interest as promising candidates for next-generation wearable electronics. However, the relationship between the structural details and properties of these perovskites is not well understood. This review summarizes recent insights into their structural and functional aspects, explaining the role of molecular structure in the packing structure and resulting properties. It also discusses important factors and challenges in designing molecular structures for future applications, aiming to enrich the library of potential structures and applications for metal-free perovskites.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biology
Ralph T. Boettcher, Nico Strohmeyer, Jonas Aretz, Reinhard Faessler
Summary: This study found that widely used antibodies against β1-pT788/pT789 integrin could not specifically detect the phosphorylation signal of the integrin. Instead, these antibodies bind to bi-phosphorylated threonine residues in multiple proteins. Additionally, the study also found that a phospho-mimicking β1-TT788/789DD integrin impairs integrin function due to the inability of kindlin to bind to the phosphorylated or phospho-mimicking β1-tail.
LIFE SCIENCE ALLIANCE
(2022)
Article
Multidisciplinary Sciences
Michal Zielinski, Jaeok Park, Barry Sleno, Albert M. Berghuis
Summary: Macrolides, commonly used antibiotics, face resistance due to enzymatic cleavage by erythromycin esterases (Eres) like EreA. Limited research has been done on Eres, but a study on EreC provides insight into the catalytic mechanism of Eres as metal-independent hydrolases. Substrate assays and residue conservation analysis suggest two active site archetypes within the Ere enzyme family.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Ziad Ibrahim, Tao Wang, Olivier Destaing, Nicola Salvi, Naghmeh Hoghoughi, Clovis Chabert, Alexandra Rusu, Jinjun Gao, Leonardo Feletto, Nicolas Reynoird, Thomas Schalch, Yingming Zhao, Martin Blackledge, Saadi Khochbin, Daniel Panne
Summary: This article investigates how acetylation reading and writing enable the binding of the oncogenic fusion protein BRD4-NUT with the acetylase p300, resulting in self-organizing reactions that enable long-range intra- and interchromosomal interactions.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Ukhyun Jo, Yves Pommier
Summary: This article reviews the molecular characteristics and structural features of Schlafen proteins, highlighting their potential therapeutic applications in cancer management. The review also discusses the functional differentiation and differential expression of SLFN genes in various tissues and species, as well as their involvement in different cellular and tissue-specific processes.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Surabhi Mehra, Laxmikant Gadhe, Riya Bera, Ajay Singh Sawner, Samir K. Maji
Summary: Abnormal accumulation of aggregated alpha-synuclein is a common feature in various neurodegenerative diseases, exhibiting clinical and pathological differences similar to prion disorders. Emerging evidence suggests that alpha-Syn self-assembles into conformationally diverse polymorphs, which may contribute to the clinical heterogeneity in synucleinopathies.
Article
Chemistry, Multidisciplinary
Anlian Huang, Linjing Tong, Xiaoxue Kou, Rui Gao, Zhi-Wei Li, Siming Huang, Fang Zhu, Guosheng Chen, Gangfeng Ouyang
Summary: This contribution comprehensively investigates the biomineralization of zeolite imidazole frameworks for one-step synthesis of an enzyme-MOF biocomposite. The study reveals that the biomineralization ability depends on the ZIF organic linker, and the biocatalytic function is highly related to the ZIF mineral species and their microstructures. Additionally, the protective effect of ZIF mineral on the hosted enzyme is associated with the synergistic effect of size dimension and chemical microenvironment of the ZIF pores.
Article
Biochemistry & Molecular Biology
Seung Han Son, Min Young Kim, Eunbi Jo, Vladimir N. Uversky, Chul Geun Kim
Summary: This study reveals unprecedented insights into the structure and function of CP2c, providing clues for its transcriptional regulation mechanism and potential therapeutic targeting.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Driti Ashok, Laura Polcik, Svenja Dannewitz Prosseda, Tanja Nicole Hartmann
Summary: The bone marrow microenvironment plays a crucial role in the function and malignant transformation of hematopoietic stem cells. It is composed of various cell types, soluble factors, and extracellular matrix. The positioning of cells within this microenvironment depends on adhesion molecules and chemotactic signaling. The interaction between cell adhesion and metabolic pathways is essential for maintaining the stability of the bone marrow niche.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Jing Shi, Zhenzhen Feng, Juncao Xu, Fangfang Li, Yuqiong Zhang, Aijia Wen, Fulin Wang, Qian Song, Lu Wang, Hong Cui, Shujuan Tong, Peiying Chen, Yejin Zhu, Guoping Zhao, Shuang Wang, Yu Feng, Wei Lin
Summary: In actinobacteria, GlnR plays the role of a master regulator and coordinates the expression of genes related to nitrogen, carbon, and phosphate metabolism. This study provides insight into the mechanism of GlnR-dependent transcription activation by determining the co-crystal structure of GlnR in complex with its regulatory DNA and the cryo-EM structure of the GlnR transcription activation complex. These structures demonstrate how GlnR engages with promoter DNA and reveal the protein-protein interactions that stabilize the GlnR complex. This research sheds light on the global transcription activation mechanism of GlnR and other related proteins, and presents a unique mode of bacterial transcription regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Andrea Tagliani, Jacopo Rossi, Christophe H. Marchand, Marcello De Mia, Daniele Tedesco, Libero Gurrieri, Maria Meloni, Giuseppe Falini, Paolo Trost, Stephane D. Lemaire, Simona Fermani, Mirko Zaffagnini
Summary: The study focuses on the catabolism of GSNO in the microalga Chlamydomonas reinhardtii, identifying two enzymatic systems with specific reliance on NADPH or NADH, one of which is named CrGSNOR1. The kinetic properties and three-dimensional structures of CrGSNOR1 were determined, revealing its strict specificity towards GSNO and NADH, as well as its resistance to oxidative modifications.
Article
Biochemistry & Molecular Biology
Juncheng Wang, Sandra Catania, Chongyuan Wang, M. Jason de la Cruz, Beiduo Rao, Hiten D. Madhani, Dinshaw J. Patel
Summary: Epigenetic evolution in Cryptococcus neoformans is mediated by DNMT5, a maintenance type cytosine methyltransferase. The study reveals the mechanism of DNMT5 in achieving high fidelity methylation reaction through specific structural changes and ATP binding.
Review
Biochemistry & Molecular Biology
Yasmin A. Kadry, David A. Calderwood
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2020)
Article
Biochemistry & Molecular Biology
Yasmin A. Kadry, Eesha M. Maisuria, Clotilde Huet-Calderwood, David A. Calderwood
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Multidisciplinary Sciences
Mo Zhou, Leena Kuruvilla, Xiarong Shi, Stephen Viviano, Ian M. Ahearn, Caroline R. Amendola, Wenjuan Su, Sana Badri, James Mahaffey, Nicole Fehrenbacher, Jane Skok, Joseph Schlessinger, Benjamin E. Turk, David A. Calderwood, Mark R. Philips
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Massimiliano Baldassarre, Virtu Solano-Collado, Arda Balci, Rosa A. Colamarino, Ivy M. Dambuza, Delyth M. Reid, Heather M. Wilson, Gordon D. Brown, Subhankar Mukhopadhyay, Gordon Dougan, Stefania Spano
Summary: The Rab32/BLOC-3 pathway in macrophages is a novel and crucial host immune defense mechanism that controls bacterial and fungal infection independently of other known antimicrobial mechanisms, helping mammals protect against various pathogens.
Article
Medicine, General & Internal
Ahlima Roumane, George D. Mcilroy, Arda Balci, Weiping Han, Mirela Delibegovic, Massimiliano Baldassarre, Philip Newsholme, Justin J. Rochford
Summary: Selective Bscl2 deficiency in macrophages does not critically impact the innate immune response to infection. Instead, increased susceptibility to infection in CGL2 patients likely results from severe metabolic disease.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Cell Biology
Eunice Cho, Hua Jane Lou, Leena Kuruvilla, David A. Calderwood, Benjamin E. Turk
Summary: This study identifies PPP6C as a crucial phosphatase for MEK in the ERK pathway, which is frequently mutated or downregulated in melanoma. Loss of PPP6C leads to hyperphosphorylation of MEK, enhancing signaling through the pathway and reducing sensitivity to MEK inhibitors. Its recurrent mutations in melanoma cause MEK hyperphosphorylation, suggesting their role in promoting the disease by activating the core oncogenic pathway.
Article
Immunology
Virtu Solano-Collado, Rosa Angela Colamarino, David A. Calderwood, Massimiliano Baldassarre, Stefania Spano
Summary: Salmonella Typhi is a human-restricted bacterial pathogen that can survive in human macrophages but not in macrophages from other animals. An optimized experimental method for shRNA screening has been developed to identify genes controlling the growth of S. Typhi in macrophages, providing insights into host-restriction mechanisms.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Emilie L. Cerezo, Thibault Houles, Oriane Lie, Marie-Kerguelen Sarthou, Charlotte Audoynaud, Genevieve Lavoie, Maral Halladjian, Sylvain Cantaloube, Carine Froment, Odile Burlet-Schiltz, Yves Henry, Philippe P. Roux, Anthony K. Henras, Yves Romeo
Summary: Studies have shown that the Ras/MAPK pathway stimulates post-transcriptional stages of human ribosome synthesis, with RIOK2 identified as a new target of the MAPK-activated kinase RSK. Phosphorylation of RIOK2 by RSK facilitates cytoplasmic maturation of late pre-40S particles, required for optimal protein synthesis and cell proliferation. This provides a detailed mechanistic link between the Ras/MAPK pathway and human pre-40S particle maturation, opening up a previously poorly explored area of ribosome biogenesis.
Article
Multidisciplinary Sciences
Bertrand Simon, Hua Jane Lou, Clotilde Huet-Calderwood, Guangda Shi, Titus J. Boggon, Benjamin E. Turk, David A. Calderwood
Summary: TLK2 selectively targets ASF1 by mimicking its client protein histone H3, promoting nucleosome assembly. This selectivity is achieved through recognition of phosphorylation site motifs in ASF1 by the catalytic domain of TLK2 and interaction between a short sequence at the N-terminus of TLK2 and the N-terminal domain of ASF1.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Kalil Batnini, Thibault Houles, Olivier Kirsh, Stanislas Du Manoir, Mehdi Zaroual, Helene Delpech, Chloe Fallet, Matthieu Lacroix, Laurent Le Cam, Charles Theillet, Claude Sardet, Genevieve Rodier
Summary: In human Triple-Negative Breast Cancer cells, E4F1 directly controls a transcriptional program that regulates the ATM/ATR-CHK1 signaling pathway and DNA damage-stress response by binding and regulating target genes like CHEK1, TTI2, and PPP5C.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Pakorn Kanchanawong, David A. Calderwood
Summary: Cell-extracellular matrix (ECM) interactions occur at specialized, multi-protein adhesion complexes, with clustered integrins as the predominant ECM receptors. Progress in characterization of adhesion composition, organization and dynamics in response to force has improved understanding of adhesion maturation and turnover and the relationships between adhesion structures and functions.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Cell Biology
Clotilde Huet-Calderwood, Felix E. Rivera-Molina, Derek K. Toomre, David A. Calderwood
Summary: Fibronectin (FN) is an important component of the extracellular matrix (ECM) that supports cell adhesion, migration, and signaling through binding to integrin receptors. This study demonstrates that FN is secreted predominantly at the ventral surface of cells in an integrin-independent manner and its secretion is regulated by cell polarization. Additionally, the deposition of FN continues during focal adhesion disassembly.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Biology
Byung Hak Ha, Sezin Yigit, Nalini Natarajan, Elizabeth M. Morse, David A. Calderwood, Titus J. Boggon
Summary: This study investigates the interaction between integrin β5 and PAK4, revealing the molecular basis of their interaction and the inhibitory effect of integrin β5 on PAK4 activity.
COMMUNICATIONS BIOLOGY
(2022)
Correction
Biology
Byung Hak Ha, Sezin Yigit, Nalini Natarajan, Elizabeth M. Morse, David A. Calderwood, Titus J. Boggon
COMMUNICATIONS BIOLOGY
(2023)