Article
Biochemistry & Molecular Biology
Lukas Schulig, Piotr Grabarczyk, Norman Geist, Martin Delin, Hannes Forkel, Martin Kulke, Mihaela Delcea, Christian A. Schmidt, Andreas Link
Summary: Transcription factors are crucial in regulating biological processes, with zinc finger proteins being the largest family of DNA-binding transcription regulators. BCL11B plays a fundamental role in various tissues and organs, and the atypical zinc finger domain identified in previous work is critical for efficient regulation of target genes. The structural basis for BCL11B interaction and the identification of key amino acid residues provide insight into its active structure and potential for inhibitor design.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
R. Ichijo, M. Kabata, H. Kidoya, F. Muramatsu, R. Ishibashi, K. Abe, K. Tsutsui, H. Kubo, Y. Iizuka, S. Kitano, H. Miyachi, Y. Kubota, H. Fujiwara, A. Sada, T. Yamamoto, F. Toyoshima
Summary: This study uncovers the regulation of stem cells in dynamic skin, specifically in the context of epidermal proliferation and differentiation during pregnancy, and how the skin adjusts its size in coordination with dermal constituents.
Article
Biochemistry & Molecular Biology
Chien- Yang, Jiwoo Kim, Shu-Ou Shan
Summary: The ribosome actively participates in diverse protein biogenesis pathways, including folding, localization, and modifications. It imposes an additional layer of substrate selection during N-terminal methionine excision (NME) in bacteria.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Computer Science, Artificial Intelligence
Jui-Hung Chang, Yin-Chung Leung
Summary: This paper proposes a novel framework for dynamic image clustering without prior knowledge of the cluster count. By using deep learning and coordinate learning models to project high dimensional data onto a two-dimensional space, a new clustering algorithm is introduced to evaluate and classify the projected data.
Article
Food Science & Technology
Anupong Joompang, Preeyanan Anwised, Sompong Klaynongsruang, Lapatrada Taemaitree, Anuwat Wanthong, Kiattawee Choowongkomon, Sakda Daduang, Somporn Katekaew, Nisachon Jangpromma
Summary: There has been a renewed interest in bioactive peptides as therapeutic agents, especially tyrosinase inhibitors. This study demonstrates the rational design of a tetrapeptide that can effectively inhibit tyrosinase activity in vitro and in cells. The tetrapeptide CRNL interacts with the enzyme through multiple intermolecular interactions and shows promising potential for hyperpigmentation treatment without toxicity.
CURRENT RESEARCH IN FOOD SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Xiaodi Gong, Yaqian Huang, Yan Liang, Yundong Yuan, Yuhao Liu, Tongwen Han, Shujia Li, Hengbin Gao, Bo Lv, Xiahe Huang, Eric Linster, Yingchun Wang, Markus Wirtz, Yonghong Wang
Summary: This study identifies HYPK as a positive regulator of NatA activity in rice and demonstrates the critical role of the OsHYPK-NatA complex in coordinating plant development and stress responses.
Article
Biochemistry & Molecular Biology
Petra Van Damme
Summary: N-terminal acetylation catalyzed by NatA, a major acetyltransferase complex, plays a crucial role in protein modification. Knockdown of human NatA resulted in significant reduction in Nt-acetylation of potential targets, including less efficient NatA substrates and some NatE substrates. The deficiency of NatA Nt-acetylation directly affected protein stability of knockdown targets, suggesting its important role in protein regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Yan Li, Kiwon Song
Summary: This study found that Bfa1 can control the spindle position checkpoint (SPOC) independent of its GTPase-activating protein (GAP) activity and spindle pole body (SPB) localization, by inhibiting the activity of Tem1 to prevent premature mitotic exit.
Article
Plant Sciences
Patrick Willems, Elvis Ndah, Veronique Jonckheere, Frank Van Breusegem, Petra Van Damme
Summary: Alternative translation initiation can shape multiple protein forms from a single gene. This study provides evidence for the existence of ~90 N-terminal proteoform pairs shaped by alternative translation initiation in Arabidopsis thaliana. The study also suggests that alternative translation initiation may serve as a common mechanism to supply protein copies in multiple cellular compartments.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Tetsuya Hirata, Jing Yang, Seita Tomida, Yuko Tokoro, Taroh Kinoshita, Morihisa Fujita, Yasuhiko Kizuka
Summary: This study investigates the ER entry pathways of GPI-APs and reveals that the N and C-terminal sequences determine the selective ER entry route and subsequent maturation processes of GPI-APs.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Bartlomiej Surpeta, Michal Grulich, Andrea Palyzova, Helena Maresova, Jan Brezovsky
Summary: Growing concerns about microbial antibiotic resistance have led to extensive research on overcoming antibiotic resistance. This study evaluated the degradation capacity of three enzymes on signaling compounds for Gram-negative bacteria and clarified the molecular mechanisms underlying their quorum quenching (QQ) activity. The study also observed substrate-dependent differences in the catalytic actions of these enzymes due to the distinct structures of their acyl-binding cavities and the dynamics of their molecular gates.
Article
Biochemistry & Molecular Biology
Charlotte L. Frankling, Megan F. Downes, Angray S. Kang, Ewan R. G. Main
Summary: Many gram-negative bacteria use a protein nanomachine called the Type Three Secretion System (T3SS) to infect. This system transports bacterial toxins using a proteinaceous channel that links the bacteria and host cell. In this study, the specificity of the binding interfaces of the translocator-chaperone complexes from Pseudomonas aeruginosa was investigated.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xiaozhuo Liu, Houtan Moshiri, Qian He, Ansuman Sahoo, Sarah E. Walker
Summary: The yeast eukaryotic initiation factor 4B plays an important role in translation preinitiation complexes. Recent studies have found that yeast mRNAs have differential dependence on eIF4B under different growth conditions. It is suggested that the activity of eIF4B in translation may alter yeast phenotypes by selecting different mRNAs. By comparing the effects of disrupting yeast eIF4B RNA- and 40S-binding motifs, it is found that the 40S-binding N-terminal Domain (NTD) is associated with stress responses and promotes yeast growth. Deletion of the NTD significantly reduces translation activity and alters the composition of ribosome-associated mRNAs. Gene ontology analysis reveals that transcripts dependent on the NTD encode proteins associated with the cellular membrane system and the cell wall.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Nutrition & Dietetics
Maria Bikaki, Nikolai Kuhnert
Summary: This study investigates the thermal degradation of dietary-relevant pentapeptides and proposes a degradation mechanism similar to lipid peroxidation, forming novel degradation products with potential toxicological relevance. A radical-based reaction mechanism is proposed, leading to distinct reaction products with specific functionalities.
FRONTIERS IN NUTRITION
(2021)
Article
Biochemistry & Molecular Biology
Gazal Kalyan, Vivek Junghare, Sourya Bhattacharya, Saugata Hazra
Summary: Functional foods, especially food-derived peptides, are considered essential for providing abundant health benefits. This study focuses on the inhibitory potential of antihypertensive peptides from food sources, showing promising results in targeting ACE. The research involves a structure-based analysis of enzyme-peptide interactions using MD simulations, revealing key insights into the mechanisms behind successful ACE inhibition by food peptides.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biotechnology & Applied Microbiology
Marco Rusnati, Giulia Paiardi, Chiara Tobia, Chiara Urbinati, Alessio Lodola, Pasqualina D'Ursi, Miriam Corrado, Riccardo Castelli, Rebecca C. Wade, Massimiliano Tognolini, Paola Chiodelli
Summary: UniPR1331, a derivative of 3 beta-hydroxy-Delta(5)-cholenic acid, has been shown to inhibit Eph-ephrin interaction and VEGFR2 activation, leading to the suppression of tumor cell-driven angiogenesis. These findings highlight the potential of Delta(5)-cholenic acid as a promising molecular scaffold for the development of multitarget antiangiogenic compounds.
CANCER GENE THERAPY
(2022)
Correction
Biotechnology & Applied Microbiology
Marco Rusnati, Giulia Paiardi, Chiara Tobia, Chiara Urbinati, Alessio Lodola, Pasqualina D'Ursi, Miriam Corrado, Riccardo Castelli, Rebecca C. Wade, Massimiliano Tognolini, Paola Chiodelli
CANCER GENE THERAPY
(2022)
Article
Biochemistry & Molecular Biology
Giulia Paiardi, Stefan Richter, Pasqua Oreste, Chiara Urbinati, Marco Rusnati, Rebecca C. Wade
Summary: Heparin has been found to have antiviral activity against SARS-CoV-2 by inhibiting viral binding to host cells, competing with binding to host heparan sulfate proteoglycan coreceptors, and preventing spike cleavage. These findings provide insights into potential strategies for SARS-CoV-2 antiviral therapy.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Federico Cerullo, Sebastian Filbeck, Pratik Rajendra Patil, Hao-Chih Hung, Haifei Xu, Julia Vornberger, Florian W. Hofer, Jaro Schmitt, Guenter Kramer, Bernd Bukau, Kay Hofmann, Stefan Pfeffer, Claudio A. P. Joazeiro
Summary: This study uncovers the function of Bacillus subtilis MutS2, a member of the conserved MutS family, in translational quality control. MutS2 acts as a ribosome-binding protein and functions in sensing collisions between stalled and translating ribosomes. It promotes ribosomal subunit dissociation, ribosome recycling, and initiation of ribosome-associated protein quality control. These findings demonstrate the conserved role of ribosome collisions in mounting a complex response to translation interruption.
Review
Biochemistry & Molecular Biology
Szymon W. Kmiecik, Matthias P. Mayer
Summary: Cells need to maintain proteome homeostasis and regulate it through the heat shock response (HSR), which is orchestrated by heat shock transcription factor 1 (Hsf1). Hsf1 plays a crucial role in regulating proteome homeostasis and is involved in aging, cancer, and neurodegenerative disorders. Multiple layers of control circuits, such as synthesis and degradation, conformational rearrangements, post translational modifications (PTMs), and molecular chaperones in negative feedback loops, regulate the transcriptional activity of Hsf1.
TRENDS IN BIOCHEMICAL SCIENCES
(2022)
Article
Microbiology
Philip Eisenberg, Leon Albert, Jonathan Teuffel, Eric Zitzow, Claudia Michaelis, Jane Jarick, Clemens Sehlke, Lisa Grosse, Nicole Bader, Ariane Nunes-Alves, Bernd Kreikemeyer, Hermann Schindelin, Rebecca C. Wade, Tomas Fiedler
Summary: The study reveals the importance of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN in Streptococcus pyogenes and its potential as a target for antimicrobial substances that selectively kill S. pyogenes and other streptococci.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Thanasis Rogdakis, Despoina Charou, Alessia Latorrata, Eleni Papadimitriou, Alexandros Tsengenes, Christina Athanasiou, Marianna Papadopoulou, Constantina Chalikiopoulou, Theodora Katsila, Isbaal Ramos, Kyriakos C. Prousis, Rebecca C. Wade, Kyriaki Sidiropoulou, Theodora Calogeropoulou, Achille Gravanis, Ioannis Charalampopoulos
Summary: A new NGF mimetic, ENT-A013, has been identified to selectively activate TrkA receptor and exert neuroprotective effects, showing potential for therapeutic development against neurodegenerative disorders, such as Alzheimer's Disease.
Article
Chemistry, Multidisciplinary
Siri C. van Keulen, Juliette Martin, Francesco Colizzi, Elisa Frezza, Daniel Trpevski, Nuria Cirauqui Diaz, Pietro Vidossich, Ursula Rothlisberger, Jeanette Hellgren Kotaleski, Rebecca C. Wade, Paolo Carloni
Summary: This study used simulation tools to uncover the molecular and subcellular mechanisms of AC function, with a focus on the AC5 isoform. The research revealed an inactive state of the enzyme in the presence of an inhibitory G alpha subunit, regardless of the presence of a stimulatory G alpha. The binding of G alpha subunits reshaped the free-energy landscape of the AC5 enzyme.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Multidisciplinary Sciences
Lukas Rohland, Roman Kityk, Luka Smalinskaite, Matthias P. Mayer
Summary: The 70 kDa heat shock proteins (Hsp70s) are versatile molecular chaperones that assist in protein-folding processes. ATP and cochaperones induce structural rearrangements in Hsp70, with peptides causing larger changes and protein clients being more effective in stimulating ATP hydrolysis. The study provides insights into the mechanics, allostery, and dynamics of Hsp70 chaperones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Chemistry, Multidisciplinary
Abraham Muniz-Chicharro, Lane W. Votapka, Rommie E. Amaro, Rebecca C. Wade
Summary: Brownian dynamics (BD) is a computational method used to simulate molecular diffusion processes, and recent developments have improved its accuracy and expanded its applications. In biological research, BD is used to study the diffusive behavior of molecules under various conditions and to compute rate constants for molecular association and examine transport properties. The development of software packages for BD simulations has provided new features and expanded the range of questions that can be addressed.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Cell Biology
Alireza Mashaghi, Fatemeh Moayed, Eline J. Koers, Yang Zheng, Katharina Till, Gunter Kramer, Matthias P. Mayer, Sander J. Tans
Summary: The chaperone heat shock protein 90 (Hsp90) plays a crucial role in promoting local intra-chain interactions and suppressing distant interactions to alter the conformations of unstable substrates, thereby protecting and cooperating with them.
Article
Chemistry, Physical
Ainara Claveras Cabezudo, Christina Athanasiou, Alexandros Tsengenes, Rebecca C. Wade
Summary: Reducing the nonbonded interactions between protein and water enables protein encapsulation in phospholipid micelles and bilayers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Medicinal
Ina Poehner, Antonio Quotadamo, Joanna Panecka-Hofman, Rosaria Luciani, Matteo Santucci, Pasquale Linciano, Giacomo Landi, Flavio Di Pisa, Lucia Dello Iacono, Cecilia Pozzi, Stefano Mangani, Sheraz Gul, Gesa Witt, Bernhard Ellinger, Maria Kuzikov, Nuno Santarem, Anabela Cordeiro-da-Silva, Maria P. Costi, Alberto Venturelli, Rebecca C. Wade
Summary: In this study, a systematic and multidisciplinary approach was used to develop selective antiparasitic compounds. Through computational fragment-based design and crystallographic structure determination, compounds with activity against multiple targets were obtained. Additionally, the combination of polypharmacology design and parasite-specific optimization led to the discovery of compounds effective against T. brucei brucei.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
A. Toral-Lopez, D. B. Kokh, E. G. Marin, R. C. Wade, A. Godoy
Summary: Biological Field-Effect Transistors (BioFETs) have shown great potential for detecting small amounts of ions and molecules. The use of two-dimensional (2D) materials can enhance their performance and enable new applications, which is particularly relevant in the current pandemic where fast, reliable, and affordable detection methods are needed. However, there is a lack of comprehensive computational approaches to understand the mechanisms underlying sensor behavior. In this study, a multiscale platform is proposed that combines atomic models of molecules with mesoscopic device-level simulations, providing a detailed description of the sensor behavior.
NANOSCALE ADVANCES
(2022)
Meeting Abstract
Biophysics
Madhura De, Mehmet A. Oeztuerk, Sebastian Isbaner, Martin Wuertz, Gabriele Mueller, Katalin Toth, Rebecca C. Wade
BIOPHYSICAL JOURNAL
(2022)