Article
Multidisciplinary Sciences
Delfim Ferreira, Ana C. C. Barbosa, Goncalo P. Oliveira, Teresa Catarino, Sofia S. Venceslau, Ines A. C. Pereira
Summary: Dissimilatory sulfur metabolism is widespread among bacteria and archaea, with DsrAB and other Dsr proteins playing key roles. DsrD acts as an activator of DsrAB and its function is still debated.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Medicinal
Xi Xu, Jubo Wang, Min Wang, Xinyu Yuan, Lei Li, Chao Zhang, Huidan Huang, Tian Jing, Chenchen Wang, Chao Tong, Liwen Zhou, Ying Meng, Pengfei Xu, Junping Kou, Zhixia Qiu, Zhiyu Li, Jinlei Bian
Summary: Inhibition of glutaminase 1 (GLS1) is a potential treatment for malignant tumors. A novel series of macrocyclic GLS1 allosteric inhibitors, with a promising candidate molecule 13b (LL202) exhibiting robust inhibitory activity and high binding affinity, have been designed through structural analysis. The study highlights the potential of macrocyclization as an alternative approach for designing small-molecule inhibitors to improve target binding affinity.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Review
Cell Biology
Yingying Li, Yingjun Feng, Xiaoyun Ye, Hanlin Peng, Jiantong Du, Xiaoli Yao, Yaqian Huang, Hongfang Jin, Junbao Du
Summary: SO2, previously known as industrial waste, has been proven to be a novel gasotransmitter in the cardiovascular system. Endogenous SO2 regulates cell apoptosis and may play a role in the pathogenesis of various cardiovascular diseases. Studies have shown that endogenous SO2 is important in the regulation of biological processes and has potential implications in cardiovascular pathophysiology.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shanker S. S. Panchapakesan, Ronald R. Breaker
Summary: The RNA World theory suggests that sophisticated ribozymes and riboswitches played a key role in metabolic processes in ancient organisms, and various types of catalytic RNAs and ligand-sensing RNA switches still exist in modern cells. However, the fusion of RNA enzyme and RNA switch components to form allosteric ribozymes is rare in today's biological systems, despite the abundance of self-cleaving ribozymes and riboswitch aptamers.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
David P. Tilly, Jean-Paul Heeb, Simon J. Webb, Jonathan Clayden
Summary: Molecular biology controls complex reaction networks by translating a chemical input into an orthogonal chemical output, but dynamic foldamers have been limited by stereochenical changes that produce spectroscopic signals. In this study, the authors introduce an artificial molecular translation device that converts a chemical input into an unrelated chemical output. This device modulates the reactivity of an imidazole moiety by the presence of chloride ions through the allosteric remote control of imidazole tautomer states.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Peipei Qin, Pinru Chen, Nan Deng, Liu Tan, Bin-Cheng Yin, Bang-Ce Ye
Summary: This study proposes a method to directly regulate the trans cleavage activity of Cas12a using an allosteric DNA probe, enabling the sensing of different types of analytes. The proposed strategy utilizes an allosteric inhibitor probe that can induce a change in conformation and remove its inhibitory function on Cas12a upon binding to a specific target. The method was validated for detecting adenosine triphosphate and let-7a, demonstrating excellent specificity.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Arek Melkonian, Elise Loppinet, Renata Martin, Matthew Porteus, Chaitan Khosla
Summary: Extracellular TG2 activity is competitively controlled by high-affinity Ca2+ ion binding and strained disulfide bond formation, leading to either enzyme protection or complete inactivation. Minor changes in redox catalysts or promoters in the extracellular matrix can significantly alter steady-state TG2 activity. TG2 serves as a molecular OR gate determining its catalytic fate upon export from cells.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Review
Microbiology
Li-Jun Liu, Zhen Jiang, Pei Wang, Ya-Ling Qin, Wen Xu, Yang Wang, Shuang-Jiang Liu, Cheng-Ying Jiang
Summary: Sulfolobales is a group of thermoacidophilic archaea, with most members being chemolithoautotrophic and using sulfur compounds as energy sources. Sulfur metabolism is the key physiological characteristic of Sulfolobales.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Raul Valente, Luis Q. Alves, Matilde Nabais, Filipe Alves, Isabel Sousa-Pinto, Raquel Ruivo, L. Filipe C. Castro
Summary: The study investigates the role of Cortistatin (CORT) in mammalian biorhythm regulation, revealing that cetaceans and other mammals with atypical biorhythms, thermal constraints, and/or energy metabolism have accumulated deleterious mutations in the CORT gene. The inactivation of this gene may have contributed to a variety of phenotypic adjustments for adaptive solutions to specific ecological niches.
Article
Biochemistry & Molecular Biology
Mohammad Roghanian, Katleen Van Nerom, Hiraku Takada, Julien Caballero-Montes, Hedvig Tamman, Pavel Kudrin, Ariel Talavera, Ievgen Dzhygyr, Simon Ekstrom, Gemma C. Atkinson, Abel Garcia-Pino, Vasili Hauryliuk
Summary: Amino acid starvation is sensed by RelA and Rel through monitoring the aminoacylation status of ribosomal A-site tRNA, with their synthetic activity controlled by the alarmone nucleotide (p)ppGpp. Stimulation by the alarmone exploits intra-NTD autoinhibition dynamics to activate Rel/RelA. Without pppGpp stimulation, starved ribosomes cannot efficiently activate Rel/RelA, compromising their function in vivo.
Article
Chemistry, Physical
Zhenzhong Zhang, Fang Wang, Kai Hu, Yu She, Sannian Song, Zhitang Song, Kailiang Zhang
Summary: This paper systematically investigates the sulfur (S)-doping technology for HfOx-based RRAM to improve its electrical performance. The optimal S content reduces V-SET/V-RESET, limits Icc, and enhances device performance with improved uniformity, stability, fast response speed, and low energy consumption. Sulfur doping effectively suppresses the random formation of conductive filaments, leading to improved performance of the TiN/HfOx/ITO device.
Article
Chemistry, Multidisciplinary
Tuhin Sahana, Dhanusree C. Kakkarakkal, Subrata Kundu
Summary: This study reveals an amine-free biologically relevant route for the reactions of sulfane sulfur and thiol, with the important role of [Zn-II] coordination motif in the reactions of sulfane sulfur. It highlights the feasible influence of biologically relevant [Zn-II] coordination motifs on sulfur chemistry in biology.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Multidisciplinary Sciences
Vitor Mendes, Simon R. Green, Joanna C. Evans, Jeannine Hess, Michal Blaszczyk, Christina Spry, Owain Bryant, James Cory-Wright, Daniel S-H Chan, Pedro H. M. Torres, Zhe Wang, Navid Nahiyaan, Sandra O'Neill, Sebastian Damerow, John Post, Tracy Bayliss, Sasha L. Lynch, Anthony G. Coyne, Peter C. Ray, Chris Abell, Kyu Y. Rhee, Helena I. M. Boshoff, Clifton E. Barry, Valerie Mizrahi, Paul G. Wyatt, Tom L. Blundell
Summary: Coenzyme A (CoA) is a crucial factor in various metabolic pathways and cellular processes, particularly in prokaryotes such as Mycobacterium tuberculosis. The biosynthesis of CoA involves five steps, with the second and third steps catalyzed by a bifunctional protein CoaBC in most prokaryotes. The researchers identified inhibitors of M. tuberculosis CoaB through a high-throughput screen and discovered a cryptic allosteric binding site within the enzyme.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Medicinal
Lung-Chun Lee, Yi-Hui Peng, Hsin-Huei Chang, Tsu Hsu, Cheng-Tai Lu, Chih-Hsiang Huang, Ching-Cheng Hsueh, Fang-Chun Kung, Ching-Chuan Kuo, Weir-Torn Jiaang, Su-Ying Wu
Summary: MTHFD2 is an important enzyme in one-carbon metabolism, upregulated in cancer and a potential target for treatment. A xanthine derivative was found to allosterically bind to MTHFD2, demonstrating uncompetitive inhibition and high selectivity. This study provides insights into the inhibition mechanism of MTHFD proteins and the development of novel inhibitors.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Yi Jin, Zhuqing Ren, Yanjie Tan, Pengxiang Zhao, Jian Wu
Summary: Lipid droplets store neutral lipids in cells and have been found to play important roles in various biological processes, such as stress resistance, immunity, cell proliferation, apoptosis, and signal transduction. Lorganelles interacts with other organelles in cells, including the endoplasmic reticulum, mitochondria, peroxisomes, and autophagic lysosomes, requiring them to be close to each other and involve the motility of the lipid droplets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Marouane Libiad, Victor Vitvitsky, Trever Bostelaar, Daniel W. Bak, Ho-Joon Lee, Naoya Sakamoto, Eric Fearon, Costas A. Lyssiotis, Eranthie Weerapana, Ruma Banerjee
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Pramod K. Yadav, Victor Vitvitsky, Hanseong Kim, Andrew White, Uhn-Soo Cho, Ruma Banerjee
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Ruddi Rodriguez-Garcia, Vladimir A. Volkov, Chiung-Yi Chen, Eugene A. Katrukha, Natacha Olieric, Amol Aher, Ilya Grigoriev, Magdalena Preciado Lopez, Michel O. Steinmetz, Lukas C. Kapitein, Gijsje Koenderink, Marileen Dogterom, Anna Akhmanova
Article
Biology
Pim J. Huis in ' t Veld, Vladimir A. Volkov, Isabelle D. Stender, Andrea Musacchio, Marileen Dogterom
Article
Biochemistry & Molecular Biology
Pramod Kumar Yadav, Victor Vitvitsky, Sebastian Carballal, Javier Seravalli, Ruma Banerjee
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Review
Cell Biology
Vladimir A. Volkov
KINETOCHORES AND CHROMOSOME SEGREGATION
(2020)
Article
Biochemistry & Molecular Biology
Victor Vitvitsky, Roshan Kumar, Marouane Libiad, Allison Maebius, Aaron P. Landry, Ruma Banerjee
Summary: The exogenously added hydrogen sulfide had a half-life of 3 to 4 minutes in human colonic epithelial cells, with a small fraction trapped as sulfane sulfur species. Sulfide stimulated aerobic glycolysis in cells, was sensitive to the mitochondrial NADH pool, and decreased ATP levels.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Sebastian Carballal, Victor Vitvitsky, Roshan Kumar, David A. Hanna, Marouane Libiad, Aditi Gupta, Jace W. Jones, Ruma Banerjee
Summary: This study demonstrates that H2S increases lipid synthesis in cells by affecting mitochondrial NAD(P)H pools and enabling reductive carboxylation of alpha-ketoglutarate. H2S also leads to time-dependent changes in various lipid classes, upregulating triglycerides while downregulating phosphatidylcholine.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Celine Alkemade, Harmen Wierenga, Vladimir A. Volkov, Magdalena Preciado Lopez, Anna Akhmanova, Pieter Rein ten Wolde, Marileen Dogterom, Gijsje H. Koenderink
Summary: This study reveals the mechanism of passive cross-linkers generating forces in the interaction between actin and microtubules, and experimentally verifies this process. The results demonstrate that passive cross-linkers can facilitate the transportation of actin filaments on microtubules, which is significant for cellular remodeling processes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biophysics
Felix Schwietert, Vladimir A. Volkov, Pim J. Huis in't Veld, Marileen Dogterom, Andrea Musacchio, Jan Kierfeld
Summary: In the mitotic spindle, microtubules attach to chromosomes via kinetochores, with the Ndc80 complex playing a crucial role in this process. The study reveals that Ndc80 complexes exhibit strain stiffening when subjected to tension, with effective stiffness increasing as tension builds up from depolymerizing microtubules. This behavior can be attributed to the specific architecture of the Ndc80 complex, thermal fluctuations of microtubules, and the bending elasticity of flaring protofilaments.
BIOPHYSICAL JOURNAL
(2022)
Article
Cell Biology
Ali Nick Maleki, Pim J. Huis in 't Veld, Anna Akhmanova, Marileen Dogterom, Vladimir A. Volkov
Summary: Microtubules are dynamic cytoskeletal filaments that can generate forces through polymerization and depolymerization. Proteins that interact with microtubule ends and facilitate force generation are essential for cellular processes. In this study, we propose a novel experimental approach using a fluorescent spring-shaped DNA origami molecule to estimate microtubule-generated forces. The DNA nanospring allows multiplexed force measurements and only requires basic laboratory equipment. We validate the performance of DNA nanosprings and demonstrate their utility in studying protein-mediated force generation during microtubule growth and shortening.
JOURNAL OF CELL SCIENCE
(2023)
Article
Cell Biology
Renu Maan, Louis Reese, Vladimir A. Volkov, Matthew R. King, Eli O. van der Sluis, Nemo Andrea, Wiel H. Evers, Arjen J. Jakobi, Marileen Dogterom
Summary: Growing microtubule ends can organize end-tracking proteins into mixed composition comets. In a reconstituted fission yeast system, these proteins can form liquid-phase droplets in solution and at microtubule ends under crowding conditions. Motor-dependent comets consist of disordered networks that may facilitate non-stoichiometric accumulation of cargo Tip1, while autonomous comet formation requires specific disordered protein regions in Mal3. The enrichment of Tip1 at microtubule ends may be attributed to motor activity and multivalent interactions.
NATURE CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Soumitra Polley, Helen Mueschenborn, Melina Terbeck, Anna De Antoni, Ingrid R. Vetter, Marileen Dogterom, Andrea Musacchio, Vladimir A. Volkov, Pim J. Huis In 't Veld
Summary: During cell division, the Ndc80 complex plays a crucial role in linking chromosomes to spindle microtubules. This study demonstrates that the Ndc80 loop promotes direct interactions between adjacent Ndc80 complexes, which are necessary for stable end-on kinetochore-microtubule attachment and spindle assembly checkpoint satisfaction. Mutations in the loop impair these interactions and lead to cell arrest in mitosis.
Article
Cell Biology
Cyntha M. van den Berg, Vladimir A. Volkov, Sebastian Schnorrenberg, Ziqiang Huang, Kelly E. Stecker, Ilya Grigoriev, Sania Gilani, Kari-Anne M. Frikstad, Sebastian Patzke, Timo Zimmermann, Marileen Dogterom, Anna Akhmanova
Summary: CSPP1, a protein associated with cilia and centrosomes, preferentially binds to slowly growing or perturbed microtubule ends, stabilizing their structure. This study reveals the mechanisms by which CSPP1 regulates the elongation and stability of cilia and other microtubule-based structures by inhibiting microtubule growth and shortening.
JOURNAL OF CELL BIOLOGY
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Victor Vitvitsky, Marouane Libiad, Trever Bostelaar, Allison Maebius, Ho-Joon Lee, Costas A. Lyssiotis, Ruma Banerjee