Article
Biochemistry & Molecular Biology
Elodie C. Leroy, Thomas N. Perry, Thibaud T. Renault, C. Axel Innis
Summary: As antimicrobial resistance becomes a threat, the development of new antibiotics with limited cross-resistance is urgent. Natural products that target the bacterial ribosome have the potential to be potent drugs if their mechanisms of action are well understood. This study provides mechanistic insights into how the aromatic polyketide tetracenomycin X inhibits peptide bond formation and suggests a path forward for the development of novel antibiotics.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Panagiotis Poulis, Anoshi Patel, Marina V. Rodnina, Sarah Adio
Summary: Slippery sequences in mRNA can cause the ribosome to change its reading frame, affecting the translation process. Research has shown that during translocation on slippery sequences, the ribosome switches from a fast and accurate translation mode to a slow and frameshifting-prone mode, reducing translation fidelity.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Matthias Thoms, Benjamin Lau, Jingdong Cheng, Lisa Fromm, Timo Denk, Nikola Kellner, Dirk Flemming, Paulina Fischer, Laurent Falquet, Otto Berninghausen, Roland Beckmann, Ed Hurt
Summary: The study isolated and described the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, Rix1-Ipi3-Ipi1 and Las1-Grc3 complex. The Rix1 complex plays a key role in pre-60S particles by inserting between the 5S rRNA tip and L1-stalk, facilitating the rotation of immature 5S RNP. The other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase cleaves and phosphorylates the nearby ITS2 pre-rRNA at the pre-60S foot. Inward movement of the L1 stalk permits the Nop53 N-terminus with AIM motif to participate in completing ITS2 removal.
Article
Biochemistry & Molecular Biology
Ying-Hui Wang, Hong Dai, Ling Zhang, Yun Wu, Jingfen Wang, Chen Wang, Cai-Huang Xu, Hai Hou, Bing Yang, Yongqun Zhu, Xing Zhang, Jie Zhou
Summary: In this study, the cryo-electron microscopy structures of archaeal ribosomes from Sulfolobus acidocaldarius were determined, revealing unstable conformations of certain ribosomal RNA and providing models for new ribosomal proteins. The structures of the 50S-aRF1 complex and 70S ribosome complexes captured at different functional states shed light on translation termination and tRNA translocation. These findings enhance our understanding of archaeal translation and ribosome translocation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ze Liu, Justin Wang, Yi Shi, Brian A. Yee, Markus Terrey, Qian Zhang, Jenq-Chang Lee, Kuo- Lin, Andrew H-J Wang, Susan L. Ackerman, Gene W. Yeo, Haissi Cui, Xiang-Lei Yang
Summary: Translational readthrough of UGA stop codons by selenocysteine-specific tRNA enables the synthesis of selenoproteins. In addition, this mechanism can also increase translational readthrough of non-selenocysteine genes to create C-terminally extended isoforms. The recognition of target mRNAs by seryl-tRNA synthetase is dependent on its enzymatic activity and a vertebrate-specific domain. The findings expand our understanding of selenoprotein biosynthesis and suggest a potential avenue for therapeutic targeting of nonsense mutations using endogenous factors.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Rachel A. Johnson, Andrew N. Chan, Ryan D. Ward, Caylie A. McGlade, Breanne M. Hatfield, Jason M. Peters, Bo Li
Summary: Hybrid antibiotics like thiomarinol A show promise in combating antibiotic resistance, with a dual mode of action targeting IleRS and potentially involving metal chelation. Thiomarinol A remains effective against high-level mupirocin-resistant MRSA and shows less resistance development compared to mupirocin, emphasizing the importance of hybridity between DTP and mupirocin for potent activity.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Hadieh Monajemi, Sharifuddin M. Zain, Wan Ahmad Tajuddin Wan Abdullah
Summary: The translational accuracy in protein synthesis is contributed to by several mechanisms in the ribosome, generally called kinetic proofreading. In addition to kinetic proofreading, the study shows the importance of aminoacyl-tRNA binding energy in ensuring fidelity of protein synthesis. The wrong addition of amino acids can lead to errors in the polypeptide chain.
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS
(2021)
Review
Cell Biology
Marianne Mercer, Seoyeon Jang, Chunyang Ni, Michael Buszczak
Summary: Regulation of mRNA translation is crucial for germ cell development and function across species, involving specific RNA binding proteins. These proteins are conserved and play similar roles in germ cells of various species, highlighting the importance of understanding the mechanisms controlling mRNA translation in germ cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Carolin Seyfferth, Bernard A. Wessels, Jorma Vahala, Jaakko Kangasjarvi, Nicolas Delhomme, Torgeir R. Hvidsten, Hannele Tuominen, Judith Lundberg-Felten
Summary: PtERF85 plays a crucial role in balancing xylem cell expansion and secondary cell wall (SCW) formation in hybrid aspen, by activating genes related to cell expansion while preventing the synthesis of SCW chemical components. The spatial expression of PtERF85 during wood development contributes to transition of fiber cells from elongation to secondary cell wall deposition.
Article
Biochemistry & Molecular Biology
Caroline Vindry, Olivia Guillin, Philippe Wolff, Paul Marie, Franck Mortreux, Philippe E. Mangeot, Theophile Ohlmann, Laurent Chavatte
Summary: This study used CRISPR/Cas9 technology to engineer heterozygous and homozygous mutant human cells with a C65G mutation in tRNA([Ser]Sec). The mutation affected the expression level of tRNA([Ser]Sec), leading to altered selenoprotein expression and reduced sensitivity to selenium supplementation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Mathias S. Heltberg, Alessandra Lucchetti, Feng-Shu Hsieh, Duy Pham Minh Nguyen, Sheng-hong Chen, Mogens H. Jensen
Summary: This study investigates the dynamic signaling in the repair process of DNA damage in cells, revealing that the oscillatory dynamics of the transcription factor p53 optimize the repair efficiency by forming sub-compartments.
Article
Environmental Sciences
Ming-Tung Chuang, Chang-Fu Wu, Chuan-Yao Lin, Wei-Che Lin, Charles C. -K Chou, Chung-Te Lee, Tang-Huang Lin, Joshua S. Fu, Steven Soon-Kai Kong
Summary: The downward trend of NOX concentrations in Taiwan does not reflect the reduction of nitrate (NO3-). Instead, the proportion of NO3- in PM2.5 has increased in recent years. This study found that the reaction between NO2 and OH during the daytime is a major contributor to HNO3, while the heterogeneous reaction is the main formation mechanism of NO3-. Controlling O-3 may be another useful strategy to reduce NO3-.
ATMOSPHERIC ENVIRONMENT
(2022)
Article
Immunology
Jinghan Ma, Hideki Kitaura, Saika Ogawa, Fumitoshi Ohori, Takahiro Noguchi, Aseel Marahleh, Yasuhiko Nara, Adya Pramusita, Ria Kinjo, Kayoko Kanou, Akiko Kishikawa, Atsuhiko Ichimura, Itaru Mizoguchi
Summary: This study investigates the influence of DHA on TNF-alpha-induced osteoclast formation and orthodontic tooth movement (OTM). The results demonstrate that DHA can inhibit TNF-alpha-induced osteoclast formation and OTM via GPR120. Therefore, DHA may have an inhibitory effect on osteoclast formation and bone resorption in OTM.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Electrochemistry
Yutaka Tabe, Naoyuki Wakatake, Yuta Ishima, Takemi Chikahisa
Summary: In startups of polymer electrolyte fuel cells at temperatures close to 0 degrees C below freezing, water produced by the cathode reaction is present in a supercooled state and may freeze, impacting the startup process.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Fenfen Wang, Naizhi Chen, Shihua Shen
Summary: This study compares the green and golden-yellow leaves of hybrid paper mulberry using physiological, cytological, and proteomic analyses. The mutants of hybrid paper mulberry exhibit golden-yellow leaves, reduced chlorophyll and carotenoid content, and increased flavonoid content. Cytological observations reveal defective chloroplasts in the mutants. Proteomic analysis identifies differentially accumulated proteins involved in chlorophyll synthesis, carotenoid metabolism, photosynthesis, and ribosome pathways, suggesting their role in adaptation to environmental conditions. This study provides insights into the formation mechanism of the golden-yellow leaf phenotype.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Huan Yang, Jonathan Perrier, Paul C. Whitford
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2018)
Article
Chemistry, Physical
Mariana Levi, Paul C. Whitford
JOURNAL OF PHYSICAL CHEMISTRY B
(2019)
Article
Chemistry, Physical
Frederico Campos Freitas, Angelica Nakagawa Lima, Vinicius de Godoi Contessoto, Paul C. Whitford, Ronaldo Junio de Oliveira
JOURNAL OF CHEMICAL PHYSICS
(2019)
Article
Chemistry, Physical
Huan Yang, Prasad Bandarkar, Ransom Horne, Vitor B. P. Leite, Jorge Chahine, Paul C. Whitford
JOURNAL OF CHEMICAL PHYSICS
(2019)
Article
Chemistry, Physical
Antonio B. Oliveira, Huan Yang, Paul C. Whitford, Vitor B. P. Leite
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2019)
Article
Biophysics
Prasad Bandarkar, Huan Yang, Robert. Y. Henley, Meni Wanunu, Paul C. Whitford
BIOPHYSICAL JOURNAL
(2020)
Article
Biology
Esteban Dodero-Rojas, Jose N. Onuchic, Paul Charles Whitford
Summary: SARS-CoV-2 is highly contagious and its transmission is influenced by vaccines and therapeutics. Research shows that the conformational changes of the Spike protein and the role of glycans are crucial for the virus to enter host cells. The study provides a new mechanistic description for understanding viral transmission.
Editorial Material
Biophysics
Paul Charles Whitford
Summary: Experts in molecular biophysics discussed the dynamics of biopolymers across various length and time scales, showcasing techniques ranging from detailed simulations to structural analysis. Topics covered biological processes at different scales, from individual atoms to phase separation on a large scale.
BIOPHYSICAL REVIEWS
(2021)
Review
Biophysics
Asem Hassan, Sandra Byju, Paul C. Whitford
Summary: The process of protein synthesis in cells is controlled by conformational rearrangements in the ribosome, which contains approximately 50-100 RNA and protein molecules. Computational and simulation methods are used to understand the mechanical properties of the ribosome, leading to insights that guide next-generation experimental measurements. Research focuses on large-scale subunit rotation events in the ribosome, revealing how its molecular structure encodes mechanical properties that control dynamics on a larger scale.
BIOPHYSICAL REVIEWS
(2021)
Article
Chemistry, Multidisciplinary
Ailun Wang, Mariana Levi, Udayan Mohanty, Paul C. Whitford
Summary: Proper ionic concentrations are crucial for the functional dynamics of RNA and RNP assemblies. This study presents a model that quantifies the impact of diffuse ions on biomolecular assembly dynamics. The model accurately predicts the excess Mg2+ ions in RNA systems and reveals the direct influence of diffuse ions on the dynamics of a ribosome and tRNA molecules during translation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Asem Hassan, Paul C. Whitford
Summary: In this study, molecular dynamics simulations were used to investigate the translocation step of the elongation cycle in the ribosome. The results reveal that the head domain of the ribosomal small subunit undergoes spontaneous rotation and tilt-like motions. Possible single-molecule probes that can isolate the rotation and tilt of the head domain were identified, providing insights into the mechanistic and kinetic aspects of the ribosome.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Yang Wang, Ailun Wang, Udayan Mohanty, Paul C. Whitford
Summary: Protein synthesis involves complex conformational changes in the ribosome, and this study focuses on the final stage of accommodation of aminoacyl-tRNA on the ribosome. By using molecular dynamics simulations, it was discovered that a distinct intermediate is induced by steric confinement of the 3'-CCA tail of aa-tRNA before it completes accommodation. Multiple pathways for the tail accommodation were found, with one pathway involving Helix 89, 90, and 92, and another involving Helix 93 and the P-site tRNA. Additionally, the study identified that C2573 in Helix 90 plays a significant role in the steric barrier of late-stage accommodation.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Biographical-Item
Chemistry, Physical
Faruck Morcos, Paul C. Whitford, Margaret S. Cheung
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Editorial Material
Chemistry, Physical
Faruck Morcos, Paul C. Whitford, Margaret S. Cheung
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Multidisciplinary Sciences
Mariana Levi, Kelsey Walak, Ailun Wang, Udayan Mohanty, Paul C. Whitford
NATURE COMMUNICATIONS
(2020)