Article
Biochemistry & Molecular Biology
Weiwei Han, Bee-Zen Peng, Chunyan Wang, Guy E. Townsend II, Natasha A. Barry, Frank Peske, Andrew L. Goodman, Jun Liu, Marina Rodnina, Eduardo A. Groisman
Summary: Protein synthesis is a vital cellular process that requires a significant amount of energy. However, cells can sustain protein synthesis under starvation conditions through the use of a bacterial elongation factor called EF-C2, which promotes translocation without hydrolyzing GTP. EF-G2, a variant of EF-C2, is crucial for bacterial gut colonization and can sustain protein synthesis at slower rates. EF-G2 is more abundant than canonical EF-C1 and specifically accumulates during carbon starvation. A unique 26-residue region in EF-G2 is essential for protein synthesis, dissociation from the ribosome, and the absence of GTPase activity. These findings provide insights into how cells minimize energy consumption while maintaining protein synthesis in fluctuating nutrient environments.
Article
Biochemistry & Molecular Biology
Wataru Nishima, Dylan Girodat, Mikael Holm, Emily J. Rundlet, Jose L. Alejo, Kara Fischer, Scott C. Blanchard, Karissa Y. Sanbonmatsu
Summary: This study combines molecular simulations with single-molecule fluorescence resonance energy transfer imaging to uncover the key steps of ribosome completion and resetting during translocation. Diffusive motions of the ribosomal small subunit head domain and the role of ribosomal RNA enable mRNA and tRNA to achieve full translocation, while the engagement of peptidyl-tRNA and disengagement of deacyl-tRNA facilitate the ribosome resetting mechanism.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Changil Kim, Mikael Holm, Chandra Sekhar Mandava, Suparna Sanyal
Summary: This study optimized a popular fluorescent-mRNA based translocation assay for studying ribosomal translocation kinetics and found that a 10-base fluorescently labelled mRNA is best suited for the assay. Comparisons between a commonly used peptidyl tRNA analog and a natural dipeptidyl tRNA showed that the analog translocates slower and produces biphasic kinetics.
Article
Biochemistry & Molecular Biology
Manuel Osorio-Valeriano, Florian Altegoer, Chandan K. Das, Wieland Steinchen, Gael Panis, Lara Connolley, Giacomo Giacomelli, Helge Feddersen, Laura Corrales-Guerrero, Pietro I. Giammarinaro, Juri Hanssmann, Marc Bramkamp, Patrick H. Viollier, Sean Murray, Lars V. Schaefer, Gert Bange, Martin Thanbichler
Summary: ParB-like CTPases play a key role in the segregation of bacterial chromosomes and low-copy number plasmids by forming large nucleoprotein complexes across the centromere. CTP hydrolysis helps limit the sliding time of ParB clamps and establish a diffusion gradient critical for DNA segregation. Understanding the CTPase cycle of ParB advances our knowledge of this prototypic CTP-dependent molecular switch.
Article
Multidisciplinary Sciences
Daniel Beckett, Gregory A. Voth
Summary: Microtubules (MTs) are large cytoskeletal polymers composed of α(3-tubulin heterodimers that undergo stochastic polymerization and depolymerization processes. Depolymerization involves the hydrolysis of guanosine triphosphate (GTP), which is favored in the MT lattice compared to the free heterodimer. This study used extensive simulations to investigate the GTP hydrolysis mechanism in different lattice states. The results revealed the catalytic role of α:E254 and demonstrated that GTP hydrolysis is variable with lattice state and slower at the MT tip.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Yasir H. Ibrahim, Spyridon Pantelios, Anders P. Mutvei
Summary: A simple tool has been developed to isolate endogenous mTORC1 protein from various cellular sources. This cost-effective and scalable method can aid in mTORC1-related research.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Maria G. Khrenova, Bella L. Grigorenko, Alexander Nemukhin
Summary: This computational study investigates the reaction mechanism of GTP hydrolysis catalyzed by the Ran and Ran-RanGAP enzymes with and without GAP. The activation barriers calculated align with experimentally estimated rate constants, and mapping the Laplacian of the electron density provides insights into substrate activation and enzyme-catalyzed features. Comparing reactions in different scenarios helps to characterize the role of GAP in the absence of an arginine finger.
Article
Biochemistry & Molecular Biology
Shixin Ye, Jean Lehmann
Summary: This study investigates the origin of genetic code degeneracy and the role of the ribosome in this process. The results show that residue A1493 in the ribosome plays a significant role in the stability of the base pair, which is crucial for the establishment of degeneracy. The study also provides evidence for the relationship between G530 in the decoding center and tRNA selection based on evolutionary models.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Sakshi Jain, Lukasz Koziej, Panagiotis Poulis, Igor Kaczmarczyk, Monika Gaik, Michal Rawski, Namit Ranjan, Sebastian Glatt, Marina V. Rodnina
Summary: m(6)A is a common mRNA modification that regulates cellular mRNA metabolism. It delays the decoding process and increases tRNA drop-off from the ribosome by favoring alternative codon conformations that are rejected by the ribosome.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Mitchell I. Parker, Joshua E. Meyer, Erica A. Golemis, Roland L. Dunbrack
Summary: Analysis of more than 700 RAS structures has expanded our understanding of RAS structural biology, including active, inactive, and druggable conformations, the structural impact of common RAS mutations, and previously uncharacterized RAS inhibitor-binding modes.
Article
Biochemistry & Molecular Biology
Soneya Majumdar, Andrew Emmerich, Sascha Krakovka, Chandra Sekhar Mandava, Staffan G. Svard, Suparna Sanyal
Summary: Using cryo-electron microscopy, we have determined high-resolution structures of six translocation intermediates from Giardia ribosomes. These ribosomes possess eukaryotic rRNAs and proteins, but also retain some bacterial features. The study elucidates the mechanism of translocation in protists and sheds light on the evolution of translation machinery.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Eric Girard, Pedro Lopes, Michael Spoerner, Anne-Claire Dhaussy, Thierry Prange, Hans Robert Kalbitzer, Nathalie Colloc'h
Summary: In this study, the researchers used high pressure crystallography to investigate the allosteric transitions of Ras protein. They found that pressure can shift the equilibria between different conformational states, providing insight into the structural plasticity involved in Ras protein's allosteric equilibria.
Article
Multidisciplinary Sciences
Thu Giang Nguyen, Christina Ritter, Eva Kummer
Summary: Mitochondria contain their own genetic information and translation system. Researchers have discovered that GTPBP10 plays a role in the folding of mitochondrial ribosomal RNA during the biogenesis process, which is related to bacterial ribosome biogenesis. Unlike bacteria, mitochondria require two biogenesis factors. This study reveals the process of maturation in the human mitoribosome and the interplay between GTPBP10 and GTPBP7.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Evgenii Kliuchnikov, Eugene Klyshko, Maria S. Kelly, Artem Zhmurov, Ruxandra Dima, Kenneth A. Marx, Valeri Barsegov
Summary: This study developed a 3D microtubule assembly and disassembly dynamics (MADDY) model to analyze the dynamic instability behavior of microtubules. By applying machine learning techniques, the study identified microtubule characteristics that distinguish different kinetic states. The results provide greater insights into the stability of kinetic states and the transitions between states involved in microtubule dynamic instability behavior.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Philipp I. Pletnev, Olga Shulenina, Sergey Evfratov, Vsevolod Treshin, Maksim F. Subach, Marina V. Serebryakova, Ilya A. Osterman, Alena Paleskava, Alexey A. Bogdanov, Olga A. Dontsova, Andrey L. Konevega, Petr Sergiev
Summary: This study identified another key enzyme, RimI, responsible for acetylation modification in bacteria and demonstrated that acetylation of EF-Tu increases the efficiency of in vitro translation. Additionally, the absence of RimI in the strain resulted in reduced growth rate and potentially promoted conservation of the acetylation mechanism in the translation apparatus.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)