Review
Cell Biology
Claudia Schneider, Katherine E. Bohnsack
Summary: Ribosomes are responsible for translating genetic information into proteins and are composed of rRNAs and RPs. Recent advances in cryo-electron microscopy have allowed the visualization of pre-ribosomal particles, providing new insights into the processing of rRNA and the regulation of ribonucleases. This understanding enhances our knowledge of ribosome assembly and target recognition by ribonucleases.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Multidisciplinary Sciences
Haina Huang, Katrin Karbstein
Summary: This passage discusses the tendency of three-helix junctions to misfold during the assembly of small ribosomal subunits in cells, and reveals the pivotal role of ribosome assembly factors in facilitating their correct folding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Eunhye Lee, Paul J. Bujalowski, Tadahisa Teramoto, Keerthi Gottipati, Seth D. Scott, Radhakrishnan Padmanabhan, Kyung H. Choi
Summary: Flaviviruses use stem-loop A (SLA) as a promoter for RNA synthesis, with NS5 recognizing SLA to initiate RNA synthesis. The crystal structures of DENV and ZIKV SLAs show differences in orientation, but these can be compensated by differences in domain arrangements in DENV and ZIKV NS5s.
NATURE COMMUNICATIONS
(2021)
Article
Mathematics, Applied
Sebastian Carrasco, Pablo Medina, Jose Rogan, Juan Alejandro Valdivia
Summary: A theoretical framework for studying the dynamics of an open city with the use of GPS navigation systems was proposed. Through simulations, unexpected consequences of the massive use of GPS navigation systems in city dynamics were assessed. Different navigation strategies were considered, and it was found that in certain scenarios, the unweighted strategy may be more optimal.
Review
Oncology
Asimina Zisi, Jiri Bartek, Mikael S. Lindstrom
Summary: Cells, especially cancer cells, need to continuously produce ribosomes to sustain their proliferation. Targeting the machinery involved in ribosome biogenesis has shown potential for developing effective cancer therapies. This review provides information on molecules that target ribosome biogenesis and discusses potential avenues for future research.
Article
Chemistry, Multidisciplinary
James S. Craig, Larry Melidis, Hugo D. Williams, Samuel J. Dettmer, Alexandra A. Heidecker, Philipp J. Altmann, Shengyang Guan, Callum Campbell, Douglas F. Browning, Roland K. O. Sigel, Silke Johannsen, Ross T. Egan, Brech Aikman, Angela Casini, Alexander Pothig, Michael J. Hannon
Summary: Holliday 4-way junctions are important for DNA processes. Metallo-supramolecular pillarplexes can interact with open DNA junction cavities. They can bind 3-way junctions but disrupt base pairing, while they can bind and increase binding sites of 4-way junctions. This offers possibilities for biological and synthetic nucleic acid nanostructures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Microbiology
Joshua Stoll, Victor Zegarra, Gert Bange, Peter L. L. Graumann
Summary: Bacteria have nucleolus-like structures where ribosomal synthesis and maturation occur in close proximity at the cell poles, facilitating efficient ribosome maturation even under nutrient-deprived conditions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anwar Mohammad, Fahd Al-Mulla, Dong-Qing Wei, Jehad Abubaker
Summary: This study found that the mutation P323L in SARS-CoV-2 RdRp has a higher binding affinity to Remdesivir, potentially offering a more favorable option for alleviating the disease.
Article
Plant Sciences
Ming Zhou, Lei Deng, Shaogui Guo, Guoliang Yuan, Chuanyou Li, Changbao Li
Summary: This study reveals the genetic control mechanism of the orange-fruited phenotype in a tomato elite inbred line. It is found that this phenotype is controlled by a single recessive gene, oft3, which leads to reduced carotenoid levels and an increased beta-carotene-to-lycopene ratio in fruit. The candidate gene SlIDI1, with a 116 bp deletion mutation, is identified through gene mapping and genome sequence analysis. Functional complementation and CRISPR-Cas9 knockout experiments confirm the role of SlIDI1 in controlling the oft3 locus. Further analysis shows that SlIDI1 is highly expressed in flowers and fruit, and its expression increases with fruit ripening or flower maturation.
HORTICULTURE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Kuokuo Li, Tengfei Luo, Yan Zhu, Yuanfeng Huang, An Wang, Di Zhang, Lijie Dong, Yujian Wang, Rui Wang, Dongdong Tang, Zhen Yu, Qunshan Shen, Mingrong Lv, Zhengbao Ling, Zhenghuan Fang, Jing Yuan, Bin Li, Kun Xia, Xiaojin He, Jinchen Li, Guihu Zhao
Summary: This study manually collected 50,000 splicing variant samples to evaluate the performance of prediction methods and found differences in recognizing splicing variants among these methods. The study also validated the feasibility of integrating splicing prediction methods in identifying splicing variants and developed a splicing analytics platform that provides detailed annotation information.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Michael R. Lawson, Laura N. Lessen, Jinfan Wang, Arjun Prabhakar, Nicholas C. Corsepius, Rachel Green, Joseph D. Puglisi
Summary: Through single-molecule fluorescence assays, researchers found that in the termination process of yeast translation, the two release factors eRF1 and eRF3 bind together to rapidly recognize stop codons and induce termination through a tightly regulated, multistep process that resembles transfer RNA selection during translation elongation.
Article
Biochemistry & Molecular Biology
Hyejeong Kim, David Aponte-Diaz, Mohamad S. Sotoudegan, Djoshkun Shengjuler, Jamie J. Arnold, Craig E. Cameron
Summary: RNA recombination is a molecular-genetic process in positive-strand RNA viruses, allowing for maximum genome evolution and playing a crucial role in stabilizing the genome against harmful effects of mutations. Enteroviruses provide a useful model for studying this process, which is catalyzed by viral RNA-dependent RNA polymerase through a template-switching mechanism. Trafficking of viral genomes to the site of replication and recombination, which is membrane-associated and isolated from the cytoplasm, remains unclear. In this study, the researchers found that translation of the viral genome is essential for colocalization of genomes for recombination. Complete inactivation of internal ribosome entry site (IRES)-mediated translation enhanced recombination, rather than impairing it. Noncanonical translation initiation factors eIF2A and eIF2D were required for IRES-independent translation, suggesting their involvement in a different mechanism when eIF2-dependent translation is inactive. The discovery of an IRES-independent translation mechanism provides an explanation for various observations, including nonreplicative recombination and persistence of enteroviral RNA lacking an IRES. The existence of an eIF2A/eIF2D-dependent mechanism in enteroviruses suggests similar mechanisms may be present in other viruses.
Article
Cell Biology
Alessandro Brombin, Daniel J. Simpson, Jana Travnickova, Hannah Brunsdon, Zhiqiang Zeng, Yuting Lu, Adelaide I. J. Young, Tamir Chandra, E. Elizabeth Patton
Summary: This study identifies Tfap2b and a set of target genes that define an McSC population in the dorsal root ganglia of zebrafish, and shows that these McSCs play important roles during embryogenesis and in adulthood.
Article
Biochemistry & Molecular Biology
Kevin J. Sweeney, Xu Han, Ulrich F. Muller
Summary: In vitro selection experiments have developed catalytic RNA using cyclic trimetaphosphate as an energy source. Lanthanides can serve as catalytic cofactors for these ribozymes, with a sensitivity to ion radius. Potassium and magnesium enhance the lanthanide-mediated catalysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Computer Science, Software Engineering
Pasquale Claudio Africa
Summary: Numerical simulations are widely used in mathematics and computational science. This study presents an open-source library called lifex, which is designed for high-performance finite element simulations of complex multiphysics, multiscale, and multidomain problems. The flexibility and parallel performance of lifex are demonstrated through various examples and applications.
Article
Astronomy & Astrophysics
Martin Ferus, Vojtech Adam, Giuseppe Cassone, Svatopluk Civis, Vaclav Cuba, Elias Chatzitheodoridis, Barbora Drtinova, Bertrand LeFloch, Alan Heays, Sohan Jheeta, Akos Kereszturi, Antonin Knizek, Miroslav Krus, Petr Kubelik, Helmut Lammer, Libor Lenza, Lukas Nejdl, Adam Pastorek, Lukas Petera, Paul Rimmer, Raffaele Saladino, Franz Saija, Laurenz Spross, Jiri Sponer, Judit Sponer, Zoe Todd, Marketa Vaculovicova, Kristyna Zemankova, Vladislav Chernov
Summary: The existence of life beyond Earth has always been an important scientific question. Future observations of terrestrial exoplanets provide a unique opportunity to investigate this question. By studying other planetary systems, we can understand how physical and chemical environments evolve and gain insights into the early Earth. Therefore, it is crucial to carefully study the chemistry on young exoplanets and prepare reference materials for spectroscopic observations.
EXPERIMENTAL ASTRONOMY
(2022)
Article
Chemistry, Applied
Giuseppe Cassone, Jiri Sponer, Franz Saija
Summary: Electric fields play a crucial role in catalysis by modifying activation barriers and shaping free-energy landscapes of chemical reactions when interacting with atoms, molecules, and complex matter. The development of novel theories and advanced computational approaches has allowed for the routine investigation of catalytic effects observed when applying intense electric fields on condensed matter. Including nuclear quantum effects in path-integral ab initio molecular dynamics simulations enables the systematic study of field-induced catalytic effects on matter treated as a fully quantum object.
TOPICS IN CATALYSIS
(2022)
Article
Biophysics
Eva Matouskova, Tomas Drsata, Lucie Pfeifferova, Jiri Sponer, Kamila Reblova, Filip Lankas
Summary: This study utilizes molecular dynamics simulations to parameterize kink-turns and extract their bending shapes and stiffness constants from different RNA functional classes. The results reveal that kink-turns have isotropic bending stiffness but are highly anisotropic with respect to lateral displacement of the stems.
BIOPHYSICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Haritha Asha, Petr Stadlbauer, Lara Martinez-Fernandez, Pavel Banas, Jiri Sponer, Roberto Improta, Luciana Esposito
Summary: The study investigates the structural behavior of a quadruplex helix sequence in human telomeres when one of the G bases is ionized to G(center dot+). It is found that the position of G(center dot+) influences structural rearrangements, electrostatic repulsion, and solvent exposure, providing new insights into guanine reactions. The research suggests structural determinants of reactivity and implications for understanding reactivity in other G-quadruplex topologies.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Multidisciplinary
Jielin Chen, Mingpan Cheng, Petr Stadlbauer, Jiri Sponer, Jean-Louis Mergny, Huangxian Ju, Jun Zhou
Summary: G-quadruplexes (G4s) are nonclassical nucleic acid structures that play important roles in gene regulation and stability maintenance, and are widely used in nanotechnology. However, a comprehensive study of the factors determining G4 structural versatility is currently lacking.
Article
Chemistry, Physical
Vojtech Mlynsky, Michal Janecek, Petra Kuhrova, Thorben Frohlking, Michal Otyepka, Giovanni Bussi, Pavel Banas, Jiri Sponer
Summary: Atomistic molecular dynamics simulations are widely used in studying RNA structural dynamics, but they still face challenges in terms of accuracy of empirical potentials and sampling limitations. In this study, the combination of REST2 and well-tempered metadynamics (ST-MetaD) is shown to improve sampling efficiency by at least two orders of magnitude. Moreover, modifications to the nonbonded terms of the AMBER OL3 RNAff potential are found to stabilize the native state of RNA structures.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Multidisciplinary Sciences
Chad R. Simmons, Tara MacCulloch, Miroslav Krepl, Michael Matthies, Alex Buchberger, Ilyssa Crawford, Jiri Sponer, Petr Sulc, Nicholas Stephanopoulos, Hao Yan
Summary: Engineered crystal architectures from DNA have become a foundational goal for nanotechnological precise arrangement. Here, the authors systematically investigate the structures of 36 immobile Holliday junction sequences and identify the features allowing the crystallisation of most of them, while 6 are considered fatal.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Pavlina Pokorna, Miroslav Krepl, Sebastien Campagne, Jiri Sponer
Summary: This study used MD simulations to explore the dynamic characteristics of FUS-RNA complexes, complementing experimental results and revealing methodological difficulties in studying complex RNA-protein interfaces. The results of this study suggest that MD simulations are a viable tool for investigating dynamic RNA-protein complexes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Medicinal
Zhengyue Zhang, Jiri Sponer, Giovanni Bussi, Vojtech Mlynsky, Petr Sulc, Chad R. Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Summary: HJ is a crucial DNA structure involved in DNA repair, recombination, and DNA nanotechnology. Molecular dynamics simulations revealed complex conformational transitions of HJs, including previously unconsidered half-closed intermediates. This study provides detailed insights into the rearrangement process of HJs and opens up possibilities for more accurate computational studies of biological processes and nanomaterials involving HJs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Petra Kuhrova, Vojtech Mlynsky, Michal Otyepka, Jiri Sponer, Pavel Banas
Summary: RNA molecules play a key role in biochemical processes and interact closely with ions and water molecules. Double-stranded RNA is important for RNA folding and the design of RNA-based nanostructures. This study used molecular dynamics simulations to investigate the effects of ion concentrations and solvation box size on A-RNA structure.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Remi Coulon, Barbora Papouskova, Elmira Mohammadi, Michal Otyepka, Sreekar Wunnava, Jiri Sponer, Judit E. Sponer
Summary: 3',5'-Cyclic nucleotides play a fundamental role in modern biochemical processes and may have played a central role in the origin of early terrestrial life. A formamide-based systems chemistry could explain their availability on early Earth, as demonstrated by the formation of 3',5'-cyclic nucleotides in liquid formamide environments at elevated temperatures.
Article
Chemistry, Medicinal
Petr Stadlbauer, Vojtech Mlynsky, Miroslav Krepl, Jiri Sponer
Summary: In this study, steered molecular dynamics simulations were performed to investigate the unfolding mechanism of human telomeric GQs. The results showed that the direction of force, pulling velocity, and pulling force all affected the unfolding process. Additionally, it was found that a GQ could continue to unfold after a force drop. Furthermore, the study revealed that different unfolding intermediates could have similar chain end-to-end distances, suggesting limitations in structural interpretations of single-molecule spectroscopic data.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Dehui Qiu, Mingpan Cheng, Petr Stadlbauer, Jielin Chen, Michal Langer, Xiaobo Zhang, Qiang Gao, Huangxian Ju, Jiri Sponer, Jean-Louis Mergny, David Monchaud, Jun Zhou
Summary: The active sites of natural and artificial enzymes play a crucial role in their catalytic performance. This study focuses on G-quadruplex (GQ)/hemin DNAzymes and investigates how their active sites can be controlled and manipulated. Experimental and molecular dynamics simulation results reveal that the topology of the GQ and the flanking nucleotides influence the activation of hemin, providing valuable insights into the biocatalytic activity of GQs.
Article
Chemistry, Physical
Vojtech Mlynsky, Petra Kuhrova, Petr Stadlbauer, Miroslav Krepl, Michal Otyepka, Pavel Banas, Jiri Sponer
Summary: Molecular dynamics simulations are commonly used to study RNA molecules. By adjusting the nonbonded parameters, the widely used AMBER OL3 ff in RNA simulations can be improved. The modified simulations show better agreement with experimental results.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Mikolaj J. Janicki, Rafal Szabla, Jiri Sponer, Robert W. Gora
Summary: This study reveals the photodestruction mechanism of aqueous guanine nucleosides by utilizing accurate quantum chemical calculations, showing that an excited-state non-bonding interaction between guanosine and a water molecule facilitates electron-driven proton transfer to form a crucial intermediate leading to guanine photodamage products.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
