Article
Biochemistry & Molecular Biology
Xiaoxiao Zhang, Peng Li, Huanhuan Zhong, Fanming Yang, Fanzhou Liu, Gabriel Yedid, Yan Zeng
Summary: Proteins involved in RNA metabolism possess a double-stranded RNA-binding domain (dsRBD), with variations in sequences and functions. A study showed that a short insertion in the dsRBD of Drosha is important for its function, and extending the L1 region in other dsRBDs reduces RNA binding. This highlights the sensitivity of dsRBDs to perturbations in the L1 region and adds to the understanding of their structural and functional diversity.
ACTA BIOCHIMICA ET BIOPHYSICA SINICA
(2021)
Article
Biology
Stephanie A. Wankowicz, Saulo H. de Oliveira, Daniel W. Hogan, Henry van den Bedem, James S. Fraser
Summary: This study measured conformational heterogeneity in a large number of crystallographic datasets and found that binding site residues become more rigid upon ligand binding, while distant residues become more flexible, especially in non-solvent-exposed regions. Additionally, protein flexibility was observed to increase as the number of hydrogen bonds decreases and relative hydrophobicity increases.
Article
Engineering, Mechanical
Wanxiang Li, Zhiwu Shang, Maosheng Gao, Fei Liu, Hu Liu
Summary: The main challenge of fault diagnosis models based on partial domain adaptation (PDA) is to promote positive transfer in the shared label space and avoid negative transfer caused by the mismatch between the outlier and the target label spaces. To address this challenge, this paper proposes a partial deep transfer diagnosis model (MICDDA) based on multi-representation structure intraclass compact and double-aligned domain adaptation. Experimental results in two case studies show that the MICDDA can effectively weaken the transfer of source outlier knowledge to the target domain, capture rich and homogeneous compact fault features in PDA diagnosis scenarios, and effectively improve diagnostic performance.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2023)
Article
Biochemistry & Molecular Biology
Esra Boz, Matthias Stein
Summary: The study utilized the CREST tool to calculate non-covalent ligand-receptor interactions and energy using the GFN2-xTB method, and blind predictions were made for the binding of 10 drug molecule ligands to the CB[8] receptor. The results demonstrate that the proposed method shows good agreement with experimental values for large molecules, showcasing the effectiveness of quantum chemistry in predicting molecular interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Engineering, Environmental
Ke Zhang, Joseph Hodge, Anamika Chatterjee, Tae Seok Moon, Kimberly M. Parker
Summary: Double-stranded RNA undergoes alkaline hydrolysis at orders-of-magnitude slower rates compared to single-stranded RNA, and can remain intact for months at neutral pH. Increasing pH effectively attenuates enzymatic degradation of dsRNA without inducing alkaline hydrolysis, which differs significantly from ssRNA. Understanding these unique properties of dsRNA allows for greater control of stability in RNAi technology and provides insights into various applications, including isolation, detection, and inactivation of dsRNA viruses.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
David S. White, Sandipan Chowdhury, Vinay Idikuda, Ruohan Zhang, Scott T. Retterer, Randall H. Goldsmith, Baron Chanda
Summary: Research has shown both positive and negative cooperativity in cAMP binding, with limited parameter resolution in bulk measurements. By using nanophotonic zero-mode waveguides, individual ligand binding dynamics to multimeric ion channels have been directly resolved, revealing different kinetics in cAMP binding and isomerization. This approach can provide insights into binding allostery at single-molecule resolution in other intact membrane proteins and receptors.
Article
Multidisciplinary Sciences
Richard de Reuver, Simon Verdonck, Evelien Dierick, Josephine Nemegeer, Eline Hessmann, Sadeem Ahmad, Maude Jans, Gillian Blancke, Filip Van Nieuwerburgh, Alexander Botzki, Lars Vereecke, Geert van Loo, Wim Declercq, Sun Hur, Peter Vandenabeele, Jonathan Maelfait
Summary: The RNA-editing enzyme ADAR1 plays an important role in limiting the accumulation of immunostimulatory dsRNA. Reduced ADAR1 activity can lead to severe inflammatory diseases, while complete loss of ADAR1 activity is embryonically lethal and causes autoinflammation. ADAR1 not only prevents overactivation of MDA5 and PKR, but also inhibits the spontaneous activation of ZBP1.
Article
Computer Science, Artificial Intelligence
Zhonghua Liu, Fa Zhu, Kaibing Zhang, Zhihui Lai, Hua Huo
Summary: In this paper, a new model framework for cross-domain image classification, called manifold transfer subspace learning based on double relaxed discriminative regression (MTSL-DRDR), is proposed. The model leverages the labeled data samples from the source domain to learn the unlabeled data samples from the target domain, achieving promising performance. The model preserves the global geometry information, projects both domains to a unified subspace, preserves the local structure information, and encodes the discriminant information from the source domain to the target domain.
ARTIFICIAL INTELLIGENCE REVIEW
(2023)
Article
Multidisciplinary Sciences
Enrico Rennella, Danny D. Sahtoe, David Baker, Lewis E. Kay
Summary: With recent advancements in calculating protein structures from amino acid sequences using AI algorithms, the next important step is to understand how dynamics is encoded in the primary protein sequence to improve function prediction. This study emphasizes the significance of dynamics in modulating the function of a designed protein called C34, which binds β-strands. By investigating the structural dynamics of C34 using NMR spectroscopy, the researchers show that manipulating conformations can enhance functionality in protein design.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Alexey D. Nikulin
Summary: The review discusses the differences in protein interactions with single- and double-stranded RNA molecules based on the structure of RNA-protein complexes. Proteins interacting with single-stranded RNAs form contacts with RNA bases for recognition of specific nucleotide sequences, while proteins interacting with double-stranded RNAs mainly interact with the RNA sugar-phosphate backbone.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Multidisciplinary Sciences
Krishna Neupane, Meng Zhao, Aaron Lyons, Sneha Munshi, Sandaru M. Ileperuma, Dustin B. Ritchie, Noel Q. Hoffer, Abhishek Narayari, Michael T. Woodside
Summary: The RNA pseudoknot of SARS-CoV-2 that induces programmed ribosomal frameshifting is a potential drug target. Through optical tweezer experiments, researchers identified two pseudoknotted conformers with distinct topologies and revealed the folding mechanism of the frameshift signal, shedding light on its conformational heterogeneity and implications for drug discovery based on structure.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Marco van den Noort, Marijn de Boer, Bert Poolman
Summary: This study demonstrates that different ligands induce distinct bound conformations, and by changing the free energies of available conformations, ligand affinity can be adjusted. Experimental data on the maltose-binding protein (MBP) from Escherichia coli reveals that ligand affinity can be modulated through altering conformations.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Computer Science, Artificial Intelligence
Xin Luo, Wei Chen, Zhengfa Liang, Chen Li, Yusong Tan
Summary: This study proposes a new unsupervised domain adaptation method that achieves fine-grained domain adaptation by differentiating individual samples and introducing a style discrepancy metric. Experimental results validate the effectiveness of the proposed method, which outperforms many existing adversarial-learning-based methods on different tasks.
Article
Computer Science, Information Systems
Mengmeng Jing, Lichao Meng, Jingjing Li, Lei Zhu, Heng Tao Shen
Summary: We propose a novel adversarial domain adaptation method called AMRC to reduce domain shifts. Our method uses mixup to generate multiple features with different mixup ratios, and learns a continuous and domain-invariant latent space by accurately estimating the mixup ratio and making the estimator uncertain about it. We also apply mixup regularizations to ensure the smoothness and continuity of the latent space, and enhance the discriminability of the target features through self-supervised learning using sharpened pseudo-labels. Experimental results on 3 benchmarks validate the effectiveness of our method.
IEEE TRANSACTIONS ON MULTIMEDIA
(2023)
Article
Chemistry, Multidisciplinary
Xianrui Zhang, Haoran Huang, Yuan Liu, Zhigang Wu, Fengzhang Wang, Xinyuan Fan, Peng R. Chen, Jie Wang
Summary: Site-specific protein decaging by light is an effective approach for manipulating protein activities. A genetically encoded photocaged Asp was developed and used for the photocontrolled manipulation of various proteins, including firefly luciferase, kinases, and GTPase. This new tool may have broad applications for studying protein functions and biological processes in living cells.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Nicolas Bourassin, Florent Barbault, Marc Baaden, Sophie Sacquin-Mora
Summary: This study investigates the adsorption behavior of an enzyme on gold surfaces and finds that the adsorption process has little impact on the protein conformation but can affect its mechanical properties and catalytic activity. Compared to functionalized surfaces, adsorption on bare gold is more stable but less specific, and more likely to disrupt the enzyme's function.
Article
Biochemistry & Molecular Biology
Orian Gilmer, Elodie Mailler, Jean-Christophe Paillart, Assia Mouhand, Carine Tisne, Johnson Mak, Redmond P. Smyth, Roland Marquet, Valerie Vivet-Boudou
Summary: Maturation of HIV-1 viral particles is essential for infectivity. While the structural rearrangements of viral proteins during maturation are well-known, the maturation of genomic RNA (gRNA) structure is less explored. This study investigates the interactions between Pr55(Gag) or its maturation products and the gRNA region, revealing their distinct contributions to gRNA structural maturation.
Review
Biochemistry & Molecular Biology
Ezgi Karaca, Chantal Prevost, Sophie Sacquin-Mora
Summary: Modeling protein-protein assemblies at the atomic level is challenging, but recent computational strategies using enhanced sampling, multi-scale modeling, and experimental data integration have provided insights into interface dynamics and their connection to the function of protein assemblies.
Article
Biochemistry & Molecular Biology
Vincent Meynier, Laura Iannazzo, Marjorie Catala, Stephanie Oerum, Emmanuelle Braud, Colette Atdjian, Pierre Barraud, Matthieu Fonvielle, Carine Tisne, Melanie Etheve-Quelquejeu
Summary: Chemical synthesis of RNA conjugates has provided new methods for studying enzymatic mechanisms in RNA biology. This study developed a new method to synthesize RNA-conjugates for studying the recognition and methyl-transfer mechanisms of SAM-dependent m(6)A RNA methyltransferases. Crystal structures of RlmJ in complex with RNA-SAM conjugates were solved, revealing the specific recognition elements and activation mechanisms of RlmJ.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Charles Bou-Nader, Ankur Bothra, David N. Garboczi, Stephen H. Leppla, Jinwei Zhang
Summary: The study reveals the selective recognition mechanism of S9.6 for hybrid double-stranded DNA and provides a framework for S9.6 protein engineering.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Elena Wei, Charles Bou-Nader, Megan L. Perry, Rasem Fattah, Jinwei Zhang, Stephen H. Leppla, Ankur Bothra
Summary: Traditional diagnosis of infectious agents amplifies unique nucleic acid sequences using methods like PCR, but an overlooked alternative is using antibodies that recognize nucleic acids. The S9.6 monoclonal antibody recognizes DNA-RNA hybrids in a sequence-independent manner. By determining the structure of S9.6 Fab bound to a DNA-RNA hybrid, reagents and methods for sensitive detection of specific DNA and RNA sequences have been developed.
BIOCONJUGATE CHEMISTRY
(2023)
Review
Chemistry, Medicinal
Marc Graille, Sophie Sacquin-Mora, Antoine Taly
Summary: The recent breakthrough in three-dimensional structure prediction by artificial intelligence software has revolutionized the field of structural biology. These models have generated enthusiasm within the scientific community and are regularly used in various applications. It is important to make users aware of the information these models offer and encourage collaboration for improvement.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Pierre Barraud, Carine Tisne
Summary: Two papers uncover the structural basis of the tRNA maturation event catalyzed by RNA methyltransferase METTL1, which modifies N-7-methylguanosine (m(7)G) at position 46 in human transfer RNAs (tRNAs) and drives tumorigenesis in various cancer types.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Plant Sciences
Magali Charvin, Thierry Halter, Romain Blanc-Mathieu, Pierre Barraud, Magali Aumont-Nicaise, Francois Parcy, Lionel Navarro
Summary: DNA methylation decreases binding of Arabidopsis WRKY transcription factors to their genomic regions and binding sites in vitro. Methylation of a single cytosine in the W-box motif repels DNA binding of AtWRKY40 in vitro through steric hindrance. This methylation-dependent mechanism could potentially be widespread across different plant species.
Article
Cell Biology
Cesar Valencia-Gallardo, Daniel-Isui Aguilar-Salvador, Hamed Khakzad, Benjamin Cocom-Chan, Charles Bou-Nader, Christophe Velours, Yosra Zarrouk, Christophe Le Clainche, Christian Malosse, Diogo Borges Lima, Nicole Quenech'Du, Bilal Mazhar, Sami Essid, Marc Fontecave, Atef Asnacios, Julia Chamot-Rooke, Lars Malmstrom, Guy Tran Van Nhieu
Summary: Shigella IpaA induces vinculin oligomerization, leading to the formation of clusters that strengthen cell adhesion at a distance from the activation site and resist the action of actin relaxing drugs. These activated vinculin homo-oligomers maintain a persistent activation state and are relevant to bacterial invasion.
Article
Biochemistry & Molecular Biology
Jules Marien, Chantal Prevost, Sophie Sacquin-Mora
Summary: The microtubule-associated protein (MAP) tau plays a crucial role in microtubule assembly and spatial organization. Phosphorylation affects its binding on the tubulin surface and is implicated in diseases such as Alzheimer's. The flexible tubulin C-terminal tails (CTTs) influence the tau-tubulin interaction and tau potentially modulates CTT activity.
Meeting Abstract
Chemistry, Multidisciplinary
Charles Bou-Nader, Frauke Muecksch, Janae Brown, Michael Summers, Paul Bieniasz, Jinwei Zhang
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2022)
Article
Biochemical Research Methods
Charles Bou-Nader, Jinwei Zhang
Summary: This protocol describes the interaction between the matrix domain (MA) of HIV-1 major structural polyprotein Gag and host tRNAs, as well as the co-crystallization and structure determination of the complex using X-ray crystallography. Rational engineering of the tRNA surface led to the formation of high-quality co-crystals. This protocol can be applied to solve the structures of other ribonucleoprotein complexes containing structured RNAs.
