Article
Biochemistry & Molecular Biology
Jeff Gaither, Yi-Hsuan Lin, Ralf Bundschuh
Summary: The study focuses on the interactions of hundreds of RNA binding proteins in the human genome with RNA in cells, introducing RBPBind as a web-based tool for quantitatively predicting the interaction by considering the effect of RNA secondary structure on binding affinity. The tool provides a quick and easy way to obtain reliable predicted binding affinities and locations for single-stranded RNA binding proteins based solely on RNA sequence.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Juan P. G. Villaluenga, Francisco Javier Cao-Garcia
Summary: Ligands can alter the properties of polymers, and our research focuses on developing an accurate kinetic model for the cooperative binding kinetics of large ligands. We found that cooperativity significantly affects the affinity of the ligands, and it can be achieved through increased binding affinity or decreased release affinity. Cooperativity is crucial for understanding and characterizing ligand binding processes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Hao Zhu, Zixuan Chen, Yun Chen, Jun-Jie Zhu
Summary: Quantifying the binding kinetics and affinities of protein-small molecule interactions is critical for biomarker validation, drug discovery, and deep understanding of various biological processes at the molecular-scale. A novel optical imaging platform based on MoS2 material is developed to measure the binding kinetics of protein-small molecules and protein-ions. The method is capable of distinguishing different inhibitors binding to different forms of kinase, and can be used for drug evaluation and mechanism exploration.
Article
Chemistry, Physical
Suguru Yoshida, Hirofumi Akamatsu, Alexandra S. Gibbs, Shogo Kawaguchi, Venkatraman Gopalan, Katsuhisa Tanaka, Koji Fujita
Summary: In this study, it is found that the competition between octahedral rotations and deformations in AgRTiO4 leads to biaxial negative thermal expansion (NTE), which is different from conventional materials. The analysis of calculated electronic structures reveals the essential role of Ag-O-Ti covalent bonding in enhancing the octahedral deformation.
CHEMISTRY OF MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Serena Monaco, Jesus Angulo, Matthew Wallace
Summary: We developed a new tool called imaging STD NMR by combining saturation transfer difference NMR (STDNMR) with chemical shift imaging (CSI) and controlled concentration gradients of small molecule ligands. This method allows for the assessment of protein-ligand interactions, determination of dissociation constants (K(D)), and evaluation of binding specificity in a single NMR tube, saving time compared to traditional titration methods. Imaging STD NMR also allows for screening of non-specific binders, making it a potential tool to speed up and optimize the drug discovery process.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Sowmya Ramaswamy Krishnan, Arijit Roy, M. Michael Gromiha
Summary: RNAs play crucial roles in cellular functions and disease conditions, making them potential therapeutic targets. Studying RNA-small molecule interactions can aid in designing more effective RNA-targeting drugs.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Emilia Kuzniak-Glanowska, Michal Glanowski, Rafal Kurczab, Andrzej J. Bojarski, Robert Podgajny
Summary: Mutual positioning and non-covalent interactions between anions and aromatic motifs play a crucial role in the functional performance of biological systems. A comprehensive screening of the Protein Data Bank (PDB) led to the identification of numerous unique anion-aromatic motifs, highlighting the importance of ion-π interactions in these motifs.
Article
Biochemistry & Molecular Biology
Malwina Hyjek-Skladanowska, Brooke A. Anderson, Vitaliy Mykhaylyk, Christian Orr, Armin Wagner, Jaroslaw T. Poznanski, Krzysztof Skowronek, Punit Seth, Marcin Nowotny
Summary: This study investigates the structural and biochemical interactions between phosphorothioate-modified antisense oligonucleotides and annexin A2 protein. The researchers found that a unique mode of hydrophobic interactions accounts for the enhanced affinity of modified nucleic acids for the protein. This mechanism of interaction is not only observed for nucleic acid-binding proteins but also accounts for the association of phosphorothioate-modified oligonucleotides with other proteins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Pan Wang, Shixian Cao, Ting Yin, Xin-Long Ni
Summary: This study demonstrates a novel tunable hydrophobic effect in self-assembly of a small cationic organic fluorophore (NI-TPy+) with aggregation-induced emission (ALE) property in aqueous solution. The amplification of hydrophobicity was found to be significantly dependent upon the increasing aggregates of NI-TPy+, enabling the study of hydrophobic binding with chaotropic anions in the Hofmeister series.
CHINESE CHEMICAL LETTERS
(2021)
Article
Plant Sciences
Ashish Prasad, Susmita Sett, Manoj Prasad
Summary: Under field conditions, plants face various detrimental stresses that impact crop productivity. Climate change and emergence of new pathogen strains worsen the situation. International trade facilitates resource sharing but also leads to the spread of viruses and pathogens. Paradigm shift in research methodology focuses on combined stress. This review discusses recent developments and strategies to tackle plant-virus-abiotic stress interactions.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Review
Biochemistry & Molecular Biology
Songjie Zheng, Min Zou, Yingfeng Shao, Huaping Wu, Helong Wu, Xiaohuan Wang
Summary: Gaining insight into the two-dimensional receptor-ligand interactions is crucial for understanding physiological and pathological mechanisms, as well as biomedical applications and drug design. This review discusses various methods for measuring in situ receptor-ligand binding kinetics, including mechanical-based and fluorescence-based approaches. The importance of combining experimental and computational methods in studying receptor-ligand interactions is emphasized, and future studies should focus on their synergistic development.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Chisato Kinoshita, Noriko Kubota, Koji Aoyama
Summary: With the increasing number of older adults, there is a rising number of patients with neurodegenerative diseases (NDs), posing a potential medical and social crisis. NDs encompass a wide range of diseases, with dysfunction of RNA-binding proteins (RBPs) and miRNAs playing important roles in these disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Wenlong Zhang, Zhenyu Wang, Yunpeng Liu, Jiangtao Feng, Jie Han, Wei Yan
Summary: This study focuses on the role of counter cations in the cation exchange process of NH4+ to enhance adsorption capacity. Different counter cations were found to affect the adsorption performance of titanates, with electrostatic interaction and ion affinity being the main influencing factors. The introduction of an affinity coefficient K-f helps explain the differences in adsorption performance among the titanates.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Medicine, Research & Experimental
Haiyang Yang, Xueyan Li, Gang Li, Huating Huang, Wenning Yang, Xiaoquan Jiang, Muli Sen, Jingjing Liu, Yang Liu, Yanli Pan, Guopeng Wang
Summary: This study emphasizes the importance of accurate quantitative determination of affinity and binding kinetics for tight binding inhibition. Recommendations on experimental design and mathematical calculation approaches are provided to evaluate affinity and BK parameters for inhibitors against xanthine oxidase. Significant differences in results and the influence of different data analytical methods on enzyme engagement in human are discussed.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Environmental Sciences
Giorgia Confalonieri, Giovanna Vezzalini, Laura Maletti, Francesco Di Renzo, Vittorio Gozzoli, Rossella Arletti
Summary: The use of NH4+-exchanged zeolite L for Ce recovery from a very diluted solution showed efficient Ce3+ exchange, with high adsorption capacity and removal efficiency under optimal working conditions.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Chemistry, Physical
Sergio Cruz-Leon, Kara K. Grotz, Nadine Schwierz
Summary: This study optimizes the description of ion interactions with nucleic acids in simulations by adjusting combination rules, significantly improving agreement with experiments and offering a more accurate method for describing metal cations in biomolecular simulations.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Jan Neumann, Nadine Schwierz
Summary: Magnesium plays a crucial role in biological processes and it is important to understand its binding pathways and the role of solvent in the binding process. By using transition path sampling and a machine learning algorithm, we revealed the coupling between solute and solvent and gained detailed insights into biochemical reactions in aqueous solutions.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Kara K. Grotz, Nadine Schwierz
Summary: This study provides accurate force field parameters for Mg2+ in combination with OPC water, showing the transferability of SPC/E parameters to OPC and presenting two optimal parameter sets, MicroMg and NanoMg, for different timescales and enhanced ion binding events observation.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Sergio Cruz-Leon, Willem Vanderlinden, Peter Mueller, Tobias Forster, Georgina Staudt, Yi-Yun Lin, Jan Lipfert, Nadine Schwierz
Summary: The structure and properties of DNA are influenced by the environment, particularly the ion atmosphere. This study investigates how DNA twist changes with the concentration and identity of surrounding ions. The results show that DNA twist increases with increasing concentration for all ions studied, and the twist strongly depends on the specific ion identity. Molecular dynamics simulations provide a microscopic explanation for the observed ion specificity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Christin Fuks, Sebastian Falkner, Nadine Schwierz, Martin Hengesbach
Summary: Riboswitch RNAs regulate gene expression through conformational changes induced by environmental conditions and specific ligand binding, which is of great significance for understanding the mechanism of RNA regulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Sergio Cruz-Leon, Nadine Schwierz
Summary: The distribution of cations around nucleic acids is crucial for various biological processes, but predicting it is challenging. This study uses molecular dynamics simulations to reveal the ion-specific distributions and binding patterns for DNA and RNA duplexes, shedding light on the opposing behavior of DNA and RNA in the same ionic conditions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Miriam Grava, Mohd Ibrahim, Akhil Sudarsan, Julio Pusterla, Julian Philipp, Joachim O. Raedler, Nadine Schwierz, Emanuel Schneck
Summary: The protonation degree and lipid packing of ionizable lipids play crucial roles in the performance of lipid-based nanoparticles, and a combination of molecular dynamics simulations and experimental measurements can provide valuable insights for further predictive modeling.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Kartikay Sharma, Sambhasan Banerjee, Dilan Savran, Cedric Rajes, Sebastian Wiese, Amandeep Girdhar, Nadine Schwierz, Christopher Lee, James Shorter, Matthias Schmidt, Lin Guo, Marcus Faendrich
Summary: In this study, the three-dimensional structure of amyloid fibrils from the hnRNPA1 protein was investigated using cryo-electron microscopy. The fibril core was found to be composed of a 45-residue segment from the low-complexity domain of the protein, while the remaining parts formed a fuzzy coat around the core. The fibril exhibited a pseudo-21 screw symmetry and contained disease-associated mutation sites. These findings suggest that the structure of full-length protein amyloid fibrils may be more complex than currently believed.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Mohd Ibrahim, Christiane Wenzel, Max Lallemang, Bizan N. Balzer, Nadine Schwierz
Summary: Ion-mediated attraction between DNA and mica is crucial in biotechnological applications and molecular imaging. The specific adsorption of ions at the mica surface compensates or overcompensates its negative charge. Different types of contacts between ions, DNA phosphate oxygens, and mica result in low- and high-force pathways and a broad distribution of detachment forces. Cs+ and water-mediated contacts lead to low detachment forces and high mobility of DNA, while direct ion-DNA or ion-surface contacts result in higher forces. K+, Mg2+, and Ca2+ are the most promising cations for imaging under physiological conditions.
Article
Chemistry, Multidisciplinary
Mohd Ibrahim, Jennifer Gilbert, Marcel Heinz, Tommy Nylander, Nadine Schwierz
Summary: Ionizable lipids, such as MC3, are crucial for the design of LNPs as drug delivery agents. Combining molecular dynamics simulations with experimental data is necessary to understand the internal structure of LNPs. The choice of force field parameters is important for simulation accuracy, and high-quality experimental data is needed for parametrization validation. This study provides parameters for cationic and neutral MC3 compatible with the AMBER Lipid17 force field, and compares different force fields using neutron reflectivity experiments. Accurate force field parameters and experimental validation are essential for reliable simulations.
Article
Biochemistry & Molecular Biology
Marijana Ugrina, Ines Burkhart, Diana Mueller, Harald Schwalbe, Nadine Schwierz
Summary: In this study, the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA were characterized using a combination of molecular dynamics simulations and circular dichroism experiments. The presence of ions stabilized the quadruplex fold, and the folding process was guided by the formation of an ion double layer surrounding the charged quadruplex. Coarse-grained simulations accurately captured the ionic double layer using a matching procedure based on all-atom simulations. The results showed that the folding progressed through a series of intermediate states, stabilized by transient Hoogsteen interactions, before reaching the final folded structure. The study also proposed that conformational entropy is a hallmark of rG4 folding, which was supported by the analysis of free energy landscapes and folding pathways of four rG4 systems with varying loop length.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Physical
Sergio Cruz-Leon, Nadine Schwierz
Summary: The distribution of cations around nucleic acids is crucial for various biological processes, but predicting the exact distribution remains challenging. DNA and RNA may react differently to the same ionic conditions. This study aims to reveal the ion-specific distributions and binding patterns for DNA and RNA duplexes through molecular dynamics simulations.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)