Review
Biochemistry & Molecular Biology
Shelby R. Lennon, Robert T. Batey
Summary: Riboswitches are genetic regulatory elements that use RNA conformational switching mediated by ligand binding to control gene expression. This review focuses on the mechanism of ligand-directed conformational changes in cobalamin riboswitches, a widely distributed class of riboswitches in bacteria. The review discusses the architectural features of cobalamin riboswitches, experimental approaches used to study them, and the importance of studying their folding landscapes in vitro and in a co-transcriptional context. The review highlights the challenges of studying cobalamin riboswitches outside of the transcriptional context and emphasizes the importance of co-transcriptional approaches for understanding their structure-function relationships. This understanding is crucial for the future development and applications of small-molecule guided RNA switches.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Fabio Amadei, Maria Reichenbach, Sofia Gallo, Roland K. O. Sigel
Summary: The RNA structural elements called riboswitches play a critical role in regulating gene expression by responding to specific cellular metabolites. The folding pathway and structure of the moaA riboswitch from E. coli, which responds to the metabolite molybdenum cofactor (Moco), were investigated. The study revealed that low ion concentrations can induce a high degree of structure formation in the riboswitch, and Mg2+ facilitates the compaction of the riboswitch towards its active structure.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
P. Broft, S. Dzatko, M. Krafcikova, A. Wacker, Robert Haensel-Hertsch, Volker Dotsch, L. Trantirek, Harald Schwalbe
Summary: This study reports the in-cell NMR-spectroscopic observation of the binding of the bacterial riboswitch ligand with the aptamer domain in eukaryotic cells, demonstrating the maintenance of binding mode in eukaryotic cellular environment. Additionally, the study shows that the in-cell NMR setup can be used for characterization of large, non-modified RNA molecules in cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemical Research Methods
Sumit Mukherjee, Matan Drory Retwitzer, Sara M. Hubbell, Michelle M. Meyer, Danny Barash
Summary: Riboswitches are conserved RNA sensors that mainly regulate genes/operons in bacteria. The challenge is to discover riboswitch classes in eukaryotes and understand the evolution of bacterial riboswitches. A novel approach based on inverse RNA folding was developed to identify potential structural candidates in fungi that could be distant homologs of bacterial riboswitches. This method transforms a structure-based search into a sequence-based search, considering the conservation of secondary structure shape and ligand-binding residues.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Lan Mei, Bo Chen, Rangrang Fan, Min Wu, Chengxin Weng, Aiping Tong, Bingwen Zou, Hui Yang, Chunlai Nie, Gang Guo
Summary: This study constructs DNase-resistant and tumor-distinguishing DNA nano-assemblies based on crossover motifs, and found that 3HB equipped with three aptamers shows the best tumor discriminating ability.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Multidisciplinary Sciences
Thinh D. N. Luong, Suhani Nagpal, Mourad Sadqi, Victor Munoz
Summary: This article introduces a method called "Molecular LEGO" that allows for the dissection of conformational landscapes of unbound intrinsically disordered proteins (IDPs) and provides insights into the functional mechanisms of these proteins. The method was applied to the protein NCBD and revealed specific energetic biases and conformational rheostatic behavior in NCBD's folding landscape, which are likely crucial for its function as a transcriptional coactivator.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Anwar Sadat, Satyam Tiwari, S. Sunidhi, Aseem Chaphalkar, Manisha Kochar, Mudassar Ali, Zainab Zaidi, Akanksha Sharma, Kanika Verma, Kannan Boosi Narayana Rao, Manjul Tripathi, Asmita Ghosh, Deepika Gautam, Atul, Arjun Ray, Koyeli Mapa, Kausik Chakraborty
Summary: The surface charge properties of the GroEL/ES chaperonin cavity, especially the negative charges, play a crucial role in its ability to assist protein folding. However, the negative-charge density varies significantly among different bacterial species and is lowest in eukaryotic GroEL/ES homologs. The chaperoning mechanism of GroEL may have changed during evolution to accommodate different mutations on their substrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
D. Funck, M. Sinn, J. R. Fleming, M. Stanoppi, J. Dietrich, R. Lopez-Igual, O. Mayans, J. S. Hartig
Summary: Nitrogen availability is crucial for growth in many habitats, and the global nitrogen cycle involves competition between prokaryotes and eukaryotes for this resource. In this study, a Ni2+-dependent guanidine hydrolase enzyme called GdmH was identified in Synechocystis sp. PCC 6803. GdmH is specific for free guanidine and its activity is dependent on two accessory proteins that load Ni2+ ions into the active site. The crystal structures of GdmH show a typical arginase family enzyme geometry and suggest the presence of guanidine hydrolases in other cyanobacteria, bacteria, and heterokont algae. The broad distribution of these enzymes suggests their ecological relevance in aquatic habitats.
Review
Cell Biology
Padmaja D. D. Wakchaure, Bishwajit Ganguly
Summary: During the last decade, riboswitches have been discovered as a new type of small-molecule sensing RNA in bacteria. The thiamine pyrophosphate (TPP) riboswitch is widely distributed and found in various organisms. This review provides comprehensive information on the structure, mechanism, and ligand design for TPP riboswitch. Experimental and theoretical techniques have been employed to study the conformational dynamics and the importance of certain helices in ligand binding. Development of potent inhibitors for TPP riboswitch is necessary for therapeutic applications, and recent advancements in ligand design show promising potential for developing new antibiotics.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Chemistry, Multidisciplinary
Chak Kui Wong, Chuyan Tang, John S. Schreck, Jonathan P. K. Doye
Summary: This study demonstrates the application of coarse-grained modeling combined with umbrella sampling to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. The approach is illustrated with examples of DNA nanotubes and DNA origami sheets. The ability to compute such landscapes is crucial for DNA mechanotechnology and understanding stress accumulation during the self-assembly process of origamis.
Article
Biochemistry & Molecular Biology
Anna Ender, Maja Etzel, Stefan Hammer, Sven Findeiss, Peter Stadler, Mario Moerl
Summary: The study describes a synthetic riboswitch element that regulates tRNA maturation by either sequestering or exposing the 5'-leader region of tRNA precursor in response to a ligand. It provides evidence for the importance of the leader region structure in tRNA maturation and demonstrates the potential of ligand-dependent structural rearrangements in addressing individual maturation steps of stable non-coding RNAs as promising targets for regulatory devices in synthetic biology.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Chengyi Du, Yujie Wang, Sha Gong
Summary: The ThiM riboswitch from Escherichia coli is a typical mRNA device that modulates downstream gene expression by sensing TPP. Its regulatory behavior in cells depends on co-transcriptional folding and a combination of transcription rate, pause, and ligand levels.
Article
Chemistry, Physical
Xiaojun Xu, Lei Jin, Liangxu Xie, Shi-Jie Chen
Summary: This article describes an alternative approach to predicting cotranscriptional RNA folding by zooming in and out of the RNA folding energy landscape. The application of this approach to specific RNAs shows promising results and provides new insights into biologically significant conformational switches and pathways.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Analytical
Yichen Zhao, Biwen Gao, Peihuan Sun, Jiawen Liu, Juewen Liu
Summary: This study investigated the effect of pH and metal ions on the fluorescence enhancement sensor OTC5 that binds to tetracycline, oxytetracycline, and doxycycline. The results showed that Mg2+ ions are crucial for the binding of OTC5 to its target and that lower pH values lead to better fluorescence enhancement.
Article
Chemistry, Multidisciplinary
Diana Muller, Irene Bessi, Christian Richter, Harald Schwalbe
Summary: The folding kinetics of RNA G4 and DNA G4 differ significantly during K+-induced folding, mainly due to differences in their folded conformations, especially regarding the chi angle preferences. Modified DNA G4 can achieve faster folding kinetics and monomorphic conformations similar to RNA G4 by adjusting the chi angle.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Physical
Yonghyun Song, Changbong Hyeon
Summary: This study reviews the trade-offs between speed, fluctuations, and thermodynamic cost in biological processes and discusses the optimization in nonequilibrium states. It finds suboptimal precision of enzymatic processes at a given thermodynamic cost, with key biological processes working around this condition. The research delves into how biological systems evolve through optimization and balancing conflicting functional requirements.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemical Research Methods
Ji Hyun Bak, Min Hyeok Kim, Lei Liu, Changbong Hyeon
Summary: This study develops a unified framework for modeling and inferring chromatin domain structures over multiple scales, offering a quantitative view of multi-scale chromatin organization and revealing its connections with genome function.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Anvy Moly Tom, Won Kyu Kim, Changbong Hyeon
Summary: The study investigates the impact of mobile polymer brushes on proteins embedded in biological membranes using theoretical models and simulations. The depletion attraction between proteins due to brush polymers changes non-monotonically with the size of the brush; the interaction increases linearly with brush size as long as the brush height is shorter than the protein size. However, when the brush height exceeds the protein size, the depletion attraction among proteins is slightly reduced.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Pureun Kim, Changbong Hyeon
Summary: Temporal order in living matters reflects the self-organizing nature of dynamical processes driven out of thermodynamic equilibrium. The precision of biochemical oscillations is constrained by the thermodynamic cost according to the thermodynamic uncertainty relation (TUR). Glycolytic oscillations under cellular conditions are found to be cost-effective, with minimal entropy production when the oscillation period is between 5-10 minutes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Multidisciplinary Sciences
Changwon Kim, Min Ju Shon, Sung Hyun Kim, Gee Sung Eun, Je-Kyung Ryu, Changbong Hyeon, Reinhard Jahn, Tae-Young Yoon
Summary: Using single-molecule methods, researchers demonstrated the cooperativity between NSF and the SNARE complex to prevent ATP consumption without productive disassembly.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Yonghyun Song, Changbong Hyeon
Summary: Spatial boundaries in animal development are formed by prepatterning of tissues by signaling molecules called morphogens. The accuracy of boundary location is limited by fluctuations in morphogen concentration, which control the expression level of target genes. Producing more morphogen molecules to reduce fluctuations can lead to more precise target boundaries, but also incurs higher thermodynamic cost. In order to achieve a precise morphogen profile with minimal cost, the characteristic length of the concentration profile should be roughly half the distance to the target boundary position from the source.
Biographical-Item
Chemistry, Physical
Margaret S. Cheung, Ruxandra I. Dima, Changbong Hyeon
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemical Research Methods
Lei Liu, Bokai Zhang, Changbong Hyeon
Summary: The study highlights the importance of multi-way chromatin contacts in gene regulation, proposing a method to predict these contacts from Hi-C data. By analyzing pairwise genomic contact frequencies, the study reveals correlations and insights into related issues, such as cell-line dependent assemblies of genes and enhancers to chromatin hubs.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biophysics
Seonghoon Kim, Changbong Hyeon
Summary: This study used molecular dynamics simulations to investigate the positioning of TEMPO spin label in lipid bilayers. The results showed that the location of TEMPO is dependent on the membrane phase, with it being stabilized above the interface in the gel phase and below the interface in the fluid phase. This finding highlights the importance of assessing lipid packing order and fluidity under specific measurement conditions.
BIOPHYSICAL JOURNAL
(2022)
Article
Biophysics
Lei Liu, Xinmeng Cao, Bokai Zhang, Changbong Hyeon
Summary: Genome architecture mapping (GAM) is a method to probe and decipher three-dimensional chromatin organization. It provides the cosegregation probability of two genomic segments from nuclear profiles. However, the cosegregation probability is different from the contact probability and has a weaker correlation with interlocus distance. The study suggests that a properly normalized version of cosegregation probability calculated from a large number of nuclear slices is needed to achieve a strong correlation with interlocus distance.
BIOPHYSICAL JOURNAL
(2022)
Article
Computer Science, Interdisciplinary Applications
Kiri Choi, Won Kyu Kim, Changbong Hyeon
Summary: This study proposes a systematic and principled method for classifying neurons based on the idea of polymer physics. By calculating the 3D coordinates of neurons and analyzing the resulting distance distribution, the authors are able to quantitatively characterize the morphology of neurons and classify them based on their structural similarities. This method provides valuable insights into the dense neural networks in the brain.
Article
Biology
Kiri Choi, Won Kyu Kim, Changbong Hyeon
Summary: Reconstructed from electron microscope images, the projection neurons of the Drosophila olfactory system provide a detailed view of neuronal anatomy and shed light on the relationship between neuronal organization and odor perception.
Article
Chemistry, Physical
Lei Liu, Changbong Hyeon
Summary: Confined polymer chains in two-dimensional planes are segregated due to topological interaction. The properties of the solution depend on the solvent quality, and the osmotic pressure increases with the area fraction, with different rates for good and bad solvents. Numerical simulations show that polymer chains in bad solvents occupy the surface in a more inhomogeneous manner and have a greater correlation length, leading to a higher and more heterogeneous interstitial void size.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Meeting Abstract
Biophysics
Seonghoon Kim, Changbong Hyeon
BIOPHYSICAL JOURNAL
(2022)
Article
Physics, Fluids & Plasmas
Davinder Singh, Changbong Hyeon
Summary: This study investigates the characteristics of thermodynamic uncertainty relations (TURs) in open quantum systems, revealing that the imaginary part of quantum coherence leads to a relaxation of the TUR bound, while the real part of coherence tightens it.
Article
Chemistry, Physical
Sergey Yu. Ketkov, Sheng-Yuan Tzeng, Elena A. Rychagova, Anton N. Lukoyanov, Wen-Bih Tzeng
Summary: Metallocenes, including methylcobaltocene, play important roles in various fields of chemistry. The ionization energy and vibrational structure of (Cp ')(Cp)Co can be influenced by introducing methyl substituents. The mass-analyzed threshold ionization spectrum and DFT calculations provide accurate information about the properties and transformations of (Cp ')(Cp)Co.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Review
Chemistry, Physical
Qifeng Mu, Jian Hu
Summary: Polymer mechanochemistry has experienced a renaissance due to the rapid development of mechanophores and principles governing mechanochemical transduction or material strengthening. It has not only provided fundamental guidelines for converting mechanical energy into chemical output, but also found applications in engineering and smart devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Da Hye Yang, Francesco Ricci, Fredrik L. Nordstrom, Na Li
Summary: Through systematic evaluation of the oiling-out behavior of procaine, we identified both stable and metastable liquid-liquid phase separation, and established phase diagrams to assist in rational selection of crystallization strategies.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Vikki Anand Varma, Simmie Jaglan, Mohd Yasir Khan, Sujin B. Babu
Summary: Designing engineering structures like nanocages, shells, and containers through self-assembly of colloids is a challenging problem. This work proposes a simple model for the subunit, which leads to the formation of monodispersed spherical cages or containers. The model with only one control parameter can be used to design cages with the desired radius.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Hainan Jiang, Yaolong He, Xiaolin Li, Zhiyao Jin, Huijie Yu, Dawei Li
Summary: The cycling lifespan and coulombic efficiency of lithium-ion batteries are crucial for high C-rate applications. The Li-ion concentration plays a crucial role in determining the mechanical integrity and structural stability of electrodes. This study focuses on graphite as the working electrode and establishes an experimental system to investigate the mechanical properties of composite graphite electrode at different C-rates. Considering the effect of Li-ion concentration in stress analysis is found to be significant.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Zhiye Wang, Yunchuan Li, Mingjun Sun
Summary: This study investigates the influence of intramolecular pi-pi interactions on the electronic transport capabilities of molecules. By designing and analyzing three pi-conjugated molecules, the researchers observe that different pi-conjugated structures have varying effects on electron transport. The findings provide a theoretical foundation for designing single-molecule electronic devices with multiple electron channels based on intramolecular pi-pi interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Yuandong Xu, Haoyang Feng, Chaoyang Dong, Yuqing Yang, Meng Zhou, Yajun Wei, Hui Guo, Yaqing Wei, Jishan Su, Yingying Ben, Xia Zhang
Summary: Hollow MoS2 cubes and spheres were successfully synthesized using a one-step hydrothermal method with the hard template method. The hollow MoS2 cubes exhibited higher specific capacitance and energy density compared to the hollow MoS2 spheres. The symmetrical supercapacitors assembled with these hollow structures showed good performance and high capacity retention after multiple cycles. These findings suggest that controlling the pore structure and surface characteristics of MoS2 is crucial for enhancing its electrochemical properties.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Ainhoa Oliden-Sanchez, Rebeca Sola-Llano, Joaquin Perez-Pariente, Luis Gomez-Hortiguela, Virginia Martinez-Martinez
Summary: The combination of photoactive molecules and inorganic structures is important for the development of advanced materials in optics. In this study, bulky dyes were successfully encapsulated in a zeolitic framework, resulting in emission throughout the visible spectrum.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Miaomiao Zhang, Cunyuan Pei, Qiqi Xiang, Lintao Liu, Zhongxu Dai, Huijuan Ma, Shibing Ni
Summary: The design of a solid electrolyte interphase (SEI) plays a crucial role in improving the electrochemical performance of anode materials. In this study, lithium difluoro(oxalate)borate (LiDFOB) is used as an electrolyte additive to form a protective SEI film on Li3VO4 (LVO) anodes. The addition of LiDFOB results in a dense, uniform, stable, and LiF-richer SEI, which enhances the Li-ion storage kinetics. The generated SEI also prevents further decomposition of the electrolyte and maintains the morphology of LVO anodes during charge/discharge processes. This work demonstrates the effectiveness of LiDFOB as a multi-functional additive for LiPF6 electrolytes and provides insights into SEI construction for high-performance LVO anodes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
B. V. Andryushechkin, T. V. Pavlova, V. M. Shevlyuga
Summary: The atomic structure of the Ag(111)-p(4 x 4)-O phase was reexamined and two phases with the same periodicity were discovered. It was demonstrated that the accepted Ag6 model is incompatible with high-resolution oxygen-sensitive STM images.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
S. L. Romo-Avila, D. Marquez-Ruiz, R. A. Guirado-Lopez
Summary: In this study, we used density functional theory (DFT) calculations to investigate the interaction between model graphene oxide (GO) nanostructures and chlorine monoxide ClO. We aimed to understand the role of this highly oxidizing species in breaking C-C bonds and forming significant holes on GO sheets. Our results showed that C-C bonds in a single graphene oxide sheet can be broken through a simple mechanism involving the dissociation of two chemically attached ClO molecules. The formation of carbonyl groups and holes on the GO surface was also observed. This study provides important insights into the degradation of carbon nanotubes and the stability of GO during the myeloperoxidase (MPO) catalytic cycle.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Alberto Garcia-Fernandez, Birgit Kammlander, Stefania Riva, Hakan Rensmo, Ute B. Cappel
Summary: In this study, the X-ray stability of five different lead halide perovskite compositions (MAPbI3, MAPbCl3, MAPbBr3, FAPbBr3, CsPbBr3) was investigated using photoelectron spectroscopy. Different degradation mechanisms and resistance to X-ray were observed depending on the crystal composition. Overall, perovskite compositions based on the MA+ cation were found to be less stable than those based on FA+ or Cs+. Metallic lead formation was most easily observed in the chloride perovskite, followed by bromide, and very little in MAPbI3. Multiple degradation processes were identified for the bromide compositions, including ion migration, formation of volatile and solid products, as well as metallic lead. CsBr was formed as a solid degradation product on the surface of CsPbBr3.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Timofei Rostilov, Vadim Ziborov, Alexander Dolgoborodov, Mikhail Kuskov
Summary: The shock-loading behavior of nanomaterials is investigated in this study. It is found that shock compaction waves exhibit a distinct two-step structure, with the formation of faster precursor waves that travel ahead of the main compaction waves. The complexity of the shock Hugoniot curve of the tested nanomaterial is described, and the effect of initial porosity on the compressed states is demonstrated.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Sergey S. Nikitin, Alexander D. Koryakov, Elizaveta A. Antipinskaya, Alexey A. Markov, Mikhail V. Patrakeev
Summary: The stability of La1/3Sr2/3Fe1-xMnxO3-delta, a perovskite-type oxide, under reducing conditions is dependent on the manganese content. Increasing the manganese content leads to a decrease in stability. The behavior of iron and manganese in the oxide shows distinct differences, which can be attributed to the difference in the enthalpy of oxidation reactions. Additionally, the change in the La/Sr ratio affects the concentration of iron and manganese ions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Mosayeb Naseri, Shirin Amirian, Mehrdad Faraji, Mohammad Abdur Rashid, Maicon Pierre Lourenco, Venkataraman Thangadurai, D. R. Salahub
Summary: Inspired by the successful transfer of freestanding ultrathin films of SrTiO3 and BiFeO3, this study assessed the structural stability and investigated the electronic, optical, and thermoelectric properties of a group of two-dimensional perovskite-type materials called perovskenes. The findings revealed that these materials are wide bandgap semiconductors with potential application in UV shielding. Moreover, they exhibit better electrical and thermal conductivity at high temperatures, enabling efficient power generation in thermoelectric devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
