Article
Chemistry, Multidisciplinary
Nikita Brodyagin, Aubrey L. Maryniak, Ilze Kumpina, John M. Talbott, Martins Katkevics, Eriks Rozners, James A. MacKay
Summary: Peptide nucleic acids (PNA) with extended isoorotamides containing nucleobases (I-o) were designed to bind A-U base pairs in double-stranded RNA. Isothermal titration calorimetry and UV thermal melting experiments showed improved affinity for A-U using the Io scaffold in PNA, with PNAs having four sequential Io extended nucleobases maintaining high binding affinity.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Andrea Mosseri, Maria Sancho-Albero, Marilisa Leone, Donatella Nava, Francesco Secundo, Daniela Maggioni, Luisa De Cola, Alessandra Romanelli
Summary: This study reports the formation of homogeneous chiral fibers through self-assembly of peptide nucleic acids. Nucleobases play a key role in determining the morphology and chirality of the fibers. By spectroscopic characterization and microscopy studies, a structural model consistent with the experimental evidence was obtained.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Analytical
Haobo Sun, Lisheng Qian, Jinming Kong, Xueji Zhang
Summary: A novel electrochemical biosensor platform with triple helix structure switch and double signal amplification strategy was proposed for nucleic acid detection, achieving ultra-sensitivity and high selectivity. The biosensor showed a detection limit as low as 1.954 aM and a linear range of 7 orders of magnitude. Additionally, it demonstrated excellent anti-interference ability when analyzing DNA in serum samples.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Biochemistry & Molecular Biology
Sophie Hertel, Richard E. Spinney, Stephanie Y. Xu, Thomas E. Ouldridge, Richard G. Morris, Lawrence K. Lee
Summary: The physical mechanisms underlying DNA hybridization rates are still not well understood. Secondary structure is one factor that affects the rates, but there are other factors at play. Research has shown that a higher number of Watson-Crick pair repetitions increases the number of initial states capable of proceeding to full hybridization, with the stability of these pairings dictating the likelihood of progression.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Mathematics
Bing Ma
Summary: This paper explores the effect of the Double-pillar regulation on promoting enterprise innovation and its influencing mechanism. The empirical results demonstrate that the Double-pillar regulation can promote enterprise innovation, particularly for state-owned enterprises. Furthermore, the Double-pillar regulation effectively reduces the financialization of enterprises, thus boosting enterprise innovation. Moreover, an increased level of financing constraint and enterprise risk-taking enhances the driving effect of the Double-pillar regulation on enterprise innovation.
JOURNAL OF MATHEMATICS
(2022)
Article
Engineering, Biomedical
Terence W. Gee, Jennifer M. Richards, Ablajan Mahmut, Jonathan T. Butcher
Summary: This study utilized a mechanically stressed 3D culture system to replicate valve interstitial cell-induced matrix calcification and investigated the collaborative interactions between valve endothelial cells and interstitial cells in calcific pathogenesis. Results showed that endothelial cells induce pathological remodeling and calcification of interstitial cells through EndMT and paracrine signaling.
Article
Chemistry, Multidisciplinary
Tomotaka Kumagai, Ban Kinoshita, Shingo Hirashima, Hiroshi Sugiyama, Soyoung Park
Summary: Fluorescent molecular rotors are versatile tools for investigating biomolecular interactions and monitoring microenvironmental changes. We report the synthesis and characterization of a highly emissive molecular rotor-containing thymine nucleoside and its analogue, which can emit vivid fluorescence via interaction with target proteins. These probes have the potential to serve as robust tools for fluorescence mapping and monitoring specific protein-binding interactions in biological systems.
Article
Biochemistry & Molecular Biology
Takaya Sato, Yusuke Sato, Seiichi Nishizawa
Summary: PNA forms a more stable triplex with dsRNA compared to dsDNA, exhibiting a favorable association process under various conditions. In contrast to DNA/RNA heteroduplexes, the DNA strand is detrimental to the stability of the PNA triplex. The key factors influencing the different triplex formation behaviors of PNA with different duplexes appear to be the conformational adaptability and geometric compatibility.
Article
Environmental Sciences
Leheng Dong, Manjia Chen, Chengshuai Liu, Yahui Lv, Xugang Wang, Qinkai Lei, Yujuan Fang, Hui Tong
Summary: This study investigated the microbial communities and processes involved in the formation of floating iron films in wetlands. The results showed that the dominant microorganisms in these films were iron-oxidizing and reducing bacteria, as well as methanotrophs, which played important roles in iron oxidation, iron supply, and methane oxidation. In addition, the oxidation of Fe(II) could trigger carbon fixation, while the reduction of Fe(III) accelerated the cycling of iron and carbon. These findings highlight the contribution of these microbial processes to the iron and carbon cycling in wetlands.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Editorial Material
Oncology
Alison A. McBride, Elizabeth A. White
Summary: In this study, the authors characterize the complex landscape of virus-host DNA molecules in HPV-positive cells, revealing diverse integrated and extrachromosomal virus-host hybrid DNAs that can drive clonal evolution.
Article
Chemistry, Multidisciplinary
Sophie Schoellkopf, Andrea Knoll, Amal Homer, Oliver Seitz
Summary: Efficient fluorogenic hybridization probes that combine high brightness and specificity of fluorescence signaling with large turn-on of fluorescence are presented. An approach to enhance signaling by combining two identical fluorescence base surrogates in FIT2 probes is proposed. The probes were used to explore the single nucleotide-specific detection of a C -> U edited RNA of the glycine receptor (GlyR) and showed strong self-quenching upon single base mismatched hybridization.
Article
Chemistry, Multidisciplinary
Daniele Rosa-Gastaldo, Andrea Dalla Valle, Tommaso Marchetti, Luca Gabrielli
Summary: A new family of duplex-forming recognition encoded oligomers was developed with the ability of sequence selective duplex formation and template directed synthesis. The duplex formation and assembly properties were studied by F-19 and H-1 NMR experiments. The use of dynamic combinatorial chemistry demonstrated the templated synthesis of complementary oligomers. The H-bond recognition played a key role in discriminating mutated donor monomers. The combination of sequence-selective duplex formation and template effect makes this system a promising target for further studies.
Article
Chemistry, Multidisciplinary
Anish Rao, Soumendu Roy, Pramod P. Pillai
Summary: This study demonstrates the ability to create transient self-assembled structures in gold nanoparticles through fine-tuned interparticle interactions on appropriately functionalized surfaces. Changes in pH and ionic strength lead to variations in electrostatic attraction between gold nanoparticles and the aggregating agent, triggering a simultaneous self-assembly response.
Article
Pharmacology & Pharmacy
Fasih Bintang Ilhami, Enyew Alemayehu Bayle, Chih-Chia Cheng
Summary: The cooperative A-U base pairing within A-R6G/BU-PEG nanogels significantly improves selective drug uptake by cancer cells and effectively promotes apoptotic programmed cell death, making it a promising smart drug delivery system for cancer chemotherapy.
Article
Chemistry, Physical
Eric Bremond, Hanwei Li, Juan Carlos Sancho-Garcia, Carlo Adamo
Summary: This study explores a method for accurately evaluating weak noncovalent interactions in large molecular systems. The PBE-QIDH/DH-SVPD protocol shows high accuracy and computational speed for large systems, but has limitations when dealing with complex molecular structures and limited reference data.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Review
Biochemistry & Molecular Biology
Amy O. Stevens, Yi He
Summary: Dynamic allosterism plays a crucial role in signal propagation within proteins. The PDZ family is a well-known example of dynamic allostery in small modular domains. This review summarizes the residues involved in dynamic allostery within the PDZ2 and PDZ3 domains of PTP-BL and PSD-95, respectively, and highlights their conservations. Future studies should focus on PDZ domains with multiple binding partners and multidomain constructs containing a PDZ domain.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Malgorzata Bogunia, Adam Liwo, Cezary Czaplewski, Joanna Makowska, Artur Gieldon, Mariusz Makowski
Summary: Hydrophobic interactions, the aggregation of nonpolar particles in a polar solvent, are crucial for complex processes like protein folding. This study used molecular dynamics simulations to investigate the hydrophobic association of adamantane and hexane under various conditions and determined the thermodynamic properties associated with their formation.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Jessica L. Binder, Joel Berendzen, Amy O. Stevens, Yi He, Jian Wang, Nikolay Dokholyan, Tudor Oprea
Summary: This paper investigates the use of confidence scores to evaluate the accuracy of AlphaFold protein models for drug discovery. It proposes criteria for useful models and residues and presents findings on the effects of disorder and sequence divergence on accuracy.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Cell Biology
Amy O. Stevens, Samuel Luo, Yi He
Summary: This study used all-atom molecular dynamics simulations to reveal the atomic-level interaction pattern between the PICK1 PDZ domain and BIO124, identifying three unique binding conformations of BIO124. The interactions between BIO124 and I35 may be the key to inducing dynamic coupling with the alpha A helix.
Correction
Chemistry, Physical
Celina Sikorska, Adam Liwo
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Pharmacology & Pharmacy
Xiaosi Li, Qi Li, Shenghan Song, Amy O. Stevens, Zach Broemmel, Yi He, Ursula Wesselmann, Tony Yaksh, Chao Zhao
Summary: This study explores the use of emulsion-induced polymersomes (EIP) as a drug delivery system for Tetrodotoxin (TTX) to provide a continuous nerve block for pain relief. The EIP/TTX formulation can increase the tolerated dose of TTX without causing systemic toxicity and produce a reliable nerve block with minimal local toxicity for 22 days when combined with a chemical penetration enhancer.
ADVANCED THERAPEUTICS
(2023)
Article
Biochemical Research Methods
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Pawel Czarnul
Summary: The UNRES-GPU package has been implemented on GPUs and achieved significant speed-up for large protein systems. It is capable of simulating large protein systems at the millisecond time scale.
Article
Chemistry, Multidisciplinary
Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipinska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo
Summary: The dynamics of HuNoV VLPs from GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains were investigated using long-time molecular dynamics simulations. The bending motion at the junction between the P1 and P2 subdomains of the major VP1 protein was found to be the main motion of the VLP units. The GII.2 strain exhibited more pronounced fluctuations and a greater angle with the VLP surface, which may explain its inability to bind HBGAs.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Adam Liwo, Maciej Pyrka, Cezary Czaplewski, Xubiao Peng, Antti J. Niemi
Summary: In this study, the long-term dynamics of three molecular motors were investigated using molecular dynamics simulations. The results show that rotational motion can occur with zero total angular momentum in both the microcanonical and canonical ensembles, and thermal motions can be converted into net rotation. These findings highlight the importance of molecular motors in facilitating movement and transportation within living organisms.
Article
Biophysics
Maciej Maciejczyk, Maciej Pyrka
Summary: 8-azaguanine is a triazolopyrimidine nucleobase analog with potent antibacterial and antitumor activities. Its tautomeric equilibrium, as well as the effects of methyl substitution and ribosylation, were investigated using quantum chemistry methods. The results supported the assumption that replacing the proton with a methyl group does not significantly alter the absorption and fluorescence properties of the compound.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2023)
Article
Chemistry, Physical
Annemarie Danielsson, Sergey. A. A. Samsonov, Adam Liwo, Adam. K. K. Sieradzan
Summary: Heparin is a negatively charged unbranched polysaccharide involved in important biological processes. This study extends the UNICORN model to heparin and accurately predicts its conformation using the SUGRES-1P force field.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Agnieszka G. Lipska, Adam K. Sieradzan, Su''meyye Atmaca, Cezary Czaplewski, Adam Liwo
Summary: A reliable representation of local interactions is crucial for accurate protein structure and dynamics modeling. Traditional approaches mainly focus on parameterizing preset formulas rather than physics-based derivation. Recent advancements suggest the consideration of virtual bond angles and multiple torsional terms. Furthermore, separating residue-based torsional potentials into regular and improper potentials is a new approach.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Christian Schulze, Annemarie Danielsson, Adam Liwo, Daniel Huster, Sergey A. Samsonov, Anja Penk
Summary: This study compares the binding of highly charged heparin with peptides of varying charge density to the regulatory protein IL-8. The results demonstrate that the peptide ligands have weaker binding affinity to IL-8 compared to GAGs. Molecular simulations suggest that the entropic loss of peptides might account for this difference.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Christian Schulze, Annemarie Danielsson, Adam Liwo, Daniel Huster, Sergey A. Samsonov, Anja Penk
Summary: This study investigates the binding process between proteins and glycosaminoglycans (GAGs) from the extracellular matrix and compares the binding affinity of highly charged heparin (HP) hexasaccharide and negatively charged peptides with different charge densities. The results suggest that the difference in binding affinity between GAGs and peptides may be attributed to the entropic loss of peptides during binding.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Tongtong Li, Stefano Motta, Amy O. Stevens, Shenghan Song, Emily Hendrix, Alessandro Pandini, Yi He
Summary: This study investigates the binding/unbinding mechanism of p53's disordered regions at the residue level. The researchers observed two different dissociation pathways and identified key residues in the N-terminal transactivation domain 2 (TAD2) of p53 that play critical roles in the dissociation process. Additionally, their analysis suggests that the binding of the Taz2-TAD2 complex is mainly governed by the Taz2 binding site.
