Article
Biochemistry & Molecular Biology
Sasidharan Perumal, MadhanaVigneshwari Gopal Samy, Dharaneedharan Subramanian
Summary: This study examined the antibacterial activity of swertiamarin extracted from Enicostema axillare against three human gram-negative pathogens. The results showed that swertiamarin had efficient activity at low doses against the tested pathogens. Molecular docking and dynamics simulations indicated that swertiamarin exhibited better antibacterial activity compared to other typhoid drugs.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Sanja Skulj, Antun Barisic, Natalie Mutter, Oliver Spadiut, Ivan Barisic, Branimir Bertosa
Summary: This study investigated the impact of different types of glycosylation on the structure and dynamics of horseradish peroxidase (HRP) and engineered split horseradish peroxidase (sHRP) using molecular dynamics simulations. The results showed that glycosylation reduced protein fluctuations and affected both the peripheral region directly and the central region near the active site through propagation. The presence of glycans also influenced the electrostatic potential of the protein and the heme cofactor.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Olga Yu. Portnyagina, Darya N. Ivashkevich, Inessa V. Duizen, Ludmila S. Shevchenko, Olga D. Novikova
Summary: It has been discovered that a single dose immunization of mice with Yersiniapseudotuberculosis porins OmpF and OmpC leads to pathological changes in the deep layers of the cerebral cortex, characterized by dystrophic changes in cells along with an increasing titer of specific antibodies. Simultaneously, an increased level of caspase-3 expression is observed in neurons, indicating the induction of proapoptotic signaling pathways. The findings suggest that nonspecific pore-forming proteins of Gram-negative bacteria's outer membrane have the potential to initiate degenerative changes in brain cells.
BIOCHEMISTRY-MOSCOW
(2023)
Article
Biochemistry & Molecular Biology
Muhammad Janees Imdad, Muhammad Naseem Khan, Hafiz Shahood Alam, Abdul Basit Khan, Zulfiqar Ali Mirani, Adnan Khan, Faraz Ahmed
Summary: This study designed and analyzed a novel mRNA vaccine construct against Salmonella by combining genes of outer membrane proteins C and F of S. Typhi. The construct demonstrated structural stability, high antigenicity, and the potential to provide broad-spectrum protection against various Salmonella serovars.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Jianzhuo Zhu, Zhuodan Zhao, Xingyuan Li, Yong Wei
Summary: This study used molecular dynamics simulations to investigate the attributes of concentrated ionic aqueous electrolytes, revealing the effects of different solute fractions on ion diffusion, hydration number, and water hydrogen bonding.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Chenxing Liang, Archith Rayabharam, N. R. Aluru
Summary: In this study, the structural and dynamical properties of water and heavy water under nanoscale confinement were investigated using path integral molecular dynamics simulations. It was found that under nanoscale confinement, the bond length and bond angle of both water and heavy water were smaller compared to the bulk state. The number of hydrogen bonds decreased, indicating a weakened hydrogen bond interaction. Heavy water had a higher dipole moment and stronger hydrogen bonding than water.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Multidisciplinary Sciences
Cecilia Herrero, Michela Pauletti, Gabrile Tocci, Marcella Iannuzzi, Laurent Joly
Summary: Water is a unique fluid that has always been studied extensively by scientists. In this research, the temperature dependence of transport properties in water was investigated using density functional theory and ab initio molecular dynamics. The study found that different functionals have varying accuracy in describing experimental data and explored the role of nuclear quantum effects in water dynamics using machine learning algorithms. The molecular mechanisms underlying the performance of different functionals were also examined, and the relationship between structural properties and transport coefficients was verified. The results provide insights for predicting transport coefficients and developing improved functionals, emphasizing the importance of considering the long-range features of the radial distribution function.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Kana Ishisone, Guido Ori, Mauro Boero
Summary: This study provides a detailed insight into the structural and electronic interactions in the ionic liquid targeted for low-power electronics and optoelectronic devices. Through first principles dynamical simulations and long-lasting dynamical simulations, the nature of bonding and non-bonding interactions, conformational changes, induced dipole moments, and the mobilities of the ionic species are revealed. Additionally, the analysis of the electronic structure and charge distributions helps to understand the electrostatic interactions, hydrogen bonding properties, and the infra-red and dielectric response of the system.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Thomas S. Hofer
Summary: The extensive re-parametrisation of the flexible SPC-mTR water potential resulted in more suitable ensemble averages for the intramolecular geometry of ambient water, improved vibrational properties, and an adequate relative static permittivity. The optimization strategy followed successful three-point water models OPC3 and H2O-DC, utilizing overpolarized partial charges and modified intramolecular geometries. The improved structural, vibrational, and dielectric properties of the new SPC-mTR2 parametrisation are expected to provide superior performance in QM/MM-type simulations aimed at determining single-ion solvation free energies.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Chemistry, Physical
Qamreen Parker, Robert G. Bell, Nora H. de Leeuw
Summary: Molecular dynamics simulations were used to study the structures and dynamics of ionic liquids, showing the significant influence of the alkyl chain on cation movement and validation of experimental values within a 2% error range. The simulations revealed the retention of short and medium-range structures in dynamical behavior.
MOLECULAR SIMULATION
(2021)
Article
Biochemical Research Methods
Alexander J. Bryer, Tyler Reddy, Edward Lyman, Juan R. Perilla
Summary: Enveloped viruses are protected by a lipid membrane, and the complex lipid composition of the envelope is closely related to its structural, mechanical, and dynamical properties.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Chemistry, Physical
Tatiana Morozova, Nicolas A. Garcia, Jean-Louis Barrat
Summary: This study investigates the temperature dependence of different water models and finds that four-point water models are more suitable than the traditional TIP3P model for modeling temperature-dependent phenomena in biomolecular systems.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Masahiko Okuda, Toru Ekimoto, Jun-ichi Kurita, Mitsunori Ikeguchi, Yoshifumi Nishimura
Summary: TFIIH is a crucial factor in transcription and DNA repair, with the p62 subunit containing a flexible PH-D domain that plays a key role in TFIIH localization and function. By establishing the solution structure of p62 PH-D and modeling its dynamic position in TFIIH, researchers have gained insights into the interaction mechanism between TFIIH and its binding partners. The study also showed that the binding partners use their intrinsically disordered acidic regions for TFIIH recruitment, providing a deeper understanding of the molecular mechanisms involved.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Chanchan Liu, Qiyu Gao, Zhuo Shang, Jian Liu, Siwei Zhou, Jingjie Dang, Licheng Liu, Iris Lange, Narayanan Srividya, B. Markus Lange, Qinan Wu, Wei Lin
Summary: This study characterized the stereoselectivity of pulegone reductases using various methods, laying a foundation for the engineering of menthone/menthol biosynthetic enzymes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Xuesen Qi, Guozhen Li, Jiahai Liu, Linkai Mou, Yusheng Zhang, Shilin Guo, Xiangyu Chen, Wenxing Li
Summary: In this study, the binding selectivity mechanism of RP-6306 towards PKMYT1 was uncovered using molecular docking, molecular dynamics simulations, and free energy calculations. The results clarified the binding specificity of RP-6306 reported in previous bioassays and showed that the selectivity largely derived from protein-ligand electrostatic interactions. The critical factor responsible for the binding selectivity was identified as the non-conserved gatekeeper residue Thr187 in PKMYT1.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Polymer Science
Jaya Baranwal, Brajesh Barse, Antonella Fais, Giovanna Lucia Delogu, Amit Kumar
Summary: Biopolymers are highly valuable functional materials that attract researchers and professionals from various disciplines. Interdisciplinary research is crucial to explore the fundamental and applied aspects of biopolymers in addressing complex problems related to health and well-being. Efforts have been made to replace synthetic polymers with biodegradable materials derived from natural resources to reduce environmental impact. This review focuses on the diverse applications of biopolymers in the food and medical industry and provides an outlook for the future of this industry.
Article
Cell Biology
Margherita Festa, Velia Minicozzi, Anna Boccaccio, Laura Lagostena, Antonella Gradogna, Tianwen Qi, Alex Costa, Nina Larisch, Shin Hamamoto, Emanuela Pedrazzini, Stefan Milenkovic, Joachim Scholz-Starke, Matteo Ceccarelli, Alessandro Vitale, Petra Dietrich, Nobuyuki Uozumi, Franco Gambale, Armando Carpaneto
Summary: This review focuses on current methods used to unravel the functional properties of lysosomal ion channels and transporters, evaluating their advantages, disadvantages, and fields of applicability.
Article
Chemistry, Medicinal
Lucile Moynie, Francoise Hoegy, Stefan Milenkovic, Mathilde Munier, Aurelie Paulen, Veronique Gasser, Aline L. Faucon, Nicolas Zill, James H. Naismith, Matteo Ceccarelli, Isabelle J. Schalk, Gaetan L. A. Mislin
Summary: This study found that TCV can mimic the binding of ENT to the outer membrane transporter PfeA in Pseudomonas aeruginosa and can cross the bacterial outer membrane through this protein. This finding provides a promising vector for using the Trojan horse strategy against P. aeruginosa.
ACS INFECTIOUS DISEASES
(2022)
Review
Physics, Multidisciplinary
C. Guardiani, F. Cecconi, L. Chiodo, G. Cottone, P. Malgaretti, L. Maragliano, M. L. Barabash, G. Camisasca, M. Ceccarelli, B. Corry, R. Roth, A. Giacomello, B. Roux
Summary: Ion channels act as gates on cellular membranes to ensure selective ion transport, serving as the molecular mechanism for basic biological functions like nerve signal transmission and muscle contraction. Recent computational research on ion channels reviews theoretical advances, simulation approaches, and modeling techniques, including applications to understand permeation, selectivity, and gating mechanisms in biological and model channels.
ADVANCES IN PHYSICS-X
(2022)
Review
Energy & Fuels
Vigneselvan Sivasubramaniyam, Suganthi Ramasamy, Manikandan Venkatraman, Gianluca Gatto, Amit Kumar
Summary: The increase in electric vehicles and their electrical appliances has led to a demand for more efficient and lightweight electrical machines with better performance. However, conventional wire windings used in these machines have limitations in meeting the current requirements. Copper, which is commonly used in electrical windings, causes a significant amount of losses due to its resistance. On the other hand, carbon nanotubes and composite materials have superior electrical conductivity and mechanical properties compared to copper. This article reviews the electrical and mechanical properties of carbon nanotubes and explores their potential as a replacement for copper windings in electrical wires.
Review
Biochemistry & Molecular Biology
Navodit Kumar Singh, Jaya Baranwal, Siddhartha Pati, Brajesh Barse, Rizwan Hasan Khan, Amit Kumar
Summary: The burning of plastic waste leads to air pollution due to the release of toxic gases. Developing biodegradable polymers with similar characteristics to those derived from petroleum is crucial. To mitigate the impact of these issues, we need to focus on alternative sources that can biodegrade naturally.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Microbiology
Mohd Athar, Silvia Gervasoni, Andrea Catte, Andrea Basciu, Giuliano Malloci, Paolo Ruggerone, Attilio Vittorio Vargiu
Summary: Bacterial resistance to antibiotics is a major concern, especially with multi-drug resistant (MDR) bacteria that are resistant to most drugs. Efflux pumps in Gram-negative bacteria play a crucial role in MDR and virulence, and understanding their interactions with antibiotics is key for designing better therapeutics. In silico studies on these pumps have flourished in recent decades, complementing experimental research and contributing to the fight against MDR bacteria.
Article
Chemistry, Medicinal
Mitul Srivastava, Lovika Mittal, Debapriyo Sarmadhikari, Vijay Kumar Singh, Antonella Fais, Amit Kumar, Shailendra Asthana
Summary: The development of potent non-nucleoside inhibitors (NNIs) as an alternative strategy to combatting the infectious bovine viral diarrhea virus (BVDV) is discussed. The RNA-dependent RNA polymerase (RdRp) is identified as a primary target for countermeasures against infectious diseases. Quinoline compounds are shown to bind at the template entrance channel of RdRp, suggesting potential for the discovery of improved antivirals.
Article
Chemistry, Multidisciplinary
Igor Bodrenko, Alessandra Satta, Claudia Caddeo, Giacomo Cozzolino, Stefan Milenkovic, Matteo Ceccarelli, Alessandro Mattoni
Summary: The possibility of using fullerenes as containers for toxic beryllium atoms is explored through a multi-scale approach combining first-principles calculations and molecular dynamics simulations. It is concluded that Be endohedral complexes can be obtained by implanting Be atoms at energies >2.3 eV, suggesting the potential use of laser implantation technologies. Optical absorption can be used as a non-destructive technique to distinguish stable endohedral complexes from metastable exohedral ones. The results also indicate the long-term thermodynamic stability and confinement ability of Be-endohedral complexes in both vacuum and aqueous solution, highlighting their potential applications in nanotechnology and nanomedicine.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Chemistry, Medicinal
Antonio Laus, Amit Kumar, Pierluigi Caboni, Maria A. De Luca, Michael H. Baumann, Enrico Pieroni, Graziella Tocco
Summary: The misuse of synthetic opioids has become a major public health concern. Through molecular modeling, we have identified the ligand-receptor interactions of U-47700 and U-50488 with MOR and KOR, providing insights into their pharmacology. Our findings suggest that U-47700 exhibits high affinity for MOR, while U-50488 shows a preference for KOR binding.
ARCHIV DER PHARMAZIE
(2023)
Article
Chemistry, Medicinal
Silvia Gervasoni, Isilay Ozturk, Camilla Guccione, Andrea Bosin, Paolo Ruggerone, Giuliano Malloci
Summary: In this study, the molecular interactions between radiopharmaceuticals and SSTR2 were carefully analyzed, and the binding modes and interaction patterns of six compounds were identified. This study provides valuable insights for the design of new ligands targeting SSTR2.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Review
Chemistry, Physical
Jaya Baranwal, Brajesh Barse, Amalia Di Petrillo, Gianluca Gatto, Luca Pilia, Amit Kumar
Summary: The use of tailored medication delivery holds great potential for improving cancer treatment outcomes by increasing efficacy and reducing side effects. Currently, chemotherapy remains a challenging topic for researchers seeking to improve clinical outcomes. Nanotechnology has revolutionized medical research by providing new and improved materials for biomedical applications, particularly in therapy and diagnostics. Metal nanoparticles are increasingly being explored as alternative chemotherapy drugs, as they possess inherent or surface-induced anticancer properties. The rapid development of metal nanoparticles offers alternative therapeutic strategies and improved outcomes for cancer treatments.
Article
Chemistry, Physical
Stefan Milenkovic, Jiajun Wang, Silvia Acosta-Gutierrez, Mathias Winterhalter, Matteo Ceccarelli, Igor V. Bodrenko
Summary: Transmembrane beta-barrel proteins are versatile candidates for various technological applications and their behavior is influenced by environmental conditions. Comparing two highly homologous porins, OmpF and OmpC, we observed subtle amino acid substitutions that can modulate mass transport properties. These differences can be attributed to the disparities in the environmental conditions under which the porins are expressed. Our analysis not only highlights the advantages of enhanced sampling methods, but also provides valuable insights into the biological function and technical applications of these proteins.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Igor Bodrenko, Matteo Ceccarelli, Silvia Acosta-Gutierrez
Summary: General porins are crucial sieving mechanisms in the outer membrane of Gram-negative bacteria, with a unique structure that protects the cell while allowing selective entry of molecules. By exploiting electrostatic interactions, the permeability of porins can be finely tuned, enabling control over the transport of molecules.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Igor Bodrenko, Matteo Ceccarelli, Silvia Acosta-Gutierrez
Summary: This study presents a theoretical framework for analyzing the filter of general porins in bacterial outer membranes. The researchers demonstrate that permeability can be finely tuned by exploiting electrostatic interactions between the pore and the translocating molecule. This research contributes to understanding the transport mechanism of general porins in bacterial outer membranes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
