Article
Biology
Shivani Gupta, Ashok Kumar Dasmahapatra
Summary: It has been reported that the therapeutic strategy of destabilizing preformed Afi fibril using natural compounds is significant in treating Alzheimer's disease (AD). This study investigates the destabilization potential of lycopene on different polymorphic forms of Afi fibril through Molecular Dynamics (MD) simulation. The results show that lycopene can bind to the outer surface of the fibril and disrupt its structure by breaking H-bonds and hydrophobic interactions.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2023)
Article
Chemistry, Physical
Phuong. H. Nguyen, Fabio Sterpone, Philippe Derreumaux
Summary: Understanding the atomistic resolution changes during the self-assembly of amyloid peptides or proteins is crucial for drug development, altering aggregation pathways, and suppressing toxicity, but it poses significant challenges.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Shivani Gupta, Ashok Kumar Dasmahapatra
Summary: The extraneuronally deposited senile plaques composed of neurotoxic Aβ fibrils define Alzheimer's disease. Natural compounds have been tested for their ability to destabilize Aβ fibrils and potentially cure Alzheimer's disease. In this study, the stability of a destabilized fibril after removal of the ligand was assessed through molecular dynamics simulation. The results indicate increased destabilization of the fibril structure and reduced interactions with residues, suggesting irreversibility to the native state. Overall, this study demonstrates the potential of destabilization techniques as a promising therapeutic approach for Alzheimer's disease.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Shivani Gupta, Ashok Kumar Dasmahapatra
Summary: The omega-3 polyunsaturated fatty acids EPA and HXA have shown potential to destabilize A beta fibrils, the pathological hallmark of Alzheimer's disease, making them promising drug leads for AD treatment.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Ryo Kawada, Katsuhiro Endo, Daisuke Yuhara, Kenji Yasuoka
Summary: Molecular dynamics simulation is a method for studying the behavior of molecules, but its high computational cost has always been a problem. MD-GAN is a machine learning-based method that accelerates the generation of molecular dynamics data. This study explores the effectiveness of incorporating information from other particles in the training process and successfully predicts molecular diffusion.
Article
Chemistry, Applied
Patrick Heasman, Aleksandar Y. Mehandzhiyski, Sarbani Ghosh, Igor Zozoulenko
Summary: Processing natural cellulose requires dissolution and regeneration. The crystallinity of re-generated cellulose does not match that of native cellulose, and the physical and mechanical properties of re-generated cellulose vary depending on the technique used. Molecular dynamics simulations were performed to simulate the regeneration of order in cellulose. The simulations show that cellulose chains have an affinity to align with each other on the nanosecond scale, but the end results still lack sufficient order. The time factor plays a major role in reclaiming the order of crystalline cellulose.
CARBOHYDRATE POLYMERS
(2023)
Article
Biochemistry & Molecular Biology
Nililla Nisoh, Viwan Jarerattanachat, Mikko Karttunen, Jirasak Wong-ekkabut
Summary: This study uses coarse-grained molecular dynamic simulations to investigate the interactions between carbon nanoparticles (CNPs) and biological membranes. It demonstrates that CNPs can spontaneously penetrate plasma membranes and preferentially locate themselves in regions enriched with highly unsaturated lipids. The findings suggest that by adjusting the lipid composition, CNPs can be loaded inside the plasma membrane, which has potential applications in drug carrier liposome design.
Article
Chemistry, Physical
Ekaterina Maximova, Eugene B. Postnikov, Anastasia Lavrova, Vladimir Farafonov, Dmitry Nerukh
Summary: In this study, the dissociation of ligand isoniazid from a protein catalase was investigated using MD simulations, with a novel method proposed to extrapolate dissociation times to the zero-force limit for comparison with experimental values. The calculated dissociation time was found to quantitatively match the experimental value, despite the extrapolation over multiple orders of magnitude in time.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Marceau Henot, Pierre-Michel Dejardin, Francois Ladieu
Summary: This study investigates the orientational dynamics of supercooled glycerol using molecular dynamics simulations and compares the results with experimental data. The findings suggest that the depolarized dynamic light scattering (DDLS) method has low sensitivity to cross-correlations, supporting the idea of directly comparing data from dielectric spectroscopy (DS) and DDLS to evaluate the impact of cross-correlations in polar liquids.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Arup Kumar Pathak, Tusar Bandyopadhyay
Summary: The capsid-like structure of virus-based protein nanoparticles has potential applications in biomedicines and nanotechnology, allowing for the release of packaged materials through heat-induced structural changes. These changes, primarily resulting from collective atomic motion, occur at widely separated temperatures and play a crucial role in facilitating translocation events of the packaged materials through the nanoparticles.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Physics, Fluids & Plasmas
Enrico Skoruppa, Aderik Voorspoels, Jocelyne Vreede, Enrico Carlon
Summary: Investigations on the influence of nonlocal couplings on DNA torsional and bending elasticities revealed strong off-site couplings for tilt-tilt and twist-twist, while they were weaker in the roll-roll case. Analysis indicated that off-site interactions generate a length-scale-dependent elasticity in DNA models. Simulation-generated data predicted significant length-scale-dependent effect on torsional fluctuations, but only a modest effect on bending fluctuations, consistent with experimental observations probing DNA mechanics.
Article
Physics, Fluids & Plasmas
Chia -Ming Chang, Yi-Hsin Lin, Victor Reshetnyak
Summary: The way water condenses on surfaces is crucial for the energy efficiency of heat transfer systems. Controlled manipulation of water condensation on tunable surfaces has potential applications in various fields and offers promising prospects for development.
Article
Chemistry, Multidisciplinary
Salar Balou, Isteaque Ahmed, Aashish Priye
Summary: Incorporating biomass-derived activated carbon with PETG enables the production of sustainable and eco-friendly 3D printing filaments, which can transform waste into valuable resources and reduce environmental impact.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Medicinal
Ebru Akkus, Omer Tayfuroglu, Muslum Yildiz, Abdulkadir Kocak
Summary: In this paper, a new strategy is introduced to estimate binding free energies using end-state molecular dynamics simulation trajectories. The method, based on linear interaction energy (LIE) and ANI-2x neural network potentials (machine learning), predicts the single-point interaction energies between ligand-protein and ligand-solvent pairs with high accuracy. Experimental results show that the method outperforms current end-state methods, while having reduced computational cost. It also allows for comparison of binding free energies between ligands with different scaffolds.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biology
Chandan Kumar, Susan Idicula-Thomas
Summary: Through molecular docking and MD simulations, the binding site and conformational changes of FSHR modulators were studied. It was observed that both agonist and antagonist bind to the same site but interact with different residues in the transmembrane domain. Agonist binding induces prominent conformational changes in TM helices 3, 4 and 6, which have also been observed in LHCGR and other GPCR members. This reveals an important and conserved mechanism of GPHR activation that can be exploited for novel modulator design.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Chemistry, Multidisciplinary
Sergio Cruz-Leon, Nadine Schwierz
Article
Chemistry, Physical
Nadine Schwierz
JOURNAL OF CHEMICAL PHYSICS
(2020)
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
Kara K. Grotz, Sergio Cruz-Leon, Nadine Schwierz
Summary: Improvements in accurately simulating the properties of magnesium ions have been made by optimizing parameters in a larger parameter space, resulting in the reproduction of experimental properties such as solvation free energy, hydration shell oxygens distance, water exchange rate, and ion-binding sites.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Sebastian Falkner, Nadine Schwierz
Summary: This study investigates the water exchange mechanism between the hydration shells of Mg2+ through molecular dynamics simulations and transition path sampling. It reveals that the choice of water model and Mg2+ model influences the exchange kinetics, with different mechanisms observed depending on the force field used. The results provide insights into the impact of force field choice on exchange dynamics 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
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)