Molecular dynamics simulations are performed on two hydrated dipalmitoylphosphatidylcholine bilayer systems: one with pure water and one with added NaCl. Due to the rugged nature of the membrane/electrolyte interface, ion binding to the membrane surface is characterized by the loss of ion hydration. Using this structural characterization, binding of Na(+) and Cl(-) ions to the membrane is observed, although the binding of Cl(-) is seen to be slightly weaker than that of Na(+). Dehydration is seen to occur to a different extent for each type of ion. In addition, the excess binding of Na(+) gives rise to a net positive surface charge density just outside the bilayer. The positive density produces a positive electrostatic potential in this region, whereas the system without salt shows an electrostatic potential of zero.
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http://dx.doi.org/10.1016/S0006-3495(03)75102-9 | DOI Listing |
Skelet Muscle
January 2025
Department of Anesthesia and Critical Care, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
Background: Duchenne muscular dystrophy (DMD) is a prevalent, fatal degenerative muscle disease with no effective treatments. Mdx mouse model of DMD exhibits impaired muscle performance, oxidative stress, and dysfunctional autophagy. Although antioxidant treatments may improve the mdx phenotype, the precise molecular mechanisms remain unclear.
View Article and Find Full Text PDFJ Transl Med
January 2025
Department of Neurosurgery, The Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China.
Background: Spinal cord injury (SCI) triggers a complex inflammatory response that impedes neural repair and functional recovery. The modulation of macrophage phenotypes is thus considered a promising therapeutic strategy to mitigate inflammation and promote regeneration.
Methods: We employed microarray and single-cell RNA sequencing (scRNA-seq) to investigate gene expression changes and immune cell dynamics in mice following crush injury at 3 and 7 days post-injury (dpi).
J Phys Chem A
January 2025
School of Environment and Safety Engineering, North University of China, Taiyuan, Shanxi 030051, China.
DNP (3,4-dinitropyrazole) has attracted much interest due to its promising melting characteristics and high detonation performances, such as low melting point, high density, high detonation velocity, and low sensitivity. In this work, first-principles molecular dynamics (MD) simulations were performed to investigate the anisotropic shock response of DNP in conjunction with the multiscale shock technique (MSST). The initial decomposition mechanism was revealed through the evolution of the chemical reaction and product analysis.
View Article and Find Full Text PDFMethods Mol Biol
January 2025
Institute of Physical Chemistry, University of Göttingen, Göttingen, Germany.
We present two innovative approaches to investigate the dynamics of membrane fusion and the strength of protein-membrane interactions. The first approach employs pore-spanning membranes (PSMs), which allow for the observation of protein-assisted fusion processes. The second approach utilizes colloidal probe microscopy with membrane-coated probes with reconstituted proteins.
View Article and Find Full Text PDFMethods Mol Biol
January 2025
Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China.
Steered Molecular Dynamics (SMD) simulation is a powerful computational simulation technique that enables the controlled manipulation of molecular systems by applying external forces. This method is frequently utilized to investigate the slow processes of biomolecular systems that occur within sub-second to second time scales, achieved through SMD simulations that only span nanoseconds. SMD simulation can be utilized to study the detailed mechanism of protein conformational changes, protein unfolding, and ligand dissociation, etc.
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