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View article: Psychedelics promote plasticity by directly binding to BDNF receptor TrkB
Psychedelics promote plasticity by directly binding to BDNF receptor TrkB Open
Psychedelics produce fast and persistent antidepressant effects and induce neuroplasticity resembling the effects of clinically approved antidepressants. We recently reported that pharmacologically diverse antidepressants, including fluoxe…
View article: Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties
Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties Open
The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid sp…
View article: Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties
Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties Open
The plasma membrane serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a d…
View article: Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations
Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations Open
The outer mitochondrial membrane (OMM) is involved in multiple cellular functions such as apoptosis, inflammation and signaling via its membrane-associated and -embedded proteins. Despite the central role of the OMM in these vital phenomen…
View article: "Maturation of the SARS-CoV-2 virus is regulated by dimerization of its main protease" TPR files
"Maturation of the SARS-CoV-2 virus is regulated by dimerization of its main protease" TPR files Open
TPR files used for generating the data for analysis of "Maturation of the SARS-CoV-2 virus is regulated by dimerization of its main protease" paper. The names of the ZIP archives with the TPR files refer to the simulation systems descripti…
View article: Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design
Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design Open
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the st…
View article: Mechanistic Insight into How PEGylation Reduces the Efficacy of pH-Sensitive Liposomes from Molecular Dynamics Simulations
Mechanistic Insight into How PEGylation Reduces the Efficacy of pH-Sensitive Liposomes from Molecular Dynamics Simulations Open
Liposome-based drug delivery systems composed of DOPE stabilized with cholesteryl hemisuccinate (CHMS) have been proposed as a drug delivery mechanism with pH-triggered release as the anionic form (CHSa) is protonated (CHS) at reduced pH; …
View article: Cholesterol‐recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: The case of TRKB
Cholesterol‐recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: The case of TRKB Open
Cholesterol is an essential constituent of cell membranes. The discovery of cholesterol‐recognition amino acid consensus (CRAC) motif in proteins indicated a putative direct, non‐covalent interaction between cholesterol and proteins. In th…
View article: Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery
Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery Open
In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is d…
View article: The F1 loop of the talin head domain acts as a gatekeeper in integrin activation and clustering
The F1 loop of the talin head domain acts as a gatekeeper in integrin activation and clustering Open
Integrin activation and clustering by talin are early steps of cell adhesion. Membrane-bound talin head domain and kindlin bind to the β integrin cytoplasmic tail, cooperating to activate the heterodimeric integrin, and the talin head doma…
View article: Cooperative Effects of an Antifungal Moiety and DMSO on Pore Formation over Lipid Membranes Revealed by Free Energy Calculations
Cooperative Effects of an Antifungal Moiety and DMSO on Pore Formation over Lipid Membranes Revealed by Free Energy Calculations Open
Itraconazole is a triazole drug widely used in the treatment of fungal infections, and it is in clinical trials for treatment of several cancers. However, the drug suffers from poor solubility, while experiments have shown that itraconazol…
View article: Tail-Oxidized Cholesterol Enhances Membrane Permeability for Small Solutes
Tail-Oxidized Cholesterol Enhances Membrane Permeability for Small Solutes Open
Cholesterol renders mammalian cell membranes more compact by reducing the amount of voids in the membrane structure. Because of this, cholesterol is known to regulate the ability of cell membranes to prevent the permeation of water and wat…
View article: Membrane-Dependent Binding and Entry Mechanism of Dopamine into Its Receptor
Membrane-Dependent Binding and Entry Mechanism of Dopamine into Its Receptor Open
Synaptic neurotransmission has recently been proposed to function via either a membrane-independent or a membrane-dependent mechanism, depending on the neurotransmitter type. In the membrane-dependent mechanism, amphipathic neurotransmitte…
View article: Cholesterol Reduces Partitioning of Antifungal Drug Itraconazole into Lipid Bilayers
Cholesterol Reduces Partitioning of Antifungal Drug Itraconazole into Lipid Bilayers Open
Cholesterol plays a crucial role in modulating the physicochemical properties of biomembranes, both increasing mechanical strength and decreasing permeability. Cholesterol is also a common component of vesicle-based delivery systems, inclu…
View article: Cholesteryl Hemisuccinate Is Not a Good Replacement for Cholesterol in Lipid Nanodiscs
Cholesteryl Hemisuccinate Is Not a Good Replacement for Cholesterol in Lipid Nanodiscs Open
Nanodiscs are suitable tools for studies of membrane proteins (MPs) due to their ability to mimic native biological membranes, and several MP structures are solved in nanodiscs. Among the various cell membrane components, cholesterol (CHL)…
View article: Cholesterol recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: the case for TRKB
Cholesterol recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: the case for TRKB Open
Cholesterol is an essential constituent of cell membranes. Recently, the discovery of cholesterol recognition amino acid consensus (CRAC) on proteins indicated a putative direct, non-covalent interaction between cholesterol and proteins. I…
View article: Complex Behavior of Phosphatidylcholine–Phosphatidic Acid Bilayers and Monolayers: Effect of Acyl Chain Unsaturation
Complex Behavior of Phosphatidylcholine–Phosphatidic Acid Bilayers and Monolayers: Effect of Acyl Chain Unsaturation Open
Phosphatidic acids (PAs) have many biological functions in biomembranes, e.g., they are involved in the proliferation, differentiation, and transformation of cells. Despite decades of research, the molecular understanding of how PAs affect…
View article: Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance
Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance Open
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features…
View article: How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative
How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative Open
Organic dye-tagged lipid analogs are essential for many fluorescence-based investigations of complex membrane structures, especially when using advanced microscopy approaches. However, lipid analogs may interfere with membrane structure an…
View article: The effect of light sensitizer localization on the stability of indocyanine green liposomes
The effect of light sensitizer localization on the stability of indocyanine green liposomes Open
Light triggered drug delivery systems offer attractive possibilities for sophisticated therapy, providing both temporal and spatial control of drug release. We have developed light triggered liposomes with clinically approved indocyanine g…