Biomembranes are integral part of the cell, the basic building block of all life. They are a two- dimensional fluid, composed of myriad proteins and lipid species, which provide identity to the cell and to many internal organelles. An intriguing aspect of membranes is their ability to assume a variety of shapes, which is crucial for many cellular processes such as food update, waste disposal,...
Molecular dynamics (MD) is a well-established simulation method that has successfully been applied to study a wide range of biomolecular processes. As a result of continuous improvements in both modeling methods and computational infrastructures, the study of mesoscopic, multi-component systems has become more attainable. However, the intricacies involved in setting up MD simulations for...
In the yeast plasma membrane, domains rich in long-chain sphingolipids are observed. Our study employs MD simulations to explore the influence of these lipids on membrane properties. We utilize both coarse-grained and all-atom models, employing a simplified lipid composition with varying concentrations of long-chain lipids. We assess the impact on diverse parameters such as order parameter,...
G protein-coupled receptors (GPCRs) play a crucial role in modulating physiological responses by transmitting extracellular signals into the cell. Moreover, they are the main target of drugs like salmeterol and salbutamol, which act against pulmonary diseases by activating the GPCR, β2-adrenergic receptor (β2AR). In this study, we employ coarse-grained molecular dynamics simulations with the...
Combining synthetic polymers with biological matter such as proteins or DNA is a cornerstone technique in nanomedicine and biotechnology. For example, antibody formulations can be stabilized through the addition of low molecular weight polymers or nucleic acid delivered by combining them with ionic polymers to form polyplexes. Exploiting the vast chemical composition space spanned by synthetic...
