Related papers: Biomolecule surface patterning may enhance membran…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that…
Membrane proteins deform the surrounding lipid bilayer, which can lead to membrane-mediated interactions between neighboring proteins. Using the mechanosensitive channel of large conductance (MscL) as a model system, we demonstrate how the…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
It was recently discovered that friction between surfaces bearing phosphatidylcholine (PC) lipid bilayers can be increased by two orders of magnitude or more via an externally-applied electric field, and that this increase is fully…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Biological membranes are self-assembled complex fluid interfaces that host proteins, molecular motors and other macromolecules essential for cellular function. These membranes have a distinct in-plane fluid response with a surface viscosity…
Using computer simulations we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic…
The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential controlled by a 20x20 random matrix. Good folding sequences,…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Exploring the protein-folding problem has been a long-standing challenge in molecular biology. Protein folding is highly dependent on folding of secondary structures as the way to pave a native folding pathway. Here, we demonstrate that a…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
In this article we review the present knowledge on the elastic properties of membranes of biological origin. Assuming the fluid mosaic hypothesis, we consider the phospholipid bilayer as the structural base of a biological membrane. We…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Membrane proteins and lipids can self-assemble into membrane protein polyhedral nanoparticles (MPPNs). MPPNs have a closed spherical surface and a polyhedral protein arrangement, and may offer a new route for structure determination of…
Cells use homeostatic mechanisms to maintain an optimal composition of distinct types of phospholipids in cellular membranes. The hydrophilic dipolar layer at the membrane interface, composed of phospholipid headgroups, regulates the…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
We propose a model that accounts for budding behavior of domains in lipid bilayers, where each of the bilayer leaflets has a coupling between its local curvature and local lipid composition. The compositional asymmetry between the two…
Many proteins have the potential to aggregate into amyloid fibrils, which are associated with a wide range of human disorders including Alzheimer's and Parkinson's disease. In contrast to that of folded proteins, the thermodynamic stability…
Reactive, semi-permeable interfaces play important roles in key biological processes such as targeted drug delivery, lipid metabolism, and signal transduction. These systems involve coupled surface reactions, transmembrane transport, and…