Related papers: Membrane-mediated protein-protein interaction: A M…
The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes of proteins in different salt solutions. We demonstrate the existence of ion-specific attractive…
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…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
Predicting the adsorption affinity of a small molecule to a target surface is of importance to a range of fields, from catalysis to drug delivery and human safety, but a complex task to perform computationally when taking into account the…
Sequential Monte Carlo methods are typically not straightforward to implement on parallel architectures. This is because standard resampling schemes involve communication between all particles. The $\alpha$-sequential Monte Carlo method was…
Cell membranes phase separate into ordered ${\rm L_o}$ and disordered ${\rm L_d}$ domains depending on their compositions. This membrane compartmentalization is heterogeneous and regulates the localization of specific proteins related to…
We study pattern formation, fluctuations and scaling induced by a growth-promoting active walker on an otherwise static interface. Active particles on an interface define a simple model for energy consuming proteins embedded in the plasma…
Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by…
Bin/Amphiphysin/Rvs superfamily proteins and other curvature-inducing proteins have anisotropic shapes and anisotropically bend biomembrane. Here, we report how the anisotropic proteins bind the membrane tube and are orientationally ordered…
Protein chains of the (FG)$_n$ ($n \simeq$ 300) type cap the cytoplasmatic side of the nucleopore complex, which connects the nucleus to the remainder of an eukaryotic cell. We study the properties of three fundamental polymer models that…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and…
Particles embedded in a fluctuating interface experience forces and torques mediated by the deformations and by the thermal fluctuations of the medium. Considering a system of two cylinders bound to a fluid membrane we show that the…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
The computational study of the interaction between charged, ligand-protected metal nanoparticles and model lipid membranes has been recently addressed both at atomistic and coarse grained level. Here we compare the performance of three…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
Many protein-protein interaction (PPI) networks take place in the fluid yet structured plasma membrane. Lipid domains, sometimes termed rafts, have been implicated in the functioning of various membrane-bound signaling processes. Here, we…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms…
Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest…