Related papers: Lattice models for protein organization throughout…
Photosystem II (PSII) and its associated light-harvesting complex II (LHCII) are highly concentrated in the stacked grana regions of photosynthetic thylakoid membranes. Within the membrane, PSII-LHCII supercomplexes can be arranged in…
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…
We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices.…
Lipid phase heterogeneity in the plasma membrane is thought to be crucial for many aspects of cell signaling, but the physical basis of participating membrane domains such as "lipid rafts" remains controversial. Here we consider a lattice…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Membrane proteins often form dimers and higher-order oligomers whose stability and spatial organization depend sensitively on their lipid environment. To investigate the physical principles underlying this coupling, we employ a lattice…
Experiments show that the movement of eukaryotic cells is regulated by a process of phase separation of two competing enzymes on the cell membrane, that effectively amplifies shallow external gradients of chemical attractant. Notably, the…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
We present a new lattice model for proteins that incorporates a tube-like anisotropy by introducing a preference for mutually parallel alignments in the conformations. The model is demonstrated to capture many aspects of real proteins.
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic…
We have constructed a model for the kinetics of rupture of membranes under tension, applying physical principles relevant to lipid bilayers held together by hydrophobic interactions. The membrane is characterized by the bulk compressibility…
Collagen fibrils, cable-like assemblies of long biological molecules, are dominant components of connective tissues. Their determinant morphological and functional roles motivated a large number of studies concerning their formation and…
Eukaryotic cells intrinsically change their shape, by changing the composition of their membrane and by restructuring their underlying cytoskeleton. We present here further studies and extensions of a minimal physical model, describing a…
Triangular lattice models for pattern formation by hard-core soft-shell particles at interfaces are introduced and studied in order to determine the effect of the shell thickness and structure. In model I, we consider particles with…
We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…