Related papers: Robust protein-protein interactions in crowded cel…
We present a simple model for the underlying structure of protein-protein pairwise interaction graphs that is based on the way in which proteins attach to each other in experiments such as yeast two-hybrid assays. We show that data on the…
Biological information processing networks consist of many components, which are coupled by an even larger number of complex multivariate interactions. However, analyses of data sets from fields as diverse as neuroscience, molecular…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to polymerize. Their assemblies should therefore not be understood…
High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
We introduce a simple model to describe the interplay between specific and non-specific interactions. We study the influence of various physical factors on the static and dynamic properties of the specific interactions of our model and show…
The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes…
The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…
It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
Multiple phenotypic protein expressions arising from one genome represent variations in the protein relative abundance and their stoichiometry. A lack of definite compositional parts challenges the modeling of protein megacomplexes and…
Protein-protein interactions (PPIs) are of fundamental importance for the human body, and the knowledge of their existence can facilitate very important tasks like drug target developing and therapy design. The high-throughput experiments…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…