Related papers: The Relation Between {\alpha}-Helical Conformation…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
Numerous experiments demonstrate a high level of promiscuity and structural disorder in organismal proteomes. Here we ask the question what makes a protein promiscuous, i.e., prone to non-specific interactions, and structurally disordered.…
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…
Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…
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…
Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native…
Functional amyloid fibrils, once primarily associated with amyloidosis, are now recognized for their exceptional potential as biomaterials due to their unique structural features, including remarkable mechanical strength, high stability,…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an…
The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…
Alzheimer's disease is characterized by dangerous amyloid plaques formed by deposits of the protein Beta-Amyloid aggregates in the brain. The specific amino acid sequence that is responsible for the aggregates of Beta-Amyloid is…
The proposal of this paper is to provide a simple angular random walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging…
The need to understand the assembly kinetics of fibril formation has become urgent because of the realization that soluble oligomers of amyloidogenic peptides may be even more neurotoxic than the end product, namely, the amyloid fibrils. In…
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…
Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address…
Structural defects within amorphous packings of symmetric particles can be characterized using a machine learning approach that incorporates structure functions of radial distances and angular arrangement. This yields a scalar field,…
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…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
The importance of understanding the mechanism of protein aggregation into insoluble amyloid fibrils relies not only on its medical consequences, but also on its more basic properties of self--organization. The discovery that a large number…