Related papers: The Relation Between {\alpha}-Helical Conformation…
Hexapeptides are widely applied as a model system for studying amyloid-forming properties of polypeptides, including proteins. Recently, large experimental databases have become publicly available with amyloidogenic labels. Using these…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible…
The hygro-thermo-expansive response of fibrous networks involves deformation phenomena at multiple length scales. The moisture or temperature induced expansion of individual fibres is transmitted in the network through the inter-fibre…
Segments with the amino acid sequence EKAYLRT appear in natural occurring proteins both in $\alpha$-helices and $\beta$-sheets. For this reason, we have use this peptide to study how secondary structure formation in proteins depends on the…
Recent years have seen tremendous developments in the use of machine learning models to link amino acid sequence, structure and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of…
To the best of the author's knowledge, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins due to the unstable, noncrystalline and insoluble nature of the amyloid…
Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various…
Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for…
Using atomic force microscopy (AFM) we investigated the interaction of amyloid beta (Ab) (1 42) peptide with chemically modified surfaces in order to better understand the mechanism of amyloid toxicity, which involves interaction of amyloid…
Alzheimer's disease causes severe neurodegeneration in the brain that leads to a certain death. The defining factor is the formation of extracellular senile amyloid plaques in the brain. However, therapeutic approaches to remove them have…
The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…
Hybridization between species is an important mechanism for the origin of novel lineages and adaptation to new environments. Increased allelic variation and modification of the transcriptional network are the two recognized forces currently…
We use numerical simulations to show how a fully flexible filament binding to a deformable cylindrical surface may acquire a macroscopic persistence length and a helical conformation. This is a result of the nontrivial elastic response to…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
The structure-function relationship is at the heart of biology and major protein deformations are correlated to specific functions. In the case of heme proteins, doming is associated with the respiratory function in hemoglobin and…
Amphiphilic molecules and their self-assembled structures have long been the target of extensive research due to their potential applications in fields ranging from materials design to biomedical and cosmetic applications. Increasing…