Related papers: Amyloid Fibril Solubility
Protein amyloid fibrils are a form of linear protein aggregates that are implicated in many neurodegenerative diseases. Here, we study the dynamics of amyloid fibril elongation by performing Langevin dynamic simulations on a coarse-grained…
Protein fibril accumulation at interfaces is an important step in many physiological processes and neurodegenerative diseases as well as in designing materials. Here we show, using $\beta$-lactoglobulin fibrils as a model, that semiflexible…
Amyloid fibrillation is a protein self-assembly phenomenon that is intimately related to well-known human neurodegenerative diseases. During the past few decades, striking advances have been achieved in our understanding of the physical…
Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study aggregation of short peptides in a coarse-grained model with…
Protein aggregation in the form of amyloid fibrils has important biological and technological implications. Although the self-assembly process is highly efficient, aggregates not in the fibrillar form would also occur and it is important to…
Recent experimental studies have shown that amyloid fibril formed by aggregation of {\beta} peptide exhibits excellent mechanical properties comparable to other protein materials such as actin filaments and microtubules. These excellent…
Many proteins have the potential to aggregate into amyloid fibrils, which are associated with a wide range of human disorders including Alzheimer's and Parkinson's disease. In contrast to that of folded proteins, the thermodynamic stability…
We study the two-filament insulin fibril's structure by incorporating recent simulation results and mechanical measurements. Our investigation suggests that the persistence length measurement correlates well with the previously proposed…
Above a critical concentration a wide variety of peptides and proteins self-assemble into amyloid fibrils which entangle to form percolating networks called hydrogels. Such hydrogels have important applications as biomaterials and in…
Bone is a multiscale heterogeneous materiel of which principal function is to support the body structure and to resist mechanical loading and fractures. Bone strength does not depend only on the quantity and quality of bone which is…
We consider nucleation of amyloid fibrils in the case when the process occurs by the mechanism of direct polymerization of practically fully extended protein segments, i.e. beta-strands, into beta-sheets. Applying the classical nucleation…
We develop a general theory for three states of equilibrium of amyloid peptides: the monomer, oligomer, and fibril. We assume that the oligomeric state is a disordered micelle-like collection of a few peptide chains held together loosely by…
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…
A microscopic model is proposed for the interactions between sickle hemoglobin molecules based on information from the protein data bank. A Monte Carlo simulation of a simplified two patch model is carried out, with the goal of…
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…
We investigate interfacial properties between two highly incompatible polymers of different stiffness. The extensive Monte Carlo simulations of the binary polymer melt yield detailed interfacial profiles and the interfacial tension via an…
This is a summary of mathematical tools we used in research of analyzing the structure of proteins with amyloid form \cite{xi2024Top}. We defined several geometry indicators on the discrete curve namely the hop distance, the discrete…
A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo…
Amyloid fibers are aggregates of proteins. They are built out of a peptide called $\beta$--amyloid (A$\beta$) containing between 41 and 43 residues, produced by the action of an enzyme which cleaves a much larger protein known as the…
We present and study a minimal structure-based model for the self-assembly of peptides into ordered beta-sheet-rich fibrils. The peptides are represented by unit-length sticks on a cubic lattice and interact by hydrogen bonding and…