Related papers: The Relation Between {\alpha}-Helical Conformation…
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…
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…
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…
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…
The formation of amyloid fibrils comprising amyloid $\beta$ (A$\beta$) peptides is associated with the pathology of Alzheimer's disease. In this study, we theoretically investigated the A$\beta$ structure at the fibril end using the density…
Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. Yet it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils, or just a dangerous by-product.…
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…
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…
Protein amyloidosis is a cytopathological process characterized by the formation of highly beta-sheet-rich fibrils. How this process occurs and how to prevent/treat the associated diseases are not completely understood. Here, we carry out a…
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…
Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…
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…
The presence of oligomeric aggregates, which is often observed during the process of amyloid formation, has recently attracted much attention since it has been associated with neurodegenerative conditions such as Alzheimer's and Parkinson's…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
Protein aggregates exhibit diverse morphology, exemplified by amyloid fibrils, gel-like structures, and liquid-like condensates. Differences in the morphologies in identical proteins play important functional roles in several diseases.…
Elongation is a fundament process in amyloid fiber growth, which is normally characterized by a linear relationship between the fiber elongation rate and the monomer concentration. However, in high concentration regions, a sub-linear…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
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…