Related papers: Self-assembly of protein amyloid: a competition be…
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…
The self-assembly of proteins into $\beta$-sheet-rich amyloid fibrils has been observed to occur with sigmoidal kinetics, indicating that the system initially is trapped in a metastable state. Here, we use a minimal lattice-based model to…
We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for…
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 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.…
In the self-assembly process which drives the formation of cellular membranes, micelles, and capsids, a collection of separated subunits spontaneously binds together to form functional and more ordered structures. In this work, we study the…
We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of…
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of…
A variety of neurodegenerative diseases are associated with the formation of amyloid plaques. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Most experimental and…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Proteins can combine into functional elements in living cells or self-assemble into unwanted structures in a number of diseases. The resulting aggregates often display filamentous morphologies across a large range of protein shapes and…
``Seeding'' is the addition of preformed fibrils to a solution of monomeric protein to accelerate its aggregation into new fibrils. It is a versatile and widely-used tool for scientists studying protein aggregation kinetics, as it enables…
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…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…
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…
We propose an exactly solvable simplified statistical mechanical model for the thermodynamics of beta-amyloid aggregation, generalizing a well-studied model for protein folding. The monomer concentration is explicitly taken into account as…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
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…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
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…