Thermodynamics of amyloid formation and the role of intersheet interactions

Irbäck, Anders; Wessén, Jonas

doi:10.1063/1.4930280

Cited by 13 publications

(10 citation statements)

References 66 publications

(97 reference statements)

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“…Indeed, the behavior of C(T ) displayed in Fig. 3(b) for the aggregation transition studied here, i.e., with C − > C + and ∆C < 0, is also supported by numerical simulations of more detailed aggregation models [44][45][46][47]. Even so, our model-independent kinetic approach can be also applied to study the behavior observed for, e.g., protein folding transitions [48], where one may find that [31] ∆C > 0 and ∆γ < 0.…”

supporting

confidence: 75%

Shape-free theory for the self-assembly kinetics in macromolecular systems

Trugilho,

Rizzi

2021

Preprint

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Self-assembly kinetics is usually described by approaches which assume that the shape of the aggregates has a definite form (e.g., spherical, cylindrical, cubic, etc), however that is unlikely to be the case in many finite-sized macromolecular and colloidal systems. Here we consider a simple aggregation model which displays a first-order phase transition in order to illustrate a rate theory based on microcanonical analysis that allows one to obtain a shape-free description of its selfassembly kinetics. Stochastic simulations are performed to validate our approach and demonstrate how the equilibrium thermostatistical properties of the system can be related to the temperaturedependent rate constants. As a model-independent kinetic approach, it may provide experimentalists a reliable method to reconstruct free-energy profiles and microcanonical entropies from kinetic data.

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supporting

confidence: 75%

Shape-free theory for the self-assembly kinetics in macromolecular systems

Trugilho,

Rizzi

2021

Preprint

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“…Here, many questions are still open, and one often considers explicit heteropolymers/peptides or proteins connected to specific problems. In this context, there has been much recent effort, including full atomistic approaches [115], heteropolymer models [62,116,117,118], tube-like homopolymers [119], extended lattice models [120] and even single-site lattice models [121,122,123], to name only a few. Of course, there is a huge amount of molecular dynamics studies.…”

Section: Aggregation Of Dilute Semiflexible Polymersmentioning

confidence: 99%

“…Flexible polymers were shown to exhibit nucleation hierarchies [124] known from droplet formation. An interesting future question is how this analogy carries over to larger system sizes or to the underlying process itself [123,125,126].…”

Section: Aggregation Of Dilute Semiflexible Polymersmentioning

confidence: 99%

Dilute Semiflexible Polymers with Attraction: Collapse, Folding and Aggregation

2016

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Abstract:We review the current state on the thermodynamic behavior and structural phases of self-and mutually-attractive dilute semiflexible polymers that undergo temperature-driven transitions. In extreme dilution, polymers may be considered isolated, and this single polymer undergoes a collapse or folding transition depending on the internal structure. This may go as far as to stable knot phases. Adding polymers results in aggregation, where structural motifs again depend on the internal structure. We discuss in detail the effect of semiflexibility on the collapse and aggregation transition and provide perspectives for interesting future investigations.

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“…The existence of a bad or malfunctioning mechanism by both large and hydrophobic sub-components could indicate a more pronounced global influence of the non-standard residues, but this mechanism is hypothetically possible to occur in other proteins not analyzed yet. The current approach based on two coarse-grained (LS and HP residues) models is suitable in quantitative analyses and when atomic or molecular details can be suppressed or uninterested, but it is rather insufficient for sharper or local measurements, or very specific difference between nonstandard and standard residues, as frequently occur in other applications utilizing coarse-grained models [45][46][47][48]. However, detailed approaches (such as semi-empirical or atomic models) are also limited in many features, since they are very CPU demanding.…”

Section: Non-standard Residues and Molecular Mechanisms In The Targetmentioning

confidence: 99%

Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications

Rocha¹

2017

BMB

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Non-standard amino acids in protein post-translational modifications aid in a wide variety of biological functions and processes, furnishing expansion from the genome to the proteome. First, from structural examinations in unmodified proteins with only standard amino acids, this work empirically obtains numeric relations that reveal how instruction transfers occur between native-state structures. Next, from these relations, the influence of non-standard amino acids inside posttranslationally modified proteins is quantified by successfully predicting the contents of large and hydrophobic residues in helices and β-strands for 210 inspections performed. This suggests a twofold molecular mechanism by the fundamental biophysicochemical properties (residue volume and hydrophobicity), and concludes that the utilized non-standard amino acids have limited global influence at the residue level. Our prediction method provides a better underlying understanding of molecular interactions and mechanisms, and is particularly promising in terms of surveying further modified proteins.

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Thermodynamics of amyloid formation and the role of intersheet interactions

Abstract: The self-assembly of proteins into β-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 explore the ther-

Cited by 13 publications

References 66 publications

Shape-free theory for the self-assembly kinetics in macromolecular systems

Shape-free theory for the self-assembly kinetics in macromolecular systems

Dilute Semiflexible Polymers with Attraction: Collapse, Folding and Aggregation

Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications

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