Self-Assembly of Amyloid-Beta (Aβ) Peptides from Solution to Near In Vivo Conditions

PH Nguyen, F Sterpone… - The Journal of Physical …, 2022 - ACS Publications
Understanding the atomistic resolution changes during the self-assembly of amyloid
peptides or proteins is important to develop compounds or conditions to alter the …

Role of conformational dynamics in pathogenic protein aggregation

X Sun, HJ Dyson, PE Wright - Current opinion in chemical biology, 2023 - Elsevier
The accumulation of pathogenic protein oligomers and aggregates is associated with
several devastating amyloid diseases. As protein aggregation is a multi-step nucleation …

Production of Distinct Fibrillar, Oligomeric, and Other Aggregation States from Network Models of Multibody Interaction

EM Diessner, LJ Thomas, CT Butts - Journal of Chemical Theory …, 2024 - ACS Publications
Protein aggregation can produce a wide range of states, ranging from fibrillar structures and
oligomers to unstructured and semistructured gel phases. Recent work has shown that many …

Evolution of large Aβ16–22 aggregates at atomic details and potential of mean force associated to peptide unbinding and fragmentation events

A Iorio, Š Timr, L Chiodo… - Proteins: Structure …, 2023 - Wiley Online Library
Atomic characterization of large nonfibrillar aggregates of amyloid polypeptides cannot be
determined by experimental means. Starting from β‐rich aggregates of Y and elongated …

Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations

LJ Walter, PK Quoika, M Zacharias - Journal of Chemical …, 2024 - ACS Publications
Many biological functions are mediated by large complexes formed by multiple proteins and
other cellular macromolecules. Recent progress in experimental structure determination, as …

Multi-eGO: Model Improvements toward the Study of Complex Self-Assembly Processes

F Bačić Toplek, E Scalone, B Stegani… - Journal of Chemical …, 2023 - ACS Publications
Structure-based models have been instrumental in simulating protein folding and
suggesting hypotheses about the mechanisms involved. Nowadays, at least for fast-folding …

Exploring the misfolding and self-assembly mechanism of TTR (105–115) peptides by all-atom molecular dynamics simulation

Y Zhang, Y Zhu, H Yue, Q Zhao, H Li - Frontiers in Molecular …, 2022 - frontiersin.org
Pathological aggregation of essentially dissociative Transthyretin (TTR) monomers protein,
driven by misfolded and self-interaction, is connected with Amyloid Transthyretin …

Probing the structure–function relationship of proteins with molecular modeling

L Boyens-Thiele, AK Buell, C Schmitt… - Functionality of Plant …, 2024 - Elsevier
Proteins are complex biopolymers responsible for key functions in plant, microbial, fungal,
and animal organisms. Due to the variability induced by the chemical composition of the 20 …

The Scope and Limitations of In Vivo and In Silico Models of Cardiac Amyloidosis

S Morozkina, P Snetkov, M Uspenskaya - Engineering Proceedings, 2023 - mdpi.com
Amyloidosis is a systemic disease, leading to the disfunction of many organs. There are
several clinical and morphological forms of amyloidosis based on the organ-specific nature …

Estimation of ligand binding free energy using multi-eGO.

B Stegani, E Scalone, FB Toplek, T Lohr, S Gianni… - 2024 - chemrxiv.org
The computational study of the binding of a ligand to a target protein provides mechanistic
insight into the molecular determinants of this process and can improve the success rate of …