Cholesterol and Lipid Rafts in the Biogenesis of Amyloid-β Protein and Alzheimer's Disease

GA Pantelopulos, CB Abraham… - Annual Review of …, 2024 - annualreviews.org
Cholesterol has been conjectured to be a modulator of the amyloid cascade, the mechanism
that produces the amyloid-β (Aβ) peptides implicated in the onset of Alzheimer's disease …

Scaling protein–water interactions in the martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments

A Claveras Cabezudo, C Athanasiou… - Journal of Chemical …, 2023 - ACS Publications
Martini 3, the latest version of the widely used Martini force field for coarse-grained
molecular dynamics simulations, is a promising tool to investigate proteins in phospholipid …

A Rigorous Framework for Calculating Protein–Protein Binding Affinities in Membranes

M Blazhynska, JC Gumbart, H Chen… - Journal of Chemical …, 2023 - ACS Publications
Calculating the binding free energy of integral transmembrane (TM) proteins is crucial for
understanding the mechanisms by which they recognize one another and reversibly …

Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane

A Majumder, JE Straub - Journal of Chemical Theory and …, 2024 - ACS Publications
The accurate calculation of equilibrium constants for protein–protein association is of
fundamental importance to quantitative biology and remains an outstanding challenge for …

The role of structural heterogeneity in the homodimerization of transmembrane proteins

A Majumder, JE Straub - The Journal of Chemical Physics, 2023 - pubs.aip.org
The equilibrium association of transmembrane proteins plays a fundamental role in
membrane protein function and cellular signaling. While the study of the equilibrium binding …

Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer

AR Sahoo, PCT Souza, Z Meng, M Buck - Structure, 2023 - cell.com
Structures and dynamics of transmembrane (TM) receptor regions are key to understanding
their signaling mechanism across membranes. Here we examine configurations of TM …

Free-energy landscapes of transmembrane homodimers by bias-exchange adaptively biased molecular dynamics

S Ito, Y Sugita - Biophysical Chemistry, 2024 - Elsevier
Membrane proteins play essential roles in various biological functions within the cell. One of
the most common functional regulations involves the dimerization of two single-pass …

Characterization of the structural and molecular interactions of Ferulic acid ethyl ester with human serum albumin and Lysozyme through multi-methods

W Tong, S Wang, G Chen, D Li, Y Wang, L Zhao… - … Acta Part A: Molecular …, 2024 - Elsevier
Ferulic acid ethyl ester (FAEE) is an essential raw material for the formulation of drugs for
cardiovascular and cerebrovascular diseases and leukopenia. It is also used as a fixed …

Simulation of neurotrophin receptor transmembrane helix interactions reveals active states and distinct signaling mechanisms

C Athanasiou, A Claveras Cabezudo, A Tsengenes… - bioRxiv, 2024 - biorxiv.org
Neurotrophin (NT) receptor signaling regulates neuronal survival, axonal and dendritic
network maintenance, differentiation, and synaptic plasticity. Signaling is initiated by NT …

[HTML][HTML] Transmembrane region dimer structures of Type 1 receptors readily sample alternate configurations: MD simulations using the Martini 3 coarse grained model …

AR Sahoo, PCT Souza, Z Meng… - … (London, England: 1993), 2023 - ncbi.nlm.nih.gov
Determination of the structure and dynamics of transmembrane (TM) regions of single-
transmembrane receptors is key to understanding their mechanism of signal transduction …