Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease

2022 ◽  
Vol 72 ◽  
pp. 103-113
Author(s):  
William Martin ◽  
Gloria Sheynkman ◽  
Felice C. Lightstone ◽  
Ruth Nussinov ◽  
Feixiong Cheng
Keyword(s):  
Artificial Intelligence ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

Destabilization of Alzheimer’s Aβ42 protofibrils with acyclovir, carmustine, curcumin, and tetracycline: Insights from molecular dynamics simulations

2021 ◽  
Author(s):  
Ishrat Jahan ◽  
Shahid M Nayeem
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Dynamics ◽  
Neurodegenerative Diseases ◽  
Molecular Dynamics Simulations ◽  
Amyloid Β ◽  
Neural Tissue ◽  
Amyloid Β Peptide ◽  
Characteristic Symptom ◽  
Dynamics Simulations

One of the most common dementia among neurodegenerative diseases is Alzheimer’s disease (AD). The characteristic symptom of AD is the deposition and aggregation of amyloid-β-peptide in the neural tissue. A...

scholarly journals Amylin–Aβ oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease

2016 ◽  
Vol 18 (4) ◽  
pp. 2330-2338 ◽  
Author(s):  
Michal Baram ◽  
Yoav Atsmon-Raz ◽  
Buyong Ma ◽  
Ruth Nussinov ◽  
Yifat Miller
Keyword(s):  
Alzheimer’S Disease ◽  
Type 2 Diabetes ◽  
Alzheimer's Disease ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Layer ◽  
Atomic Resolution ◽  
Aβ Oligomers ◽  
Dynamics Simulations

Aβ1–42 oligomers prefer to interact with Amylin1–37 oligomers to form single layer conformations.

scholarly journals Out-of-Register Aβ42 Assemblies as Models for Neurotoxic Oligomers and Fibrils

2017 ◽  
Author(s):  
Wenhui Xi ◽  
Elliott K. Vanderford ◽  
Ulrich H.E. Hansmann
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amyloid Formation ◽  
Explicit Solvent ◽  
The Stability ◽  
Dynamics Simulations ◽  
Nmr Signals

ABSTRACTWe propose a variant of the recently found S-shaped Aβ1‒42-motif that is characterized by out-of-register C-terminal β-strands. We show that chains with this structure can not only form fibrils that are compatible with the NMR signals, but also barrel-shaped oligomers that resemble the ones formed by the much smaller cylindrin peptides. Running at physiological temperatures long all-atom molecular dynamics simulations with an explicit solvent, we study the stability of these constructs and show that they are plausible models for neurotoxic oligomers. Analyzing the transitions between different assemblies we suggest a mechanism for amyloid formation in Alzheimer’s disease.

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