Molecular dynamics simulations reveal the mechanism of graphene oxide nanosheet inhibition of Aβ1–42 peptide aggregation

2019 ◽  
Vol 21 (21) ◽  
pp. 10981-10991 ◽  
Author(s):  
Yibo Jin ◽  
Yunxiang Sun ◽  
Yujie Chen ◽  
Jiangtao Lei ◽  
Guanghong Wei
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Graphene Oxide ◽  
Molecular Dynamics Simulations ◽  
Salt Bridge ◽  
Graphene Oxide Nanosheets ◽  
Peptide Interactions ◽  
Graphene Oxide Nanosheet ◽  
Dynamics Simulations ◽  
Β Sheet

Graphene oxide nanosheets inhibit Aβ1–42 aggregation by weakening inter-peptide interactions and reducing β-sheet contents mostly via salt bridge, hydrogen bonding and cation–π interactions with charged residues.

Characterization of a graphene oxide/poly(acrylic acid) nanocomposite by means of molecular dynamics simulations

RSC Advances ◽  
2016 ◽  
Vol 6 (111) ◽  
pp. 109267-109277 ◽  
Author(s):  
Kostas Karatasos ◽  
Georgios Kritikos
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Graphene Oxide ◽  
Thermal Properties ◽  
Acrylic Acid ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Poly Acrylic Acid

Graphene oxide/poly(acrylic acid) nanocomposite: static, dynamic, thermal properties and hydrogen bonding, as studied by molecular dynamics simulations.

Confinement effects of graphene oxide nanosheets on liquid–solid phase transition of water

RSC Advances ◽  
2015 ◽  
Vol 5 (118) ◽  
pp. 97446-97457 ◽  
Author(s):  
Meymanat Zokaie ◽  
Masumeh Foroutan
Keyword(s):  
Phase Transition ◽  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Transition Temperature ◽  
Molecular Dynamics Simulations ◽  
Phase Transition Temperature ◽  
Solid Phase ◽  
Graphene Oxide Nanosheets ◽  
Solid Phase Transition ◽  
Dynamics Simulations

In this work, the liquid–solid phase transition temperature of water confined between two graphene oxide (GO) sheets is investigated using molecular dynamics simulations.

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid State ◽  
Crystalline State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Linear Alcohols ◽  
Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

scholarly journals Structural Influence and Interactive Binding Behavior of Dopamine and Norepinephrine on the Greek-Key-Like Core of α-Synuclein Protofibril Revealed by Molecular Dynamics Simulations

Processes ◽  
2019 ◽  
Vol 7 (11) ◽  
pp. 850
Author(s):  
Yu Zou ◽  
Zhiwei Liu ◽  
Zhiqiang Zhu ◽  
Zhenyu Qian
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Therapeutic Strategy ◽  
Binding Capacity ◽  
Salt Bridges ◽  
Drug Candidates ◽  
Binding Behavior ◽  
Dynamics Simulations ◽  
Structural Influence ◽  
Β Sheet

The pathogenesis of Parkinson’s disease (PD) is closely associated with the aggregation of α-synuclein (αS) protein. Finding the effective inhibitors of αS aggregation has been considered as the primary therapeutic strategy for PD. Recent studies reported that two neurotransmitters, dopamine (DA) and norepinephrine (NE), can effectively inhibit αS aggregation and disrupt the preformed αS fibrils. However, the atomistic details of αS-DA/NE interaction remain unclear. Here, using molecular dynamics simulations, we investigated the binding behavior of DA/NE molecules and their structural influence on αS44–96 (Greek-key-like core of full length αS) protofibrillar tetramer. Our results showed that DA/NE molecules destabilize αS protofibrillar tetramer by disrupting the β-sheet structure and destroying the intra- and inter-peptide E46–K80 salt bridges, and they can also destroy the inter-chain backbone hydrogen bonds. Three binding sites were identified for both DA and NE molecules interacting with αS tetramer: T54–T72, Q79–A85, and F94–K96, and NE molecules had a stronger binding capacity to these sites than DA. The binding of DA/NE molecules to αS tetramer is dominantly driven by electrostatic and hydrogen bonding interactions. Through aromatic π-stacking, DA and NE molecules can bind to αS protofibril interactively. Our work reveals the detailed disruptive mechanism of protofibrillar αS oligomer by DA/NE molecules, which is helpful for the development of drug candidates against PD. Given that exercise as a stressor can stimulate DA/NE secretion and elevated levels of DA/NE could delay the progress of PD, this work also enhances our understanding of the biological mechanism by which exercise prevents and alleviates PD.

Molecular dynamics simulations of Aβ fibril interactions with β-sheet breaker peptides

Peptides ◽  
2010 ◽  
Vol 31 (11) ◽  
pp. 2100-2108 ◽  
Author(s):  
Neil J. Bruce ◽  
Deliang Chen ◽  
Shubhra G. Dastidar ◽  
Gabriel E. Marks ◽  
Catherine H. Schein ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Β Sheet
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