Expanded ensemble and replica exchange methods for simulation of protein-like systems

2003 ◽  
Vol 119 (22) ◽  
pp. 11998-12010 ◽  
Author(s):  
Michael K. Fenwick ◽  
Fernando A. Escobedo
Keyword(s):  
Replica Exchange ◽  
Expanded Ensemble

scholarly journals A generalized linear response framework for expanded ensemble and replica exchange simulations

2018 ◽  
Vol 149 (7) ◽  
pp. 072315 ◽  
Author(s):  
Brian K. Radak ◽  
Donghyuk Suh ◽  
Benoît Roux
Keyword(s):  
Linear Response ◽  
Replica Exchange ◽  
Expanded Ensemble

Computational Investigations of the Transmembrane Italian-Mutant (E22K) 3A\(\beta_{11 - 40}\) in Aqueous Solution

2018 ◽  
Vol 28 (3) ◽  
pp. 265 ◽  
Author(s):  
Son Tung Ngo
Keyword(s):  
Structural Changes ◽  
Replica Exchange ◽  
Aβ Oligomers ◽  
Replica Exchange Molecular Dynamics ◽  
Charged Residue ◽  
Intermolecular Contacts ◽  
Structural Details ◽  
Positively Charged ◽  
Dynamic Fluctuation ◽  
Good Agreement

The Amyloid beta (Aβ) oligomers are characterized as critical cytotoxic materials in Alzheimer’s disease (AD) pathogenesis. Structural details of transmembrane oligomers are inevitably necessary to design/search potential inhibitor due to treat AD. However, the experimental detections for structural modify of low-order Aβ oligomers are precluded due to the extremely dynamic fluctuation of the oligomers. In this project, the transmembrane Italian-mutant (E22K) 3Aβ11-40 (tmE22K 3Aβ11-40) was extensively investigated upon the temperature replica exchange molecular dynamics (REMD) simulations. The structural changes of the trimer when replacing the negative charged residue E22 by a positively charged residue K were monitored over simulation intervals. The oligomer size was turned to be larger and the increase of β-content was recorded. The momentous gain of intermolecular contacts with DPPC molecules implies that tmE22K 3Aβ11-40 easier self-inserts into the membrane than the WT one. Furthermore, the tighter interaction between constituting monomers was indicated implying that the E22K mutation probably enhances the Aβ fibril formation. The results are in good agreement with experiments that E22K amyloid is self-aggregate faster than the WT form. Details information of tmE22K trimer structure and kinetics probably yield the understanding of AD mechanism.

The enhanced sampling in parallel finite-time dynamics method with replica exchange

2021 ◽  
Vol 263 ◽  
pp. 107911
Author(s):  
Chudong Xu ◽  
Shengdong Lu ◽  
Yongfeng Kong ◽  
Wanjie Xiong
Keyword(s):  
Finite Time ◽  
Replica Exchange ◽  
Enhanced Sampling ◽  
Time Dynamics ◽  
Dynamics Method

Molecular Mechanism of Amyloidogenicity and Neurotoxicity of a Pro-aggregated Tau Mutant in the Presence of Histidine Tautomerism via Replica-Exchange Simulation.

2021 ◽  
Author(s):  
Sompriya Chatterjee ◽  
Abbas Salimi ◽  
Jin Yong Lee
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Mechanism ◽  
Replica Exchange

The accumulation of ΔK280 tau mutant resulting in neurotoxic oligomeric aggregates is an important but yet mysterious procedure in Alzheimer’s disease (AD) development. Recently, we proposed a histidine tautomerization hypothesis...

Solution Study of Engineered Quartz Binding Peptides Using Replica Exchange Molecular Dynamics

2010 ◽  
Vol 11 (12) ◽  
pp. 3266-3274 ◽  
Author(s):  
Rebecca Notman ◽  
E. Emre Oren ◽  
Candan Tamerler ◽  
Mehmet Sarikaya ◽  
Ram Samudrala ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Solution Study ◽  
Binding Peptides
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