Molecular Dynamics Study To Investigate the Effect of Chemical Substitutions of Methionine 35 on the Secondary Structure of the Amyloid β (Aβ(1−42)) Monomer in Aqueous Solution

2008 ◽  
Vol 112 (7) ◽  
pp. 2159-2167 ◽  
Author(s):  
Luciano Triguero ◽  
Rajiv Singh ◽  
Rajeev Prabhakar
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Secondary Structure ◽  
Amyloid Β ◽  
Methionine 35

Molecular Dynamics Study on an Adipokinetic Hormone Peptide in Aqueous Solution

2000 ◽  
Vol 55 (1-2) ◽  
pp. 125-128 ◽  
Author(s):  
Igor Z. Zubrzycki
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Secondary Structure ◽  
Room Temperature ◽  
Dynamics Simulation ◽  
Red Pigment ◽  
Adipokinetic Hormone ◽  
Extended Conformation ◽  
Flying Insects

Lom-AKH-I is a member of the adipokinetic hormone/ red pigment concentrating hormone (AKH / RPCH) family of peptides found in flying insects. A molecular dynamics simulation at room temperature (293 K) in water has been performed to survey the folding path of the Lom-AKH-I peptide in water and to establish the secondary structure of Lom-AKH-I. The obtained results indicate the presence of an undefined extended conformation.

scholarly journals Remarked Suppression of Aβ 42 Protomer-Protomer Dissociation Reaction Elucidated by Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Ikuo Kurisaki ◽  
Shigenori Tanaka
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Amyloid Fibrils ◽  
Protein Complexes ◽  
Amyloid Β ◽  
Dynamics Simulation ◽  
Physicochemical Condition ◽  
Technical Limitation ◽  
Amyloid Fibril Formation ◽  
Dynamics Simulations

Multimeric protein complexes are molecular apparatuses to regulate biological systems and often determine their fate. Among proteins forming such molecular assemblies, amyloid proteins have drawn attention over a half-century since amyloid fibril formation of these proteins is supposed to be a common pathogenic cause for neurodegenerative diseases. This process is triggered by the accumulation of fibril-like aggregates, while the microscopic mechanisms are mostly elusive due to technical limitation of experimental methodologies in individually observing each of diverse aggregate species in the aqueous solution. We then addressed this problem by employing atomistic molecular dynamics simulations for the paradigmatic amyloid protein, amyloid-β (1-42) (Aβ ). Seven different dimeric forms of oligomeric Aβ fibril-like aggregate in aqueous solution, ranging from tetramer to decamer, were considered. We found additive effects of the size of these fibril-like aggregates on their thermodynamic stability and have clarified kinetic suppression of protomer-protomer dissociation reactions at and beyond the point of pentamer dimer formation. This observation was obtained from the specific combination of the Aβ protomer structure and the physicochemical condition that we here examined, while it is worthwhile to recall that several amyloid fibrils take dimeric forms of their protomers. We could thus conclude that the stable formation of fibril-like protomer dimer should be involved in a turning point where rapid growth of amyloid fibrils is triggered.

Dimerization of the Full-Length Alzheimer Amyloid β-Peptide (Aβ42) in Explicit Aqueous Solution: A Molecular Dynamics Study

2012 ◽  
Vol 116 (15) ◽  
pp. 4405-4416 ◽  
Author(s):  
Xiaoxia Zhu ◽  
Ram Prasad Bora ◽  
Arghya Barman ◽  
Rajiv Singh ◽  
Rajeev Prabhakar
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Amyloid Β ◽  
Full Length ◽  
Amyloid Β Peptide

Molecular Dynamics Study of Aqueous Solution of Polyethylene Oxide: Critical Test of Force Field Models

2013 ◽  
Vol 11 (4) ◽  
pp. 371-383 ◽  
Author(s):  
Yong-Lei Wang ◽  
Rochelle S. Lawrence ◽  
Zhong-Yuan Lu ◽  
Aatto Laaksonen
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Force Field ◽  
Polyethylene Oxide ◽  
Critical Test
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