scholarly journals In Silico Protein Folding Simulation of Amyloid A4 Peptide

2012 ◽  
Vol 8 (4) ◽  
Author(s):  
Fatahiya Mohamed Tap ◽  
Nurul Bahiyah Ahmad Khairudin
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Protein Folding ◽  
Magnetic Resonance ◽  
In Silico ◽  
Md Simulation ◽  
Nmr Structure ◽  
Folding Simulation ◽  
Folding Pathways ◽  
Nuclear Magnetic

The objective of this study is to investigate the folding pathways of Amyloid A4 peptide (PDB ID: 1AML). The structure and trajectories of this protein has been studied using Molecular Dynamics (MD) simulation. The simulation was run at 300K for 50nsec. The model at 2nsec was aligned to the Nuclear Magnetic Resonance (NMR) structure with the RMSD value of 7.85Å for the overall structure. It was found that the 3_10_helix started to form (ILE32 GLY33 LEU34 MET35) at 4nsec until 7nsec.

scholarly journals Structure and Dynamics of Spider Silk Studied with Solid-State Nuclear Magnetic Resonance and Molecular Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (11) ◽  
pp. 2634
Author(s):  
Tetsuo Asakura
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Solid State ◽  
Magnetic Resonance ◽  
Solid State Nmr ◽  
Md Simulation ◽  
Isotope Labeling ◽  
Dynamics Simulation ◽  
Structure And Dynamics ◽  
Nuclear Magnetic

This review will introduce very recent studies using solid-state nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulation on the structure and dynamics of spider dragline silks conducted by the author’s research group. Spider dragline silks possess extraordinary mechanical properties by combining high tensile strength with outstanding elongation before breaking, and therefore continue to attract attention of researchers in biology, biochemistry, biophysics, analytical chemistry, polymer technology, textile technology, and tissue engineering. However, the inherently non-crystalline structure means that X-ray diffraction and electron diffraction methods provide only limited information because it is difficult to study the molecular structure of the amorphous region. The most detailed picture of the structure and dynamics of the silks in the solid state experimentally have come from solid-state NMR measurements coupled with stable isotope labeling of the silks and the related silk peptides. In addition, combination of solid-state NMR and MD simulation was very powerful analytical tools to understand the local conformation and dynamics of the spider dragline silk in atomic resolution. In this review, the author will emphasize how solid-state NMR and MD simulation have contributed to a better understanding of the structure and dynamics in the spider dragline silks.

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