Folding transition-state and denatured-state ensembles of FSD-1 from folding and unfolding simulations
Article Abstract:
An investigation of the free-energy landscape of FSD-1 protein by a total of four sets of folding and unfolding molecular dynamics simulations with explicit solvent is conducted. Analyses revealed interesting nonnative interactions in the denatured-state ensemble and early-stage folding and the possibility that destabilization of these interactions could help to enhance the stability and folding rate of the protein.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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Fs-21 peptides can form both single helix-turn-helix
Article Abstract:
All atom molecular dynamic simulations are used to investigate the detailed folding processes and mechanisms of two alanine-based peptides, Fs-21 and MABA-Fs. The differences in their folding processes highlight the contribution of the bulky N-terminal MABA group and it was seen that helix-turn-helix conformation was the most stable state at 300 K, instead of the expected full helix conformation.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2004
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Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation
Article Abstract:
The AMBER FF03 all-atom force field (FF03) and a generalized-Born solvation model are used to obtain the folding mechanism of albumin binding domain (ABD) at higher accuracy. The folding of the three studied helix bundle protein followed a diffusion-collision process where substantial formation of the individual helices is critical and preceded the global packing.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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