
doi: 10.1021/jp300074f
pmid: 22417236
We have carried out all-atom action-derived molecular dynamics (ADMD) folding simulations of the full-size FSD-1. FSD-1 is a designed mini-protein of 28 residues containing both α and β secondary structure elements. Multiple folding pathways are found for FSD-1, which is consistent with existing computational studies. Hydrophobic collapse is observed first, and then subsequent folding events proceeds by forming either α-helix or β-hairpin. Concurrent formation of the full tertiary structure and the secondary structure elements of α-helix and β-hairpin is observed. The folding pathway of FSD-1 elucidated by ADMD simulations does not follow the scenario of the framework model. ADMD simulations provide significant insights for the general mechanisms of protein folding and conformational changes.
DNA-Binding Proteins, Models, Molecular, Protein Folding, Molecular Dynamics Simulation, Protein Structure, Secondary, Transcription Factors
DNA-Binding Proteins, Models, Molecular, Protein Folding, Molecular Dynamics Simulation, Protein Structure, Secondary, Transcription Factors
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