A combination of φ/ψ dihedral order parameters, essential dynamics and fuzzy clustering of trajectories was used to investigate the presence of domain movement consistent with the mitten model in the peptides murine epidermal growth factor (mEGF), human epidermal growth factor (hEGF) and human transforming growth factor-alpha (hTGF-α). Local decreases in the φ/ψ dihedral order parameters identified Val35and Gly36 in hEGF and Val33and Cys34 in hTGF-α as possible hinge residues. Essential dynamics analysis characterized domain movement in hEGF and hTGF-α. The domain movement in hEGF involved Val35 and Gly36 as hinge residues and in hTGF-α, Val33 and Cys34. The fuzzy clustering of hEGF and hTGF-α trajectories resulted in two clusters that showed domain movement and involved the same hinge residues as identified by φ/ψ dihedral order parameters and characterized by the essential dynamics analysis. mEGF had no local decrease in the φ/ψ dihedral order parameters in the region of the proposed hinge residue. Essential dynamics showed only minor gaussian fluctuations within the peptide. Fuzzy clustering identified two clusters with minor variations in backbone conformation. hTGF-α is the only peptide that demonstrated domain movement consistent with the mitten model.
All Science Journal Classification (ASJC) codes
- Condensed Matter Physics
- Physical and Theoretical Chemistry