Application of principal component analysis in protein unfolding: an all-atom molecular dynamics simulation study.
We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide-ubiquitin and melittin. To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding. Unfolding of ubiquitin was found to be a three-state process, while that of melittin, though smaller and mostly helical, is more complicated.
Das
Atanu
A
Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Kolkata 700009, India.
Mukhopadhyay
Chaitali
C
D000818:Animals; D016880:Anisotropy; D003198:Computer Simulation; D006801:Humans; D006860:Hydrogen Bonding; D008555:Melitten / Q000737:chemistry*; D025341:Principal Component Analysis; D011489:Protein Denaturation; D017510:Protein Folding; D025801:Ubiquitin / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D025801:Ubiquitin; D014867:Water; D008555:Melitten