Paper Citing NAMD - Abstract
Chen, Xin; Duan, Danhui; Zhu, Shuyan; Liu, Yafang
Dynamics study on the stability of animal prion proteins
TURKISH JOURNAL OF BIOCHEMISTRY-TURK BIYOKIMYA DERGISI, 39:188-195, 2014
Aim: Structural conversion of normal cellular prion protein (PrPc) into the scrapie isoform (PrPsc) is the central event in the development of prion diseases. Materials and Methods: To get more insight into the molecular basis of the stability of animal prion protein, 10 ns molecular dynamics (MD) and flow molecular dynamics (FMD) simulations of turtle prion protein (tPrPc) and bank vole prion protein (bvPrPc) have been performed in this paper. Results: The dynamics and mechanical properties of the two model proteins have been studied. Conclusion: Various motions of beta-sheet appeared in the two proteins, such as twisting, elongation and unfolding. For alpha-helix, it is more readily to unfold in bvPrPc system. Furthermore, the protective wall staggered with helix is found to be strong enough to stabilize PrPc under the shear flow.
