The effect of the Ala-substitution, the N- and C-terminal capping and the presence of Ca2+, Mg2+ and Zn2+ on the structure of amyloid peptide fragment, Aβ(25-35), and its analog, [Ala31,32,34,35]Aβ(25-35), was studied. One nanosecond NPT molecular dynamics simulation was used to examine the structural stability of the peptides in water. Calculations were performed using the modified GROMOS-87 force field with SPC/E water model, applying the weak temperature and pressure coupling method. During the simulation of the Aβ(25-35) structure, an initial helical structure was destroyed. In Ac-[Ala31,32,34,35]Aβ(25-35)-NHCH3, however, the helix was stable and even more so in the presence of Ca2+, Mg2+ and Zn2+ cations. Between residues 27 and 34, mainly turn/bend and less frequently helix, respectively, characterized the secondary structure of Aβ(25-35) and [Ala31,32,34,35]Aβ(25-35).
All Science Journal Classification (ASJC) codes
- Physical and Theoretical Chemistry
- Computational Theory and Mathematics
- Atomic and Molecular Physics, and Optics