Inhibition of Aggregation of Amyloid Peptides by Beta-Sheet Breaker Peptides and Their Binding Affinity
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- 作者：Man Hoang Viet ; Son Tung Ngo ; Nguyen Sy Lam ; Mai Suan Li
- 刊名：Journal of Physical Chemistry B
- 出版年：2011
- 出版时间：June 9, 2011
- 年：2011
- 卷：115
- 期：22
- 页码：7433-7446
- 全文大小：1524K
- 年卷期：v.115,no.22(June 9, 2011)
- ISSN：1520-5207
文摘
The effects of beta-sheet breaker peptides KLVFF and LPFFD on the oligomerization of amyloid peptides were studied by all-atom simulations. It was found that LPFFD interferes the aggregation of A尾16鈥?2 peptides to a greater extent than does KLVFF. Using the molecular mechanics-Poisson鈥揃oltzmann surface area (MM-PBSA) method, we found that the former binds more strongly to A尾16鈥?2. Therefore, by simulations, we have clarified the relationship between aggregation rates and binding affinity: the stronger the ligand binding, the slower the oligomerization process. The binding affinity of pentapeptides to full-length peptide A尾1鈥?0 and its mature fibrils has been considered using the Autodock and MM-PBSA methods. The hydrophobic interaction between ligands and receptors plays a more important role for association than does hydrogen bonding. The influence of beta-sheet breaker peptides on the secondary structures of monomer A尾1鈥?0 was studied in detail, and it turns out that, in their presence, the total beta-sheet content can be enhanced. However, the aggregation can be slowed because the beta-content is reduced in fibril-prone regions. Both pentapeptides strongly bind to monomer A尾1鈥?0, as well as to mature fibrils, but KLVFF displays a lower binding affinity than LPFFD. Our findings are in accord with earlier experiments that both of these peptides can serve as prominent inhibitors. In addition, we predict that LPFFD inhibits/degrades the fibrillogenesis of full-length amyloid peptides better than KLVFF. This is probably related to a difference in their total hydrophobicities in that the higher the hydrophobicity, the lower the inhibitory capacity. The GROMOS96 43a1 force field with explicit water and the force field proposed by Morris et al. (Morris et al. J. Comput. Chem. 1998, 19, 1639) were employed for all-atom molecular dynamics simulations and Autodock experiments, respectively.