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Atomistic characterization of binding modes and affinity of peptide inhibitors to amyloid-β protein

Frontiers of Chemical Science and Engineering 2014年第4期8卷 433-444页

作者： Fufeng LIU Wenjie DU Yan SUN Jie ZHENG Xiaoyan DONG Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin 300072 China Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China

Abstract The aggregation of amyloid β-protein （Aβ） is tightly linked to the pathogenesis of Alzheimer＇s disease. Previous studies have found that three peptide inhibitors （i.e., KLVFF, VVIA, and LPFFD） can inhibit Aβ aggregation and alleviate Aβ-induced neurotoxicity. How- ever, atomic details of binding modes and binding affinities between these peptide inhibitors and Aβ have not been revealed. Here, using molecular dynamics simulations and molecular mechanics Poisson Boltzmann surface area （MM/PBSA） analysis, we examined the effect of three peptide inhibitors （KLVFF, VVIA, and LPFFD） on their sequence-specific interactions with Aβ and the molecular basis of their inhibition. All inhibitors exhibit varied binding affinity to Aβ, in which KLVFF has the highest binding affinity, whereas LPFFD has the least. MM/PBSA analysis further revealed that different peptide inhibitors have different modes of interaction with Aβ, consequently hotspot binding residues, and underlying driving forces. Specific residue-based interactions between inhibitors and Aβ were determined and compared for illustrating different binding and inhibition mechanisms. This work provides structure-based binding information for further modifica- tion and optimization of these three peptide inhibitors to enhance their binding and inhibitory abilities against Aβ aggregation.

关键词： Alzheimer's disease amyloid β-protein pep-tide inhibitors protein-protein interaction moleculardynamics simulation

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