Coupling of the non-amyloid-component (NAC) domain and the KTK(E/Q)GV repeats stabilize the α-synuclein fibrils

Liang Xu, Ruth Nussinov, Buyong Ma

Research output: Contribution to journalArticlepeer-review

Abstract

The aggregates of α-synuclein (αS) are a major pathological hallmark of Parkinson's disease (PD) making their structure-function relationship important for rational drug design. Yet, the atomic structure of the αS aggregates is unavailable, making it difficult to understand the underlying aggregation mechanism. In this work, based on available experimental data, we examined plausible molecular structures of αS(20/30–110) fibrils for the first time by employing computational approaches. The optimized structure was used to investigate possible interactions with aggregation inhibitors. Our structural models characterize the essential properties of the five-layered fold of the αS fibril. The distribution of the β-strands and the topology of the five β-strands in the relatively stable models are in good agreement with experimental values. In particular, we find that the KTK(E/Q)GV repeat motifs significantly stabilize the αS fibrils. The charged residues within each repeat prefer exposure to the solvent in order to further stabilize the inter-layered interactions by salt-bridges. The organization of the repeat K58T59K60E61Q62V63between the β2 and β3 layers significantly affects the stability of the non-amyloid-component (NAC) domain. The coupling between the NAC domain and the KTKEGV repeats indicates that both regions can be potential binding sites for inhibitor design. The distinct binding modes of chemical agents that alter αS aggregation highlight the potential of our models in inhibitor design.

Original languageEnglish
Pages (from-to)841-850
Number of pages10
JournalEuropean Journal of Medicinal Chemistry
Volume121
DOIs
StatePublished - 2016

Keywords

  • Alpha-synuclein
  • Drug design
  • Fibril structure
  • Molecular dynamics
  • Parkinson's disease

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