An Alpha Synuclein- Peptide Docking Study to Select Appropriate Peptides Interacting with the Protein NAC Domain

α-synuclein (AS) is one of the presynaptic intrinsically disordered proteins. However, the change in environmental factors (such as pH, ionic strength, severe shaking) induces the formation of AS aggregations and amyloid fibrils in vitro. Lewy bodies are aggregates that are seen in Parkinson s patients. The main component of the Lewy bodies are the amyloid fibers of AS. The exact function of this protein and the mechanisms that cause toxicity and cell death are still not well defined. Inhibition AS aggregations may be an approach to preventing and treating Parkinson s disease. A number of polyphenol antioxidants have been discovered that inhibit AS fibers. However, their effects are non-specific. Generally, protein-protein interactions are highly specific and well-regulated. In this study, we attempted to design using computational methods and synthesize a new peptide according to AS sequence 68-83, and its inhibitory effects on AS accumulations will be examined. Approximately 78 modified linear peptides were designed in sequences AS (68-83). The circular forms of these peptides (N to C terminal cyclization) were also considered. The protein-peptide docking with the HADDOCK web server performed on these linear and circular peptides and their binding energy and interaction with the protein were determined. Based on HADDOCK scores, RMSD and Pose, the proper linear and cyclic peptides were selected and will be synthesized. A scramble peptide with similar amino acid composition with different sequence will be synthesized to examine the significance of the sequence in the future.

Keywords:

Alpha synuclein , Parkinson s disease , HADDOCK , Peptide- based inhibitors