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

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Year: 2018
COI code: CBC15_032
Paper Language: English

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

  Mitra Pirhaghi - Institute of Biochemistry & Biophysics (IBB), University of Tehran, Tehran, Iran
  Ali Akbar Saboury - Institute of Biochemistry & Biophysics (IBB), University of Tehran, Tehran, Iran
  Sajjad Gharaghani - Institute of Biochemistry & Biophysics (IBB), University of Tehran, Tehran, Iran
  Ali Akbar Meratan - Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran

Abstract:

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

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Pirhaghi, Mitra; Ali Akbar Saboury; Sajjad Gharaghani & Ali Akbar Meratan, 2018, An Alpha Synuclein- Peptide Docking Study to Select Appropriate Peptides Interacting with the Protein NAC Domain, 14th Conference on Biophysical Chemistry, گرگان, دانشگاه آزاد اسلامي واحد گرگان -انجمن بيوشيمي فيزيك ايران, https://www.civilica.com/Paper-CBC15-CBC15_032.htmlInside the text, wherever referred to or an achievement of this article is mentioned, after mentioning the article, inside the parental, the following specifications are written.
First Time: (Pirhaghi, Mitra; Ali Akbar Saboury; Sajjad Gharaghani & Ali Akbar Meratan, 2018)
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Paper No.: 55951
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