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All-Atom Molecular Dynamics Study of Four RADA 16-I Peptides: The Effects of Salts on Cluster Formation

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Abstract

RADA 16-I is a synthetic amphiphilic peptide, composed of 16 amino acids, designed to self-assemble in a controlled way into fibrils and higher ordered structures depending on solvent condition. This peptide has many applications in tissue engineering and wound healing. We have studied the cluster formation of four RADA 16-I peptide chains in the presence of different concentrations of NaCl and CaCl2 as solvents, using all-atom molecular dynamics simulation. Nine independent simulations over 20 ns were performed. The results show that the fastest cluster formation rate occurs in the presence of 0.2 M NaCl following by water. In these simulations cluster formation doesn’t occur in the presence of CaCl2. It is also found that the cluster formation depends on two solvent-related factors: (a) salt concentration and (b) salt type. The effect of salts may act through changing the compactness and secondary structure of this peptide. In fact NaCl helps each peptide to adopt transitional expanded α-helical conformation in order to induce better interaction sites for self-assembly. The results gave insight into the effect of ionic strength in self-assembly mechanism of RADA 16-I in the bulk solution.

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Authors and Affiliations

  1. Biochemistry-Biophysics Group, Department of Bioscience and Biotechnology, Malek-Ashtar University of Technology, P.O.Box: 16765-3454, Tehran, Iran

    Asieh Aramvash

  2. Chemical Engineering Group, Department of Bioscience and Biotechnology, Malek-Ashtar University of Technology, Tehran, Iran

    Mansooreh Sadat Seyedkarimi

Authors
  1. Asieh Aramvash
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  2. Mansooreh Sadat Seyedkarimi
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Correspondence to Asieh Aramvash.

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Aramvash, A., Seyedkarimi, M.S. All-Atom Molecular Dynamics Study of Four RADA 16-I Peptides: The Effects of Salts on Cluster Formation. J Clust Sci 26, 631–643 (2015). https://doi.org/10.1007/s10876-014-0836-8

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  • DOI: https://doi.org/10.1007/s10876-014-0836-8

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