caa a22 4500 606182330 CHVBK 20210128100815.0 cr unu---uuuuu 210128e20150301xx s 000 0 eng 10.1007/s10876-014-0836-8 doi (NATIONALLICENCE)springer-10.1007/s10876-014-0836-8 All-Atom Molecular Dynamics Study of Four RADA 16-I Peptides: The Effects of Salts on Cluster Formation [Elektronische Daten] [Asieh Aramvash, Mansooreh Seyedkarimi] 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 20ns were performed. The results show that the fastest cluster formation rate occurs in the presence of 0.2M 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. Springer Science+Business Media New York, 2015 Peptide cluster nationallicence Molecular dynamics simulation nationallicence RADA 16-I nationallicence Self-assembly nationallicence Salts nationallicence Aramvash Asieh Biochemistry-Biophysics Group, Department of Bioscience and Biotechnology, Malek-Ashtar University of Technology, P.O.Box: 16765-3454, Tehran, Iran aut Seyedkarimi Mansooreh Chemical Engineering Group, Department of Bioscience and Biotechnology, Malek-Ashtar University of Technology, Tehran, Iran aut Journal of Cluster Science Springer US; http://www.springer-ny.com 26/2(2015-03-01), 631-643 1040-7278 26:2<631 2015 26 10876 https://doi.org/10.1007/s10876-014-0836-8 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s10876-014-0836-8 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Aramvash Asieh Biochemistry-Biophysics Group, Department of Bioscience and Biotechnology, Malek-Ashtar University of Technology, P.O.Box: 16765-3454, Tehran, Iran aut NATIONALLICENCE 700 1- Seyedkarimi Mansooreh Chemical Engineering Group, Department of Bioscience and Biotechnology, Malek-Ashtar University of Technology, Tehran, Iran aut NATIONALLICENCE 773 0- Journal of Cluster Science Springer US; http://www.springer-ny.com 26/2(2015-03-01), 631-643 1040-7278 26:2<631 2015 26 10876