All-Atom Molecular Dynamicsstudy of Four RADA 16-I Peptides: the Effects of Salts on Cluster

All-atom molecular dynamicsstudy of four RADA 16-I peptides: the effects of salts on cluster formation

Asieh Aramvash*a, Mansooreh Seyed karimib

a*Asieh aramvash, Biochemistry-Biophysics Group, Department of Bioscience and Biotechnology, Malek-Ashtar Universityof Technology, Tehran, Iran.

bMansooreh seyed karimi, Chemical Engineering Group, Department of Bioscience and Biotechnology, Malek-Ashtar Universityof Technology, Tehran, Iran.

*Correspondence: Asieh Aramvash, Biochemistry-Biophysics Group, Department of Bioscience and Biotechnology, Malek-Ashtar Universityof Technology, Tehran, Iran, Email: , P.O.Box: 16765-3454, Tehran, Iran, Phone: (+9821)22970165, Fax: (+9821)22974612.

Results and discussion

Center of mass of peptide chains

Fig. S1 shows that the four peptidesfused rapidly toforma completecluster until 2.5 ns in 0.2 M NaCl. Fig S2 (in 0.5 M NaCl) shows that peptides 1 and 4 first move closer to each other to form a pair by the time t= 2.5 ns,then they moved away from each other quickly.Finally, all four peptides join until t=10 ns and form four peptide cluster and distance between their center of mass become stabilize. In Fig. S3 the peptides form pairs and two pairs (1,3 and 2,4) of peptides have formed by t= 5 ns. The pairs are stable and can not come closer to each other, but they will most likely form a cluster of four peptides if the simulation time were to be extended. Fig. S4 shows that a stabilized peptide pair (2 and 3) form at 2.5 ns and after 10 ns peptide 4 join to the cluster and form three peptide cluster. In simulation 7 (Fig. S5) peptides 1 and 2 have moved closer to each other compared to their initial positions by t=7 ns and this distance become stable in the rest of simulation. Fig. S6 shows that peptides 1, 3 and 4 make contact to each other and the distance between their center of mass decrease in 16 ns and this distance become stable. Fig. S7 shows that peptides 1 and 4 in time more than 15 ns come incloseproximity toeach other and maintained their distance and peptides 2 and 3 at approximately 10 ns come near to each other and make a weak bond through a slow and gradual approach. Fig S8 showsthe peptides 1 and 2 gradually come closer, and begin to form a pair by t=15 ns and peptides 3 and 4 form another pair at approximately 5 ns. These peptides remain in the pair status for the rest of the simulation. Fig. S9 shows cluster formation in the water at approximately 10 ns. Actually this cluster form by combining two peptide pair (3, 4 and 1, 2) and confirm the tendency of cluster formation even in water. The rate of approach was fastest in the case of 0.2 M NaCl (simulation 3) followed by water (simulation 1). In simulation 3 from the first moments electrostatic or hydrogen bonding potential from different group make the cluster formation possible.

Figure S1: The distances between the centers of mass of each pair peptide in 0.2 M NaCl. DCMR: Distance between Center of Masses of RADA 16-I.

Figure S2:The distances between the centers of mass of each pair peptide in 0.5 M NaCl. DCMR: Distance between Center of Masses of RADA 16-I.

Figure S3: The distances between the centers of mass of each pair peptide in 0.7 M NaCl. DCMR: Distance between Center of Masses of RADA 16-I.

Figure S4: The distances between the centers of mass of each pair peptide in 1 M NaCl. DCMR: Distance between Center of Masses of RADA 16-I.

Figure S5: The distances between the centers of mass of each pair peptide in 0.2 M CaCl2. DCMR: Distance between Center of Masses of RADA 16-I.

Figure S6:The distances between the centers of mass of each pair peptide in 0.5 M CaCl2. DCMR: Distance between Center of Masses of RADA 16-I.

Figure S7: The distances between the centers of mass of each pair peptide in 0.7 M CaCl2. DCMR: Distance between Center of Masses of RADA 16-I.

Figure S8: The distances between the centers of mass of each pair peptide in 1 M CaCl2. DCMR: Distance between Center of Masses of RADA 16-I.

Figure S9: The distances between the centers of mass of each pair peptide in water. DCMR: Distance between Center of Masses of RADA 16-I.