Human body.MD Trajectory AnalysisThe trajectories of molecular dynamics simulations were analyzed using AMBER [42] and VMD [43] programs. To see the dynamics process of peptide adsorption, the contact number of ?atoms between peptides and NPs with a criterion of 3.5 A over the whole simulation time was calculated. To further probe the interaction between NP and peptides, we Nafarelin web determined the probability distribution of the minimum distance between the side chain of each residue and the nanomaterial surface for the last 50 ns simulation. The STRIDE algorithm [44] was used to compare the impacts of NPs on the secondary structure of IAPP22?28 peptides. Here, the b-sheet size is defined as the number of strands in an n-strands b-sheet, e.g., the b-sheet size of four-strands b-sheet is four. Two chains are considered to form a b-sheet if (i) at least two consecutive residues in each chain visit the b-strand state; (ii) they have at least two inter-peptide H-bonds. One H-bond is taken as formed if the Donor… Acceptor distance is less than 0.35 nm and the Donor-H… Acceptor angle is less than 30u in VMD [43].Materials and Methods Model Built and Molecular Dynamics SimulationsIn our simulations, the IAPP22?8 (NFGAILS) peptides were capped with ACE and NME at two ends. The initial structure of the peptide was generated by a 10 ns molecular dynamics (MD) simulation at 500 K. Three classes of carbon NPs were used to explore their effects on the oligomerization process of disordered IAPP22?8 peptides: graphene (with dimensions of 4.92 nm65.40 nm and 7.13 nm65.40 nm for the tetramer and octamer, respectively), capped (5, 5)-SWCNT (3.69 nm in length and 0.68 nm in diameter), and C60. The atomic coordinates of NPs were provided in the Supporting 47931-85-1 information (Text S1, S2, S3, S4). The disordered IAPP22?8 tetramer and octamer in the absence of NP were also simulated. The initial minimum distance ?between peptides and the NP surfaces is more than 5 A, and we also ensure that the peptides are well separated not contacting with each other at the beginning of the simulations. The detailed setup information including the initial place of NP and peptides together with PBC information for each system can be found in the Supporting Information (Figure S1 and Table S1). Initially, the NPs and peptides were well separated, and the complex systems were then solvated in a rectangular box with periodic boundary conditions, and the minimum distance between the solutes and the box boundary was chosen to be about 0.8 nm as reference [35]. All MD simulations were carried out using the AMBER 10.0 package together with the ff99SB force field [36]. The TIP3P [37] solvent model was used to describe water. 2 fs time step was used to integrate the equations of motion. The long-range electrostatic interactions were treated with the particle mesh Ewald method [38]. A nonbond pair list cutoff of 1.0 nm was used. All bond lengths were constrained by using the SHAKE algorithm [39]. Temperature (310 K) and pressure (1 atm) were controlled by the Berendsen thermostat and barostat [40] with coupling constants of 0.1 and 1.0 ps, respectively. Initial configurations were minimized in three steps, first keeping the peptides fixed, and then only keeping the backbones fixed, and finally keeping all of the molecules free. The systems were warmed up from 0 t o 310 K. Equilibration and subsequent MD stages were carried out without any restrictions on pepetides in the isothermal isobaric (NPT.Human body.MD Trajectory AnalysisThe trajectories of molecular dynamics simulations were analyzed using AMBER [42] and VMD [43] programs. To see the dynamics process of peptide adsorption, the contact number of ?atoms between peptides and NPs with a criterion of 3.5 A over the whole simulation time was calculated. To further probe the interaction between NP and peptides, we determined the probability distribution of the minimum distance between the side chain of each residue and the nanomaterial surface for the last 50 ns simulation. The STRIDE algorithm [44] was used to compare the impacts of NPs on the secondary structure of IAPP22?28 peptides. Here, the b-sheet size is defined as the number of strands in an n-strands b-sheet, e.g., the b-sheet size of four-strands b-sheet is four. Two chains are considered to form a b-sheet if (i) at least two consecutive residues in each chain visit the b-strand state; (ii) they have at least two inter-peptide H-bonds. One H-bond is taken as formed if the Donor… Acceptor distance is less than 0.35 nm and the Donor-H… Acceptor angle is less than 30u in VMD [43].Materials and Methods Model Built and Molecular Dynamics SimulationsIn our simulations, the IAPP22?8 (NFGAILS) peptides were capped with ACE and NME at two ends. The initial structure of the peptide was generated by a 10 ns molecular dynamics (MD) simulation at 500 K. Three classes of carbon NPs were used to explore their effects on the oligomerization process of disordered IAPP22?8 peptides: graphene (with dimensions of 4.92 nm65.40 nm and 7.13 nm65.40 nm for the tetramer and octamer, respectively), capped (5, 5)-SWCNT (3.69 nm in length and 0.68 nm in diameter), and C60. The atomic coordinates of NPs were provided in the Supporting Information (Text S1, S2, S3, S4). The disordered IAPP22?8 tetramer and octamer in the absence of NP were also simulated. The initial minimum distance ?between peptides and the NP surfaces is more than 5 A, and we also ensure that the peptides are well separated not contacting with each other at the beginning of the simulations. The detailed setup information including the initial place of NP and peptides together with PBC information for each system can be found in the Supporting Information (Figure S1 and Table S1). Initially, the NPs and peptides were well separated, and the complex systems were then solvated in a rectangular box with periodic boundary conditions, and the minimum distance between the solutes and the box boundary was chosen to be about 0.8 nm as reference [35]. All MD simulations were carried out using the AMBER 10.0 package together with the ff99SB force field [36]. The TIP3P [37] solvent model was used to describe water. 2 fs time step was used to integrate the equations of motion. The long-range electrostatic interactions were treated with the particle mesh Ewald method [38]. A nonbond pair list cutoff of 1.0 nm was used. All bond lengths were constrained by using the SHAKE algorithm [39]. Temperature (310 K) and pressure (1 atm) were controlled by the Berendsen thermostat and barostat [40] with coupling constants of 0.1 and 1.0 ps, respectively. Initial configurations were minimized in three steps, first keeping the peptides fixed, and then only keeping the backbones fixed, and finally keeping all of the molecules free. The systems were warmed up from 0 t o 310 K. Equilibration and subsequent MD stages were carried out without any restrictions on pepetides in the isothermal isobaric (NPT.
