Figure 1.
Side view of the energy-minimized molecular structure of the (a) part of 4 nm SNPs, (b) part of 11 nm SNPs and (c) different chemical groups (-CH3, -COOH, -NH2, -OH) coated onto 2 nm SNPs.
Figure 2.
The molecular dynamics simulation box of SNPs and enzymes with water.
(a) 4 nm SNP with the enzyme. The box size is 8.0×8.0×8.0 nm3; (b) 11 nm SNP with the enzyme. The box size is 11.0×11.0×8.0 nm3; (c) 2 nm SNP with the enzyme. The box size is 6.0×6.0×10.0 nm3.
Figure 3.
Time evolutions for (a) cytochrome c, (b) RNase A, and (c) lysozyme during 100 ns MD simulations.
The values are the average value from two independent MD simulations.
Figure 4.
Calculated RMSF of Cα atoms vs protein residue number for (a) cytochrome c (103 residues), (b) RNase A (124 residues), and (c) lysozyme (130 residues) during the MD simulation.
A comparison between the RMSF plot for natural structures of proteins, proteins adsorbed onto the surface of 4 nm SNPs, and the proteins adsorbed onto the surface of 11 ns SNPs.
Figure 5.
The structure of cytochrome c adsorbed onto the surface of SNPs.
(a) with 4 nm SNP, (b) with 11 nm SNP. The structures are the conformations after 100 ns MD simulation.
Figure 6.
Structure of RNase A adsorbed onto the surface of SNPs.
(a) with 4 nm SNP, (b) with 11 nm SNP. The structures are the conformations after 100 ns MD simulation.
Figure 7.
Structure of lysozyme adsorbed onto the surface of SNPs.
(a) with 4 nm SNP, (b) with 11 nm SNP. The structures are the conformations after 100 ns MD simulation.
Figure 8.
Comparison of the structure of cytochrome c adsorbed onto different diameter of SNPs.
(a) align the crystal structure (gray) with the structure adsorbed onto 4 nm SNP (blue), (b) align the crystal structure (gray) with the structure adsorbed onto 11 nm SNP (red). The structures are the conformations after 100 ns MD simulation.
Figure 9.
Comparison of the structure of RNase A adsorbed onto different diameter of SNPs.
(a) align the crystal structure (gray) with the structure adsorbed onto 4 nm SNP (blue), (b) align the crystal structure (gray) with the structure adsorbed onto 11 nm SNP (red). The structures are the conformations after 100 ns MD simulation.
Figure 10.
Comparison of the structure of lysozyme adsorbed onto different diameter of SNPs.
(a) align the crystal structure (gray) with the structure adsorbed onto 4 nm SNP (blue), (b) align the crystal structure (gray) with the structure adsorbed onto 11 nm SNP (red). The structures are the conformations after 100 ns MD simulation.
Figure 11.
The active site of cytochrome c after it absorbs onto (a) 4 nm SNP, (b) 11 nm SNP.
The structures are the conformations after 100 ns MD simulation.
Figure 12.
Conformation changes of active site of cytochrome c.
(a) active site of cytochrome c in the crystal structure, (b) active site of cytochrome c after it absorbs onto 4 nm SNP (after 100 ns MD simulation), (c) active site of cytochrome c after it absorbs onto 11 nm SNP (after 100 ns MD simulation).
Figure 13.
The binding mode of TBU (tertiary-butyl alcohol, highlighted in the stick model) in (a) the crystal structure of RNase A, (b) the structure of RNase A adsorbed onto 4 nm SNP (after 100 ns MD simulation), (c) the structure of RNase A adsorbed onto 11 nm SNP (after 100 ns MD simulation).
Figure 14.
Cytochrome c adsorbed onto 2 nm SNPs coated with (a)-CH3, (b)-COOH, (c)-NH2 and (d)-OH.
The structures are the conformations after 100 ns MD simulation.
Figure 15.
Time evolutions for cytochrome c adsorbed onto different chemical groups coated onto silica nano-particles during 100 ns MD simulations.
(a) RMSD of cytochrome c adsorbed onto SNPs coated with -CH3 and with -COOH, (b) RMSD of cytochrome c adsorbed onto SNPs coated with -NH2 and with -OH.
Figure 16.
Conformation changes of active site of cytochrome c.
(a) active site of cytochrome c of the crystal structure, (b) active site of cytochrome c after it adsorbs onto 2 nm SNP coated with -CH3, (c) active site of cytochrome c after it adsorbs onto 2 nm SNP coated with -COOH, (d) active site of cytochrome c after it absorbs onto 2 nm SNP coated with -NH2, (e) active site of cytochrome c after it adsorbs onto 2 nm SNP coated with -OH. The structures of (b), (c), (d), (e) are the conformations after 100 ns MD simulation.