Chem. J. Chinese Universities ›› 2015, Vol. 36 ›› Issue (11): 2171.doi: 10.7503/cjcu20150546
• Physical Chemistry • Previous Articles Next Articles
GUO Kai, ZHANG Heng, SUN Jichao, YUAN Shiling*(), LIU Chengbu
Received:
2015-07-14
Online:
2015-11-10
Published:
2015-10-12
Contact:
YUAN Shiling
E-mail:shilingyuan@sdu.edu.cn
Supported by:
CLC Number:
TrendMD:
GUO Kai, ZHANG Heng, SUN Jichao, YUAN Shiling, LIU Chengbu. Molecular Dynamics Simulation on Self-Assembly of Fmoc-FF Dipeptide†[J]. Chem. J. Chinese Universities, 2015, 36(11): 2171.
Fig.2 Views of the configurations at different time(A—E) and top view of configuration at 50 ns(F) Time/ns: (A) 0; (B) 1; (C) 5; (D) 30; (E) 50. Orange represents the fluorenyl group of Fmoc, blue is the peptide chain, and gray is the benzene ring of peptide chain. Fmoc-FF molecules are represented by CPK pattern. Water molecules are represented by red and white lines.
Fig.4 Non-normalized RDF plot of distance between fluorenyl rings(A) and MD simulation of π-π stacking of the aggregate after 50 ns(B) Water molecules are omitted to show the structure clearly.
Fig.5 Overall interaction energy and the decomposed VDW, Coulomb and hydrogen bond terms (A) The whole interaction energy of dipeptide and water molecules. a. Peptide-peptide; b. peptide-H2O. (B) The individual interaction energy between different parts of Fmoc-FF dipeptide. a. Fmoc-Fmoc; b. Fmoc-Chain; c. Chain-Chain; d. Ben-Ben; e. Ben-Chain; f. Ben-Fmoc. All data are averaged using the last 20 ns MD simulations.
Fig.7 Views of water bridge structure (A) Dipeptides formed water bridge through one water molecule; (B) dipeptides formed water bridge by two water molecules.
Certain atoms of Fmoc-FF dipeptide | 105Diffusion coefficient(cm2·s-1) | Residence time, τr/ps |
---|---|---|
O1, O3 | 3.87 | 7.09 |
O4 | 4.27 | 9.52 |
O2, O5 | 2.91 | 10.65 |
N1 | 4.42 | 1.71 |
N2 | 4.58 | 1.43 |
Table 1 Dynamic properties of water around certain atoms of Fmoc-FF dipeptide
Certain atoms of Fmoc-FF dipeptide | 105Diffusion coefficient(cm2·s-1) | Residence time, τr/ps |
---|---|---|
O1, O3 | 3.87 | 7.09 |
O4 | 4.27 | 9.52 |
O2, O5 | 2.91 | 10.65 |
N1 | 4.42 | 1.71 |
N2 | 4.58 | 1.43 |
Fig.9 Illustration of definition of Pi Pi(t1)=1 when water molecule in the first shell at t0 and t1.The location of water molecule during t0—t1 does not count.
Atom type | Number of hydrogen bonds | Residence time/ps |
---|---|---|
O1, O3 | 12.68 | 16.53 |
N1H12 | 0.92 | 2.23 |
O4 | 22.77 | 12.56 |
N2H14 | 1.61 | 1.01 |
O2, O5 | 105.82 | 9.54 |
Table 2 Averaged hydrogen bond number and residence time between certain atoms of Fmoc-FF dipeptide and water molecules
Atom type | Number of hydrogen bonds | Residence time/ps |
---|---|---|
O1, O3 | 12.68 | 16.53 |
N1H12 | 0.92 | 2.23 |
O4 | 22.77 | 12.56 |
N2H14 | 1.61 | 1.01 |
O2, O5 | 105.82 | 9.54 |
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