Molecular and Thermodynamic Basis for EGCG-Keratin Interaction - Part I:
Molecular Dynamics Simulations
Jan K. Marzinek, Yanyan Zhao, Guoping Lian, Athanasios Mantalaris,
Efstratios N. Pistikopoulos, Peter J. Bond, Massimo G. Noro, Lujia Han, Longjian Chen.
Supplementary Material
1
Figure S1. Monomeric self-assembly simulation of EGCG molecule and keratin at 298K: A)
Buried hydrophobic surface area between EGCG and keratin during the simulation; B) Number
of hydrogen bonds between keratin and EGCG vs simulation time.
2
Figure S2. The buried surface area between keratin and EGCG at 318 K. After 47 ns EGCG
molecule fell off suggesting weaker interactions at higher temperatures.
3
Figure S3. Binding of 20 EGCG molecules to keratin segment 1B at 298K: A) The number of
hydrogen bonds between 20 EGCG molecules; B) The number of hydrogen bonds between
keratin and 20 EGCG molecules at 298K. At the constant number of hydrogen bonds between
EGCG molecules the increase in EGCG-keratin hydrogen bonds is observed. This proves the
spreading of EGCG molecules over the keratin surface as multilayer.
4
Figure S4. Hydrophobic surface area of 20 EGCG molecules during the simulation of binding to
keratin 1 (segment 1B). EGCG molecules cluster and elongate on the keratin surface which
results in decreasing their overall hydrophobic area.
5
Figure S5. Force vs time of pulling EGCG 4 nm away from keratin 1 (α-helical segment 1A) at
298K using pulling rate of 1 nm ns-1 and spring constant of 360 kcal mol-1nm-2.
6
Figure S6. Force vs time of pulling EGCG of 4 nm away from keratin 1 (α-helical segment 1A)
at 298K using pulling rate of 10 nm ns-1 and spring constant of 120 kcal mol-1nm-2.
7
Figure S7. Potential of mean force profiles obtained from windows generated by different pulling
simulations of EGCG (Fig. S5-S6) from the same initial coordinates of keratin-EGCG complex.
Nearly identical values of the free energy difference were achieved.
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Figure S8. The convergence of the potential of mean force curves. By increasing the simulation
time in each window a reasonable convergence is achieved. Hence, in all systems the umbrella
sampling windows were carried out for 50 ns.
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Figure S9. Umbrella sampling histograms along the reaction coordinate (distance). 20 umbrella
potentials with spacing of 0.2 nm and 50 ns of sampling show excellent overlap.
10
Figure S10. Force vs time for pulling EGCG 4 nm away from keratin coiled-coil at 308K using
pulling rate of 10 nm ns-1 and spring constant of 120 kcal mol-1nm-2. Three very similar profiles
were obtained from the same initial coordinates providing approximately the same breaking
point (maximum) confirming simulation reproducibility.
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Figure S11. The Number of hydrogen bonds between EGCG and water molecules decreased
during the simulation time at 298 K. EGCG during the binding process expelled water molecules
from the keratin surface.
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Table T1. The contribution of the average number of hydrogen bonds between EGCG and acidic
residues as well as occupied amino acids.
Initial position
of EGCG
around the
Keratin segment
1B
1.
Average no of
hbonds
(EGCG-protein )
Average no of
hbonds
(EGCG-charged
residues )
Contribution of
hbonds with
charged residues
[%]
1.034
0.485
47
Asp258, Glu264
2.
0.799
0.249
31
Glu239, Ser247
3.
1.355
1.034
76
4.
1.169
1.144
98
5.
2.484
2.429
98
Asp225, Asn226,
Asp233
Asp251, Asp260,
Glu261
Glu261, Asp292
6.
1.002
0.604
60
7.
0.746
0.541
73
8.
1.560
1.365
88
Occupied
Residues
Tyr230, Phe231,
Glu232
Asp272, Glu249,
Asn275
Asp265, Ala231,
Tyr266
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