Table 4 Molecular dynamics simulation results of proteins in free and complex forms.

From: Design of a multi-epitope vaccine against Staphylococcus Aureus lukotoxin ED using in silico approaches

 

Vaccine

Free TLR

Complex

TLR1

TLR2

Vaccine

TLR1

TLR2

Temperature(K)

309.97 ± 1.85

310.00 ± 0.92

309.97 ± 1.06

Normalized-pot

-14.50 ± 0.02

-14.25 ± 0.01

-14.29 ± 0.01

RMSD (nm)

0.58 ± 0.02

1.07 ± 0.07

0.77 ± 0.07

0.47 ± 0.01

0.22 ± 0.03

0.25 ± 0.03

SASA (nm2)

144.29 ± 2.37

231.70 ± 3.09

220.46 ± 3.01

147.37 ± 2.59

198.19 ± 2.91

264.31 ± 3.25

Rg (nm)

2.06 ± 0.01

3.29 ± 0.03

3.10 ± 0.03

2.13 ± 0.01

2.86 ± 0.01

3.18 ± 0.04

Ave RMSF (nm)

0.10 ± 0.04

0.19 ± 0.07

0.18 ± 0.07

0.10 ± 0.04

0.11 ± 0.03

0.11 ± 0.04

hbond-pro-pro

238.89 ± 7.54

436.20 ± 12.87

407.38 ± 10.27

236.81 ± 7.74

379.09 ± 8.49

462.38 ± 12.94

hbond-pro-sol

552.15 ± 15.09

889.28 ± 19.15

790.80 ± 18.30

545.49 ± 16.14

709.17 ± 22.43

931.19 ± 20.30

hbond-A-B

–

12.74 ± 3.09

–

27.23 ± 3.68

Structure

56.45 ± 7.56

55.52 ± 1.47

57.58 ± 2.48

56.97 ± 1.27

Coil

26.53 ± 5.56

27.21 ± 0.97

23.91 ± 1.90

27.33 ± 0.93

B-Sheet

44.05 ± 6.25

35.02 ± 1.36

44.52 ± 1.96

37.02 ± 1.30

B-Bridge

1.75 ± 2.54

2.81 ± 0.53

2.98 ± 0.89

2.29 ± 0.48

Bend

16.45 ± 5.65

13.13 ± 0.81

17.02 ± 1.59

14.60 ± 0.83

Turn

6.82 ± 4.01

6.26 ± 0.69

6.06 ± 1.31

5.99 ± 0.66

A-Helix

3.83 ± 1.00

11.42 ± 0.58

4.03 ± 0.45

11.67 ± 0.43

5-Helix

0.54 ± 2.38

0.00 ± 0.01

1.46 ± 0.60

0.00 ± 0.01

3-Helix

0.03 ± 0.49

1.67 ± 0.45

0.03 ± 0.18

1.10 ± 0.33

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