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Table 2 Sensitivity of the most stable salt bridges in the NIP7-ABY, the NIP7-FUR models to increase in temperatures and pressures

From: Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species

Salt bridge

Marker

Function

NIP7-ABY

NIP7-FUR

   

S T

F (T)

S p

F (P)

S T

F (T)

S p

F (P)

10-4

All

α1-α1

0.94

2.74

1.04

0.83

0.99

1

1.01

1

75-37

All

β6-β4

1.06

0.52

1.11

0.91

0.99

1.89

1.00

0.36

37-10

All

β4-α1

1.04

0.16

1.14

0.99

1.18

2.87

0.88

4.68

148-109

All

RNA binding - RNA binding

0.95

0.40

1.09

0.45

u

u

u

u

33-4

All

β3-β1

0.92

0.59

0.94

0.69

0.98

0.10

1.00

0.20

20-17

All

α1-α1

0.92

2.65

1.02

0.13

0.89

2.96

0.98

0.36

16-12

P.a.&P.f.

α1-α1

1.14

3.77

0.91

1.68

1.08

1.60

0.89

2.76

147-113

P.a.&P.f.

RNA binding - RNA binding; α6

0.98

0.02

0.72

3.18

u

u

u

u

33-2

2p38&P.a.

β3 - N-terminal

0.98

0.01

0.99

2.07

-

-

-

-

131-116

All

C-terminal - β9

1.93

12.23

0.94

0.49

0.98

0.72

0.99

0.43

51-5

P.a.&P.f.

α2-β1

1.25

1.50

1.03

0.03

0.88

1.11

1.18

0.74

76-70

P.a.&P.f.

β6 - N-terminal

1.20

6.59

0.84

3.42

0.83

8.19

0.95

1.98

147-146

P.a.

RNA binding - C-terminal

1.84

4.12

0.95

0.12

-

-

-

-

48-45

P.a.&P.f.

α2-α2

1.06

0.14

0.92

1.42

0.99

0.00

0.88

1.29

88-23

P.a.

β7-β2

1.26

5.91

0.87

1.72

-

-

-

-

151-109

All

RNA binding; β12 - RNA binding

0.93

0.09

0.75

1.49

0.86

2.74

0.92

0.42

119-117

P.a.

β9-β9

0.98

0.04

1.26

2.31

-

-

-

-

48-44

2p38&P.a.

α2-α2

0.99

0.00

0.98

0.01

-

-

-

-

146-112

All

C-terminal - α5

u

u

u

u

1.01

0.00

1.11

0.50

76-17

P.a.&P.f.

β6-α1

u

u

u

u

0.83

1.07

0.95

0.56

  1. Columns: residue pairs forming salt bridges; occurrence of a salt bridge in the different structures (ALL, the NIP7-ABY, the NIP7-FUR models, and the crystal 2P38:A structure; ABY & FUR for only the NIP7-ABY, NIP7-FUR models and so on); the values of the indices of sensitivity for the NIP7-ABY; for the NIP7-FUR models; the F-value for a concrete parameter. Values expressing significant changes, maintenance of a salt bridge when pressure or temperature changes are in bold. Unstable salt bridges (occurrence less than 20%) are marked with the symbol u.