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Table 4 Electric moments of RNA-binding proteins as pairs of RNA-complexed and monomeric structures*.

From: Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction

 

Detailed protein-wise comparison

ED

Protein name

P

Q

 
 

Complex.

Monomer.

Complex.

Monomer.

 

30S Ribosomal protein S15 (1fjgO, 2fkxA, 100%)

4.37

4.44

5.77

7.36

rRNA binding: ED(P) = 0.7 ED(Q) = 1.6

30S Ribosomal protein S6 (1fjgF, 1louA, 99%)

2.34

2.66

7.90

8.74

 

30S Ribosomal protein S7 (1fjgG, 1rssA, 100%)

4.95

3.30

22.12

9.56

 

30S Ribosomal protein S19 (1ibmS, 1qkfA, 100%)

5.04

3.83

12.96

8.43

 

30S Ribosomal protein S16 (1hnwP, 1emwA, 100%)

4.27

4.31

7.22

6.76

 

Ribosomal protein L11 (1hc8A, 2f0wA, 100%)

1.79

1.84

6.64

6.41

 

Ribosomal protein L25 (1d6kA, 1b75A, 100%)

3.59

3.35

10.26

9.90

 

60S Ribosomal protein L30 (1cn8A, 1cn7A, 100%)

2.94

2.41

4.61

4.97

 

Glutaminyl-tRNA synthetase (1euyA, 1nylA, 98%)

1.10

1.15

14.24

15.46

tRNA binding: ED(P) = 0.6 ED(Q) = 1.2

Queuine tRNA-ribosyltransferase (1q2rA, 1r5yA, 100%)

2.19

2.26

2.83

3.75

 

Glutamyl-tRNA synthetase (1g59A, 1j09A, 99%)

1.64

1.50

13.21

13.77

 

Aspartyl tRNA-synthetase (1asyA, 1eovA, 100%)

4.03

5.06

7.48

9.39

 

Elongation factor TU (1b23P, 2c78A, 98%)

3.62

3.44

12.65

11.21

 

Arginyl tRNA synthetase (1f7uA, 1bs2A, 100%)

2.22

2.31

12.44

13.83

 

Small protein B (1p6vA, 1k8hA, 98%)

0.69

1.71

16.40

18.62

 

Pseudouridine synthase B (1k8wA, 1r3fA, 100%)

1.65

1.90

18.31

17.41

 

Tyrosyl tRNA synthetase (1j1uA, 2ag6A, 96%)

1.34

1.75

16.60

15.22

 

Bactereophage coat protein MS2 (1aq3A, 1mscA, 98%)

2.08

2.08

4.77

3.65

Viral RNA binding: ED(P) = 0.7 ED(Q) = 1.9

Minor core protein lambda 3 (1n1hA, 1mukA, 100%)

1.65

1.42

11.95

12.44

 

RNA polymerase HC-J4 (1nb7A, 1gx5A, 96%)

3.81

2.77

12.44

10.34

 

HIV-I nucleocapsid protein (1a1tA, 1mfsA, 100%)

4.24

3.65

12.74

23.69

 

NHP2-like protein 1 (1e7kA, 2jnbA, 100%)

3.27

5.06

4.28

8.61

Others: ED(P) = 0.9 ED(Q) = 2.0

Splicosomal U1A protein (1audA, 1fhtA, 98%)

1.36

2.60

7.93

12.88

 

Pumilo homology domain (1m8yB, 1m8zA, 100%)

4.00

4.05

20.01

20.46

 

Rho transcription termination factor (2a8vA, 1a62A)

1.84

1.86

12.42

10.87

 

Transcription factor IIIA (**) (1un6B, 2j7jA, 100%)

3.92

1.94

16.83

30.18

 

VP39 protein (1av6A, 4dcgA, 98%)

3.18

3.09

6.53

6.25

 
  1. *P and Q stands for dipole moment and quadrupole moment (first eigen value) respectively. Euclidean distance (ED) here refers to the root mean squared difference between bound and unbound moments for the given pair. (**) This protein is reported to have two modes of interaction and shows very large conformational change via domain movement (rigid body RMSD is 9.2Å). However, domain-wise comparison shows almost no change in moments (see Table 5).
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BMC Structural Biology

ISSN: 1472-6807

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