Table 1 Properties of metastable binding configurations between MR1 and ligands.

From: Molecular recognition of natural compounds by MR1 and their implication in MAIT cell activation elucidated through McMD-based dynamic docking simulations

Struc.

CFE

Population (%)

RASA

R(ref)-value

RMSD (Ã…)

R-value 300 K

R-value 400 K

r11VY

0.00

74.72

0.13

0.627

5.77

0.937 (0.116)

0.787 (0.267)

r21VY

0.88

17.19

0.17

0.139

12.32

0.966 (0.147)

0.614 (0.330)

r31VY

1.36

7.64

0.15

0.962

0.84

0.999 (0.004)

0.908 (0.174)

ref

–

–

0.05

1.000

0.00

–

–

r1PLI

0.00

73.25

0.14

0.542

5.89

0.960 (0.033)

0.920 (0.064)

r2PLI

0.60

26.69

0.07

0.926

2.00

0.969 (0.027)

0.838 (0.098)

ref

–

–

0.05

1.000

0.00

–

–

r1PLIII

0.00

70.45

0.11

0.809

1.86

0.994 (0.010)

0.855 (0.117)

r2PLIII

0.76

19.78

0.20

0.401

6.87

0.980 (0.020)

0.802 (0.163)

r3PLIII

1.28

8.29

0.13

0.364

7.95

0.985 (0.019)

0.835 (0.177)

ref

–

–

0.04

1.000

0.00

–

–

r1RBF

0.00

57.20

0.26

0.308

6.61

0.923 (0.058)

0.829 (0.080)

r2RBF

0.87

13.21

0.12

0.348

7.47

0.988 (0.016)

0.899 (0.119)

r3RBF

0.99

10.80

0.30

0.018

16.15

0.934 (0.049)

0.561 (0.335)

r4RBF

1.42

5.31

0.29

0.000

18.22

0.910 (0.091)

0.618 (0.251)

r5RBF

1.46

4.91

0.20

0.314

7.11

0.945 (0.045)

0.865 (0.151)

r6RBF

1.62

3.76

0.28

0.202

8.76

0.831 (0.227)

0.616 (0.187)

ref

–

–

0.04

1.000

0.00

–

–

  1. Characteristics for representative structures \(\mathrm{\textbf{r}_k}\) (from McMD). Shown are, the cluster free energy (CFE) value in kcal/mol of the corresponding cluster k, the fraction of the relative accessible surface area (RASA) of the ligand, the R(ref)-value with respect to the reference structure (approximation of the complex structure based on binding of 1VY in 4L4V) and the RMSD of the ligand in Å with respect to the reference structure (see the Materials and Methods section), the stability R-value (with respect to the initial structure measured by our canonical MD simulations) of the final 40 ns over 10 parallel trajectories at 300 K (with standard deviation), and the stability R-value of the final 40 ns over 10 parallel trajectories at 400 K (with standard deviation). The R-value is a measure of stability and indicates the fraction of contacts maintained between receptor and ligand during a 100 ns MD simulation at the given temperature. Only the metastable structures, i.e., those with a CFE within 2.0 kcal/mol, are shown. The full multicanonical sampling process yields a total population of 100% across all sampled structures (including those with CFE > 2.0 kcal/mol), which represent transient or less stable states not considered metastable. The reference structure is derived from the ligand position in PDB 4L4V and serves as a structural benchmark; however, there is no experimental evidence confirming the actual complex structure for the PLI, PLIII, and RBF complexes.
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