Table 1.

Average occurrence of hydrogen bonds and salt bridges for lipid A, lipid IVa and DA193 in complex with hMD-2, together with the atom positional root mean square displacement (RMSD) of Phe126.^a

MD-2 ligand	Pose (orientation)	H-bondsb (nm)	Salt bridges (nm)	RMSDc F126 (nm)
Lipid A	A as in 3FXI	12.4 ± 0.1	0.3	0.18
Lipid A	B	13.0 ± 0.3	0.5	0.37
Lipid IVa	A	13.3 ± 0.2	0.2	0.69
Lipid IVa	B as in 2E59	12.8 ± 0.1	0.6	0.38
DA193	A	11.4 ± 0.1	2.1	0.43
DA193	B	12.7 ± 0.2	1.0	0.31

^aError estimates are calculated from block averages.

^bAverage total number of hydrogen bonds, including the protein and the solvent. In pure water or octane–water environment, the number of hydrogen bonds is, on average, 14.5 (lipid A); 13.6 (lipid IVa); 12.8 (DA193) nm.

^cAtom-positional RMSD of Phe126 at the end of the simulations with respect to the initial MD-2 structure calculated after a rotational fit on the Cα atoms of the MD-2 backbone. All simulations were started from the agonistic MD-2 structure (3FXI). The Phe126 remained relatively close to its original position (small RMSD) in the simulations of lipid A^hMD-2 in pose A, while the crystallographically not-observed binding poses (lipid A in pose B and lipid IVa in pose A) induced a larger conformational change of Phe126. Larger deviations are observed when hMD-2 antagonist (lipid IVa or DA193) is placed in an agonistic protein structure (3FXI). Thus, the dynamic behavior of Phe126 was in line with the antagonistic role of DA193.