Fig 1.
The Illustration of the dimer interfaces in the free energy calculations.
a) (TLR4-MD2)/(TLR4*-MD2*), b) TLR4/MD2, c) TLR4/TLR4*, and d) TLR4/MD2* interface. The TLR4 and MD2 are colored in blue, and TLR4* and MD2* are colored in red. Displayed images were created with UCSF Chimera software [63].
Table 1.
The binding free energies (ΔG) in kcal/mol at the five interfaces computed by both molecular mechanics generalized Born surface area (MM-GBSA) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods.
These interfaces are TLR4/MD2 (and its symmetry-related image TLR4*/MD2*), TLR4/TLR4*, and TLR4/MD2* (and its symmetry-related images TLR4*/MD2). The free energies in each of the ligand-free TLR4-MD2 heterodimer, (TLR4-MD2)2 tetramer, lipopolysaccharide (LPS)-bound (TLR4-MD2)2 tetramer, and neoseptin3-bound (TLR4-MD2)2 tetramer complexes are averaged over the average of their 4 different trajectories consisting of overall 4000 frames. A negative value is a favorable free energy, while a positive value is an unfavorable. The values in parenthesis are standard deviation. ΔEMM is molecular mechanics free energy which is divided into ΔEele and ΔEvdw representing the contributions from the electrostatic and van der Waals interactions, respectively. ΔGsol is solvation free energy expressed by ΔGpol and ΔGnonpol, the polar and non-polar contributions, respectively.
Table 2.
The binding free energies (ΔG) in kcal/mol between TLR4-MD2 and TLR4*-MD2* at the (TLR4-MD2)/(TLR4*-MD2*) interface computed by both molecular mechanics generalized Born surface area (MM-GBSA) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods.
The free energies in each of the ligand-free (TLR4-MD2)2 tetramer, lipopolysaccharide (LPS)-bound (TLR4-MD2)2 tetramer, and neoseptin3-bound (TLR4-MD2)2 tetramer complexes are averaged over the average of their 4 different trajectories consisting of overall 4000 frames. A negative value is a favorable free energy, while a positive value is an unfavorable. The values in parenthesis are standard deviation. ΔEMM is molecular mechanics free energy which is divided into ΔEele and ΔEvdw representing the contributions from the electrostatic and van der Waals interactions, respectively. ΔGsol is solvation free energy expressed by ΔGpol and ΔGnonpol, the polar and non-polar contributions, respectively.
Fig 2.
The structure of mouse MD2 in the lipopolysaccharide (LPS)-bound (TLR4-MD2)2 tetramer complex.
a) The residue sequences of MD2 and the residues within secondary structures of β-sheet and helix are colored in yellow and cyan shadow respectively. The C strand in the neoseptin3-bound complex starts at residue S45. In the ligand-free complex: the A strand ends at S27, the C strand starts at S45, the D strand starts at T57, the F and G strands are combined together as one strand (i.e., I85 to V93), the H strand ends at F121, and the I strand starts at C133. b) The three-dimensional crystal structure of MD2. The secondary structures of β-sheet and helix are colored in yellow and cyan respectively.
Fig 3.
The per residue free energy contribution spectrums of TLR4 and MD2* in the TLR4/MD2* interface.
a) the ligand-free (TLR4-MD2)2 tetramer, b) the lipopolysaccharide (LPS)-bound (TLR4-MD2)2 tetramer, and c) the neoseptin3-bound (TLR4-MD2)2 tetramer complex. Only the binding areas are shown with standard errors as red bars, estimated as standard deviation divided by square root of 1000.
Table 3.
The key residues of TLR4 and MD2 identified by per-residue free energy decomposition (kcal/mol) in the TLR4/MD2* and TLR4*/MD2 interfaces of the ligand-free (TLR4-MD2)2 tetramer, lipopolysaccharide (LPS)-bound (TLR4-MD2)2 tetramer, and neoseptin3-bound (TLR4-MD2)2 tetramer complexes.
The values are averaged over the 1000 frames of the combined 4 trajectories of each system. A negative value is a favorable free energy, while a positive value is an unfavorable.
Fig 4.
Illustration of key residues of MD2 in the TLR4/MD2* and TLR4*/MD2 interfaces.
a) the ligand-free (TLR4-MD2)2 tetramer, b) the lipopolysaccharide (LPS)-bound (TLR4-MD2)2 tetramer, and c) the neoseptin3-bound (TLR4-MD2)2 tetramer complex. MD2 are shown in surface. LPS and neoseptin3 are shown in sticks. F126 and H155 are colored in orange and magenta, respectively. I85, L87, P88, R90, I124, L125, P127, K128 are colored by elements (red: oxygen; blue: nitrogen; gray: carbon) and the remaining residues of MD2 are colored in light gray. Displayed images were created with UCSF Chimera software [63].