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. 2011 Sep 6;286(43):37793–37803. doi: 10.1074/jbc.M111.245472

FIGURE 3.

FIGURE 3.

Computational prediction of LPS-binding sites on Hb. A, prediction of phospho-group binding patches. An algorithm for computing phospho-group binding propensity was applied on human Hb (Protein Data Bank code 1HGB). FhuA protein in complex with LPS (Protein Data Bank code 1QFG) and MD2 protein with bound lipid A (Protein Data Bank code 2E59) served as positive controls. The binding propensity is represented by surface coloring, which varies linearly from white to blue over favorable propensity values from 1 to 30, and from red to white over the unfavorable propensity values from −1 to 0. The ligands, LPS and lipid A, are shown in a licorice representation, with the phosphate atoms colored green. The phosphate atoms of the ligands in FhuA and MD2 are outlined in yellow. Insets show magnified images of the phospho-groups of the ligand along with the surface coloring for the proteins. B, structure-based sequence alignment of vertebrate Hbα chains. Vertebrate Hb proteins were aligned on the basis of structure using the MultiSeq tool of VMD. The alignment for Hbα is shown here. Residues are color-shaded on the basis of predicted propensity of phospho-residue contact in a decreasing order from green to red to blue. Residues with no propensity of contact are indicated in black. Buried residues are indicated in yellow. The helix designations, A–F, for Hb (according to Kendrew's nomenclature (39)) are shown above the alignment. C, molecular docking of the ligand to the predicted LPS-binding sites. The diglucosamine head group of lipid A (1,4′-bisphospho-β-(1,6)-2,2′-N-acetyl-3,3′-O-acetyl-d-glucosamine disaccharide) was used for docking analysis to the predicted LPS-binding sites. Panels I–VIII, top ranking docked poses of the ligand to the predicted LPS-binding sites. Dockings were performed using GLIDE (version 5.0; Schrodinger, LLC, 2007). The residues participating in hydrogen bonding with the ligand and the computed binding energies are indicated. The α subunits are colored gold, and the β subunits are colored violet. The ligand is in stick representation, whereas the polypeptide chains are shown as ribbons. The hydrogen bonds are indicated as dashed lines.