Figure 4.
A, model of the tetrahedral intermediate of C(cyan)
bound to PAF-AH with catalytic triad residues (Ser^273, His^351,
and Asp^296) in green and interfacial-binding residues (Thr^113,
His^114, Trp^115, Leu^116, Met^117, Ile^120, Leu^123, Leu^124,
Ile^364, Ile^365, Met^368, and Leu^369) in yellow. The
coordinates of the tetrahedral intermediate were modeled based
on the crystal structure of the DEP moiety complexed to PAF-AH
(tetrahedral mimic). The C[18]-alkyl chain was oriented to
penetrate into the hydrophobic portion of the LDL particle. The
predicted plane of the hydrophilic-hydrophobic interface, which
was predicted by the OPM method (47, 48), is displayed with
small gray spheres. B, the view from A was rotated by 90° on
the y axis to show a side view of the interface and
substrate-bound model. A prominent cluster of 10 carboxylate
residues (Asp^374, Asp^376, Asp^382, Asp^401, Asp^403, Asp^406,
Glu^410, Asp^412, Asp^413, and Glu^414) are shown in red, and
three basic residues (Lys^55, Arg^58, and Lys^363) are shown in
blue ball and stick. C, electrostatic surface view of A. D,
electrostatic surface view of B. The figure was prepared using
the program PyMOL (51).
The above figure is reprinted
from an Open Access publication published by the ASBMB:
J Biol Chem
(2008,
283,
31617-31624)
copyright 2008.
(cyan)
bound to PAF-AH with catalytic triad residues (Ser^273, His^351,
and Asp^296) in green and interfacial-binding residues (Thr^113,
His^114, Trp^115, Leu^116, Met^117, Ile^120, Leu^123, Leu^124,
Ile^364, Ile^365, Met^368, and Leu^369) in yellow. The
coordinates of the tetrahedral intermediate were modeled based
on the crystal structure of the DEP moiety complexed to PAF-AH
(tetrahedral mimic). The C[18]-alkyl chain was oriented to
penetrate into the hydrophobic portion of the LDL particle. The
predicted plane of the hydrophilic-hydrophobic interface, which
was predicted by the OPM method (47, 48), is displayed with
small gray spheres. B, the view from A was rotated by 90° on
the y axis to show a side view of the interface and
substrate-bound model. A prominent cluster of 10 carboxylate
residues (Asp^374, Asp^376, Asp^382, Asp^401, Asp^403, Asp^406,
Glu^410, Asp^412, Asp^413, and Glu^414) are shown in red, and
three basic residues (Lys^55, Arg^58, and Lys^363) are shown in
blue ball and stick. C, electrostatic surface view of A. D,
electrostatic surface view of B. The figure was prepared using
the program PyMOL (51).