Volume 6, Issue 5, Pages 637-648 (May 1998) Solution structure of the heparin-binding domain of vascular endothelial growth factor  Wayne J Fairbrother, Mark A Champe, Hans W Christinger, Bruce A Keyt, Melissa A Starovasnik  Structure  Volume 6, Issue 5, Pages 637-648 (May 1998) DOI: 10.1016/S0969-2126(98)00065-3

Figure 1 A schematic representation of the VEGF165 homodimer. The lightly shaded regions (residues 1–115) include exons 1–4, and the darker shaded regions (residues 116–165) include exons 7 and 8. Disulfide bridges are represented by lines. The disulfide assignments were determined by X-ray crystallography for the amino-terminal receptor-binding domain [24,25], and by amino-terminal sequencing of tryptic fragments for the carboxy-terminal heparin-binding domain [29]. The plasmin cleavage site is indicated by the arrow. The amino acid sequence of the carboxy-terminal 55-residue heparin-binding domain used in the present study is shown. Structure 1998 6, 637-648DOI: (10.1016/S0969-2126(98)00065-3)

Figure 2 1H–15N HSQC spectrum of the 15N-labeled VEGF heparin-binding domain. The assignments made in this study are indicated. Sidechain amide resonances of asparagine and glutamine residues are connected by horizontal lines. Structure 1998 6, 637-648DOI: (10.1016/S0969-2126(98)00065-3)

Figure 3 Residue-based structural statistics for VEGF55. (a) Residue-based summary of NOE distance restraints. Intraresidue, sequential, medium-range (1 < |i–j| < 5), and long-range (|i–j| ≥ 5) NOEs are indicated by open, dark shaded, lightly shaded, and black bars, respectively. (b) Atomic rmsds (mean ± SD) of the backbone heavy atoms (N, Cα and C) of the 20 final structures about the mean coordinates. (c) and (d) Angular order parameters for φ and ψ angles calculated from the 20 final structures. The positions of secondary structure elements are indicated schematically at the top of the figure (arrow, β sheet; block, α helix). Structure 1998 6, 637-648DOI: (10.1016/S0969-2126(98)00065-3)

Figure 4 Stereoviews showing selected best fit superpositions of the 20 final structures of VEGF55. The backbone atoms of residues 6–53 and the sidechain heavy atoms of the eight cysteines are shown. (a) The superposition was optimized for the backbone atoms of residues 18–52; rmsds with respect to the mean coordinates for this superposition are 0.60 ± 0.26 å. (b) The superposition was optimized for residues 18–29 giving rmsds with respect to the mean coordinates of 0.32 ± 0.08 å. The sidechain heavy atoms of the four cysteine residues in the amino-terminal subdomain are labeled. (c) The superposition was optimized using residues 29–52 giving rmsds with respect to the mean coordinates of 0.26 ± 0.06 å. The sidechain heavy atoms of the four cysteine residues in the carboxy-terminal subdomain are labeled. This figure was produced using the program INSIGHT II (Molecular Simulations, Inc.). Structure 1998 6, 637-648DOI: (10.1016/S0969-2126(98)00065-3)

Figure 5 A schematic stereo representation of the VEGF55 structure, highlighting the elements of secondary structure, disulfide bridges and hydrophobic packing of selected sidechains. The χ1 angular order parameters of the depicted sidechains are all > 0.98. The figure was produced using the program MOLMOL [69]. Structure 1998 6, 637-648DOI: (10.1016/S0969-2126(98)00065-3)

Figure 6 The 1H–15N NOE values of VEGF55 plotted as a function of residue number. Structure 1998 6, 637-648DOI: (10.1016/S0969-2126(98)00065-3)

Figure 7 The solvent-accessible molecular surface of the minimized mean structure of VEGF55 color coded according to electrostatic surface potential; red, −10 kT; white, 0 kT; and blue, +10 kT. The positions of charged sidechains are labeled. The two views are related by a 180° rotation about the vertical axis. The figure was produced using the program GRASP [70]. Structure 1998 6, 637-648DOI: (10.1016/S0969-2126(98)00065-3)