Heparin Linked Acidic Fibroblast Growth Factor (FGF 1) by Larry P. Taylor, Ph. D.
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FGF Site: FGF Intro Nomenclature Notes References FGF Sequences FGFR Sequences
Acidic fibroblast growth factor (FGF 1) and its interaction with heparin (a poly-sulfated carbohydrate).
The unit cell for the
acidic growth factor (FGF 1)-heparin complex is shown in Kinemage
1 . The secondary structure cartoon for the monomer is shown in Kinemage
2. The heparin-linked dimer is shown in Kinemage 3. The
characteristics of the unit cell for this structure are summarized at pdbsum.
Heparin (or a heparin-like molecule) is a necessary component for growth factor binding to its receptors leading to a biological response. Heparin bound FGF species show increased stability in the presence of acid, heat, mild oxidation, and proteolysis. The heparin-stabilization appears particularly important in humans since human FGF 1, in the absence of sugar poly anions, tends to unfold at physiological temperature. This heat instability may be involved in regulation of FGF mediated biological processes.
In particular, note the location of heparin relative to the C-terminus of FGF 1 (Kinemage 4 ). The basic trefoil shape of the FGF molecule is stabilized by the juxtaposition of the first (N-terminal) and last (C-terminal) beta sheets. The heparin-FGF interaction limits conformational mobility at the C-terminus of the molecule. This restriction in ability to move at the C-terminus stabilizes the overall molecular shape by keeping the C and N terminals together. The poly-anionic nature of heparin may also reduce intra chain repulsion from the abundant positively charged basic groups (which would tend to destabilize the C terminal to N-terminal junction) found in the heparin binding region of the FGF 1 molecule.
Acidic FGF contains three Cys residues at position 16, 83, and 117 (Kinemage
5 ). While both acidic and basic FGF contain Cys residues at positions 16 and 83, basic FGF
(FGF 2) has no Cys corresponding to the acidic FGF Cys-117. Acidic FGF contains no disulphide bonds. Exposure to thiol oxidizing agents inactivates the FGF protein. Since the disulphides in acidic FGF are mostly solvent non-accessible, any disulphide formation would involve significant molecular distortion. Cys-16 (entirely non-accessible to solvent) is presumed to be the most structurally disruptive potential disulphide linkage.
One characteristic of the beta trefoil architecture is an internal cavity of about 50 cubic angstroms (volume, of course, will vary with side chain
variability of various FGF ligands).
The central cavity in acidic FGF is marked by residues Leu-14, Leu-23, Leu-44, Ile-56, Leu-65, Phe-85, Tyr-97, Val-109, and Phe-132.
This cavity is shown in Kinemage 6.
Acidic FGF has both a high affinity receptor binding site comprised of a non-contiguous set of residues (Tyr-15, Arg-35, Asn-92, Tyr-94, Leu-133,
and Leu-135) and a second lower affinity site (~ 250 times weaker) that is primarily the loop region of residues 101-107 with Lys-101, His-102 and Trp-107 being the defining
residues (Kinemage 7). These sites for both chains A and B
of the dimer are shown in Kinemage 8. A ribbon rendering
cartoon of the binding sites is shown in Kinemage 9.
The FGF ligand region that
binds heparin is known as the "basic canyon" because the protein
surface of this region is a long cleft populated by a series of positive
charges. These basic residues (Kinemage 10) in FGF 1
are Lys-112, Lys-113, Lys-118, Arg-122, and Lys-128.
Acidic and basic FGF share a common structural motif (three-dimensional architecture)
with about 55% residue identity. So, their approach to receptor binding will be similar, but the differences in sequence in the high and low affinity regions provide a difference in FGF to receptor binding characteristics. The low affinity binding site is particularly noticeable since the length and composition of this region of the known FGF molecules is the most divergent, suggesting this loop region as a primary means of ligand-receptor discrimination.
A Calpha backbone trace comparing FGF 1 and FGF 2 is shown in Kinemage
11. A comparison of several FGF molecular sequences and backbones is shown
in this Kinemage (fgfcomp).
The human gene for FGF 1 encodes a 155 residue protein. However, because of N-terminal enzymatic degradation, protein isolation schemes from biological sources typically shorten the full sequence. Thus, biological activity studies have been primarily carried out on a protein of 140 residues. The X-ray diffraction experiment on the 140 residue
FGF 1 only resolves positions 26-137 because both terminal ends have conformational mobility and thus, do not provide an interpretable x-ray diffraction pattern.
The Kinemages
The real-time visualization using KiNG of the structures on this site requires a java-enabled (JRE from Java) browser.
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A single click on the KiNG logo will launch the appropriate kinemage.
Kinemage 1: The Unit Cell for FGF 1 (1AXM)
View 1 "top view" of the Heparin-FGF1 Dimer Complex
View 2 view 1 rotated 90 degrees to give a "side view"
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Click on KiNG to see | Unit Cell for Acidic FGF (FGF 1) |
Kinemage 2: Secondary Structure Cartoon for the Acidic FGF (FGF 1) Monomer
View 1 "top view" of the FGF 1 monomer
View 2 view 1 rotated 90 degrees to give a "side view"
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Click on KiNG to see | Cartoon Rendering of Acidic FGF (FGF 1) |
Kinemage 3: The Heparin-Linked Dimer
View 1 "top view" of the Heparin-FGF 1 Dimer Complex
View 2 view 1 rotated 90 degrees to give a "side view"
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Click on KiNG to see | Calpha Trace of Heparin-Linked FGF 1 Dimer |
Kinemage 4: The Acidic FGF1-Heparin Linked Dimer
In particular, note the location of heparin relative to the C-terminus of FGF 1. The basic trefoil shape of the FGF molecule is stabilized by the juxtaposition of the first (N-terminal) and last (C-terminal) beta sheets. The heparin-FGF interaction limits conformational mobility at the C-terminus of the molecule. This restriction in ability to move at the C-terminus stabilizes the overall molecular shape by keeping the C and N terminals together. The poly-anionic nature of heparin may also reduce intra chain repulsion from the abundant positively charged basic groups (which would tend to destabilize the C terminal to N-terminal junction) found in the heparin binding region of the FGF 1 molecule.
View 1 "top view" of the Heparin-FGF2 Dimer Complex
View 2 view 1 rotated 90 degrees to give a "side view"
View 3 highlights residues (Asn-18, Lys-113 & Lys-118) on chain A that have been implicated in binding the sulfate ion..
To view:
toggle on: chain A, side chains A, and ion binding.
turning off ribbon B facilitates examination of the highlighted residues.
View 4 highlights residues Lys-112, Lys-118, Arg-122 & Gln-127 on chain A that are implicated in binding heparin analogues.
from view 3, turn off ion binding and toggle on SOS binding.
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Click on KiNG to see | Ribbon Cartoon of Heparin-Linked FGF 1 Dimer |
Kinemage 5: The Cys Residues of Acidic FGF
Acidic FGF contains three Cys residues at position 16, 83, and 117.
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Click on KiNG to see | Cys Residues of the Heparin-Linked FGF 1 Dimer |
Kinemage 6: The Internal Cavity
The nine residues (Leu-14, Leu-23, Leu-44, Ile-56, Leu-65, Phe-85, Tyr-97, Val -109, & Phe-132) of chain A define the internal cavity
View 1 the "side view" of the dimer complex with heparin.
View 2 closer view of the cavity in chain A.
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Click on KiNG to see | Internal Cavity of FGF 1 |
Kinemage 7: The Receptor Binding Residues
Tyr-15, Arg-35, Asn-92, Tyr-94, Leu-133, & Leu-135 are the major residues defining the high affinity binding site. Lys-101, His-102 and Trp-107 define the low affinity site.
View 1 "top view" of the heparin-FGF 1 dimer complex
View 2 "side view" of the dimer complex with heparin.
View 3 highlights the residues defining the high affinity binding site of chain A.
View 4 highlights the residues defining the low affinity finding site of chain A.
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Click on KiNG to see | Acidic FGF Receptor Binding Sites |
Kinemage 8: The Receptor Binding Sites For Chains A and B
Kinemage 7 with residues from both chains highlighted
View 1 "top view" of the heparin-FGF 1 dimer complex
View 2 "side view" of the dimer complex with heparin.
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Click on KiNG to see | Receptor Binding Sites for Both Chains |
Kinemage 9: The Receptor Binding Sites For Chains A and B
The receptor high and low binding regions are highlighted in ribbon format.
View 1 "top view" of the heparin-FGF 1 dimer complex
View 2 "side view" of the dimer complex with heparin.
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Click on KiNG to see | Ribbon Rendering of the Binding Sites For FGF 1 |
Kinemage 10:The "Basic Canyon"
The basic residues ( Lys-112, Lys-113, Lys-118, Arg-122, and Lys-128) which form the "basic canyon" of the heparin binding region are highlighted in one FGF 1 molecule.
View 1 "top view" of FGF 1
View 2 "side view" of FGF 1
View 3 highlights the residues defining the "basic canyon."
View 4 closer view facing directly into the "basic canyon"
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Click on KiNG to see | "Basic Canyon" of Acidic FGF |
Kinemage 11: Backbone of Acidic FGF (FGF 1) Superimposed On Basic FGF (FGF
2)
The backbone of FGF 1 superimposed on the backbone of FGF 2.
View 1 Calpha trace for the two receptors
View 2 the low affinity (receptor selectivity) loop at the center-bottom of the image
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Click on KiNG to see | Backbone of FGF 1 Superimposed upon FGF 2 |
Sequence: (The X-ray resolved residues are 10-138 of the human FGF 1 sequence.)
Unresolved N-Terminal: MAEGEITTFTALTEKFNLPPGNYK
X-Ray Resolved: KPKLLYCSNGGHFLRILPDGTVDGTRDRSDQH
IQLQLSAESVGEVYIKSTETGQYLAMDTDGLLYGSQTPNEECLFLERL
EENHYNTYISKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV
Unresolved C-Terminal: SSD
Source:
The human sequence was expressed in escherichia coli cell line jm109 de3; Structural coordinates were taken from the Brookhaven Data Base File1AXM.
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FGF Site: FGF Intro
Nomenclature Notes
References FGF
Sequences FGFR Sequences
My University Home Harris Links Chemistry / Modeling Links
Copyright 2005-2020 by Larry P. Taylor
Molecular & Behavioral Neuroscience Institute
The University of Michigan
All Rights Reserved
Supported by the Pritzker Neuropsychiatric Disorders Research Consortium, and by NIH Grant 5 P01 MH42251, Conte Center Grant #L99MH60398, RO1 DA13386 and the Office of Naval Research (ONR) N00014-02-1-0879 to Huda Akil & Stanley J. Watson. at the Molecular & Behavioral Neuroscience Institute.