RGD loop

Leahy, D. J., Aukhil, L, and Erickson, H. P. (1996). 2.0 angstrom crystal structure of a four-domain segment of human fibronectin encompassing the RGD Loop and synergy region. Cell 84, 155-164. 

To further examine the interactions between FMDV and neutralizing antibodies, the atomic structures of peptide—Fab complexes and the cryo-TEM structures of the Fab—virus complexes were determined [136]. In the image reconstructions, SD6 has a well-defined orientation on the virion surface whereas the density for 4C4 is extremely diffuse. One possible reason for this difference is that, while the RGD loop is in an extended conformation in the SD6 complex, a hinge rotation at the base of the loop may bring it closer to the capsid surface and stabilize the orientation. 

To localize the RGD residues on the Ad penton base, a cryo-EM reconstruction was performed of adenovirus type 2 (Ad2) complexed with an RGD-specific Eab fragment from an mAb directed against the penton base (Stewart et al, 1997). This structural analysis revealed that the RGD regions are at the top of protrusions on the pentameric penton base protein. In addition, it was deduced from the diffuse nature of the Fab density that the RGD residues were in a structurally variable surface loop. Comparison of the knovra sequences of the penton base protein from various adenovirus serotypes suggested that type 12 adenovirus (Adl2) would have the least structurally variable RGD loop, as Ad 12 has 45 fewer residues in the variable region flanking the conserved RGD residues than are found in Ad2 (Chiu et al, 1999). 

Marcinkiewicz, C., Vijay-Kumar, S., McLane, M.A., and Niewiarowski, S. (1997). Significance of RGD loop and C-terminal domain of echistatin for recognition of a P, and a,p, integrins and expression of ligand-induced binding site. Blood. 90 1565-1575. 

Pfaff, M McLane, M.A., Beviglia, L., Niewiarowski, S., and Timpl, R. (1994). Comparison of disintegrins with limited variation in the RGD loop in their binding to purified integrins a,nP, a,Pj, and a,p, and in cell adhesion inhibition. Cell Adhes. and Comm. 2 491-501. 

All of the oncosphere antigens cloned to date contain either one of two copies of a predicted Fnlll domain. These domains are widely distributed in eukaryotic proteins and occur also in some prokaryotic proteins (Bork and Doolittle, 1992). Approximately 2% of animal proteins include Fnlll domains. Many, but not all, of these proteins are extracellular and some have roles as adhesins. The structure of this 100 amino acid domain is highly conserved and consists of two layers with three p strands in one plane and four p strands in another (Potts and Campbell, 1996). Overall, amino acid sequence identity between different Fnlll domains is low, even between Fnlll repeat domains within fibronectin itself (Plaxco et al., 1997). Nevertheless, certain residues are highly conserved and maintain the tertiary structure of the proteins (Bork and Doolittle, 1992). Other conserved motifs such as an Arg-Gly-Asp (RGD) motif within a loop of some Fnlll domains is associated with proteins having cell adhesion properties, as discussed above (Ruoslahti and Pierschbacher, 1987 D Souza et al., 1991). 

In an alternative scenario, 7-mer or 20-mer oligolysine sequences (which interact with heparan sulfate) have been fused to the C terminus of the fiber protein. This modification led to a dramatically increased and CAR-independent transduction of endothelial cells, smooth muscle cells, and macrophages in vitro and in vivo (up to > 100-fold) [33, 34], of myeloma cells and AML blast cells in vitro [35, 36], and of cultured glioma cells in vitro [37, 38], A similar approach has been used to fuse an RGD peptide (RDG-4C) to the C terminus of the fiber, which led to an increased transduction of endothelial cells in vitro and in vivo [33, 39], The same RGD-containing peptide has also been incorporated into the HI-loop of the fiber protein, resulting in an up to 1000-fold increased and CAR-independent transduction of primary endothelial cells and ovarian and head and neck cancer cells in vitro [40, 41]. 

FMDV is the outlier of picornavirus structures (Fry et al, 1990), with capsid proteins that are 20% shorter than in the other viruses. The VPl loops near the 5-fold axis are sheared off, so that there is not the pronounced 5-fold protrusion and canyon of rhinoviruses and polioviruses (Acharya et al, 1989). This leaves a longer VPl GH loop as the prominent surface feature, which is highly antigenic, the site of the RGD receptor attachment sequence, but disordered in structure unless a disulfide is reduced (Acharya et al, 1989 Fox et al, 1989 Lea et al, 1994 Rowlands et al, 1994). FMDV VP2 is more similar to its homologs, except that the GH loop puff is 50 residues shorter than in poliovirus, and its space is occupied pardy by the longer VPl GH loop. 

Recent studies indicate that a limited region of GPIIIa (V275GSDNH280) (58) expressed in an extended loop of the metal ion-dependent adhesion site appears to involved in heterodimer assembly. In addition, the expression of isolated residues 1-233 of GPIIb and 111 -318 of GPIIIa leads to the formation of soluble peptide heterodimers that recognize the RGD sequence (58). 

---