Structure

The overall secondary structure of ADP-Ribosylation Factor 1 is that of an alpha/beta protein. It is a structure of mixed beta sheets with a core surrounded by alpha-helices. To view the secondary structure of ARF 1 click on the button. This gave you a look at the backbone structure of the ARF 1 protein which as stated before is made up of alpha helices and parallel beta-sheets. The tertiary structure of the protein is how the protein folds and packs its hydrophobic residues into the center of the protein. The tertiary structure of the ARF 1 protein is made up of the two monomers each being open twisted beta-sheets. To view one of the monomers more closely click on the button. Both of the domains are open twisted beta-sheets because they have parallel beta-sheets and alpha helices are on both sides of the sheet. The beta sheets are also connected to one another by beta-turns that can be viewed by clicking on the button. The ARF 1 protein appears as a dimer in an asymmetric unit. This is what makes up the quaternary structure, which is how the final protein relates its two chains. Its two monomers interact by 2 backbone hydrogen bonds, van der Waals interactions and hydrophobic forces. Although the ARF 1 protein is similar to other G-binding proteins it differs in three manners: it has an N-terminal alpha-helix and loop region; it has a different Mg⁺² ligation; and it has the non-crystallographic dimer(Amor,etal.,1994).

The N-terminal alpha-helix and loop region is amphipathic and lies in a grove parallel with the the C-terminal alpha-helix region. The N-terminal helix is held inside the grove by hydrophobic forces in the cleft of unmyristoylated, GDP-bound form. The N-terminal helix is composed of hydrophobic residues and is buried in the protein core of ARF 1. In the crystalline form the helix ends at residue 11 which is followed by a loop region. There does seem to be some suggestion of an extension of the helical region with Phe 13(Losconczi, etal., 1998). The hydrophobic side chains of the amphipathic helix tend to face towards the inside of the protein and the hydrophilic side chains face the aqueous environment(Losonczi, etal., 1998). When the ARF 1 protein is interacting with the membrane the helical peptides lay flat on the surface of the membrane with the hydrophobic side chain facing into the membrane. The N-terminal helix region act as an anchor for the myristoyl group which are localized when it is covalently bound to the N-terminal glycine.

Another unique aspect of ARF 1 is its different Mg ⁺². Compared to other GTP-binding proteins the Mg⁺² ligation is linked to a shift in the registration of the ß4 by two amino acids towards the C-terminus. This shift changes the position of Gln 71 in ARF. In other G-binding proteins this region is important for the hydrolysis of GTP. This shift of the magnesium ligation pushes the Gln 71 about 5 angstroms away from the putative binding site of the gamma-phosphate that other G-binding proteins do. This may explain the lack of the GTPase activity in ARF 1(Amor, etal., 1994).

The ARF-GDP form binds weakly to vesicles by hydrophobic interactions of the myristoylated chain and by electrostatic interactions of the cationic residues with the anionic residues of the lipid membrane. It also needs a high lipid concentration in order for the GDP to bind. This charge-charge interaction with the membrane is the activator of the release of the GDP by ARF. So this interaction causes the GTP to bind to the ARF protein so there is a conformational change that exposes the lipid chain or myristoylated chain(Antonny, etal., 1997). Since there is an insertion of the mytristoyl group into the membrane then a conformation change is needed at the helix-loop region of the N-terminal(Amor, etal., 1994). The myristoyl group can be inserted because the loop and helix form a continuous stretch in response to nucleotide exchange. The residues in the loop region contribute to the positive patch that is formed on the surface of the ARF protein. The insertion of the myristoylated chain is not enough to anchor the ARF protein to the membrane of the lipid, but the conformation change also exposes the hydrophobic surface to other parts of the lipid protein so they can interact(Losonczi, etal., 1998).