Amphipathic P-strands

The protein is a 12-stranded anti-parallel p-barrel with amphipathic P-strands traversing the membrane (Fig. 4). The active-site catalytic residues are similar to a classical serine hydrolase triad except that in addition to the serine (Ser-144) and histidine (His-142), there is an asparagine (Asn-156) in place of the expected aspartic acid. Calcium at the active site is predicted to be involved in the reaction mechanism facilitating hydrolysis of the ester. 

Membrane import machinery protein mas6 yeast was predicted with a maximum of only two short transmembrane helices 101-116 and 201-215, instead of four expected, but with many potential amphipathic P-strands. High peak in P-amphipathicity just next to the LDL or IDI motif is found at the mas6 yeast residue 69, mpcp rat (from mitochondrial carrier family) residue 83 and achl xenla residue 350. Observed amphipathic P-structure of a leucine rich repeat peptide LRP32 also contains LDL motif [99]. This motif may be important... 

Possible secondary structures of pardaxin (6) were predicted by the Delphi program (12) using decision constants (DHA = -75, DHE = 50) that favor a helices over extended segments and by the Amphi program that identified possible amphipathic a helices and p strands (Guy, unpublish data). Delphi predicted that pardaxin segments 1-8 and 16-25 were a helices and the remainder may be coils or turns. Amphi predicted that segments 1-12 and 13-28 could form amphipathic a helices. 

Shown in the upper panel of Scheme 2 is the top view of the GS14 backbone showing the positions of potential H-bonds (dashed lines) in each five-residue p-strand and the two type II p-turns defined by the D-Tyr-Pro sequence which link the two P-strands. The side view of GS14 (2) is shown in the lower panel of Scheme 2 where the P-sheet structure of the backbone is evident and the relative orientation of successive side chains within the 3-strands can be seen. The P-sheet structure gives GS14 (2) a highly amphipathic nature with a large hydrophobic face made up of Val and Leu residues and a basic face made up of Lys residues. 

Oleosins have unique secondary structures that enable the proteins to interact with other molecules on the surface of oil bodies. Each oleosin molecule has three structural domains an N-terminal amphipathic domain, a central antiparallel p-stranded hydrophobic domain, and a C-terminal amphipathic domain. The central domain anchors the protein onto the oil body or in the lipid-containing organelles, whereas the N-terminal and C-terminal domains are exposed to the exterior. Among oleosins of different organs and plant species, only the central hydrophobic stretches (72 residues) are highly conserved, whereas the N-terminal and C-terminal sequences are quite dissimilar. 

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