page_title: RiAFP
section_title: RiAFP Ice Binding
hierarchical_section_title: RiAFP / RiAFP Ice Binding
caption_attribution_description: English: A sequence logo constructed from the 13-nucleotide repeats present in RiAFP (Rhagium inquisitor antifreeze protein) found using RADAR.
context_page_description: RiAFP refers to an antifreeze protein produced by the Rhagium inquisitor longhorned beetle. It is a type V antifreeze protein with a molecular weight of 12.8 kDa; this type of AFP is noted for its hyperactivity. R. inquisitor is a freeze-avoidant species, meaning that, due to its AFP, R. inquisitor prevents its body fluids from freezing altogether. This contrasts with freeze-tolerant species, whose AFPs simply depress levels of ice crystal formation in low temperatures. Whereas most insect antifreeze proteins contain cysteines at least every sixth residue, as well as varying numbers of 12- or 13-mer repeats of 8.3-12.5kDa, RiAFP is notable for containing only one disulfide bridge. This property of RiAFP makes it particularly attractive for recombinant expression and biotechnological applications.
context_section_description: The primary structure of RiAFP (the sequence may be found here) determined by Mass Spectroscopy, Edman degradation and by constructing a partial cDNA sequence and PCR have shown that a TxTxTxT internal repeat exists . Sequence logos constructed from the RiAFP internal repeats, have been particularly helpful in the determination of the consensus sequence of these repeats. The TxTxTxT domains are irregularly spaced within the protein and have been shown to be conserved from the TxT binding motif of other AFPs. The hydroxyl moiety of the T residues fits well, when spaced as they are in the internal repeats, with the hydroxyl moieties of externally facing water molecules in the forming ice lattice. This mimics the formation of the growth cone at a nucleation site in the absence of AFPs. Thus, the binding of RiAFP inhibits the growth of the crystal in the basal and prism planes of the ice.
caption: Figure 1: A sequence logo constructed from the 13-nucleotide repeat regions found by EBI-RADAR, showing a clear TxTxTxT binding motif embedded within these regions.
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