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Research |
| Folding When a peptide or protein folds, it of necessity creates an "outer" and an "inner" surface. The folding process is controlled largely by the tendency of amino acids to interact with water or to interact with each other. If they interact with water, they must have functional groups that are attractive to water. These are called polar groups which have O-H and N-H bonds, for example. If they interact with each other, then they have functionality that does not interact well with water. They have structures like benzene rings and alkyl groups.They find themselves on the interiors of folded proteins or peptides, where they interact with each other instead of with water. This inner surface is interesting since it can serve to protect functional groups such as thiols. Please see our publication on amino acid hydropathy for more details. |
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Clam Shell If the Arginine Turn is simply expressed twice in a peptide, with a two-amino acid spacer, the two turns fold separately and arrange themselves with their amino and carboxy ends close together (as in a clam shell), as judged by the GFP-peptide fusion's high IMAC affinity. These clam shells have a deep cleft (that is, the clam's "mouth") that is a potential binding pocket for ligands. |
| Arginine Turn A serendipitous discovery made while designing small molecule binding peptides, this six amino acid peptide folds well in solution around a central arginine core to bring its amino and carboxy termini close together, which can be easily detected using IMAC chromatography. If the ends of the peptide are elaborated with three amino acid long "arms," the arms are held in close proximity, which imparts interesting binding features to the peptide, including the ability to bind phosphate and hydroxylated aromatics. We are exploring this as well as a two-cysteine mutant which has the ability to control its binding allosterically via formation of a disulfide bond. |
Clam Shell Binding The binding observed so far for the Arginine Turn is impressive. The clam shell structure, with its high degree of structure and pre-organization, is envisioned to also have small organic molecule binding capabilities. So far we have seen reasonable binding to certain dyes which opens the possibility of energy transfer from GFP to the dye molecule (FRET). |