Topology

Home
What are Cyclotides?
Uses of Cyclotides
About Us
Discovery of Cyclotides
Sequences
Biological Activity
Structures
Topological Features
Synthesis
Cyclotide Genes
Cystine Knots
Other Circular Proteins
Cybase: The Cyclotide Database
Publications
Commercial Opportunities
Contact Us

movie

Check out a movie of the cyclic cystine knot motif.

The unusual aspects of cyclotide structure introduce novel concepts not normally applied in protein chemistry. Topological considerations include the concept of acyclic permutations, the conceptual twist in the backbone which enables cyclotides to be classed as bracelet or moebius cyclotides and the possibility that cyclotides represent a true knot.

Acyclic Permutants

To help understand the significance and role of the circular backbone in the cyclotides we recently introduced the concept of acyclic permutation of circular proteins (Daly and Craik, 2000). This effectively involves breaking the backbone to produce acyclic homologues. We synthesized the six acyclic permutants corresponding to opening the backbone in each of the six loops between successive Cys residues in the prototypic cyclotide kalata B1. We found that four of the six permutants folded into native-like conformations, but two did not. These were precisely the two that involved breaking the embedded ring of the cystine knot (Daly and Craik, 2000). This emphasises the importance of the cystine knot in folding and confirms that it is the crucial structural core of the cyclotides.

Acyclic permutants of kalata B1. Only two of the permutants did not fold into a native conformation - permutants (4) and (1) - which are the two involved in the embedded loop of the cystine knot.

Moebius Strips

Moebius strips are a geometric shape with only one surface. They are a strip which is twisted halfway around and attached to itself (Figure Two). It has been proposed that a cis-Pro peptide bond in loop 5 can be thought of as providing a twist in the conceptual ribbon of the peptide backbone, leading to the circular backbone being regarded as a Möebius strip. When this cis-Pro is not present, all backbone peptide bonds are in the trans arrangement, making the backbone bracelet-like.

Moebius strip has a half-twist that gives it only one surface, (a) Shows a moebius strip with a half twist giving it only one surface, (b) shows a bracelet with a full twist with the two surfaces or sides colored differently. The defining feature of the moebius strip is a half twist, therefore strips with twists of 1.5, 2.5 .. are all moebius strips while those with whole number twists are bracelets with two distinct surfaces.

Knots

The cyclic backbone of the cyclotides introduces interesting concepts not normally asscoiated with peptides. One of the considerations is whether the cyclotides can be regarded as a true knot. Other cystine knotted peptides are topologically simple and are able to be unfolded (see below). Cyclotides on the other hand are not topologically simple and may not be unfolded. Whether this makes them a true knot, or a link (another mathematical formulation of a knot like construct) is being investigated by members of our group.

The unfolding of a non-cyclic cystine knot peptide, cyclotides on the other hand are unable to be unfolded in this way.

References

Daly NL and Craik DJ: Acyclic Permutants of Naturally Occurring Cyclic Proteins. Characterization of cystine knot and beta -sheet formation in the macrocyclic polypeptide kalata B1. J. Biol. Chem. (2000) 275:19068-19075.