Team:Slovenia/Coiled-coil polyhedra Idea Approach.html
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Latest revision as of 02:35, 22 October 2009
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Summary
We set to prepare complex polyhedra as well as two-dimensional lattice; both can be constructed from interacting rigid polypeptide rods, assuming the polypeptide being equivalent of DNA origami. This could produce structures that do not exist in nature. Coiled-coil interactions represent the best candidate for this type of assembly as their sequence dictates the selectivity and orientation for interactions with other coiled-coil segments. In the section on modeling we analyzed the potentials of this approach and designed amino acid sequences of their building blocks.
![]() Figure 1: TEM image of the self-assembled nanostructure made of K2. Idea & ApproachBased on modeling of self-assembly of interacting coiled-coil-forming segments, we selected one of the simplest combinations that could theoretically form a box as well as cover the plane in a polyhedral lattice. This combination comprised two parallel coiled-coil heterodimers (designed P1 and P2) and one parallel homodimer (Gcn4-p1(I-L)). Between each coiled-coil-forming domain we introduced a dipeptide linker Gly-Ser, to allow the limited flexibility of coiled-coil segments. Additionally the polypeptide construct (Figure 1) included a hexahistidine peptide tag, to facilitate purification, detection and attachment site of additional functions, such as metal or fluorophore binding, to the assembled product. We designed artificial heterodimeric parallel coiled-coil-forming segments (P1 and P2), as described in the modeling section. For parallel homodimeric segment we used Gcn4-p1(I-L) domain described in the literature (Harbury et al., 1993). P1 and P2 were designed to form a stable parallel coiled-coil heterodimer, which strongly prefers this combination and at the same time destabilizes formation of parallel coiled-coil homodimers, antiparallel heterodimers or pairs with central GCN domain. The GCN parallel homodimer coiled-coil was selected for the similar properties. The proposed combination of three coiled-coil segments should enable the self-assembly of a box or a hexagonal network as shown on Figure 2.
![]() Figure 1: Scheme of the K2 polypeptide construct. Gene coding for the described polypeptide was cloned into the vector according to the standard BBC RFC37. Polypeptide consists of a histidine peptide tag, P1, a designed parallel heterodimeric coiled-coil-forming segment, dipeptide linker SG, a parallel homodimeric coiled-coil-forming segment GCN, another dipeptide linker SG and P2, a designed parallel heterodimeric coiled-coil-forming segment that can pair with P1 in a parallel orientation. ![]() Figure 2: Scheme of the self-assembly of a single type of a polypeptide chain comprising three coiled-coil-forming segments (A) where two of them form parallel heterodimers (a-a’) and one forms a parallel homodimer (b). Two chains can form dimers (B, C), which can further assemble into a box (D) or into a hexagonal lattice (E). Arrows denote the orientation of the interacting coiled-coil-forming segments in the assembly. a and a’ denote complementary segments of parallel heterodimer and b denotes the parallel homodimeric segment.
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