Intertwined assemblies

FROM FUNCTIONALISED CATENANES, ROTAXANES AND KNOTS TO HIGHER INTERTWINED ASSEMBLIES... 

The asymmetric unit contains one copy each of the subunits VPl, VP2, VP3, and VP4. VP4 is buried inside the shell and does not reach the surface. The arrangement of VPl, VP2, and VP3 on the surface of the capsid is shown in Figure 16.12a. These three different polypeptide chains build up the virus shell in a way that is analogous to that of the three different conformations A, C, and B of the same polypeptide chain in tomato bushy stunt virus. The viral coat assembles from 12 compact aggregates, or pen tamers, which contain five of each of the coat proteins. The contours of the outward-facing surfaces of the subunits give to each pentamer the shape of a molecular mountain the VPl subunits, which correspond to the A subunits in T = 3 plant viruses, cluster at the peak of the mountain VP2 and VP3 alternate around the foot and VP4 provides the foundation. The amino termini of the five VP3 subunits of the pentamer intertwine around the fivefold axis in the interior of the virion to form a p stmcture that stabilizes the pentamer and in addition interacts with VP4. 

SNARE motifs spontaneously assemble into SNARE complexes. These consist of a bundle of four intertwined a-helices that are connected by a total of 16 layers of mostly hydrophobic amino acid side chains. In the middle of the bundle, there is a highly conserved and polar 0-layer consisting of three glutamine and one arginine residue. These residues are among the most conserved in the SNARE superfamily and led to a classification of SNAREs into Q- and R-SNAREs, respectively. Different fusion steps require different sets of SNAREs but some SNAREs can participate in different complexes, and some fusion steps involve several SNARE complexes that appear to operate in parallel and independently. 

The inner structure of polyelectrolyte multilayer films has been studied by neutron and X-ray reflectivity experiments by intercalating deuterated PSS into a nondeut-erated PSS/PAH assembly [94, 99]. An important lesson from these experiments is that polyelectrolytes in PEMs do not present well-defined layers but are rather interpenetrated or fussy systems. As a consequence, polyelectrolyte chains deposited in an adsorption step are intertwined with those deposited in the three or four previous adsorption cycles. When polyelectrolyte mobility is increased by immersion in NaCl 0.8 M, the interpenetration increases with time as the system evolves towards a fully mixed state in order to maximize its entropy ]100]. From the point of view of redox PEMs, polyelectrolyte interpenetration is advantageous in the sense that two layers of a redox polyelectrolyte can be in electrochemical contact even if they are separated by one or more layers of an electroinactive poly ion. For example, electrical connectivity between a layer of a redox polymer and the electrode is maintained even when separated by up to 2.5 insulating bUayers [67, 101-103]. 

Metal-directed Self-assembly of Complex Supramolecular Architecture Chains, Racks, Ladders, Grids, Macrocycles, Cages, Nanotubes and Self-intertwining Strands (Helicates)... 

An individual polypeptide in the a-keratin coiled coil has a relatively simple tertiary structure, dominated by an a-helical secondary structure with its helical axis twisted in a left-handed superhelix. The intertwining of the two a-helical polypeptides is an example of quaternary structure. Coiled coils of this type are common structural elements in filamentous proteins and in the muscle protein myosin (see Fig. 5-29). The quaternary structure of a-keratin can be quite complex. Many coiled coils can be assembled into large supramolecular complexes, such as the arrangement of a-keratin to form the intermediate filament of hair (Fig. 4-1 lb). 

There are many different polymers which are long chains of molecules linked by covalent bonds. The chains can be either intertwined in a loose assembly, or they can be cross-linked by covalent bonds to form a very strong lattice. Chromophoric molecules can be included in polymers in two different ways they can be dispersed at random, rather like in a glassy matrix, or they can be part of the polymer chains themselves. 

The functionalisation also allows extending the complexity of intertwined molecular assemblies involving molecular catenanes, rotaxanes and knots. Elaborate interlocked assemblies constructed by means of metal-templation techniques and ji-ji-stacking preorganisation were reviewed [3, 11], Our last survey was devoted to the hydrogen bond templated synthesis of amide-based catenanes and rotaxanes [32], Since then a considerable advancement in elucidation of mechanisms of templation and derivatisation of the amide-based interlocked structures has been reached. Moreover, in 2000 we reported a one pot synthesis of amide-based knots such as 8 [21], which is so far the easiest preparation of molecular knots. In the following, specific possibilities of functionalisation of amide-based catenanes, rotaxanes and knots will be discussed. 

The advantages of all above amide-based assemblies include the electro-neutral character of the compounds, their relative inertness and, last but not least, possibility of their further functionalisation. The latter can be performed both by wise selection of reagents prior to the assembly of an intertwined compound and by its post-assembly derivatisation or by combination of these two methods. The next section discusses the state-of-the-art in derivatising of the amide-based topologies. 

In the introduction we mentioned extravagant interlocked structures of higher complexity such as doubly intertwined catenane and molecular composite knots of Sauvage et al. and multicatenanes made up of 4 to 7 interlocked rings obtained by Stoddart et al. In this section, we will discuss assemblies made up of amide-based catenanes, rotaxanes and knots. Here we use the term assembly to describe covalent or... 

Sauvage, Fujita, and coworkers have combined both their copper template and palladium self-assembly methodologies to form both a doubly-intertwined... 

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