Complex motifs

Simple motifs combine to form complex motifs... 

Figure 2.21 illustrates the 24 possible ways in which two adjacent p hairpin motifs, each consisting of two antiparallel p strands connected by a loop region, can be combined to make a more complex motif. 

A survey of all known structures in 1991 showed that only those eight arrangements shown in Figure 2.21a occurred either as a complete p sheet or as a fragment of a p sheef with more than four strands. The number of times that these complex motifs occurred were 65, 29, 23, 11, 9, 3, 2, 1 for (i) to... 

The 16 possible motifs shown in Figure 2.21b never occur. Even if this database is limited compared with the universe of existing proteins, the survey clearly demonstrates that a few topological arrangements occur much more frequently than others, and that most possible complex motifs never occur or occur only in a few cases. In 1995 a preliminary survey of a much larger database of known structures yielded the same basic conclusions. 

Both Sfi fchair) and ferown) are all -cis con-foratations, but larger rings have more complex motifs. 

Suppression of the Pummerer reaction (Fig. 24) could also be a manifestation of the stabilization of the persulfoxide which prevents its interconversion to the hydro-peroxysulfonium ylide, HPSY (Fig. 25), which is the intermediate that has been suggested to undergo a 1,2-shift of the hydroperoxy group and ultimately produces the SC bond cleavage products.92 However, the situation is probably more complex since the intrazeolite reaction of /1-chlorosulfide, 29 (Fig. 28A), requires 7-hydrogen abstraction. The complexation motif (Fig. 28B) which favors the extended rather than folded M+-PS may also play an important role. A complete understanding of these reactions will require additional studies. 

Following these rules, complex motifs can be built up from simple ones. For example, a series of /3-a-/3 loops, arranged so that the /3 strands form a barrel, creates a particularly stable and common motif called the a//3 barrel (Fig. 4-21). In this structure, each parallel /3 segment is attached to its neighbor by an a-helical segment. All connections are right-handed. The a//3 barrel is found in many enzymes, often with a binding site for a... 

The familiar dsDNA is a linear molecule not suitable for forming complex motifs. To build complex DNA nano architectures, branched DNA molecules are needed. Fortunately, this key problem was resolved. By designing appropriate DNA sequences, the branched DNA molecules can be produced by the conventional solid support synthesis. 

Virtual vertical cutting of this unimolecular barrel gives the barrel-stave , horizontal cutting the barrel-hoop , horizontal and vertical cutting the barrel-rosette motif (Fig. 11.2). More complex motifs that include modification of the lipid bilayer are summarized as micellar pores. 

The diamond lattice representation of a protein, while reasonable for idealized models of / and a proteins, cannot reproduce the chain geometry of more complex motifs such as a// proteins. To remove this fundamental limitation, the chess-knight model [54] of the protein backbone was developed. In contrast to a diamond lattice model, it allows all possible protein folding motifs to be represented at low resolution [121]. The force field requirements for a unique native state are essentially the same in this finer lattice representation as for diamond lattice models. 

Scheme 2 Popular metal complexation motifs used for supramolecular polymer-network formation. py pyridine, bpy bipyridine, tpy terpyridine, BTP 2,6-bis(l,2,3-triazol-4-yl)pyridine, BIP 2,6-bis(l-methylbenzimidazolyl)pyridine, DOPA dihydroxy-phenylalanine, PAA poly (acrylic acid)...

---