Helical Motifs

It has been suggested that helix packing can be explained by the interaction of the helical dipoles [33-35]. However, in our opinion this is unlikely to be a major determinant of helix packing geometry. 

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RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

This knowledge and understanding may be helpful to characterize local conformations of other optically active polysilanes in solution. For example, poly(methyl-(-)-(3-pinanylsilane) [(+)-7 Mw = 10,200] prepared by Shinohara and co-workers.281 showed a bisignate CD band at 280 and 303 nm, associated with a broad UV absorption at 300 nm in chloroform at 15°C. Since the spectroscopic features are quite similar to those of i,28d-28e it is possible that the main chain in 7 may contain diastereomeric helical motifs with opposite screw senses and different screw pitches. 

To quantitatively characterize the PM populations using chiroptical characteristics, it may be useful to use the gabs values of 16 at each temperature with reference to the regression curve of these gabs values in 17, which is assumed to adopt a purely P 73-helical structure, instead of the Ae value. The analysis is based on the assumption that the weak temperature dependence of the ymax for 17 is due to a minute modification in the screw pitch of the P helix, rather than any formation of the M-helical motif. 

Andersson M. An amphipathic helical motif common to tumourolytic polypeptide NK-lysin and pulmonary surfactant polypeptide SP-B. FEBS Lett 1995 362(3) 328-332. 

The crystal structure of the peptide substrate-binding domain (140—245 of 517 residues of human al subunit) of the human type I enzyme forms 2.5 tetratricopeptide (TPR) repeat domains with five a helices (PDB accession number ITJC). The organization of tyrosine residues is suggested to be key to its interaction with the substrate peptide in a polyproline II helix. The TPR motif is composed of a 34 amino acid repeated a helical motif, and is typically involved in protein-protein interactions. The tandem repeats of TPR motifs are found in many proteins related to chaperone, cell cycle, transcription, and protein transport... 

The nucleotides are linked together via the phosphate groups, which connect the 5 -hydroxyl group of one nucleotide and the 3 -hydroxyl group of the next to form a polynucleotide chain (Fig. la). DNA is not a rigid or static molecule rather, it can adopt a variety of helical motifs. 

Despite the dominance of the a-helical motif as a recognition unit, the /3-sheet motif has been used in a limited number of cases. In these cases (three are known) two chains in the anti-parallel orientation interact with half-sites in adjacent large grooves of the DNA (see fig. 30.28 for an example). (The /3-sheet motif obviously works in these cases de-... 

Tetracopper helicate 26 thus appears only to be isolable as a result of its greater solubility, with respect to higher oligomers. The use of more-soluble subcomponents might thus allow for the preparation of soluble polymers based upon the stacked-helicate motif of 26. 

One may have a question of whether an optically active helical polymer obtained from an enantiopure monomer adopts a purely P- (or M-) screw sense helical main chain in solution at a given temperature, or is composed of an ensemble of pseudo-diastereomeric mixed helical motifs containing P- and M-screw senses. Fluorescence (FL) studies combined with circular dichroism (CD), UV, and NMR spectra of the main chain constitute a powerful probe in identifying the main chain chirality (screw sense, uniformity, and rigidity) and optical purity of helical polymers, since the photoexcited energy above... 

There are many examples of compounds, usually short polymers, that spontaneously form double helical structures. A classic example involves a number of bipyridyl ligands joined by short, flexible spacers. In the presence of Cu(I), which has both an affinity for nitrogen-containing ligands and a preference for a tetrahedral disposition of donor atoms, discrete double helical complexes are formed [23], A similar phenomenon gives rise to a triple helical motif when a metal that preferentially adopts an octahedral coordination geometry is used [24],... 

Figure 39 (a) ORTEP view of the molecular adduct 29 36. (b) H-bonding network of 29 36 (top view down the a axis, (c) Side view of the H-bonding network, (d) Simplified representation of the view in (c) showing the left handed helical motif of the core, (e) Single strand for H-bonded units, (f) Stereoview of the H-bonding network (side view along the b axis) from the X-ray analysis. The helical motif formed by the peripheral residues is of the left-handed type [60],... 

Notably, as was observed for neutral supraminols [51,60], the complex (R,R)-29 (R,R)-44 assumes a helical motif in which chirality is determined by the absolute configuration of the trans-1,2-diaminocyclohexane. 

M. Du, Z.-H. Zhang, W. Guo, X.-J. Fu, Multi-component hydrogen-bonding assembly of a pharmaceutical agent pamoic acid with piperazine or 4,4 -bipyridyl a channel hydrated salt with multiple-helical motifs vs a bimolecular cocrystal, Cryst. Growth Des. 9 (2009) 1655-1657. 

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