Biopolymers, helical structures

The suggestion of a helical host molecule was originally put forward by Hanes 136) and then developed by Freudenberg and his colleagues 137). Chemical 138 140) and X-ray diffraction studies by Rundle et al.141 143) and by Bear 144,145) demonstrated that these ideas were correct, and revealed that the helical structure had an outer diameter of 13.0 A, an inner diameter of 5 A, and a pitch of 8.0 A with six glucose units per turn. The iodine atoms were arranged in a linear fashion with an average I-I separation of approximately 3.1 A. These early results have been reviewed 146, 147). They represent the first confirmed example of helical structure for a biopolymer. 

Kishimoto T, Morihara Y, Osanai M, Ogata S-1, Kamitakahara M, Ohtsuki C, Tanihara M. Synthesis of poly(Pro-Hyp-Gly)n by direct polycondensation of (Pro-Hyp-Gly)n, where n = 1, 5, and 10, and stability of the triple-helical structure. Biopolymers 2005 79 163-172. 

As discussed in Section 3.1.6.1., natural biopolymers are useful chiral selectors, some of which are readily available they are constructed from chiral subunits (monomers), for instance, from L-amino acids or D-glucose. If synthetic chiral polymers of similar type are to be synthesized, appropriate chiral starting materials and subunits, respectively, must be found. Chiral polymers with, for example, a helical structure as the chiral element, are built using a chiral catalyst as chirality inducing agent in the polymerization step. If the chirality is based on a chiral subunit, the chirality of the polymer is inherent, whereas if the polymer is constructed from chiral starting materials, chiral subunits are formed which lead to chirally substituted synthetic polymers that in addition may order or fold themselves to a supramolecular structure (cf. polysaccharides). 

In both starch and glycogen the glucose emits of the main chains are linked with a-1,4 linkages. An extended conformation is not possible and the chains tend to undergo helical coiling. One of the first helical structures of a biopolymer to be discovered (in 1943)76 77 was the left-handed helix of amylose wound around molecules of pentaiodide (I5 ) in the well-known blue starch-iodine complex78 (Fig. 4-8). Tire helix contains six residues per turn, with a pitch of 0.8 nm and a diameter of nearly 14 nm. Amylose forms complexes of similar structure with many other small molecules.79... 

Discrimination between stereoisomers in biological environments should in fact not be unexpected, as at a molecular level such environments are composed of handed macromolecules, i.e., proteins, glycolipids and nucleic acids, from the chiral precursors of L-amino acids and D-carbo-hydrates. In addition, the macromolecular structures of these biopolymers also give rise to chirality as a result of helicity, e.g., the protein a-helix and DNA double helix. Such helical structures may have either a left or right handed turn in the same way that a spiral staircase may be left or right handed. In the case of the DNA double helix and the protein ot-helix, the biopolymers have a right-handed turn. 

In some molecules intramolecular H-bonding, i.e. H-bonding within one molecule, can take place, which usually leads to the formation of helical structures. Such structures are particularly important in biopolymers e.g. the ot-helical conformation of polypeptides (fig. 3.5(a)). The hydrogen bond is a loose kind of bond that is largely electrostatic in nature and its strength lies somewhere between that of the covalent bond and the weak van der Waals attractive forces that are exerted by different neutral molecules when they come within about a molecular radius of each other. 

In an attempt to estimate the energetics and kinetics of nonequilibrium transformations in metastable biopolymers the physical chemical behavior of a model system exhibiting pronounced hysteresis loops was investigated.The model hysteresis to be briefly discussed results from the acid-base titration of the polyelectrolyte complex poly(A) 2poly(U). The overall process underlying the hysteresis loop is the cyclic transition between two helical structures the triple helix poly(A) -2poly(U) and the protonated double helix poly(A) poly(A). 

DNA is a biopolymer characterized by a backbone formed by alternating phosphate and sugar residues and bearing chromophores (the nucleobases) capable of interacting each other to form a structurally complex supramolecular entity. The double helical structure of DNA is stabilized by two interaction types, namely, hydrogen bond and stacking interactions among the nucleobases, which form a column inside... 

Proteins are biopolymers formed by one or more continuous chains of covalently linked amino acids. Hydrogen bonds between non-adjacent amino acids stabilize the so-called elements of secondary structure, a-helices and / —sheets. A number of secondary structure elements then assemble to form a compact unit with a specific fold, a so-called domain. Experience has shown that a number of folds seem to be preferred, maybe because they are especially suited to perform biological protein function. A complete protein may consist of one or more domains. 

In biological systems molecular assemblies connected by non-covalent interactions are as common as biopolymers. Examples arc protein and DNA helices, enzyme-substrate and multienzyme complexes, bilayer lipid membranes (BLMs), and aggregates of biopolymers forming various aqueous gels, e.g, the eye lens. About 50% of the organic substances in humans are accounted for by the membrane structures of cells, which constitute the medium for the vast majority of biochemical reactions. Evidently organic synthesis should also develop tools to mimic the Structure and propertiesof biopolymer, biomembrane, and gel structures in aqueous media. 

Carrageenans and alginates present different conformations egg-box structure (alginates) and double helices (carrageenan) but both natural biopolymers are able to form gels and consequently, to control nanoparticle growth. 

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