Poly coiled-coil structures

Early attempts used data obtained from homopolypeptides, such as poly(Lys), for their basis spectra [87, 88]. In the past fifteen years, approaches using data from globular proteins have emerged [18, 89-101]. Basically, a data base comprised of proteins with known secondary structure compositions is assembled and far UV CD spectra recorded. The choice of the proteins to be included is critical and various combinations have been examined. Mathematical matrix methods can be used to extract basis spectra which represent the contributions from the various secondary structures. Typically, four or five basis spectra can be obtained (corresponding to a helices, jj sheets, p turns, and random coil structures). In some approaches, such as those developed by Johnson and co-workers [11, 12, 51, 52, 102], separate basis spectra can be obtained for parallel and antiparallel p sheets. These basis spectra are then linearly combined to reconstruct the CD spectrum of the protein of interest The proportion of the basis spectra used to provide the best fit to the spectrum corresponds to the percentage of that secondary structure in the protein of interest Complete details of the mathematical algorithms that have been employed can be found elsewhere [10, 12, 17, 89, 103]. 

Conformations of the polymers were studied by CD and optical rotation measurements. Poly-L-lysine is known to exist in disordered, helical and -conformation, depending on the temperature, pH of the system and the solvent used. The side chain of the polymer has a significant effect on the backbone conformation. At neutral pH, poly-L-lysine exists in a random coil structure while at pH above 10, the e-amino group becomes a neutral form and the polymer undergoes transition to a helical structure. In order to elucidate the effect of base substituents on the conformation of poly-L-lysine, CD spectra of the copolymer were measured. 

The helical structure observed here may be stabilized by interactions which is revealed by the formation of a double helix of poly A in acidic aqueous solution74. With rising pH of the system, helicity of the polymer increases due to release of the electrostatic repulsion between positively charged side chains. Above pH 2.5, the spectra cannot be measured, as the polymer begins to precipitate in aqueous solution. By adding EG, helicity tends to increase (Fig. 22). In EG, however, poly-L-lysine - HBr still exists in a random coil structure. Therefore, it can be assumed that EG rather depresses the electrostatic repulsion between piotonated adenine units. 

For PLL-T-93 and PLL-T-79, the values of [0]222 in alkaline pH region are plotted against the pH (Fig. 23). These polymers tend to exist in a helical conformation at neutral pH while poly-L-lysine exists in a random coil structure. In contrast to the latter, helicity of PLL-Ts decreases with increasing pH of the system. The decrease in helicity may be caused by the electrostatic repulsion between negatively charged thymine basses which are formed by deprotonation at N-3 in the base. The helicity of PLL-T-79 is lower at neutral pH and higher at alkaline pH than that of PLL-T-93. This can be explained by the fact that the unreacted free amino units in poly-L-lysine at neutral pH assume a random coil structure, whereas at alkaline pH they exist in a helical conformation. A similar tendency was observed in the case of PLL-U-93 and PLL-U-76. 

We have recently reported that the low molecular weight poly-L-lysine derivatives are present in a random coil structure, in spite of the high content of the base, and are unable to form the polymer complex79. The formation of such a complex was not observed for the polyMAOA low molecular weight PLL-T system. This fact indicates that polyMAOA and PLL-T occurring in a random coil structure are incompatible and unable to penetrate each other. 

The exponent a in the intrinsic viscosity-molecular weight relationship ([rj] = K.M ) of a polymer is associated with the expansion of the polymer in solution, and hence with the conformation and stiffness of the polymer (Table 24). The a values of tobacco mosaic virus, Kevlar and helical poly(a-amino acids) are close to 2, which means that they take rigid-rod structures. The a values of vinyl polymers are usually 0.5-0.8, indicating randomly coiled structures. In contrast, the a values of substituted polyacetylenes are all about unity. This result indicates that these polymers are taking more expanded conformations than do vinyl polymers. This is atrributed to their polymer-chain stiffness stemming from both the alternating double bonds and the presence of bulky substituents. 

Poly(7V-isopropylacrylamide) (PNlPAAm) is a well-known thermo-responsive polymer and exhibits a lower critical solution temperature (LCST) of 32°C in water. It assnmes a random coil structure (hydrophilic state) below the LCST and a collapsed globnlar stractnre (hydrophobic state) above. Because of this sharp reversible transition, this polymer finds a vast array of applications,... 

FIGURE 2.1 Schematic representation of linear homopolymer formation from one type of monomer unit and the possibly resulting coil structure supplemented by the examples of polystyrene and poly(e-caprolactam) (or nylon 6). 

A comparison of polymers with different polymer backbones is shown in Fig. 5.13 for the non-ionic polymers poly(ethylene oxide) (PEO), poly(acrylamide) (PAAm), and methyl cellulose (ME) in aqueous solution. The heteroatom in the backbone of PEO leads to an expanded coil structure compared to PAAm with the heteroatom in the side chain. Cellulose derivatives have in addition to the heteroatom the ring structure of the anhydroglucose unit in the polymer backbone. The methyl cellulose in this example has a less expanded coil than the synthetic PAAm and PEO. Again, it is hard to distinguish between the influence of the solvation of the polar backbone and the pure steric hindrance of the different backbone structures. 

At least two other secondary structures are observed with peptides a P pleated sheet and a random coil. Poly(aspartic) acid, mentioned previously, forms a random coil structure. A random coil, as its name implies, does not assume a regular structure such as the a-helix because hydrogen bonds are not easily formed. Rotation about the / and ( ) angles (see 126) leads to a random orientation of the various amino acid residues. The -pleated sheet, on the other hand, does involve intramolecular hydrogen bonding. In other words, there are hydrogen bonds between two different peptide chains rather than within a single peptide chain. 

The 2,5-coupling of thiophene monomeric units leads to two possible structures for poly thiophene—a linear and a coiled structure. If the sulfur atoms are oriented trans to each other, a linear polymer results as illustrated in Fig. 13a. If the atoms are cis to each other, the coil structure is favored as shown in Fig. 13b [265,266]. Other heterocyclic polymers [265], such as polypyrrole, are believed to form linear structures. Hence, a linear structure would seem favored for polythiophene. However, the possibility of an alternative structure is quite interesting and two studies have provided some possible evidence for a coil-type structure. 

Out of a number of known polymers known to exhibit this behavior, water-soluble poly(N-isopropylacrylamide) (PNIPAAM) is a very common and extensively studied material. It has a lower critical solution temperature (LCST) of about 32°C [1-6], and below this temperature, the chains exhibit chain-extended conformations and random coil structure. The intermolecu-lar hydrogen bonding with the water molecules due to the chain extended morphology generates the hydrophilic nature of the chains. The chains transform into a more collapsed globular form above the lower critical... 

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