Coiled coil structures structural parameters

Chapter 13 - It was shown, that limiting conversion (in the given case - imidization) degree is defined by purely structural parameter - macromolecular coil fraction, subjected evolution (transformation) in chemical reaction course. This fraction can be correctly estimated within the framework of fractal analysis. For this purpose were offered two methods of macromolecular coil fractal dimension calculation, which gave coordinated results. 

The deterioration of the solvent qnality, that is, the weakening of the attractive interactions between the polymer segments and solvent molecules, brings about the reduction in the coil size down to the state when the interaction between polymer segments and solvent molecules is the same as the mutual interaction between the polymer segments. This situation is called the theta state. Under theta conditions, the Flory-Huggins parameter % assumes a value of 0.5, the virial coefficient A2 is 0, and exponent a in the viscosity law is 0.5. Further deterioration of solvent quality leads to the collapse of coiled structure of macromolecules, to their aggregation and eventually to their precipitation, the phase separation. 

All factors related to the arrangement of the polymer chain in space are classified as tertiary structure. Parameters measurable directly (the radius of gyration RG, the end-to end distance h, the hydrodynamical radius RH, and the asymmetry in light scattering intensity) or indirectly (interaction parameters, the second virial coefficient A2) are related to the dimensions, such as size and shape of the polymer chain in a specific solvent under given conditions of temperature and pressure. For the exact determination of the coil size of macromolecules, it is necessary to ensure that measure-... 

Fig. 2. Parameters of coiled-coil structure. The schematic cross sections are viewed from the amino-terminal end of the structures.

Values for the Main Structural Parameters in Coiled Coils with Various Periodicities, Determined Using the Program TWISTER... 

Two of the hydrophihcity scales in Table 2 were derived from experimental measures of the behavior of amino acids in various solvents, namely partitioning coefficients [K-D index of Kyte and Doolittle (30)] or mobility in paper chromatography [Rf index of Zimmerman et al. (31)]. By contrast, the Hp index was obtained from quantum mechanics (QM) calculations of electron densities of side chain atoms in comparison with water (32). The Hp index is correlated highly with these two established hydrophobicity scales (Table 4). Therefore, like the polarizability index, it is possible to represent fundamental chemical properties of amino acids (hydrophUicity, Hp) with parameters derived from ab initio calculations of electronic properties. However, in contrast to polarizabihty (steric effects), hydrophihcity shows significant correlation with preference for secondary structure. Thus, hydrophobic amino acids prefer fi-strands (and fi-sheet conformations) and typically are buried in protein structures, whereas hydrophilic residues are found commonly in turns (coil structure) at the protein surface. 

The investigations presented focus on interpretation of polarization of fluorescence measurements and use of these measurements to study the structure of a representative spectrum of linear synthetic polypeptides, a vinyl polymer, and an intramolecularly cross-linked synthetic polypeptide. The methodological studies investigate the validity of the transition temperature as a structural parameter, the interaction of the fluorescent dye and the polymer to which it is conjugated, and the influence of the dye-polymer interaction on the measurements of various molecular parameters. The structural studies focus on the structure of the random coil, the helix-coil transition, the a-helix to conformation transition in polylysine, and the stability of the spatial structure in intramolecularly cross-linked synthetic polypeptides. 

Early attempts by Greenfield and Fasman (6) centered around the derivation of [0]x from model polypeptides, and by assuming only three conformations common to polypeptides and proteins (a-helix, a (3-sheet, and coil), it was possible to obtain structural parameters relatively consistent with x-ray data using ellipticity values at two wavelengths ... 

Hence, the stated above results demonstrated the possibility of the prediction of molecule (molecules totality) structure of organic solvents, characterized by its fiactal dimension, on the basis of one characteristic only, that is, the solvent solubility parameter 6. In its turn, this circumstance gives the possibility of prediction of a macromolecular coil structure, characterized by its fractal dimension in diluted solutions with different solvents participation. A number of specific features of systems polymier-solvent was obtained and considered, is due to their structural characteristics. 

In Table 17 the comparison of different parameters for PAr on the basis of phenolphthaleine (F-2 according to the designation, accepted in Ref. [5]) for different solvents, in which Maik-Kuhn-Houwink parameters were determined. Firstly, 6 calculation according to the Eq. (18) of Chapter 1 gave these dimension values of 0.36-0.84 for F-2, received by equilibrium polycondensation, and 8 0—for received by interphase polycondensation. This means that the solvent molecules stmcture does not influenced (does not screened repulsive interactions) on F-2 macromolecular coil structure, received by interphase polycondensation, and influences on the similar factor for F-2, received by high-temperature polycondensation. In other words, if the solvent influences on formation of coil structure in synthesis process, then it will be influenced and on this polymer formed coil structure at subsequent... 

The Eqs. (175)-(177) reflect the change dynamics of macromolecular coil structure in solution and nonaccounting for this factor serious enough errors in estimation can be introduced. The intrinsic viscosity [rj] values, calculated according to the Eq. (10), are adduced in Table 23, from which their both qualitative and quantitative correspondence to this parameter experimental values [rj] follows (the average discrepancy of [rj] and [rj] makes up 8%). 

PAASO is shown, from which the linear correlation between these parameters follows. Hence, the heterogeneity parameter h physical significance can be defined as follows the macromolecular coil structure heterogeneity is defined by this coil fraction, surviving in chemical reaction process. This means that the fractal object degradation process includes memory effects [36]. From the plot of Fig. 3.5 the analytical relationship between h and can be obtained [32] ... 

Hence, the stated above results have shown that melt viscosity extreme change of nanocomposites HDPE-EP could be described within the framework of the fractal model. The main structural parameter, controlling this effect, is the change of the fractal dimension of macromolecular coil in melt. The main physical cause, defining the mentioned effect, is a partial interaction of HDPE matrix and epoxy polymer particles. In this case the... 

A prerequisite for a qualitative as well as quantitative analyses of ehemieal shift data of proteins with elevating pressure is the eomparison with standard parameters from random-eoil peptides to separate speeilie structural features from unspecific factors characteristic for a given amino acid residue. Very early in NMR spectroscopy, Bundi and Wuthrich introduced the tetrapeptides Gly-Gly-X-Ala as reference compounds for the random-coil structures. They reported the H-chem-ical shifts of these peptides in aqueous solution with X representing one of the 20 DNA-encoded amino acids. Later on, and N-chemical shifts of these peptides were published. H- and P-chemical shifts are also reported for the phosphorylated forms of these peptides with X = P-His, P-Asp, P-Ser, P-Thr, P-Tyr and P-Hyp. ... 

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