Coiled conformation

Anisotropic behaviour is also exhibited in optical properties and orientation effects can be observed and to some extent measured by birefringence methods. In such oriented materials the molecules are in effect frozen in an unstable state and they will normally endeavour to take up a more coiled conformation due to rotation about the single bonds. If an oriented sample is heated up the molecules will start to coil as soon as they possess sufficient energy and the mass will often distort. Because of this oriented materials usually have a lower heat distortion temperature than non-oriented polymers. 

Universal SEC calibration reflects differences in the excluded volume of polymer molecules with identical molecular weight caused by varying coil conformation, coil geometry, and interactive propenies. Intrinsic viscosity, in the notation of Staudinger/ Mark/Houwink power law ([77]=fC.M ), summarizes these phenom-... 

A very interesting steric effect is shown by the data in Table 7-12 on the rate of acid-catalyzed esterification of aliphatic carboxylic acids. The dissociation constants of these acids are all of the order 1(T, the small variations presumably being caused by minor differences in polar effects. The variations in esterification rates for these acids are quite large, however, so that polar effects are not responsible. Steric effects are, therefore, implicated indeed, this argument and these data were used to obtain the Es steric constants. Newman has drawn attention to the conformational role of the acyl group in limiting access to the carboxyl carbon. He represents maximum steric hindrance to attack as arising from a coiled conformation, shown for M-butyric acid in 5. 

Proteins fold on a time scale from p seconds to seconds. Starting from a random coil conformation, proteins can find their stable fold quickly, although the number of possible conformations is astronomically high. 

The inability of the strain softened molecules to recover their random coil conformation when unloaded. 

Typically in solution, a polymer molecule adopts a conformation in which segments are located away from the centre of the molecule in an approximately Gaussian distribution. It is perfectly possible for any given polymer molecule to adopt a very non-Gaussian conformation, for example an all-trans extended zig-zag. It is, however, not very likely. The Gaussian set of arrangements are known as random coil conformations. 

The typical shape of most polymer molecules in solution is the random coil. This is due to the relative ease of rotation around the bonds of the molecule and the resulting large number of possible conformations that the molecule can adopt. We should note in passing that where rotation is relatively hindered, the polymer may not adopt a random coil conformation until higher temperatures. 

These studies showed thaL in the absence of nucleic acid, the backbone 1 aPNA had significant a-hehcal content at pH 7 whereas the backbone 2 aPNA was largely in a random coil conformation at physiological pH. The latter aPNA did become a-helical at higher pHs in a manner reminiscent of the structurally related amphipathic peptides. 

After secretion from the cell, certain lysyl residues of tropoelastin are oxidatively deaminated to aldehydes by lysyl oxidase, the same enzyme involved in this process in collagen. However, the major cross-links formed in elastin are the desmosines, which result from the condensation of three of these lysine-derived aldehydes with an unmodified lysine to form a tetrafunctional cross-hnk unique to elastin. Once cross-linked in its mature, extracellular form, elastin is highly insoluble and extremely stable and has a very low turnover rate. Elastin exhibits a variety of random coil conformations that permit the protein to stretch and subsequently recoil during the performance of its physiologic functions. 

Fresh solutions of pustulan, which are presumably in a random-coil conformation, have a positive c.d. at 180 nm (see Fig. 8). The c.d. spectrum... 

Relationships between dilute solution viscosity and MW have been determined for many hyperbranched systems and the Mark-Houwink constant typically varies between 0.5 and 0.2, depending on the DB. In contrast, the exponent is typically in the region of 0.6-0.8 for linear homopolymers in a good solvent with a random coil conformation. The contraction factors [84], g=< g >branched/ <-Rg >iinear. =[ l]branched/[ l]iinear. are another Way of cxprcssing the compact structure of branched polymers. Experimentally, g is computed from the intrinsic viscosity ratio at constant MW. The contraction factor can be expressed as the averaged value over the MWD or as a continuous fraction of MW. 

The conformations adopted by polyelectrolytes under different conditions in aqueous solution have been the subject of much study. It is known, for example, that at low charge densities or at high ionic strengths polyelectrolytes have more or less randomly coiled conformations. As neutralization proceeds, with concomitant increase in charge density, so the polyelectrolyte chain uncoils due to electrostatic repulsion. Eventually at full neutralization such molecules have conformations that are essentially rod-like (Kitano et al., 1980). This rod-like conformation for poly(acrylic acid) neutralized with sodium hydroxide in aqueous solution is not due to an increase in stiffness of the polymer, but to an increase in the so-called excluded volume, i.e. that region around an individual polymer molecule that cannot be entered by another molecule. The excluded volume itself increases due to an increase in electrostatic charge density (Kitano et al., 1980). 

Random coil conformations can range from the spherical contracted state to the fully extended cylindrical or rod-like form. The conformation adopted depends on the charge on the polyion and the effect of the counterions. When the charge is low the conformation is that of a contracted random coil. As the charge increases the chains extend under the influence of mutually repulsive forces to a rod-like form (Jacobsen, 1962). Thus, as a weak polyelectrolyte acid is neutralized, its conformation changes from that of a compact random coil to an extended chain. For example poly(acrylic acid), degree of polymerization 1000, adopts a spherical form with a radius of 20 nm at low pH. As neutralization proceeds the polyion first extends spherically and then becomes rod-like with a maximum extension of 250 nm (Oosawa, 1971). These pH-dependent conformational changes are important to the chemistry of polyelectrolyte cements. 

Altschuler EL, Hud NY, Mazrimas JA, Rupp B. Random coil conformation for extended polyglutamine stretches in aqueous soluble monomeric peptides. J Peptide Res 1997 50 73-75. 

We now report that in the region of the absorption band the flow linear dichroism of a solution of 1 is positive (Fig. 3). Assuming that the nature of the flow orientation is of the usual kind, i.e., that the polymer chains in a random coil conformation which dominates in solution (34) tend to align with the flow direction, this observation provides additional support for the absolute assignment of the transition moment direction along the chain direction, even in solution. Similar conclusions based on polarization studies on a stretched film of poly(di-n-hexyl silane) have recently been reported (36). 

M molar mass), where I and III are the tricritical or -regions. Here, the chain molecules exhibit an unperturbed random coil confirmation. In contrast, I and II are the critical or good solvent regimes, which are characterized by structural fluctuations in direction of an expanded coil conformation. According to the underlying concept of critical phenomena, the phase boundaries have to be considered as a continuous crossover and not as discontinuous transitions. 

Fig. 44. Distribution of Ala in the Ramachandran plot when using (A) all secondary structure conformations in the protein database or (B) only those Ala residues in a coil conformation. (From Serrano, 1995. 1995, with permission from Academic Press.)...

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