Random coiling

The basic features of folding can be understood in tenns of two fundamental equilibrium temperatures that detennine tire phases of tire system [7]. At sufficiently high temperatures (JcT greater tlian all tire attractive interactions) tire shape of tire polypeptide chain can be described as a random coil and hence its behaviour is tire same as a self-avoiding walk. As tire temperature is lowered one expects a transition at7 = Tq to a compact phase. This transition is very much in tire spirit of tire collapse transition familiar in tire theory of homopolymers [10]. The number of compact... 

Proteins or sections of proteins sometimes exist as random coils, an arrangement that lacks the regularity of the a helix or pleated p sheet... 

Use the Simha equation and these data to criticize or defend the following proposition These polymer molecules behave like rods whose diameter is 16 A and whose length is 1.5 A per repeat unit. The molecule apparently exists in fully extended form in this solvent rather than as random coils. 

The statistical model of the random coil discussed in Chap. 1 illustrates many of these items. 

The three-dimensional radius of gyration of a random coil was discussed in Sec. 1.10 and found to equal one-sixth the mean-square end-to-end distance of the polymer [Eq. (1.59)]. What we need now is a connection between two-and three-dimensional radii of gyration. Since the molecule has spherical symmetry r, r> = V + r + r, = 3r . If only two of these contributions are present, we obtain (2/3)rg 3 = rg2o- this result and Eq. (1.59) to... 

Although the emphasis in these last chapters is certainly on the polymeric solute, the experimental methods described herein also measure the interactions of these solutes with various solvents. Such interactions include the hydration of proteins at one extreme and the exclusion of poor solvents from random coils at the other. In between, good solvents are imbibed into the polymer domain to various degrees to expand coil dimensions. Such quantities as the Flory-Huggins interaction parameter, the 0 temperature, and the coil expansion factor are among the ways such interactions are quantified in the following chapters. 

Equation (8.97) shows that the second virial coefficient is a measure of the excluded volume of the solute according to the model we have considered. From the assumption that solute molecules come into surface contact in defining the excluded volume, it is apparent that this concept is easier to apply to, say, compact protein molecules in which hydrogen bonding and disulfide bridges maintain the tertiary structure (see Sec. 1.4) than to random coils. We shall return to the latter presently, but for now let us consider the application of Eq. (8.97) to a globular protein. This is the objective of the following example. 

We saw in Chap. 1 that the random coil is characterized by a spherical domain for which the radius of gyration is a convenient size measure. As a tentative approach to extending the excluded volume concept to random coils, therefore, we write for the volume of the coil domain (subscript d) = (4/3) n r, and combining this result with Eq. (8.90), we obtain... 

The above argument shows that complete overlap of coil domains is improbable for large n and hence gives plausibility to the excluded volume concept as applied to random coils. More importantly, however, it introduces the notion that coil interpenetration must be discussed in terms of probability. For hard spheres the probability of interpenetration is zero, but for random coils the boundaries of the domain are softer and the probability for interpenetration must be analyzed in more detail. One method for doing this will be discussed in the next section. Before turning to this, however, we note that the Flory-Huggins theory can also be used to yield a value for the second virial coefficient. 

We begin our attempt to reconcile these two expressions for the excluded volume of the random coil by reviewing some ideas about random coils from Chap. 1 ... 

In addition to an array of experimental methods, we also consider a more diverse assortment of polymeric systems than has been true in other chapters. Besides synthetic polymer solutions, we also consider aqueous protein solutions. The former polymers are well represented by the random coil model the latter are approximated by rigid ellipsoids or spheres. For random coils changes in the goodness of the solvent affects coil dimensions. For aqueous proteins the solvent-solute interaction results in various degrees of hydration, which also changes the size of the molecules. Hence the methods we discuss are all potential sources of information about these interactions between polymers and their solvent environments. 

Both the intrinsic viscosity and GPC behavior of random coils are related to the radius of gyration as the appropriate size parameter. We shall see how the radius of gyration can be determined from solution viscosity data for these... 

One thing that is apparent at the outset is that polymer molecules in solution are very different species from the rigid spheres upon which the Einstein theory is based. On the other hand, we saw in the last chapter that the random coil contributes an excluded volume to the second virial coefficient that is at least... 

The viscosity of a polymer solution is one of its most distinctive properties. Only a minimum amount of research is needed to establish the fact that [77] increases with M for those polymers which interact with the solvent to form a random coil in solution. In the next section we shall consider the theoretical foundations for the molecular weight dependence of [77], but for now we approach this topic from a purely empirical point of view. 

Random coils. Equation (9.53) gives the Kirkwood-Riseman expression for the friction factor of a random coil. In the free-draining limit, the segmental friction factor can, in turn, be evaluated from f. In the nondraining limit the radius of gyration can be determined. We have already discussed f in Chap. 2 and (rg ) in this chapter and again in Chapter 10, so we shall not examine the information provided by D for the random coil any further. 

The extension of these ideas to random coils can proceed along two lines. In one analysis the coil domain is visualized as a sphere, as in the case above, with r taking the place of R. Alternatively, statistical methods can be employed... 

An interesting outgrowth of these considerations is the idea that In r versus K or Vj should describe a universal calibration curve in a particular column for random coil polymers. This conclusion is justified by examining Eq. (9.55), in which the product [i ]M is seen to be proportional to (rg ), with r = a(rg 0 ) - This suggests that In rg in the theoretical calibration curve can be replaced by ln[r ]M. The product [r ]M is called the hydrodynamic volume, and Fig. 9.17 shows that the calibration curves for a variety of polymer types merge into a single curve when the product [r ]M, rather than M alone, is used as the basis for the cafibration. 

Figure 10.13 Variation of the dissymmetry ratio z with a characteristic dimension D (relative to X) for spheres, random coils, and rods. (Data from Ref. 4.)...

Figure 10.13 shows such plots of z versus D/X, where D is r for random coils, R for spheres and disks, and L for rods. More detailed theories permit these curves to be extended to larger values of than is justified by consideration of Eq. (10.97) alone. In the following example we illustrate an application of this simple method for estimating particle dimensions. 

With appropriate caUbration the complex characteristic impedance at each resonance frequency can be calculated and related to the complex shear modulus, G, of the solution. Extrapolations to 2ero concentration yield the intrinsic storage and loss moduH [G ] and [G"], respectively, which are molecular properties. In the viscosity range of 0.5-50 mPa-s, the instmment provides valuable experimental data on dilute solutions of random coil (291), branched (292), and rod-like (293) polymers. The upper limit for shearing frequency for the MLR is 800 H2. High frequency (20 to 500 K H2) viscoelastic properties can be measured with another instmment, the high frequency torsional rod apparatus (HFTRA) (294). 

Films or membranes of silkworm silk have been produced by air-drying aqueous solutions prepared from the concentrated salts, followed by dialysis (11,28). The films, which are water soluble, generally contain silk in the silk I conformation with a significant content of random coil. Many different treatments have been used to modify these films to decrease their water solubiUty by converting silk I to silk II in a process found usehil for enzyme entrapment (28). Silk membranes have also been cast from fibroin solutions and characterized for permeation properties. Oxygen and water vapor transmission rates were dependent on the exposure conditions to methanol to faciUtate the conversion to silk II (29). Thin monolayer films have been formed from solubilized silkworm silk using Langmuir techniques to faciUtate stmctural characterization of the protein (30). ResolubiLized silkworm cocoon silk has been spun into fibers (31), as have recombinant silkworm silks (32). 

The secondary stmcture of the plasminogen molecule, as determined by circular dichroism spectra, is 80% random coil, 20% beta-stmcture, and 0% alpha-helix. Electron microscopy has demonstrated the tertiary stmcture of plasminogen to be a 22- to 24-nm long spiral filament with a diameter of 2.2 to 2.4 nm. 

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