Random compact

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... 

Figure C2.5.7. The native confonnation of fast folding sequence (N= 27) witli random bond potentials is shown. This stmcture has c = 22 non-bonded contacts, tlierefore it is not a maximally compact confonnation for which c = 28. The figure was created using RasMol 2.6 [8].

Analysis of tlie global statistics of protein sequences has recently allowed light to be shed on anotlier puzzle, tliat of tlie origin of extant sequences [170]. One proposition is tliat proteins evolved from random amino acid chains, which predict tliat tlieir length distribution is a combination of the exponentially distributed random variable giving tlie intervals between start and stop codons, and tlie probability tliat a given sequence can fold up to fonii a compact... 

A visual inspection of a two-sample chart provides an effective means for qualitatively evaluating the results obtained by each analyst and of the capabilities of a proposed standard method. If no random errors are present, then all points will be found on the 45° line. The length of a perpendicular line from any point to the 45° line, therefore, is proportional to the effect of random error on that analyst s results (Figure 14.18). The distance from the intersection of the lines for the mean values of samples X and Y, to the perpendicular projection of a point on the 45° line, is proportional to the analyst s systematic error (Figure 14.18). An ideal standard method is characterized by small random errors and small systematic errors due to the analysts and should show a compact clustering of points that is more circular than elliptical. 

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. 

Figure 4-150 shows the major components and design of the PDC bit. The polycrystalline diamond compacts, shown in Figure 4-151. The polycrystalline diamond compacts (of which General Electric s) consist of a thin layer of synthetic diamonds on a tungsten carbide disk. These compacts are produced as an integral blank by a high-pressure, high-temperature process. The diamond layer consists of many tiny crystals grown together at random orientations for maximum strength and wear resistance.

The outer layer (beyond the compact layer), referred to as the diffuse layer (or Gouy layer), is a three-dimensional region of scattered ions, which extends from the OHP into the bulk solution. Such an ionic distribution reflects the counterbalance between ordering forces of the electrical field and the disorder caused by a random thermal motion. Based on the equilibrium between these two opposing effects, the concentration of ionic species at a given distance from the surface, C(x), decays exponentially with the ratio between the electro static energy (zF) and the thermal energy (R 7). in accordance with the Boltzmann equation ... 

Fig. 8 The Haug triangle. The three extremes of conformation compact sphere, random coil and rigid rod) are placed at the apices of a triangle. The conformation of a given macromolecule is represented by a locus along the sides of the triangle between these extremes. Knowledge of the power law exponents (see text) can help to give us an idea of the conformation type. From [61]...

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. 

It is essential that the solution be sufficiently dilute to behave ideally, a condition which is difficult to meet in practice. Ordinarily the dilutions required are beyond those at which the concentration gradient measurement by the refractive index method may be applied with accuracy. Corrections for nonideality are particularly difficult to introduce in a satisfactory manner owing to the fact that nonideality terms depend on the molecular weight distribution, and the molecular weight distribution (as well as the concentration) varies over the length of the cell. Largely as a consequence of this circumstance, the sedimentation equilibrium method has been far less successful in application to random-coil polymers than to the comparatively compact proteins, for which deviations from ideality are much less severe. 

A simplified analysis of the effect of particle shape or molecular conformation on SEC calibration has led to the prediction that the more open structure of rigid rod shaped solutes gives a relatively flat SEC-MW calibration curve. As the solute conformation becomes more compact (random-coil to solid-sphere), the SEC-MW calibration curve becomes increasingly steep... 

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. 

Why is this reconciliation important After all, a 6 M GuHCl solution hardly recapitulates the physiologically milieu, and proteins unfolded under more physiologically relevant conditions are often (though not always see Hoshino et al., 1997) much more compact than expected for an excluded-volume random coil. Still, the chemically or thermally... 

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