Coil-compact structure

The described theoretical model involves a basic molecular actuator constituted by an ideal and lineal polymeric chain. We can imagine this basic chain coimected to a metallic electrode and immersed in an electrolyte (Figure 16.5). The strong intramolecular interactions produce a coil-compact structure of the chain. During oxidation, consecutive electrons are extracted from the chain, positive charges are... 

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. 

Under a variety of conditions, plasmid DNA undergoes a dramatic compaction in the presence of condensing agents such as multivalent cations and cationic polymers. Naked DNA coils, typically with a hydrodynamic size of hundreds of nanometers, after condensation it may become only tens of nanometer in size. Contrary to proteins which show a unique tertiary structure, DNA coils do not condense into unique compact structure. Cationic polymers execute their gene carrier function by their condensation effect on gene materials and, furthermore, their protection effect on DNA from nuclease digestion. Currently, the most widely used cationic polymers in research include linear or branched PEI (poly (ethyleneimine) (161-165), polypeptides such as PLL (poly-L-lysine) (166-169), PLA (poly-L-arginine) (170). 

Figure 27-5 (A, B) Two possible models of the 30-nm chromatin fiber.55 (A) Thoma et al.85 (B) Woodcock et al.6i 87 The fully compacted structure is seen at the top of each figure. The bottom parts of the figures illustrate proposed intermediate steps in the ionic strength-induced compaction. (C) Possible organization of the DNA within a metaphase chromosome. Six nucleosomes form each turn of a solenoid in the 30-nm filament as in (A). The 30-nm filament forms 30 kb-loop domains of DNA and some of these attach at the base to the nuclear matrix that contains topoisomerase II. About ten of the loops form a helical radial array of 250-nm diameter around the core of the chromosome. Further winding of this helix into a tight coil 700 nm in diameter, as at the top in (C), forms a metaphase chromatid. From Manuelidis91.

Calsequestrin is a calcium-storage protein found in the sacroplasmic reticulum, which binds about 50 calcium ions per monomer (molecular weight 40 000) with binding constants in the range 103-105 dm3 mol. Release and uptake of Ca2+ during muscle contradion and relaxation involve this store. Calsequestrin from rabbit skeletal muscle has a random coil conformation in the absence of calcium. Binding of Ca2+ is associated with a change to a more compact structure.267... 

The monomer-monomer correlation functions of flexible polyelectrolytes exhibit qualitatively the same behavior as those for rod-like molecules. The conformational changes, however, result in more pronounced and shifted peaks. From Fig. 8 we deduce a shift of the peaks of flexible chains to larger distances compared to those of rod-like chains. This is a consequence of a smaller overlap between flexible chains compared to the one between rodlike molecules. Naturally, the effect is most pronounced for densities larger than the overlap densities. The increased peak intensity corresponds to a more pronounced order in the system of flexible chains, and is a result of the more compact structure of a polymer coil. (The structural properties of flexible polyelectrolytes without medium-induced potential have been studied in [48].)... 

In the nucleus, DNA is packed in chromatin. In this compact structure, most DNA-sequences are structurally inaccessible and functionally inactive. The nucleosomes are the fundamental subunits of chromatin, they consist of a core of histones with two turns of DNA coiled around it. Despite... 

Two major kinds of secondary structure found in proteins are the a-helix (conventionally represented as a cylinder) and the (3-strand (represented as a flat sheet with an arrow head indicating the N- to C-terminal direction). The a-helix can be envisaged as a tightly coiled, compact spring whereas the (3-strand is like a spring that has been stretched out. 

It should be noted that, due to the difficulty of perfect mutual packing of two flexible polymer chains, the complex structure is imperfect and, along with complexed parts, there may exist imperfect ones such as loops. Mutual screening of hydrophilic parts of the interacting macromolecules leads to strong hydrophobization of the polymer complex in aqueous solution and its coiling up into a compact structure. 

A highly idealized model has been postulated for the albumin molecule to account for the behavior of albumin at low pH, and for the destruction, upon isomerization, of the 10 or 12 strong binding sites for detergent ions (F15). Observations of the X-ray diffractions of bovine albumin at pH 3.6 also indicated that the molecule was not uniform or compact. It was considered that at acidic pH about one third of the polypeptide chain unraveled and assumed a loose random-coil-like structure while the rest of the molecule remained folded in a compact particle (L21). Under natural conditions, i.e., in blood plasma, albumin exists partly in the a-helix and partly in the random form (D13). 

The degree of swelling of a random coil depends on the quality of the solvent. While 6 M GuCl or 8 M urea are moderately good solvents for randomly coiled proteins [2,3], water is certainly a rather bad one for denatured proteins, as demonstrated by the compact structure of the native state and suggested by their strong propensity to aggregate when unfolded in water, after heat denaturation for example. The problem is to know whether the size of denatured pro-... 

The thermodynamic affinity of cyclohexane to polystyrene is known to increase with temperature and, naturally, increasing the temperature must further raise the volume of the polystyrene networks in cyclohexane. There is, however, an additional point we should consider. The plot of Q vs. temperature exhibits a steplike discontinuity at around 30°C (Fig. 1.14). This discontinuity, resemhling very much a -transition, is located 3-5°C below the -temperature for linear polystyrene in cyclohexane and about 8°C above the -point for star-shaped polystyrene macromolecules. This phenomenon is outside the scope of the questions discussed here, but, naturally, the first assumption of the authors [143] seems to be very logical, according to which the discontinuity reflects a transition from Gaussian coil to a supercoiled compact structure on cooling the swollen gel below that temperature zone. 

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