Structure coil conformation

Proteins fold on a time scale from [is to s. Starting from a random coil conformation, proteins can find their stable fold quickly although the number of possible conformations is astronomically high. The protein folding problem is to predict the folding and the final structure of a protein solely from its sequence. 

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. 

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. 

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.)...

The reversible recovery of a deformed elastomer to its original (undeformed) state is due to an entropic driving force. The entropy of polymer chains is minimum in the extended conformation and maximum in the random coil conformation. Cross-linking of an elastomer to form a network structure (IX) is... 

Larsen et al. reported the enzymatic cleavage of a desB30 insuhn B-chain from a presequence (Lys(Boc))6. This spacer shifts the conformation of the growing peptide chain from a y9-structure to a random coil conformation and reduces pep-tide-chain aggregation, which otherwise causes serious synthetic problems. Nova-syn KA [18] was employed as a solid support, but unfortunately, no information about the enzyme used was reported [19]. 

Leonchiks A, Liepinsh E, Barishev M, Sharipo A, Masucci MG, and Otting G (1998) Random coil conformation of a Gly/Ala-rich insert in iKB-a excludes structural stabilization as the mechanism for protection against proteasomal degradation. FEBS Lett. 440 365-369. 

Independently, Ruan etal. (1990) demonstrated that unnatural metal-ligating residues may likewise be utilized toward the stabilization of short a helices by transition metal ions (including Zn " ")—these investigators reported that an 11-mer is converted from the random coil conformation to about 80% a helix by the addition of Cd at 4°C. These results suggest that the engineering of zinc-binding sites in small peptides or large proteins may be a powerful approach toward the stabilization of protein secondary structure. 

Elastomers exhibit this behavior due to their unique, crosslinked structure (cf. Section 1.3.2.2). It has been found that as the temperatme of an elastomer increases, so does the elastic modulus. The elastic modulus is simply a measme of the resistance to the uncoiling of randomly oriented chains in an elastomer sample under stress. Application of a stress eventually tends to untangle the chains and align them in the direction of the stress, but an increase in temperatme will increase the thermal motion of the chains and make it harder to induce orientation. This leads to a higher elastic modulus. Under a constant force, some chain orientation will take place, but an increase in temperatme will stimulate a reversion to a randomly coiled conformation and the elastomer will contract. 

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