Helix-coil transitions

Although dispersed polymer chains usually adopt the random coil configuration in dilute solution, there are some important exceptions. These exceptions occur 

Specific inter- and intramolecular bonding are not necessary for ordered structures to persist in dilute solution. Ordered structures, that lead to highly asymmetric molecules, can be perpetuated by severe steric repulsions of substituents or an inherent restraint to rotations about single bonds. Such structures are known, even among synthetic macromolecules, and they form liquid-crystal systems. Some examples are polymeric aramides, poly(N-alkyl isocyanates) and some cellulose derivatives. 

When individual, isolated molecules exist in helical, or other ordered forms, environmental changes, either in the temperature or solvent composition, can disrupt the ordered structure and transform the chain to a statistical coil. This conformational change takes place within a small range of an intensive thermodynamic variable and is indicative of a highly cooperative process. This reversible intramolecular order-disorder transformation is popularly called the helix-coil transition. It is an elementary, one-dimensional, manifestation of polymer melting and crystallization. 

Many examples of this type of transformation are available in the literature, particularly among polymers of biological interest. One example is the polypeptide poly-L-glutamic acid that exists as a coiled molecule in dilute neutral or alkaline solutions. However, when the pH is lowered below about 5.0 the ordered alpha-helical form is generated. This molecular transformation results in large changes in 

An example of a similar type of cooperative transformation is shown in Fig. 3.17 for different molecular weight nucleic acids (obtained by shear degradation) from T2 bacteriophage.(62) This temperature induced transformation is quite clear in the figure. At low temperature all the appropriate bases are bonded, one to another at high temperature, in the disordered state, the bases are no longer bonded. The 

---

The conformational transitions in the presented model take place accord-itig to the all-or-nothing law, i.e. they occur at the certain r.h. value. The same behaviour has been observed, for example, for the helix-coil transition of the model double-stranded structure A(pA)i7-U(pU)i7 [24]. It is worth noting that this structure is homogeneous, the same is supposed in our model. 

Theory of helix-coil transitions in biopolymers. (Poland, D., Scheraga, H.A., eds) Academic Press, New York (1970)... 

Porschke, D., Eigen, M. Cooperative nonenzymic base recognition. HI. Kinetics of the helix-coil transition of the oligoribouridylic oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J. Mol. Biol. 62 (1971) 361-381... 

Porschke D. Elementary steps of base recognition and helix-coil transitions in nucleic acids. Mol. Biol. Biochem. Biophys. 24 (1977) 191-218... 

Okamoto Y and U H E Hansmann 1995. Thermodynamics of Helix-coil Transitions Studied 1 Multicanonical Algorithms. Journal of Physical Chemistry 99 11276-11287. 

It is not the purpose of this book to discuss in detail the contributions of NMR spectroscopy to the determination of molecular structure. This is a specialized field in itself and a great deal has been written on the subject. In this section we shall consider only the application of NMR to the elucidation of stereoregularity in polymers. Numerous other applications of this powerful technique have also been made in polymer chemistry, including the study of positional and geometrical isomerism (Sec. 1.6), copolymers (Sec. 7.7), and helix-coil transitions (Sec. 1.11). We shall also make no attempt to compare the NMR spectra of various different polymers instead, we shall examine only the NMR spectra of different poly (methyl methacrylate) preparations to illustrate the capabilities of the method, using the first system that was investigated by this technique as the example. 

Helix-coil transition Hormone activation Milleseconds (ms) to hours... 

Teramoto, A. and Fujita, H. Conformation-dependet Properties of Synthetic Polypeptides in the Helix-Coil Transition Region. Vol. 18, pp. 65— 149. 

Thermodynamic Aspects of the Triple Helix-Coil Transition. . 186... 

In 1% aqueous acetic acid, the peptides of the sequence (Ala-Gly-Pro)n, bridged with Lys-Lys and beginning with n = 8 show a cooperative transition, which was interpreted as a triple helix-coil transition (see Figs. 35, 36). 

Because of these observations, comparative experiments with peptides of different proline content in a solvent less polar than water, are recommended. (Pro-Pro-Gly)n and (Pro-Ala-Gly)n, in methanol/acetic add (volume ratio 9 1) show a temperature-induced triple helix-coil transition which is characterized by the following parameters92,150) (Pro-Pro-Gly)n AH°s = -1.9 kJ/rnol tripeptide AS° = -5.4 J tnor1 K (Pro-Ala-Gly) A HI = -0.9 kJ/mol tripeptide A 5° = -3.8 J mol-1 K ... 

E Pefferkorn, A Schmitt, R Varoqui. Helix-coil transition of poly(a,L-glutamic acid) at an interface Correlation with static and dynamic membrane properties. Biopolymers 21 1451-1463, 1982. 

Lifson, S. Roig, A., Theory of helix-coil transition in polypeptides, J. Chem. Phys. 1961, 34, 1963-1974. 

Typical examples are the conversion of the neutral form of an amino acid into its zwitterionic form, the helix-coil transitions in polypeptides and polynucleotides, and other conformational changes in biopolymers. Reactions of higher molecularity in which reactants and products have different dipole moments are subject to the same effect (association of the carboxylic acids to form hydrogen-bonded dimers). Equilibrium involving ions are often more sensitive to the application of an electric field ... 

Bond DNA vibrations twisting Hinge motions Helix-coil transitions Protein folding Protein aggregation ... 

Both ORD and CD are important tools in the study of molecular conformation in solution. These techniques are of special importance in the study of biomolecules, their helical content, and helix-coil transitions. 

The NMR data (James et al., 1997 Liu et al., 1999) show a slight reverse turn in the HI domain, similar to that proposed from X-ray diffraction (Inouye and Kirschner, 1998) however, NMR indicates that the turn is close to Alai 17. A molecular dynamics study of the helix-coil transition of PrP106—126 (Levy et al., 2001) indicates that the turn is near Alai 15, such that Hislll would interact with Vall22 rather than with Alall7. The HI domain, initially modeled as an z-helix. also adopts a /Miairpin fold as shown by molecular dynamics simulation (Daidone et al., 2005). 

Levy, Y., Hanan, E., Solomon, B., and Becker, O. M. (2001). Helix-coil transition of PrP106-126 Molecular dynamic study. Proteins 45, 382-396. 

Very recently, however, two papers were published by the group of Fujiki which report successful solid-state CD studies of chiral polysilanes. In the first, a helix-coil transition was described for film samples of poly[(A)-3,7-dimethyloctyl- -propylsilylene)], 113.327 This polymer has a relatively low glass transition temperature, T, which was considered critical for the observation of a helix-helix transition in the solid state, since helical inversion would be precluded if the inversion temperature, Tc, were below Ts as the segmental motion of the chain,... 

In this section we introduce the matrix method to rewrite the GPF of a linear system of m sites in a more convenient form. This is both an elegant and a powerful method for studying such systems. We start by presenting the so-called Ising model for the simplest system. We assume that each urrit can be in one of two occupational states empty or occupied. Also, we assirme only nearest-neighbor (nn) interactions. Both of these assumptions may be removed. In subsequent sectiorrs and in Chapter 8 we shall discuss four and eight states for each subunit. We shall not discuss the extension of the theory with respect to interactions beyond the nn. Such an extension is used, for example, in the theory of helix-coil transition. 

---