Structural transitions coil-helix

The structural transition (coil-hehx/helix-coil transition) of polypeptides shows the following features ... 

This one-dimensional intramolecular structural transition, the helix-coil transition, has received extensive theoretical treatment by many investigators.(65-75) Although a variety of models and mathematical techniques have been brought to bear on this problem the basic conclusions have been essentially the same. The methods involved, and the results, have been eloquently summarized in the treatise by Poland and Scheraga.(76) As an example, we will outline the theoretical basis for the transformation in dilute solution of an isolated polypeptide chain from the alpha-helical to the coil form. 

Alanine-derived optically active A-propargylamide 22 and azobenzene-containing monomer 25 afford a co-polymer forming a helix. The azobenzene moiety isomerizes from trans-ioxm to cis-ioxm upon UV light irradiation, accompanying transition from helix to random coil. Then upon irradiation of visible light, the m-azobenezene moiety re-isomerizes into trans, while the polymer main chain keeps a random structure. This is presumably due to large steric repulsion around the azobenzene moiety to disturb recovery of a helical structure. 

Spin-lattice relaxation times and 13C chemical shifts were used to study conformational changes of poly-L-lysine, which undergoes a coil-helix transition in a pH range from 9 to 11. In order to adopt a stable helical structure, a minimum number of residues for the formation of hydrogen bonds between the C = 0 and NH backbone groups is necessary therefore for the polypeptide dodecalysine no helix formation was observed. Comparison of the pH-dependences of the 13C chemical shifts of the carbons of poly-L-lysine and (L-Lys)12 shows very similar values for both compounds therefore downfield shifts of the a, / and peptide carbonyl carbons can only be correlated with caution with helix formation and are mainly due to deprotonation effects. On the other hand, a sharp decrease of the 7] values of the carbonyl and some of the side chain carbons is indicative for helix formation [854]. 

We approached the problem of establishing a structure of the "random coil" conformation by first establishing the limits of the present computational model for a known polymeric structure, the a-helix. Coordinates, created by program MacroModel [22] for the carbonyl groups of a-helical oligomers were used, along with published and experimental dipole transition moments, to compute the VCD and absorption spectra of the a-helical conformer. We found that VCD spectra, independent of chain length, can be calculated for octamers, and that the choice of side chain residues is immaterial for the computed spectra. Both calculated and experimental data were normalized to one residue, to permit a comparison between computed and observed spectra. 

Water molecules and three-center hydrogen bonds as lubricants in structural transitions. If water participates and contributes to protein helix-to-coil transition as illustrated in Fig. 25.4, then one can also envisage comparable and more general schemes of tertiary- and secondary-structure unfolding and folding for proteins,... 

The helix-coil transition is an important structural transition in polypeptides, and it has been extensively studied by a variety of methods. 

Typically, the in vitro folding of a single domain globular protein resembles a first-order phase transition in the sense that the thermodynamic properties undergo an abrupt change, and the population of intermediates at equilibrium is very low. In other words, the process is cooperative and is well described by a two-state model [8]. The first attempts to explain protein folding cooperativity focused on the formation of secondary structure. Theoretical and experimental analysis of coil-helix transitions indeed proved that the process is cooperative [167]. However, the helix-coil transition is always continuous [168], and thus it cannot explain the two-state behavior of the protein folding transition. 

Fig. 3 Schematic view of the human vimentin protein and force-strain curves of coiled-coil intermediate filament under tensile loadings, (a) Schematic representation of vimentin structure, (b) Force-strain behaviors of a coiled-coil a-helical structures revealing the loading rate dependency of the molecular-level stiffness under tensile loading. (Reprinted from [66], with kind permission from Springer Science and Business Media), (c) a-p secondary structural transition of coiled-coil a-helix under tensile loading. (Reprinted from [67])...

FIGURE 14.8 Coil helix transition for meta-linked PPE oligomer (a) and solvent dependence of absorption and fluorescence of m-OPPE-18 (b). Structure of m-OPPE-18 (c) is also shown. (Reprinted from Lahiri, S., J.L. Thompson, and J.S. Moore. /. Am. Chem. Soc., 122, 11315-11319, 2000. With permission.)... 

Figure 7. A list of frequent residue exchanges in making secondary structural transitions in pentapeptide pairs of unrelated protein structures. The pentapeptides differed by only one amino acid. The terms H, E, T, 0, refer respectively to helix, strand, turn conformations and other unclassifiable structures (coil).

Experiments reveal that the formation of the elements of various internal structures in macromolecules changes the IMM of the latter The appearance of local regions with internal structures in the molecules of PMAA the coil-helix transition in synthetic polypeptides and, finally, the formation of a globular structure in poly(l,2-dimethoxyethylene) molecules " lead to a several fold increase in the relaxation times characterizing IMM an, when the globular structure appears, the relaxation times increase by an order of magnitude (Table 11). 

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