Coil-to-helix transition

If Pn is the dominant conformation for oligo (Ala), the traditional description of helix formation in Ala-rich model peptides as a helix-to-coil transition may be a misnomer. Questions that remain to be addressed include the following Where does the energetic barrier come... 

Both the denaturation process in proteins and the melting transition (also referred to as the helix-to-coil transition) in nucleic acids have been modeled as a two-state transition, often referred to as the all-or-none or cooperative model. That is, the protein exists either in a completely folded or completely unfolded state, and the nucleic acid exists either as a fully ordered duplex or a fully dissociated monoplex. In both systems, the conformational flexibility, particularly in the high-temperature form, is great, so that numerous microstates associated with different conformers of the biopolymer are expected. However, the distinctions between the microstates are ignored and only the macrostates described earlier are considered. For small globular proteins and for some nucleic acid dissociation processes,11 the equilibrium between the two states can be represented as... 

PI6.4 The tetramethylammonium ion (Me4N+) has been reported to stabilize oligonucleotides. Marky et a/.20 have studied its effect on the helix-to-coil transition in poly(dA-dT). They compared their results with similar studies conducted in solutions containing the sodium ion of the same concentration. The results are summarized below ... 

L.A. Marky, D. Patel, and K. J. Breslauer, Effect of Tetramethylammonium Ion on the Helix-to-Coil Transition of Poly(deoxyadenylylthymidine) A Nuclear Magnetic Resonance and Calorimetric Investigation , Biochemistry, 20, 1427-1431 (1981). 

Most of the DNA in nature has the double helical secondary structure. The hydrogen bonds between the base pairs provide the stability of the double helix. Under certain conditions the hydrogen bonds are broken. During the replication process itself, this happens and parts of the double helix unfold. Under other conditions, the whole molecule unfolds, becomes single stranded, and assumes a random coil conformation. This can happen in denaturation processes aided by heat, extreme acidic or basic conditions, etc. Such a transformation is often referred to as helix-to-coil transition. There are a number of techniques that can monitor such a transition. One of the most sensitive is the measurement of viscosity of DNA solutions. 

Which will have a greater surface of interaction—DNA in a double helix or the same DNA denatured, single-stranded random coil Justify your answer with a diagram of helix-to-coil transition. 

At what pH values did you observe helix-to-coil transitions ... 

Triphenylmethyl methacrylate (TrMA) and azobenzene-modified methacrylates were randomly copolymerized in toluene at — 78°C with chiral catalysts to give optically active helical copolymers (19 in Fig. 6) [65]. The optical activity (optical rotation) of the copolymers decreased with the increasing content of the azobenzene-modified methacrylates in the copolymers. The single helical conformation of PTrMA is quite stable in solution, but the copolymers of TrMA with less bulky methacrylates cannot keep their helical structure and lose their optical activity during the polymerization or after the polymerization in solution, which is highly dependent on the bulkiness of the comonomers [22]. The copolymer (19 x = 2) containing 26 mol% azobenzene units, also lost its optical activity upon irradiation within 20 min. This change is due to the helix-to-coil transition of the copolymer and can occur in the dark. 

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,... 

DSC was used to characterize the thermodynamic properties of the collagen triple helix to coil transition in individual molecules and in fibrils. Many microscopy techniques were used to visualize individual collagen molecules and their supramolec-ular assemblies. 

Figure 21-3 Model of metal-ion activation of DtxR helix-to-coil transition [30]. (A) Vacant metalion binding region of apo-DtxR [18], in which the side chains of Met 10, Cys 102, Glu lOS and His 106, and the main chain oxygen of Cys 102 are shown. The amino-terminus is indicated with N. (B) Metal-ion binding region of Ni(II)-activated DtxR(C102D) [22]. Shown are the ligands of the metal ion (sphere), which are the side chains of Met 10, Asp 102, Glu 105 and His 106, the main chain oxygen of Asp 102, and a water molecule. The main chain of residues 3-6 is also illustrated. (C) As in (B) but for the ternary complex Ni(II)-DtxR(C102D)-toxO [30]. For simplicity, only four nucleotides are shown.

Duplex stability is dependent on DNA conformation. Classic B conformation has a lower free energy of helix-to-coil transition and lower T than B conformation, whereas B conformation has a higher thermal stability than A conformation [106]. Base pairs also influence duplex stability. 

X-ray diffraction studies (68-78) of the possible conformations available in hyaluronic acid in solution indicate that helices packed together in various arrangements are possible. It is therefore appropriate to relate the present analysis to the theory of the helix-to-coil transition. In the model developed by Zimm and Rice (79) for helix-to-coil transitions in charged macromolecules, the fraction, 6, of intact hydrogen bonds in the helix is given by ... 

Hanlon and Klotz (1968) have discussed the use of near-infrared spectroscopy for studying structural problems of biochemistry. In particular, they have considered the equilibrium state of the peptide unit in a number of synthetic polyamino acids (poly-L-alanine, poly-L-leucine, poly-L-methionine, and poly-y-benzyl-L-glutamate) as a function of solvent composition under conditions where the transitions in other physical properties of these polymers have been interpreted as simple peptide, hydrogen-bonded, helix-to-coil transitions. Their spectral data demonstrate that these conversions involve protonated peptide species and are far more complicated than investigators of these processes had assumed. 

Fig. 10 Illustration of the helix-to-coil transition, anisotropic-to-isotropic transition, and shape change of the uniaxial PHEG gel. Reprinted with permission from [94], Copyright 2012 American Chemical Society...

It was later demonstrated that such fiber swelling effects are due to the helix-to-coil transitions of the collagen, increasing in the series (von Hippel and Wong 1964) ... 

ABSTRACT The principle of electrical spectrography and its measurement system is discussed. The phenomenon of noise in electrolytes and interfaces receives attention. Noise spectrography is found to have applications in some biomolecular systems, viz., DNA helix-to-coil transition, thermal transconformation, and salt-free premelting effects. Noise conductivity emission spectra of collagen solutions gave information on permanent dipole fluctuations and hydrodynamic properties of the system. 

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