Helix formation

Several years ago Makino et al. 86) studied the influence of anions on the conformation of poly-[L-methionine-S-methylsulfonium] salts in solution. They found that especially perchlorate will induce a-helix formation whereas Cl- and Br do not. Since then several authors 87 92) have found a similar a-helix inducing effect in the case of poly-L-lysine (Lys) and other BPAA at low pH-values where the polymer molecules usually attain an extended conformation due to the electrostatic repulsion of the ammonium groups. Therefore, the a-helix inducing effect is obviously an... 

As Fig. 16 shows, the preferential binding of DMSO, DMF and NMF from aqueous solution to (Lys HBr)n at low contents of the organic solvent x increases with its concentration. However, at approximately x3 = 0,2 a maximum is reached and then preferential hydration between x3 = 0,3 and 0,5 occurs. No preferential binding was observed for NMP, EG or 2 PrOH, however increasing hydration occured with x3. Only in 2 PrOH at x3 > 0,3 a-helix formation occured. Furthermore binding parameters for the systems NMP + DMSO, EG + DMSO and DMF + DMSO have been determined. An initial preferential binding of DMSO by (Lys HBr)n, a maximum and a subsequently inversion of the binding parameter was also observed in these mixtures. The order of relative affinity is DMSO > DMF > EG > NMP. In DMF/DMSO-mixtures (Lys HBr) attains an a-helical conformation above 20 vol.- % DMF and in 2-PrOH/water above 70 vol.- % 2 Pr-OH. 

The structure of the chain, i.e., whether it is a helix or a random coil, might influence not only the rate but also the stereospecificity of the growing polymer. For example, it is plausible to expect that in normal vinyl polymerization helix formation might favor specific placement, say isotactic, while either placement would be approximately equally probable in a growing random coil. Formation of a helix requires interaction between polymer segments, and this intramolecular interaction is enhanced by bad solvents particularly those which precipitate the polymer. 

Antisense therapy means the selective, sequence-specific inhibition of gene expression by single-stranded DNA oligonucleotides. By hybridizing to the target mRNA, which results in a subsequent double-helix formation, gene expression is blocked. This process can occur at any point between the conclusion of transcription and initiation of translation or even possibly during translation. 

Kinetic Aspects of Triple-Helix Formation of Peptide Models Compared with... 

Since these investigations could be carried out only in the crystalline state, the question of the dynamics of the triple-helix formation and of the correlation of its stability with the amino acid sequence could be answered only with the help of other methods working in solution. 

Figure 13 shows that the analogous dependence on temperature after longer incubation time at 1 °C becomes nonlinear with higher oligomers. Helix formation starts with n = 6. The ellipticity, depending on the chain lengths at random coil conditions, is shown in Fig. 14. 

Figures 15 and 16 demonstrate folding in the l,l,l,3,3,3-hexafluoro-2-propanol/ethylene glycol (HFP/EG) mixture (1 2) and in 1,3-propandiol in comparison to Fig. 13, which describes helix formation in water. The structure formation is much more pronounced. This is indicated by the more negative signals of the CD spectrum at 198 nm. The negative values of 0 for the octamer increase from -1.8 x 10-4 deg cm2 dmol-1 in...

It is well known that native collagen containes tripeptide sequences, which alone are not capable of building up a triple helix (e.g. Gly-Pro-Leu, Gly-Pro-Ser) when they exist as homopolypeptides. The synthesis of threefold covalently bridged peptide chains opens up the possibility of investigating the folding properties of such weak helix formers, because the bridging reduces the entropy loss during triple-helix formation and thereby increases the thermodynamic stability of the tertiary structure. Therefore, we have... 

Weidner and Engel142 used the relatively short collagen peptide al-CB2 as a model peptide for kinetic measurements. They observed that the rate at the beginning of the helix formation, starting from purely coiled chains, obeys the following equation ... 

In comparison to the constant of propagation of the a-helix formation (kp — 1010s 1) and the double-helix formation (kp — 107s-1), a comparatively small parameter concerning the formation of triple helix has been found (fcp = 8 x 10 3s1). A higher entropy of activation is assumed as the main cause of this occurrence which means a lower frequence factor in the Arrhenius equation. 

This gives an important hint at what kind of model peptides are synthesized to obtain detailed information about the thermodynamics and kinetics of the collagen triple-helix formation. A first success was already achieved by synthesizing peptides of the following general structure37 ... 

This model does not say anything about the mechanism of triple-helix formation, because even in the case of an AON mechanism, nucleation may take place at many positions of the chains and may lead to products the chains of which are staggered. The AON model is based on the assumption that these products are too instable to exist in measurable concentration. As already mentioned, Weidner and Engel142 succeeded in proving by relaxation measurements of al CB2 that the kinetics of in vitro triple-helix formation is governed by more than one relaxation time. This rules out an AON mechanism, but the fitting to the experimentally found equilibrium transition curves nevertheless showed good accommodation and AH° computed from these curves could be confirmed by calorimetric measurement. 

According to Eq. (1), the triple-helix formation can be imagined as a process which may be divided into 3n - 2 steps of equilibrium with the same values of Aand AS each. This means that AG° is a linear function of 3n - 2 for the whole process. 

The covalent bridging of the three polypeptide chains with the sequence Ala-Gly-Pro has facilitated, as expected, the nucleation step for triple-helix formation. This is also... 

Fig. 37. Dependence of the thermodynamic parameters AH and AS of triple-helix formation on the imino acid content of the peptides (obtained by cleavage of calf skin-type I collagene with cyanogene and subequent isolation by column chromatrography)3) and of the native neutral salt-soluble skin collagene of various animals. The entropy values are denoted by dotted lines...

Fig. 39. Dependence of AHC of triple-helix formation on the proline content of the CNBr peptides and synthetic model peptides, respectively...

The thermodynamic stability of the 3i4-hehx in addition to the requirements for 3i4-helix formation have been studied extensively by NMR spectroscopy, circular dichroism and molecular dynamics. 

Fig. 2.16 Effect of electrostatic interactions on 3i4-helix formation in an aqueous environment [1 75 a, 175 b, 176]. y -Peptides 86 and 87 adopt a stable helical conformation mediated by salt bridges near neutral pH. While the propensity of these peptides to adopt a helical conformation is strongly de-...

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