Helix initiation parameter

The shortest helical sequence that can be created in an a-helix-forming polypeptide is hhh, and its statistical weight is as. Since s is of the order of unity in the helix-coil transition region, the probability that such a nucleus for the growth of a helical sequence will be produced is essentially equal to a. For this reason, a is also called the helix-initiation parameter. 

The proportionality constant between theoretical helix content and optical rotation is found by fitting the data at the highest concentration of 5.66% measured. Then, theoretical results at other concentrations automatically fit the experimental data with high accuracy. It turned out that, for (n) = 50, the helix initiation parameter cf2 should be as small as 0.001 to obtain good fit. One of the main reasons why t-carrageenan does not form gels is the smallness of this helix initiation probability. The coil-helix transition temperature at dilute limit is fixed at To = 65°C. 

Thermal and charge induced random coil to a-helix transitions of polyll-glutamic acid) (PGA) are measured by optical rotatory dispersion in various solvents. The data of PGA in 0.1 M NaCI are analyzed by the Zimm-Rice theory. The initiation parameter, o, of the Zimm-Rice theory is given by a value of 5 ( 1) x 10 3. Random copolymers of L-glutamic acid and L-alanine containing 10, 30, and 40 molar percents of alanyl residue are analyzed as well. 

Helix initiation (represented by the helix nucleation parameter a) in a random coil conformation is the slowest and energetically least favored step, whereas subsequent growth of the helix nucleus (represented by the helix propagation factor, s) is rapid and relatively favored. 83 ... 

IS.Sugimoto N, Nakano S, Yoneyama M and Honda K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24 4501-4505. 

S.6 Thermodynamic parameters for helix initiation and propagation in 1 M NaCl... 

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 solid lines in Fig. 11 show values of for unperturbed random-coils) as a function of fN computed from Nagai s equation for several N, with c — 2x 10-4, o0 = 22.4A, and Oj = 1.5A. These values of the parameters are typical of actual systems, as can be seen from the numerical data given later. A most interesting feature, among many others, would be that initially declines, passes through a broad minimum, and then rises sharply on proceeding from random-coil to helix. Similar behavior appears also in the relation between and fN, as will be illustrated later. It should be noted, however, that the appearance of a minimum in or depends on the values of N, g, a0, and at. 

With a sequence alignment and secondary structure, one can reasonably assess the length requirement for each helix, as this is an important parameter in creating an initial library of variants. For example, crystals of a k... 

Initially, we thought there might not be measurable differences in the B-sheet propensities because extended B-sheet structure is much more similar to the unfolded state than the constrained a-helix. Hence, the B-sheet might be merely a "default" structure into which any amino acid may fit, and the Chou-Fasman statistical parameters (12) may therefore result from the strict conformational requirements of a-helices alone. Because B-sheets are more often found fully buried than are a-helices, the statistical distribution of the hydrophobic, B-branched residues in B-sheets may reflect only a hydrophobic requirement rather than a B-sheet forming propensity. 

The titration curves of the three polypeptides can be analyzed by adapting the Zimm-Bragg theory for the helix-coil transition " to the cooperative binding of the surfactant to the polypeptide, provided that the thermodynamic contribution of any conformational change accompanying the binding is comparatively small and that the electrical potential on the surface of the polypeptide molecule can be regarded to be constant. The theory defines two parameters the equilibrium constant s and an initiator a. If the polypeptide sequence is schematically written as... 

The first equation of (10.156) ensures that a chain doesn t form helices by itself. The second equation is described by the weight 02 for the initiation (nucleation) of a double helix, i.e., the probability for an arbitrarily chosen pair of monomers on different chains to start winding. This is the counterpart of single-chain helix nucleation. The cooperativity parameter a is expected to be small, but <72 can be of order unity if there is no strict restriction on monomer conformation in starting chain winding. 

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