Fraction helical bonds

Figure 9 Fraction helical bonds as a function of the temperature T of the discotic compound 1 of Figure 6 in the solvent n-butanol. Symbols indicate experiments done in the range of concentrations of 10 6-10 2 M (van der Schoot et al., 2000). The temperature has been scaled to the helical transition temperature Th and a temperature Tc = Th(AcBTh/ /Jh )exp(//ArBTh) that depends on the frustration energy j and the excess enthalpy of the helical bond h. Remarkably, data taken over four orders in concentration collapse onto the theoretical curve, indicated by the drawn line.

Figure 14 Master curve for the mean fraction helical bonds d as a function of a dimensionless temperature scale. T is the temperature and the temperature at the helical transition temperature. The symbols give the experimental results obtained from a solution of the C3 discotic molecules shown in Figure 13 [3,71], Different symbols represent data taken at different concentration in the range from 10 to 10 2 M in the solvent n-butanol. The drawn curve is obtained from the theory of [73] that fits the data reasonably well [73].

Within the ground-state approximation, the mean fraction of helical bonds 9 (N) in a chain can easily be calculated [3]... 

Rgureie Diagram of states of the C3 discotic of Figure 13 in the solvent n-butanol. The symbols represent data obtained by various experimental methods, and the lines the theoretical fits to the experimental data [75]. At low concentrations of material the monomers polymerize directly into helical polymers, while at higher concentrations a nonhelical polymerized regime intervenes. The demarcation of the monomeric and the polymeric regimes is set at 50% fraction material in polymers, rt= and that between the helical and nonhelical states by a 50% fraction of helical bonds, 0 =. ... 

The helical fraction has here been defined as the number of helix units present in the chain under consideration relative to the total number of residues in the same chain that can assume a-helical conformation, i.e. N — 2. It should be noted that this way of defining fN differs from that of Zimm and Bragg (4), who adopted the number of hydrogen bonds formed in the chain. The difference, however, becomes important only for short chains. 

The use of infrared is not limited to p structure detection, however. The erythrocyte study reported here clearly illustrates the information available when spectra are taken in D20. Optical changes permit one to estimate the extent and rapidity of proton exchange in proteins and hence to estimate the availability of peptide bonds to water protons as well as the contributions from random coil and a-helical conformations. The results with erythrocytes indicate that about two-thirds to three-fourths of the protein amide groups are freely accessible to water and that most of the protein exists in an open, mostly random, conformation. The fraction of non-exchangeable protons agrees reasonably well with the helical content determined by ORD. 

For blood cell membranes the agreement of optical rotatory dispersion and infrared spectroscopy is reassuring. About one-third to one-fourth of the protons in the peptide bonds do not exchange in D20. This non-exchangeable fraction can be equated with the helical content of... 

Analysis of the CD spectrum has yielded values of 14% a helix and 31 % p strand, with a possible increase in helix content observed with increase of temperature (Loucheaux-Lefebvre et al., 1978). In a more recent study (Ono et al., 1987), a lower fraction of a helix was calculated, but the results vary with the method of calculation. Structure prediction methods have also been applied to this protein and have given results that encourage the view that K-casein has a number of stable conformational features. Loucheaux-Lefebvre et al. (1978) applied the Chou and Fasman (1974) method and predicted an a-helical content of 23%, with 31% P strand and 10% p turns. Raap et al. (1983) preferred the method of Lim (1974) to predict a-helix and P-strand content, because the method of Chou and Fasman, as published in 1974, was considered to overpredict these elements (Lenstra, 1977). They also tested their predictions for the structure about the chymosin-sensitive bond using the later boundary analysis method... 

Electron diffraction assessments of single crystals from inulin fractions indicate two antiparallel six-fold helices (Andre et al., 1996) a five-fold model has also been proposed (Marchessault et al., 1980). The hemihydrate molecule contains one water molecule for each two fructosyl units, while the monohydrate has one water molecule per fructosyl unit. When intermolecular hydrogen bonds are present, however, there is no evidence of intramolecular hydrogen bonding in the crystals. Crystal structures of 1-kestose (GF2) (Jeffrey and Park, 1972), nystose (GF3) (Jeffrey and Huang, 1993), and cycloinulohexaose (cF6) (Sawada et al., 1990) have been reported. 

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