Hydrophobic moment profile

Hydrophobic moment profile is calculated as described by Eisenberg et al. [48] to collect information about possible amphipathic helices and strands. We used only the PRIFT scale ( 27 in Table 5) to find hydrophobic moments. Scales used for the calculation of hydrophobic moments were not normalized. The PRIFT scale produces high moments (sometimes higher than 2.0) for sequence segments known to be highly amphipathic. An ideal a-helix twist angle of 100 was used to associate a-helix hydrophobic moments with all 

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Most existing methods for identifying protein domains include a refinement scheme to assess the quality of the domains that have been identified. Domain quality is computed according to accessible surface area, hydrophobic moment profile, size, compactness, number of protein segments involved, and presence of intact p sheets. ... 

Averaged helical hydrophobic moment ratios are evaluated in order to assess the potential of amphiphilic regions contributing to the helix-helix interaction responsible for stabilization of tropomyosin dimers. These ratios yield profiles that are higher in the amino-terminal half than in the carboxyl-terminal half of a and p tropomyosin chains. The higher profiles found in the amino-terminal half of a tropomyosin may contribute to the greater stability of the dimer in this region. 

Figure 4 Score profiles for porin from Rhodobacter capsulatus are obtained by subtraction of turn preferences from helical preferences (full line) and as sum of P-sheet preferences and hydrophobic moment scores for assumed p-sheet conformation (dotted line). Kyte-Doolittle scale [17] is used to calculate preferences, while PRIFT scale [50] is used to calculate hydrophobic moments. Observed transmembrane strands are shown as bold horizontal bars at the score level 2.0.

Membrane-embedded or surface-attached P-strands can also be recognized from the sum of prediction profiles for P-strand preferences and of hydrophobic moments for assumed P-strand conformation. 

One may consider that the structures and bioacdvity profiles of compounds 1 and 6 are not spectacular. They were new, however, and patented (16), The reason why this class of compounds have not been disclosed might be due to some "implicit" preconceptions that the oxime 0-ether structures are not very stable and/or that the structural transformations to increase polarity of the molecule are not favorable to the insecticidal activity. At the moment, it is uncertain whether further trials towards their development for the practical use are worth making. The hydrophobicity of compound 1 in terms of log P (P is the partition coefficient measured widi the l-octanol/water system) was approximately estimated as being about 6.0 (Leo, A. Pomona College, Claremont, CA, i rsonal communication, 1993) which is lower than that of phenothdn, 7.56 (77). This could be an advantage to the formulation of water-based aerosols for domestic uses. The less hydrophobic compounds are believed to be safer in terms of undesirable toxic side effects (7 ). Because compound 1 shows an almost equivalent miticidal activity with phenothrin, the use of compound 1 could be more favorable for domestic use without loss of efficacy. 

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