Hydrophobic moment analysis

In terms of the overall amino acid composition, mTPs stand out by virtue of their high content of positively charged residues (particularly Arg) and their almost complete lack of negatively charged Asp and Glu residues. In addition, hydrophobic moment analysis indicates that mTPs can be folded into higMy amphiphilic a-helices with an apolar face and a polar, positively charged face, Fig.l. 

Hydrophobic moment analysis, A search can be made for amphipathic segments using the periodic nature of the segregation between polar and nonpolar residues. The periodic difference in residue hydrophobicity creates a hydrophobic moment. 

It is also possible that a combination of both modes suggested above is involved in the formation of membrane channel for the translocation botulinum neurotoxin. The main assumptions of the hypothesis are (i) The presence of amphiphilic and transmembrane segments in the light and heavy chains as predicted by the hydrophobic moment analysis, (ii) Existence of botulinum neurotoxin in oligomeric form. 

Be, X., Fu, F. -N. and Singh, B. R., 1994, Hydrophobic moment analysis of amino acid sequences of botulinum and tetanus neurotoxins to identify functional domains. J. Natural Toxins 3 49-68. 

A characteristic of immobilized enzymes that is often ignored is the potential partitioning of ions and substrates and/or products due to electrostatic potentials or hydrophobic moments. This factor could be used to advantage, for example, if the optimal conditions for enzyme activity do not match those of the process stream. To use the example cited earlier, a succinamidopropyl surface was shown by electrostatic partitioning of ions and independent chemical analysis to have 96 ymol charged groups/g dry beads (25). Attachment of 2 ymol trypsin/g did not significantly alter this characteristic. 

The major features defined by CONSENSUS/SNORKEL analysis of class Ai (Fig. lOB) are two Arg residues at the polar-nonpolar interface and four Leu residues in the center of the nonpolar face. From Table III, class Ai has a nonpolar face hydrophobicity comparable to that of class A2, but the mean hydrophobic moment is considerably lower, and, unlike class Ai, Arg residues are twice as prevalent as Lys residues Fig. 11 shows a COMBO analysis for the distribution of Lys versus Arg for class A2 versus class Ai. A typical example of the class Ai domain, apoA-I[165-186], is shown in Fig. 8C and D. 

The GOR method phrases a very similar approach in an information theoretic framework, computing not only preferences for individual residues but aiming at the delineation of preferences for short stretches of amino acids. Since the given data set will generally not supply sufficient data for estimation of the log-odds for every k-tuple certain approximations have to made [23]. At the same time it has become clear that even this approach is unlikely to give perfect predictions because, in known crystal structures, one and the same 5-mer of residues will be found in different secondary structures [24]. Other approaches like the one due to Solovyev and Salamov [25] assemble different characteristics for a short stretch (singlet and doublet secondary structure preferences, hydrophobic moment) of amino acids and apply linear discriminant analysis in order to derive a predictor for the secondary structure of a region. 

D. Eisenberg, E. Schwartz, M. Komaromy. and R. Wall, Analysis of membrane and surface protein sequences with the hydrophobic moment plot, J. Mol. Biol. 179, 125-142 (1984). 

Drug binding is enhanced by hydrophobicity in that portion of the drug that binds to the pocket toe. Quantitative structure-activity relationship (QSAR) analysis of these compounds have consistently shown that the most predictive parameter of antiviral activity is a measure of hydrophobicity, the octanol water partition coefficient (logP) [80,82,85]. These studies have also consistently shown that there is no apparent correlation between electrostatic potential or dipole moment and potency. 

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