Hydrophobic moment

Eisenberg, D., Weiss, R.M., Terwilliger, T.C. The hydrophobic moment detects periodicity in protein hydropho-bicity. Proc. Natl. Acad. Sci. USA 82 140-144, 1984. 

In addition to these determinants, the success of immune system molecules such as host defense peptides relies upon the selectivity for the pathogen rather than the host. Host defense peptides have been optimized throughout evolution to selectively target a broad range of pathogens. This selectivity is defined by a number of specific biophysical themes, namely, conformation, charge, amphipathicity, hydrophobic moment (TIh), hydro-phobicity, and polar angle. ... 

Mean-Square Hydrophobic Moment (or Partially Helical Polypeptides" Hamed, M. M. Mattice, W. L. Biopolymers 1984, 23, 201. 

A mean-square helical hydrophobic moment,

, is defined for polypeptides in analogy to the mean-square dipole moment, , for polymer chains. For a freely jointed polymer chain, is given by X rr , where mi denotes the dipole moment associated with bond /. In the absence of any correlations in the hydrophobic moments of individual amino acid residues In the helix,

is specified by X Wj2, where H denotes the hydrophobicity of residue /, Matrix-generation schemes are formulated that permit rapid evaluation of

and . The behaviour of

I

is illustrated by calculations performed for model sequential copolypeptides. 

Helical hydrophobic moment ratios, I , are evaluated for 34 polypeptides under conditions where the helix content is dictated solely by the short-range interactions operative in aqueous media. The mean-square helical hydrophobic moment is denoted by , and is the averaged of the squared hydrophoblcltles. This ratio would be one in absence of any correlation in the hydrophoblcltles of amino acid residues in helices. 

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. 

Triangular Matrix Representation of Dimensionless Helical Hydrophobic Moment Ratios Maroun, R. C. McCord, R. W. Mattice, W. L. Int. J. Biol. Macromoi. 1986, 8, 73. 

Lysine also may form complexes with anionic ligands and thereby increase Am values. In addition, lysine may have an unfavorable effect on protein structure. Because it has a considerable hydrophobic moment, it may interact with hydrophobic sites on the protein, leading to perturbation of structure. Compatible solutes lack a propensity for interacting with peptide backbone linkages or amino acid side-chains, as discussed later. 

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. 

An effective measure of local context to predict protein local structures is the hydrophobic moment. The overall amphipathicity of any periodic structure has been quantitated in the hydrophobic moment. Even if the atomic coordinates of a protein are not known, the sequence hydrophobic moment can be estimated, as in... 

Other sequence features and information content can be extracted by various scoring mechanisms (e.g., Uberbacher et al1996). Another example of indirect sequence encoding is the computation of hydrophobic moment (Chapter 6.4). 

The hydrophobic/hydrophilic nature of the different helical faces is clearly illustrated by this projection. The amphipathic character of a segment of a protein can be calculated by use of a Fourier series and calculation of a hydrophobic moment [18],... 

The hydrophobic moment gives an orientation of the a-helix with respect to the lipid environment and the aqueous interface of the membrane surface for single a-helices or the hydrophilic core formed from a cluster of transmembrane a-helices (seven and twelve helices are quite common). Other methods, conceptually along similar lines, have produced power spectra which are cleaner, facilitating the identification of the lipophilic moment [12]. 

Class A amphipathic helix I I Class G amphipathic helix 0 Hydrophobic moment/residue < b Lipid-binding firagment... 

Table III is a compilation of physical and chemical properties derived from COMBO analyses of the different sets of potential amphipathic helical classes from all exchangeable apolipoproteins. Two of these physical and chemical properties distinguish the class A2 amphipathic helices from the rest (1) both the mean hydrophobic moment ((/ih)) and the...

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