Helix dipole model

Mattliew, M. K., and Balaram, A., 1983. A helix dipole model for alamedii-cin and related tran.smembrane channels. FEES Letters 157 1-5. 

It is now known that amino acids with high propensities for the middle of helices are not necessarily favored at the ends. Polar and charged amino acids are more prevalent at the helix termini, whereas the middle of an a-helix contains predominantly hydrophobic residues. 61 This is rationalized by what is now known as the helix dipole model, 62 65 first proposed by Blagdon and Goodman (Figure l). 62 ... 

Fairman, R., Shoemaker, K. R., York, G. J., Stewart, J. M., and Baldwin, R. L. Further studies of the helix dipole model effects of a free a-NHg or a-COO group on helix stability. Proteins Structure, Function, and Genetics 5, 1-7 (1989). 

Figure 11. Adaptation of the schematic diagram of the alamethicin helix dipole model of Mathew and Balaram (97). A top view of the alamethicin aggregate is shown. The + and — signify opposite orientation of helix dipoles in the lipid bilayer. Bars that connect helices represent hydrogen bonding of polar side chains. The central core helix (shown as a filled circle) is not hydrogen-bonded to the aggregate and is ejected in response to an applied voltage to form the open channel. Conductance of the channels is modulated by changes in...

The situation changes dramatically in solution. QM/MM simulations of these two helices in solution modeled by water droplets showed that the larger helix dipole of the a-helix leads to a stronger Coulomb interaction with the solvent [17], which leads... 

Figure 4. Folded and twisted conformations of (/i)3-hydroxybutanoate oligolides (left) containing one (heptamer, octamer) or two (hexamer) single turns of a right-handed 3i-helix, a model of which is shown on the right side in views from the side and along the helix axis. The helix is covered with methyl groups and has a dipole moment resulting from the unidirectional arrangement of the C=0 bonds parallel to the helix axis [4].

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. 

The double helix has unbalanced charge on many atoms. The displacements associated with vibrational modes generate oscillating dipole moments. These moments are constructed from our eigenvector displacements and models of atomic net charge taken from the literature (2, 3). These dipole moment matrix elements have been calculated (4). 

We approached the problem of establishing a structure of the "random coil" conformation by first establishing the limits of the present computational model for a known polymeric structure, the a-helix. Coordinates, created by program MacroModel [22] for the carbonyl groups of a-helical oligomers were used, along with published and experimental dipole transition moments, to compute the VCD and absorption spectra of the a-helical conformer. We found that VCD spectra, independent of chain length, can be calculated for octamers, and that the choice of side chain residues is immaterial for the computed spectra. Both calculated and experimental data were normalized to one residue, to permit a comparison between computed and observed spectra. 

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