Helical wheel representation

Fig. 2.40 Sequences and helical wheel representation of amphiphilic 2.5,2-helical jS-pep-tide 17-mers evaluated for antimicrobial activity [234, 248]. These peptides are exclusively composed of hydrophobic trans-ACPC...

B) Helical wheel representation of residues 2-31 of the coiled coil portion of the leucine zipper (residues 249-281) of the related transcription factor GCN4 from yeast. The view is from the N terminus and the residues in the first two turns are circled. Heptad positions are labeled a-g. Leucine side chains at positions d interact with residues d and e of the second subunit which is parallel to the first. However, several residues were altered to give a coiled coil that mimics the structure of the well-known heterodimeric oncoproteins Fos and Jun (see Chapter 11). This dimer is stabilized by ion pairs which are connected by dashed lines. See John et al.172... 

For proteins with multiple transmembrane domains, it is not necessary to have exclusively hydrophobic amino acids a pair of amino acids with opposite charges may be present in the lipophilic environment of the membrane. Therefore a search for amphipathic a-helices must be undertaken. Amphipathic helices have well-defined hydrophobic character, the hydrophobic face which would project towards the membrane/lipid environment, and a hydrophilic face, which would project out into the aqueous phase or towards the core of a helix bundle. Often times the distinction is not clear and there are regions of mixed hydrophobic/hydrophilic character. Graphically this can be realized with a helical-wheel representation in which the amino acid side chains project out, at 100 degree intervals, from the view along the long, helical axis. 

Figure 3 Helical wheel representation illustrating the hydrophilic (boxed amino acids) and hydrophobic (circled amino acids) character of an amphipathic helix. All of the hydrophobic residues are on one face of the helix (bottom half of the figure), while the hydrophilic residues are on the top half.

Here, residues a, d, and g (1,4, and 7) often carry nonpolar side chains. These come together in the coiled coil as is illustrated in the helical wheel representations in Fig. 2-21B and provide a longitudinal hydrophobic strip along the helix. Charged groups are often present in other locations and in such a way as to provide electrostatic stabilization through interactions... 

Figure 5.2. Helical wheel representation of helical bundle proteins to illustrate principles of design. Helix-loop-helix dimers are predominantly antiparallel to neutralize helical dipole moments and can fold in two ways with consequences for which residues can form active sites. Hydrophobic residues in a and d positions form cores in the folded state and...

Fig. 3. TVpe-A amphipathic helix corresponding to residues 7-24 of apo Cl. (Left) Helical wheel representation with the oi-helix axis in the center of the wheel and consecutive amino acids at 100° from each other. The nonpolar residues are at the top of the wheel, basic residues occur at the interface between the non-polar and polar sides of the helix, and negatively charged residues appear in the middle of the polar face (at the bottom of the wheel). (Right) The helix is represented as a flattened cylinder cut along the center of the polar face.

Fig. 2 A nitroxide scan on KcsA. (a) Linear representation of the putative transmembrane topology of KcsA and the nitroxide scan (linear scale with arrows), (b) Room temperature CW EPR spectra for two regions in TMl and TM2. Multiple nitroxide components are highlighted by red arrows in selected spectra, (c) Mobility and accessibility plots. Periodical pattern are visible. On the right, helical wheel representation showing the trends of the EPR parameters extracted from the spectra in a polar coordinate representation, (d) Example of dipolar broadening on position 108, and effect of underlabeling on the spectral shape. On the right the shortest distance...

Fig. 6 Structural details obtained by lineshape analysis, (a) In KcsA, labeling at any residue position renders a tetramer with potentially four spin labels, (i) Tandem dimer construct (ii) with cys residues in both protomers (control used to evaluate the effects of the intersubunit linker) and (iii) with only one of the protomers containing a cys (used in the analysis), (b) Rigid-limit X-band EPR spectra obtained at pH 7 (thick line, closed state) and at pH 4 (thin line, open state). Right panel, absorption spectra obtained from integration and relative fits obtained with convolution superimposed, (c) Simulated spin- and amplitude-normalized spectra for the two interspin distances in the figure (100% spin labeling efficiency), (d) Helical wheel representation of residues 100-119. Both closed (top) and open (bottom) states are represented as pairs of helical wheel...

Scheme 1 Self-replication cycle based on the coded-coil motif, (a) Helical wheel representation of a coiled-coil peptide showing the heptad repeat, (b) The reaction cycle for a self-replicating peptide with its fragments. (Reprodnced from Ref. 93. Elsevier, 2004.)...

The largest group of facial amphiphilic peptides consists of the alpha-helical peptides. Facial amphiphilic alpha helices, often referred to as amphipathic alpha helices, are not amphiphilic in their random coil conformation and their amphiphilicity is not directly obvious from then-sequence. However, folding of the peptide into its preferred secondary structure, leads to the formation of an alpha helix, of which the hydrophilic amino acids occupy one face and the hydrophobic amino acids are located at the other face. Alpha-helical peptides have a periodicity of 3.6 amino acid residues per turn, and because of this, for two turns, roughly every third and seventh amino acids are on the same face of the alpha helix. In order to make a helix amphiphilic, the sequence of amino acids should alternate between hydrophobic and hydrophilic every three to four residues, which becomes more clear in a helical wheel representation (Figure 3). An example of such a facial amphiphilic alpha helix is magainin 2, a 23 amino acid antibiotic peptide. Studies have shown that magainin... 

Figure 30.3 (A) Fluorescence Image of a POPC GUV and the membrane-attached dansyl-labeled model peptide (molar ratio POPC peptide = 30 1, bar = 50 pm). (B) and (C) Phase contrast image of peptide-mediated GUV-GUV clustering (incubation time > 45 nun, bar = 50 pm). (D) Diagram of peptide (helical wheel representation) - membrane interaction triggering GUV-GUV attachment.

Fig. 24 Coiled-coil-based self-assembling peptide system designed by Woolfson s group. A Amino acid sequences of self-assembing fiber (SAF) peptides (SAF-pl, -p2 and -p3). B Concept for a sticky-end assembly process. Complementary charges in companion peptides direct the formation of staggered, parallel heterodimers the resultant sticky-end are also complementary and promote longitudinal association into extranded nanofibers. C Helical wheel representation of coiled-coil conformation. (Adapted from [85])...

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