Coiled coil helical wheel

Figure 1 A helical wheel diagram of a dimeric coiled-coil. Letters a through g denote the seven amino acid residues of a heptad repeating unit. 

Figure 14.3 Helical wheel diagram of the YZl peptide and the schematic representation of the staggered dimer formation with an axial displacement of three heptad repeating units, which promote elongation into coiled coil fibrils. Reprinted from Zimenkov et al. (2004). Copyright 2004 Elsevier Science.

Fig. 7. Helical wheel and sequence representation of the parental homodimeric coiled coil. The substitution positions within the hydrophobic domain are highlighted with open squares and those in the charged domain with open circles. Their interaction partners are highlighted with shaded squares and circles, respectively. The arrows mark the ligation site of nucleophilic and electrophilic fragments. (See Colour Plate Section at the end of this book.)...

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... 

The coiled-coil library sequence and helical-wheel diagram of this coiled-coil template is shown in Scheme 9. 

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 1. Amino acid sequence consisting of multiple heptad repeats (top) schematic cartoon of a parallel coiled-coil (l ft) helical wheel diagram...

Figure 1 Schematic representation of a parallel dimeric coiled coil. The helical wheel diagram in (a) top view down the axis of the a-helices from N-terminus to C-terminus. Panel (b) provides a side view. The residues are labeled as a-g in one helix and a -g in the other. (Reproduced from Ref. 52. Wiley-VCH, 2004.)...

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 7 Helical-wheel diagram of the template peptide in the dimeric a-helical coiled-coil configuration emphasizing the heptad repeat motif. The interhelical recognition surface consists of amino acids allowing for hydrophobic packing interactions (positions a and d) and electrostatic interactions (positions e and g). Amino acids at positions b, c, and / lie on the solvent-exposed surface of the helical structure and do not participate in the molecular recognition processes. Arrows indicate the ligation site between a cysteine and an alanine residue.

Figure 6 Helical wheel presentation of coiled-coil trimers with productive interactions, (a) Perfect charge matching in homotrimer coiled coil containing K to E interactions in the e and g positions. This peptide can act as a productive autocatalyst in the network, (b) A stable heterotrimer coiled coil with almost perfect matching of opposing amino acids. The two weaker K to A interactions in this particular example are emphasized by gray dashed lines across the interface. Here, a dimer of one peptide (P) can act as a cross-catalyst for the formation of another peptide (P ).

Figure 11 Helical wheel presentation of caged coiled-coil assembly. Lysines, marked in black, were modified to possess the light-sensitive Nvoc group. This group destabilizes the coiled-coU structures by disrupting specific ionic interactions (emphasized by X over the dashed line across the local K to E interactions).

Figure 4 The a-helical coiled coil, (a) KIH packing—the residues forming the hole are gray (with the positions in the heptad repeat labeled) and the knob is black (b) Helical wheel diagram for a parallel dimeric coiled coU, showing how the hydrophobic residues (at a and d) form the hydrophobic interface (c) A top-down view of a dimeric coiled coil (d) A side view of the same, showing the left-handed supercoil.

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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