Coiled-coil a helix

Coiled-coil a helices contain a repetitive heptad amino acid sequence pattern... 

Fibrous proteins can serve as structural materials for the same reason that other polymers do they are long-chain molecules. By cross-linking, interleaving and intertwining the proper combination of individual long-chain molecules, bulk properties are obtained that can serve many different functions. Fibrous proteins are usually divided in three different groups dependent on the secondary structure of the individual molecules coiled-coil a helices present in keratin and myosin, the triple helix in collagen, and P sheets in amyloid fibers and silks. 

Fibrous proteins are long-chain polymers that are used as structural materials. Most contain specific repetitive amino acid sequences and fall into one of three groups coiled-coil a helices as in keratin and myosin triple helices as in collagen and p sheets as in silk and amyloid fibrils. 

In thinking about X-ray diffraction from this assembly, a number of the sarcomere components contribute to the observed patterns in ways that have been the subject of detailed analysis. In the A-band, these include the myosin filament backbone, where the coiled-coil a-helical myosin rods pack together, the myosin head arrays in the bridge regions of the myosin filaments, the non-myosin A-band proteins titin and C-protein (MyBP-C), and the A-band parts of the actin filaments. Very little has been seen in X-ray patterns so far that appears to be related to the M-band, probably... 

Advances in isolating and identifying cDNA clones for laminin provided considerable additional information on the amino acid sequences at the carboxyl end of the B1 and B2 chains (Barlow et al., 1984). These analyses showed that at least 350 residues of the B1 chain and over 200 residues of the B2 chain had the a-helical heptad repeat and predicted that these chains would be aligned together, along the long arm of laminin in a coiled-coil a-helical structure. 

Fig. 3 Schematic view of the human vimentin protein and force-strain curves of coiled-coil intermediate filament under tensile loadings, (a) Schematic representation of vimentin structure, (b) Force-strain behaviors of a coiled-coil a-helical structures revealing the loading rate dependency of the molecular-level stiffness under tensile loading. (Reprinted from [66], with kind permission from Springer Science and Business Media), (c) a-p secondary structural transition of coiled-coil a-helix under tensile loading. (Reprinted from [67])...

Figure 10.18 Side-chain interactions in the leucine zipper structure, (a) The hydrophobic side chains in spikes a and d (see Figure 10.17) form a hydrophobic core between the two coiled a helices, (b) Charged side chains in spikes and g can promote dimer formation by forming complementary charge interactions between the two a helices.

As the last example of a helix-sheet transition, Pagel et al. (2006) demonstrate a coiled coil peptide adopting three types of secondary structures and the transition between random coil, a-helical, and /3-sheet hbers can be simply triggered by changing the pH or peptide concentration. 

Two guest amino acids (G) are incorporated into two adjacent positions of a host peptide which is potentially able to exist in a random coil, a-helical and p-sheet conformation, depending on the expo imental conditions. The guest amino adds are supposed to alter the conformational state of the sequence reflecting the strudural preferences of the guest ... 

Fig. 12.39 Representative CD spectra of polypeptides and polynucleotides (a) random coils, a helices, andp sheets have different CD features in the spectral region where the peptide link absorbs (b) B- and A-DNA can be distinguished on the basis of CD spectroscopy in the spectral region where the bases absorb.

Structural Domains Random coils a-helices p-sheets... 

Variations on the a helix in which the chain is either more loosely or more tightly coiled, with hydrogen bonds to residues n + 5 or n + 3 instead of n + 4 are called the n helix and 3io helix, respectively. The 3io helix has 3 residues per turn and contains 10 atoms between the hydrogen bond donor and acceptor, hence its name. Both the n helix and the 3to helix occur rarely and usually only at the ends of a helices or as single-turn helices. They are not energetically favorable, since the backbone atoms are too tightly packed in the 3io helix and so loosely packed in the n helix that there is a hole through the middle. Only in the a helix are the backbone atoms properly packed to provide a stable structure. 

Figure 3.1 Schematic diagram of the coiled-coil structure. Two a helices are intertwined and gradually coil around each other.

Detailed structure determinations of GCN4 and other coiled-coil proteins have shown that the a helices pack against each other according to the "knobs in holes" model first suggested by Francis Crick (Figure 3.5). Each side chain in the hydrophobic region of one of the a helices can contact four side chains from the second a helix. The side chain of a residue in position "d"... 

Figure 3.3 Schematic diagram showing the packing of hydrophobic side chains between the two a helices in a coiled-coil structure. Every seventh residue in both a helices is a leucine, labeled "d." Due to the heptad repeat, the d-residues pack against each other along the coiled-coil. Residues labeled "a" are also usually hydrophobic and participate in forming the hydrophobic core along the coiled-coil.

Figure 3.S Schematic diagram of packing side chains In the hydrophobic core of colled-coll structures according to the "knobs In holes" model. The positions of the side chains along the surface of the cylindrical a helix Is pro-jected onto a plane parallel with the heUcal axis for both a helices of the coiled-coil. (a) Projected positions of side chains in helix 1. (b) Projected positions of side chains in helix 2. (c) Superposition of (a) and (b) using the relative orientation of the helices In the coiled-coil structure. The side-chain positions of the first helix, the "knobs," superimpose between the side-chain positions In the second helix, the "holes." The green shading outlines a d-resldue (leucine) from helix 1 surrounded by four side chains from helix 2, and the brown shading outlines an a-resldue (usually hydrophobic) from helix 1 surrounded by four side chains from helix 2.

In most four-helix bundle structures, including those shown in Figure 3.7, the a helices are packed against each other according to the "ridges in grooves" model discussed later in this chapter. However, there are also examples where coiled-coil dimers packed by the "knobs in holes" model participate in four-helix bundle structures. A particularly simple illustrative example is the Rop protein, a small RNA-binding protein that is encoded by certain plasmids and is involved in plasmid replication. The monomeric sub unit of Rop is a polypeptide chain of 63 amino acids built up from two... 

Figure 3.8 Schematic diagram of the dimeric Rop molecule. Each subunit comprises two a helices arranged in a coiled-coil structure with side chains packed into the hydrophobic core according to the "knobs in holes" model. The two subunits are arranged in such a way that a bundle of four a helices is formed.

Cohen, C., Parry, D.A.D. Alpha-helical coiled coils—a widespread motif in proteins. Trends Biochem. Sci. 

Crick, F.H.C. The packing of a-helices simple coiled coils. Acta Cryst. 6 689-697, 1953. 

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