A helix region

FIGURE 19.20 One of the four polypeptide chains that make up the human hemoglobin molecule. The chains consist of alternating regions of a helix and p sheet. The a-helix regions are represented by red helices. The oxygen molecules that we inhale attach to the iron atom (blue sphere) and are curried through the bloodstream. 

Fig. 7. Schematic picture ot the proposed model for the B800-850 antenna complex. The basic unit consists of four BChl 850 molecules (upper boxes), 2 BChl 800 molecules (lower boxes), three carotenoids (zigzag lines) and two proteins, each consisting of two subunits. The helices symbolize the a-helix regions, which are supposed to be transmembrane. The Qy transitions (open arrows) of two of the BChl 850 molecules (left front and right back) are in the same plane, while the Qy transitions of the remaining BChl 850 molecules are in a parallel plane, which is vertically displaced by about 1 A. The Qx transition moments (solid black arrows) of the BChl 850 are perpendicular to these planes. The Qy transitions of the BChl 800 molecules are both in a plane parallel to BChl 850 Qy transitions, while the Qx molecules are tilted out of this plane at an angle smaller than 24°. The bar represents 5 A. Taken from Ref. 40.

Which of the following characterize a-helix regions of proteins ... 

Figure 6 Model for ArsR repressor protein based on crystal structure of the related SmtB repressor of cyanobacterial metaUothionein (smtA) mRNA synthesis. (Top) Dimer of ArsR with a-helix-loop-a-helix region proposed to bind to operator DNA. (Bottom left) Tri-cysteine region folded as a-helix, with Cys32, Cys34, and Cys37 not suitably spaced to bind As(III). (Bottom right) Tri-cysteine region unfolded and coordinately binding As(III).

Figure 9 compares the amino acid sequences of the second transmembrane a-helix region of GABA receptor subunits. The alanine-to-serine mutation of the pore-lining amino acid of the housefly RDL subunit accounts for the... 

The possibility of HjO as the hydrogen donor is unlikely, because D is in all likelihood buried inside the strongly hydrophobic, membrane-spanning a-helix region of the Dj protein subunit. We therefore suggest that the proton donating species is an amino acid. The folding of the Dj polypeptide proposed in [14] results in four possiblities hisidine or serine in the second, or tryptophan or serine in the fifth intramembrane a-helix. A selection between these donors can only be made when a more precise location of the different a-helices relative to the tyrosyl donor is known. 

The qualitative idea underlying definition (4.7.12) is that whenever three successive units are oriented in such a way that they fall in the a-helix region, the i — 2 and / + 2 units... 

An a helix can in theory be either right-handed or left-handed depending on the screw direction of the chain. A left-handed a helix is not, however, allowed for L-amino acids due to the close approach of the side chains and the CO group. Thus the a helix that is observed in proteins is almost always right-handed. Short regions of left-handed a helices (3-5 residues) occur only occasionally. 

Figure 2.12 Two a helices that are connected by a short loop region in a specific geometric arrangement constitute a helix-turn-helix motif. Two such motifs are shown the DNA-binding motif (a), which is further discussed in Chapter 8, and the calcium-binding motif (b), which is present in many proteins whose function is regulated by calcium.

The hairpin motif is a simple and frequently used way to connect two antiparallel p strands, since the connected ends of the p strands are close together at the same edge of the p sheet. How are parallel p strands connected If two adjacent strands are consecutive in the amino acid sequence, the two ends that must be joined are at opposite edges of the p sheet. The polypeptide chain must cross the p sheet from one edge to the other and connect the next p strand close to the point where the first p strand started. Such CTossover connections are frequently made by a helices. The polypeptide chain must turn twice using loop regions, and the motif that is formed is thus a p strand followed by a loop, an a helix, another loop, and, finally, the second p strand. 

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"... 

The proteins thus adapt to mutations of buried residues by changing their overall structure, which in the globins involves movements of entire a helices relative to each other. The structure of loop regions changes so that the movement of one a helix is not transmitted to the rest of the structure. Only movements that preserve the geometry of the heme pocket are accepted. Mutations that cause such structural shifts are tolerated because many different combinations of side chains can produce well-packed helix-helix interfaces of similar but not identical geometry and because the shifts are coupled so that the geometry of the active site is retained. 

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