The a-helix

The primary structure of a peptide is its ammo acid sequence We also speak of the secondary structure of a peptide that is the conformational relationship of nearest neighbor ammo acids with respect to each other On the basis of X ray crystallographic studies and careful examination of molecular models Linus Pauling and Robert B Corey of the California Institute of Technology showed that certain peptide conformations were more stable than others Two arrangements the a helix and the (5 sheet, stand out as... 

Proteins or sections of proteins sometimes exist as random coils, an arrangement that lacks the regularity of the a helix or pleated p sheet... 

Section 27 19 Two secondary structures of proteins are particularly prominent The pleated sheet is stabilized by hydrogen bonds between N—H and C=0 groups of adjacent chains The a helix is stabilized by hydrogen bonds within a single polypeptide chain... 

Secondary structure (Section 27 19) The conformation with respect to nearest neighbor ammo acids m a peptide or pro tern The a helix and the pleated 3 sheet are examples of protein secondary structures... 

Figure 1.10 Helical conformations in polymer molecules, (a) A vinyl polymer with R substituents has three repeat units per turn, (b) The a helix of the protein molecule is stabilized by hydrogen bonding. [From R. B. Corey and L. Pauling,/ end. Inst. Lombardo Sci. 89 10 (1955).]...

For the a-helix, the length per residue is about 1.5 A. Use this figure with the molecular weight to estimate the length 2a of the particle. Use the estimated a/b ratios to calculate the diameter 2b of the helix, which should be approximately constant if this interpretation is correct. Comment on the results. 

S. Hoffmann, in R. Janoschek, ed.. Chirality—Erom Weak Bosons to the a-Helix, Springer-Vedag, Berlin, Heidelberg, 1991, p. 206. 

Ot-HehcalBundles. The a-helix is the most extensively studied protein stmctural motif. Because a-hehces form internal hydrogen bonds between the C=0 of residue i and the N—H of residue i + 4 (see Fig. 2), the individual helix is stabili2ed and can exist in isolation. Individual heUces can be manipulated as independent stmctural modules designed to associate in some predetermined manner. Often, a minimalist approach to the design of a-hehces has been taken. In this approach the goal is to obtain the desired stmctural motif using the simplest possible constmction. 

Fig. 1. The two principal elements of secondary stmcture in proteins, (a) The a-helix stabilized by hydrogen bonds between the backbone of residue i and i + 4. There are 3.6 residues per turn of helix and an axial translation of 150 pm per residue. represents the carbon connected to the amino acid side chain, R. (b) The P sheet showing the hydrogen bonding pattern between neighboring extended -strands. Successive residues along the chain point...

Attempts have also been made at predicting the secondary stmcture of proteins from the propensities for residues to occur in the a-helix or the P-sheet (23). However, the assignment of secondary stmcture for a residue only has an average accuracy of about 60%. A better success rate (70%) is achieved when multiple-aligned sequences having high sequence similarity are available. 

Figure 2.2 The a helix is one of the major elements of secondary structure in proteins. Main-chain N and O atoms ate hydrogen-bonded to each other within a helices, (a) Idealized diagram of the path of the main chain in an a helix. Alpha helices are frequently illustrated in this way. There are 3.6 residues per turn in an a helix, which corresponds to 5.4 A (1.5 A pet residue), (b) The same as (a) but with approximate positions for main-chain atoms and hydrogen bonds Included. The arrow denotes the direction from the N-terminus to the C-termlnus.

Ramachandran plot (see Figure 1.7a). The a helix has 3.6 residues per turn with hydrogen bonds between C =0 of residue n and NH of residue n + 4 (Figure 2.2). Thus all NH and C O groups are joined with hydrogen bonds except the first NH groups and the last C O groups at the ends of the a helix. As a consequence, the ends of a helices are polar and are almost always at the surface of protein molecules. 

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. 

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. 

Fhe amino acid side chains project out from the a helix (see Figure 2.2e) and do not interfere with it, except for proline. The last atom of the proline side... 

Figure 4.12 Schematic diagram illustrating the role of the conserved leucine residues (green) in the leucine-rich motif in stabilizing the P-loop-(x structural module. In the ribonuclease inhibitor, leucine residues 2, 5, and 7 from the P strand pack against leucine residues 17, 20, and 24 from the a helix as well as leucine residue 12 from the loop to form a hydrophobic core between the P strand and the a helix.

Figure 4.17 Schematic diagram of bound tyrosine to tyrosyl-tRNA synthetase. Colored regions correspond to van der Waals radii of atoms within a layer of the structure through the tyrosine ring. Red is bound tyrosine green is the end of P strand 2 and the beginning of the following loop region yellow is the loop region 189-192 and brown is part of the a helix in loop region 173-177.

Figure 4.18 Side chains of the tyrosyl-tRNA synthetase that form hydrogen bonds to tyrosyl adenylate. Green residues are from p strand 2 and the following loop regions, yellow residues are from the loop after P strand S, and brown residues are from the a helix before P strand S. (Adapted from T. Wells and A. Fersht, Nature 316 656-657, 1985.)...

Figure 6.21 Schematic diagram of the conformational changes of calmodulin upon peptide binding, (a) In the free form the calmodulin molecule is dumhhell-shaped comprising two domains (red and green), each having two EF hands with bound calcium (yellow), (b) In the form with bound peptides (blue) the a helix linker has been broken, the two ends of the molecule are close together and they form a compact globular complex. The internal structure of each domain is essentially unchanged. The hound peptide binds as an a helix.

Figure 6.21a) comprising two domains separated by a long straight a helix, similar in shape to troponin-C described in Chapter 2 (see Figure 2.13c). Each domain comprises two EF hands (see Figure 2.13a), each of which binds a calcium atom. The two domains are clearly separated in space at the two ends of the a helix linker. 

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