Residues per turn

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...

Unit cells of pure cellulose fall into five different classes, I—IV and x. This organization, with recent subclasses, is used here, but Cellulose x is not discussed because there has been no recent work on it. Crystalline complexes with alkaU (50), water (51), or amines (ethylenediamine, diaminopropane, and hydrazine) (52), and crystalline cellulose derivatives also exist. Those stmctures provide models for the interactions of various agents with cellulose, as well as additional information on the cellulose backbone itself. Usually, as shown in Eigure la, there are two residues in the repeated distance. However, in one of the alkah complexes (53), the backbone takes a three-fold hehcal shape. Nitrocellulose [9004-70-0] heUces have 2.5 residues per turn, with the repeat observed after two turns (54). 

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. 

The most common location for an a helix in a protein structure is along the outside of the protein, with one side of the helix facing the solution and the other side facing the hydrophobic interior of the protein. Therefore, with 3.6 residues per turn, there is a tendency for side chains to change from hydrophobic to hydrophilic with a periodicity of three to four residues. Although this trend can sometimes be seen in the amino acid sequence, it is not strong enough for reliable stmctural prediction by itself, because residues that face the solution can be hydrophobic and, furthermore, a helices can be either completely buried within the protein or completely exposed. Table 2.1 shows examples of the amino acid sequences of a totally buried, a partially buried, and a completely exposed a helix. 

Figure 10.17 Amino acid sequences, represented as a helical wheels with 3.5 residues per turn, of a region of 28 residues from the DNA-binding domains of the transcription factors (a) GCN4, (b) Max,...

In the crystalline region isotactic polystyrene molecules take a helical form with three monomer residues per turn and an identity period of 6.65 A. One hundred percent crystalline polymer has a density of 1.12 compared with 1.05 for amorphous polymer and is also translucent. The melting point of the polymer is as high as 230°C. Below the glass transition temperature of 97°C the polymer is rather brittle. 

There are several other far less common types of helices found in proteins. The most common of these is the Sjq helix, which contains 3.0 residues per turn (with 10 atoms in the ring formed by making the hydrogen bond three residues up the chain). It normally extends over shorter stretches of sequence than the a-helix. Other helical structures include the 27 ribbon and the 77-helix, which has 4.4 residues and 16 atoms per turn and is thus called the 4.4ig helix. 

The 18 hydroxymethyl groups in one turn of the triple helix have quite different orientations. b The two residues per turn are conformationally independent. 

A peptoid pentamer of five poro-substituted (S)-N-(l-phenylethyl)glycine monomers, which exhibits the characteristic a-helix-like CD spectrum described above, was further analyzed by 2D-NMR [42]. Although this pentamer has a dynamic structure and adopts a family of conformations in methanol solution, 50-60% of the population exists as a right-handed helical conformer, containing all cis-amide bonds (in agreement with modeling studies [3]), with about three residues per turn and a pitch of 6 A. Minor families of conformational isomers arise from cis/trans-amide bond isomerization. Since many peptoid sequences with chiral aromatic side chains share similar CD characteristics with this helical pentamer, the type of CD spectrum described above can be considered to be indicative of the formation of this class of peptoid helix in general. 

Krimm, 1968a,b Mattice and Mandelkern, 1971 Krimm and Tiffany, 1974). This conformation is similar to that of a single strand from collagen, with average backbone dihedrals of (0,0) = ( 75°, +145°). These dihedrals lead to an extended left-handed helical conformation with precisely three residues per turn and 9 A between residues i and i + 3 (measured Cft to C/3). A cartoon of a seven-residue alanine peptide in this conformation is shown in Figure 1. Notably, backbone carbonyl and amide groups point perpendicularly out from the helical axis into the solvent and are well-exposed. 

Alternate up and down helices, having six residues per turn, pack in a pseudotetragonal cell with a = b = 19.21 A (1.921 nm) and c = 8.12 A (812 pm). The space group is P2i2i2i. There are 8 molecules of dimethyl sulfoxide in the cell, three of which are inside the helix. 

The unit cell is tetragonal, with a = b = 10.7 A (1.07 nm) and c = 16.1 A (1.61 nm). The amylose helix is left-handed, with four D-glucose residues per turn. Both ions are located in a water-like environment. The atoms 0-2, 0-3, and 0-4 from D-glucose residues on adjacent chains coordinate around K+. The R factor is 41%. 

Electron diffraction by lamellar, single crystals leads to a two-dimensional, tetragonal unit-cell with a = b = 22.9 A (2.29 nm). From X-ray diffraction data obtained from a film of sedimented, lamellar crystals, it was found that the c axis spacing (7.8 A 780 pm) is equivalent to that in 6-fold and 7-fold amylose helices. The true helical diameters of the 1-butanol, isopropyl alcohol, and 1-naphthol complexes were calculated from experimental data. The ratios of 6 7 8 indicated that the 1-naphthol complex has eight D-glucose residues per turn. The diversity of helical orientations in V-amylose crystals was discussed. 

While a polar-zipper model was initially proposed for Asp2Glni3Lys2 (Perutz et ah, 1994), more recently a water-filled nanotube was proposed in which the homopolymer in the / -conformation forms a helical array having 20 residues per turn (Perutz et ah, 2002a,b). (In the earlier work, the diffraction pattern had been interpreted as a fiber pattern—that is, with the 4.8-A reflection in the fibril direction.) Rather than being attributed to intersheet stacking, the 8.4-A reflection was not accounted for. Further,... 

The more compact nature of each a chain explains why we find so few different amino acids present in the primary structure. Glycine has the smallest side chain group of the amino acids, just a single hydrogen atom, as anything more bulky would prevent the tight coiling required to achieve the three residues per turn. 

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