Bond, antiparallel

Watson and Crick were the first to appreciate the significance of strong 3.4-A and 34-A spacings and the central crosslike pattern, which reflects a helix structure in the x-ray diffraction pattern of DNA. They interpreted this as arising from the hydrogen-bonded antiparallel double-helix structure. 

Furthermore, the backbone of the Pro-Arg segment formed a hydrogen-bonded antiparallel (1-chain with the Ser214-Gly216 sequence in thrombin. 

Parallel and antiparallel sheets have different patterns of hydrogen bonding. Antiparallel sheets have unevenly spaced hydrogen bonds per-... 

Within a cell, the DNA molecule actually consists of two hydrogen-bonded antiparallel strands as depicted in Figure 1.2b. The strands are antiparallel because the end of one strand has a free 3 OH while the adjacent end of the companion strand has a free 5 OH. Thus, one strand is said to run in the 3 5 direction, while the other has the opposite 5 3 polarity. This allows the A, G, C, and T bases... 

Similar models for the crystal stmcture of Fortisan Cellulose II came from two separate studies despite quite different measured values of the diffraction intensities (66,70). Both studies concluded that the two chains in the unit cell were packed antiparallel. Hydrogen bonding between chains at the corners and the centers of the unit cells, not found in Cellulose I, was proposed to account for the increased stabiUty of Cellulose II. The same model, with... 

Cellulose III. Cellulose III results from treatment of cellulose with Hquid ammonia (ammonia mercerization) or amines. Cellulose III can be made from either Cellulose I or II. When treated with water. Cellulose III can revert to its parent stmcture. Some cellulose III preparations are much more stable than other preparations. The intensities on diffraction patterns from Cellulose III differ slightly depending on whether the Cellulose III was made from Cellulose I or II, and thus these allomorphs are called IIIj or IHjj- Workers studying III concluded, based partiy on the results of I and II, that the packings of IIIj and IIIjj are parallel and antiparallel, respectively (67). IIIjj also is thought to have hydrogen bonds between the corner and center chains. 

Figure 2.5 Schematic illustrations of antiparallel (3 sheets. Beta sheets are the second major element of secondary structure in proteins. The (3 strands are either all antiparallel as in this figure or all parallel or mixed as illustrated in following figures, (a) The extended conformation of a (3 strand. Side chains are shown as purple circles. The orientation of the (3 strand is at right angles to those of (b) and (c). A p strand is schematically illustrated as an arrow, from N to C terminus, (bj Schematic illustration of the hydrogen bond pattern in an antiparallel p sheet. Main-chain NH and O atoms within a p sheet are hydrogen bonded to each other.

Beta strands can also combine into mixed P sheets with some P strand pairs parallel and some antiparallel. There is a strong bias against mixed P sheets only about 20% of the strands inside the p sheets of known protein structures have parallel bonding on one side and antiparallel bonding on the other. Figure 2.7 illustrates how the hydrogen bonds between the p strands are arranged in a mixed P sheet. 

Figure 2.8 Adjacent antiparallel P strands are joined by hairpin loops. Such loops are frequently short and do not have regular secondary structure. Nevertheless, many loop regions in different proteins have similar structures, (a) Histogram showing the frequency of hairpin loops of different lengths in 62 different proteins, (b) The two most frequently occurring two-residue hairpin loops Type I turn to the left and Type II turn to the right. Bonds within the hairpin loop are green, [(a) Adapted from B.L. Sibanda and J.M. Thornton, Nature 316 170-174, 1985.]...

The interiors of protein molecules contain mainly hydrophobic side chains. The main chain in the interior is arranged in secondary structures to neutralize its polar atoms through hydrogen bonds. There are two main types of secondary structure, a helices and p sheets. Beta sheets can have their strands parallel, antiparallel, or mixed. 

The simplest topology is obtained if each successive p strand is added adjacent to the previous strand until the last strand is joined by hydrogen bonds to the first strand and the barrel is closed (Figure 5.2). These are called up-and-down P sheets or barrels. The arrangement of p strands is similar to that in the a/P-barrel structures we have just described in Chapter 4, except that here the strands are antiparallel and all the connections are hairpins. The structural and functional versatility of even this simple arrangement will be illustrated by two examples. 

Figure 6.6 Schematic diagram of the structure of the enzyme lysozyme which folds into two domains. One domain is essentially a-helical whereas the second domain comprises a three stranded antiparallel p sheet and two a helices. There are three disulfide bonds (green), two in the a-helical domain and one in the second domain.

Dimerization of pairs of Cro monomers depends primarily on interactions between p strand 3 from each subunit (Figure 8.4). These strands, which are at the carboxy end of the chains, are aligned in an antiparallel fashion and hydrogen bonded to each other so that the three-stranded p sheets of the monomers form a six-stranded antiparallel p sheet in the dimer (Figure 8.5). 

---