Arrangement, helical

Fibrous protein sequences are often characterized by the presence of simple repetitive motifs. Some are exact in length and/or sequence, but others are only approximate and display considerable variation. Some motifs contain residues that are absolutely conserved in some positions, whereas in others it is only the sequence character that is maintained over the repeat length. In many fibrous proteins the repeats occur contiguously, whereas in others they are found widely separated in the sequence. The varieties of sequence repeat that have been observed are typed and catalogued here by Parry (Chapter 2). Each motif forms a discrete element of structure in many instances, these are arranged helically with respect to one another. In many cases an elongate structure is formed, and this can lead naturally to molecular aggregation and the formation of functional filaments. 

Microtubules Fiber-like cytoplasmic structures that consist of units of the protein tubufin arranged helically to form a hollow tube. They are involved in various kinds of cellular motility, including the beating of cilia and flagella and the movement of... 

The discrete complexes are arranged helically to yield supercoiled structures. The chiral information of the small chiral part is amplified to result in much larger three-dimensional chiral structures in the crystals. 

In addition to hydrogen bonding between the two polynucleotide chains the double helical arrangement is stabilized by having its negatively charged phosphate groups on the outside where they are m contact with water and various cations Na" Mg and ammonium ions for example Attractive van der Waals forces between the... 

Section 28 9 Within the cell nucleus double helical DNA adopts a supercoiled terti ary structure m which short sections are wound around proteins called histones This reduces the effective length of the DNA and maintains it m an ordered arrangement... 

FIG. 18-21 Effect of impeller speed on circulation time for a helical impeller in the Reynolds niimher arranged less than 10. 

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

Figure 2.1 Kendrew s model of the low-resolution structure of myoglobin shown in three different views. The sausage-shaped regions represent a helices, which are arranged in a seemingly Irregular manner to form a compact globular molecule. (Courtesy of J.C. Kendrew.)...

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.

Secondary structure occurs mainly as a helices and p strands. The formation of secondary structure in a local region of the polypeptide chain is to some extent determined by the primary structure. Certain amino acid sequences favor either a helices or p strands others favor formation of loop regions. Secondary structure elements usually arrange themselves in simple motifs, as described earlier. Motifs are formed by packing side chains from adjacent a helices or p strands close to each other. 

Domains are formed by different combinations of secondary structure elements and motifs. The a helices and p strands of the motifs are adjacent to each other in the three-dimensional structure and connected by loop regions. Sequentially adjacent motifs, or motifs that are formed from consecutive regions of the primary structure of a polypeptide chain, are usually close together in the three-dimensional structure (Figure 2.20). Thus to a first approximation a polypeptide chain can be considered as a sequential arrangement of these simple motifs. The number of such combinations found in proteins is limited, and some combinations seem to be structurally favored. Thus similar domain structures frequently occur in different proteins with different functions and with completely different amino acid sequences. 

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. 

Figure 3.6 Four-helix bundles frequently occur as domains in a proteins. The arrangement of the a helices is such that adjacent helices in the amino acid sequence are also adjacent in the three-dimensional structure. Some side chains from all four helices are buried in the middle of the bundle, where they form a hydrophobic core, (a) Schematic representation of the path of the polypeptide chain in a four-helrx-bundle domain. Red cylinders are a helices, (b) Schematic view of a projection down the bundle axis. Large circles represent the main chain of the a helices small circles are side chains. Green circles are the buried hydrophobic side chains red circles are side chains that are exposed on the surface of the bundle, which are mainly hydrophilic.

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.

Fi re 3.9 Schematic diagram of the structure of one domain of a bacterial muramidase, comprising 450 amino acid residues. The structure is built up from 27 a helices arranged in a two-layered ring. The ring has a large central hole, like a doughnut, with a diameter of about 30 A. 

In the next class of a/p structures there are a helices on both sides of the p sheet. This has at least three important consequences. First, a closed barrel cannot be formed unless the p strands completely enclose the a helices on one side of the p sheet. Such structures have never been found and are very unlikely to occur, since a large number of p strands would be required to enclose even a single a helix. Instead, the p strands are arranged into an open twisted p sheet such as that shown in Figure 4.1b. 

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