Helical number

Fig. 1. Hypothetical secondary structure of a human plasma membrane Na /H exchanger. (Adapted from Sardet et al. [53].) Shaded bars, putative transmembrane segments. Hatched bars, putative amphipathic helices (numbers at tops and bottoms of bars refer to positions of amino acids). CHO, possible site of N-linked glycosylation. Solid bars, regions of the porcine renal Na /H exchanger used for immunolocalization in LLC-PK cells.

FIGURE 7.3 Superposition of the seven transmembrane helices (numbered 1-7) of a GPCR on the outer surface of a G-protein. Abbreviations CT, C-terminus NT, N-terminus icl, ic2, and ic3, first, second, and third intracellular loops of the GPCR. (From Bourne, H. R., Curr. Opin. Cell. Biol., 9, 134, 1997. With permission.)... 

FIGURE 16.18. (a) Overall diagram of a (/ / ) barrel (o-xylose isomerase) (Ref. 89). The 0 strands form a lining for the barrel, and the a helices, numbered sequentially from the N terminus, pack around the 0 lining and provide a stable structure. 

Figure 11. The crystal structure of the red abalone lysin monomer. The a-carbon trace shows the five a-helices numbered a-1 to a-5 and the two basic tracks of Arg and Lys residues. The left basic track contains nine residues and the right track 14 residues (Arg and Lys are not visible in the crystal structure). The two termini are labeled N and C. The N-terminal segment of residues 1 to 12 extends away from the helical bundle and the hypervariable N- and C- termini are in proximity (from Shaw et al., 1993). In the Arg and Lys side chains, carbon atoms are white and nitrogen atoms dark gray.

Spiral coils are curved ducts with varying curvature. The friction factor and heat transfer rate for spiral coils are also included in this section. In addition to the dimensionless parameters used in straight pipes, the following parameters are particularly useful in the case of curved ducts or helicoidal pipes the Dean number De the helical number He, and the effective radius of curvature Rc. These are defined as follows ... 

Cro repressor is a protein in bacteriophage that is a homodimer of 66-residue subunits folded into three oi-helical regions and three strands (Figure 26.28). Two of the helices, numbered 2 and 3 in the figure, are separated by a short turn, forming a helix - turn - helix motif (see here). 

Number of residues/tum, + for right-handed and — for left-handed helices. Number of atoms in hydrogen-bonded ring . 

Proteins are biopolymers formed by one or more continuous chains of covalently linked amino acids. Hydrogen bonds between non-adjacent amino acids stabilize the so-called elements of secondary structure, a-helices and / —sheets. A number of secondary structure elements then assemble to form a compact unit with a specific fold, a so-called domain. Experience has shown that a number of folds seem to be preferred, maybe because they are especially suited to perform biological protein function. A complete protein may consist of one or more domains. 

Fig. 5.17 Histogram of the normal modes calculated for a polyalanine polypeptide in an a-helical conformation. The height of each bar indicates the number of normal modes in each 50cm section.

Coils For flow inside helical coils, Reynolds number above 10,000, multiply the value of the film coefficient obtained from the apphcable equation for straight tubes by the term (1 + 3..5 D /DJ. 

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. 

Figure 4.8 The active site in all a/p barrels is in a pocket formed by the loop regions that connect the carboxy ends of the p strands with the adjacent a helices, as shown schematically in (a), where only two such loops are shown, (b) A view from the top of the barrel of the active site of the enzyme RuBisCo (ribulose bisphosphate carboxylase), which is involved in CO2 fixation in plants. A substrate analog (red) binds across the barrel with the two phosphate groups, PI and P2, on opposite sides of the pocket. A number of charged side chains (blue) from different loops as welt as a Mg ion (yellow) form the substrate-binding site and provide catalytic groups. The structure of this 500 kD enzyme was determined to 2.4 A resolution in the laboratory of Carl Branden, in Uppsala, Sweden. (Adapted from an original drawing provided by Bo Furugren.)...

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. 

Upha/beta (a/p) structures are the most frequent and most regular of the pro-kein structures. They fall into three classes the first class comprises a central core of usually eight parallel p strands arranged close together like the staves pf a barrel, surrounded by a helices the second class comprises an open twisted parallel or mixed p sheet with a helices on both sides of the p sheet and Ihe third class is formed by leucine-rich motifs in which a large number of parallel p strands form a curved p sheet with all the a helices on the outside bfthis sheet. 

---