In a/p structures

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.

The most frequent of the domain structures are the alpha/beta (a/P) domains, which consist of a central parallel or mixed P sheet surrounded by a helices. All the glycolytic enzymes are a/p structures as are many other enzymes as well as proteins that bind and transport metabolites. In a/p domains, binding crevices are formed by loop regions. These regions do not contribute to the structural stability of the fold but participate in binding and catalytic action. 

The packing interactions between a helices and p strands are dominated by the residues Val (V), He (I), and Leu (L), which have branched hydrophobic side chains. This is reflected in the amino acid composition these three amino acids comprise approximately 40% of the residues of the P strands in parallel P sheets. The important role that these residues play in packing a helices against P sheets is particularly obvious in a/P-barrel structures, as shown in Table 4.1. 

Figure 4.5 The polypeptide chain of the enzyme pyruvate kinase folds into several domains, one of which is an a/p barrel (red). One of the loop regions in this barrel domain is extended and comprises about 100 amino acid residues that fold into a separate domain (blue) built up from antiparallel P strands. The C-terminal region of about 140 residues forms a third domain (green), which is an open twisted a/p structure.

Each repeat forms a right-handed P-loop-a structure similar to those found in the two other classes of a/p structures described earlier. Sequential p-loop-a repeats are joined together in a similar way to those in the a/P-bar-rel stmctures. The P strands form a parallel p sheet, and all the a helices are on one side of the P sheet. However, the P strands do not form a closed barrel instead they form a curved open stmcture that resembles a horseshoe with a helices on the outside and a p sheet forming the inside wall of the horseshoe (Figure 4.11). One side of the P sheet faces the a helices and participates in a hydrophobic core between the a helices and the P sheet the other side of the P sheet is exposed to solvent, a characteristic other a/p structures do not have. 

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. 

In almost every one of the more than 100 different known a/p structures 1 of this class the active site is at the carboxy edge of the p sheet. Functional residues are provided by the loop regions that connect the carboxy end of the strands with the amino end of the a helices. In this one respect a fun-I damental similarity therefore exists between the a/p-barrel structures and the I open a/p-sheet structures. 

The general shapes of the active sites are quite different, however. Open I a/p structures cannot form funnel-shaped active sites like the barrel struc-Itures. Instead, they form crevices at the edge of the p sheet. Such crevices loccur when there are two adjacent connections that are on opposite sides of Ithe P sheet. One of the loop regions in these two connections goes out from... 

Figure 4.14 Examples of different types of open twisted a/p structures. Both schematic and topological diagrams are given. In the topological diagrams, arrows denote strands of p sheet and rectangles denote a helices, (a) The FMN-binding redox protein flavodoxln. (b) The enzyme adenylate kinase, which catalyzes the reaction AMP +...

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. 

Figure S.l The enzyme superoxide dismutase (SOD). SOD is a P structure comprising eight antiparallel P strands (a). In addition, SOD has two metal atoms, Cu and Zn (yellow circles), that participate in the catalytic action conversion of a superoxide radical to hydrogen peroxide and oxygen. The eight p strands are arranged around the surface of a barrel, which is viewed along the barrel axis in (b) and perpendicular to this axis in (c). [(a) Adapted from J.S. Richardson. The stmcture of SOD was determined in the laboratory of J.S. and D.R. Richardson, Duke University.)...

Assume that we have eight antiparallel p strands arranged in a barrel structure. We decide that we want to connect strand number n to an antiparallel strand at the same end of the barrel. We do not want to connect it to strand number n -e 1 as in the up-and-down barrels just described, nor do we want to connect it to strand number n - 1 which is equivalent to turning the up-and-down barrel in Figure 5.2 upside down. What alternatives remain ... 

Figure 13.4 Schematic diagram (a) and topology diagram (b) of the polypeptide chain of cH-ras p21. The central p sheet of this a/p structure comprises six p strands, five of which are parallel a helices are green, p strands are blue, and the adenine, ribose, and phosphate parts of the GTP analog are blue, green, and ted, respectively. The loop regions that are involved in the activity of this protein are red and labeled Gl-GS. The Gl, G3, and G4 loops have the consensus sequences G-X-X-X-X-G-K-S/T, D-X-X-E, and N-K-X-D, respectively. (Adapted from E.R Pai et al., Nature 341 209-214, 1989.)...

In resonance tenns, electron delocalization in a,p-unsaturated caibonyl compounds is represented by contributions from three principal resonance structures ... 

The structure of heart myocytes is different from that of skeletal muscle fibers. Heart myocytes are approximately 50 to 100 p,m long and 10 to 20 p,m in diameter. The t-tubules found in heart tissue have a fivefold larger diameter than those of skeletal muscle. The number of t-tubules found in cardiac muscle differs from species to species. Terminal cisternae of mammalian cardiac muscle can associate with other cellular elements to form dyads as well as triads. The association of terminal cisternae with the sarcolemma membrane in a dyad structure is called a peripheral coupling. The terminal cisternae may also form dyad structures with t-tubules that are called internal couplings (Figure 17.31). As with skeletal muscle, foot structures form the connection between the terminal cisternae and t-tubule membranes. 

To see why allylic radicals are so stable, look at the orbital picture in Figure 10.3. The radical carbon atom with an unpaired electron can adopt sp2 hybridization, placing the unpaired electron in a p orbital and giving a structure that is electronically symmetrical. The p orbital on the central carbon can therefore overlap equally well with a p orbital on either of the two neighboring carbons. 

Poly(VPGVG) (Fig. 6) has been smdied most thoroughly and it was shown that it exhibits an inverse phase transition. The biopolymer undergoes phase separation from solution upon increasing temperature, resulting in a p-spiral structure and simultaneous release of water molecules associated with the polymer chain (Fig. 7). 

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