Side chain hydrophobic

The amino acids are usually divided into three different classes defined hy the chemical nature of the side chain. The first class comprises those with strictly hydrophobic side chains Ala (A), Val (V), Leu (L), He (1), Phe (F), Pro (P), and Met (M). The four charged residues, Asp (D), Glu (E), Lys (K), and Arg (R), form the second class. The third class comprises those with polar side chains Ser (S), Thr (T), Cys (C), Asn (N), Gin (Q), His (H), Tyr (Y), and Trp (W). The amino acid glycine (G), which has only a hydrogen atom as a side chain and so is the simplest of the 20 amino acids, has special properties and is usually considered either to form a fourth class or to belong to the first class. 

Figure 2.4 The helical wheel or spiral. Amino acid residues are plotted every 100° around the spiral, following the sequences given in Table 2.1. The following color code is used green Is an amino acid with a hydrophobic side chain, blue is a polar side chain, and red is a charged side chain. The first helix is all hydrophobic, the second is polar on one side and hydrophobic on the other side, and the third helix is all polar.

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. 

Alpha helices are sufficiently versatile to produce many very different classes of structures. In membrane-bound proteins, the regions inside the membranes are frequently a helices whose surfaces are covered by hydrophobic side chains suitable for the hydrophobic environment inside the membranes. Membrane-bound proteins are described in Chapter 12. Alpha helices are also frequently used to produce structural and motile proteins with various different properties and functions. These can be typical fibrous proteins such as keratin, which is present in skin, hair, and feathers, or parts of the cellular machinery such as fibrinogen or the muscle proteins myosin and dystrophin. These a-helical proteins will be discussed in Chapter 14. 

Figure 3.3 Schematic diagram showing the packing of hydrophobic side chains between the two a helices in a coiled-coil structure. Every seventh residue in both a helices is a leucine, labeled "d." Due to the heptad repeat, the d-residues pack against each other along the coiled-coil. Residues labeled "a" are also usually hydrophobic and participate in forming the hydrophobic core along the coiled-coil.

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.

Branched hydrophobic side chains dominate the core of oi/p barrels... 

In barrels the hydrophobic side chains of the a helices are packed against hydrophobic side chains of the p sheet. The a helices are antiparallel and adjacent to the p strands that they connect. Thus the barrel is provided with a shell of hydrophobic residues from the a helices and the p strands. 

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. 

Third, in open-sheet structures the a helices are packed against both sides of the p sheet. Each p strand thus contributes hydrophobic side chains to pack against a helices in two similar hydrophobic core regions, one on each side of the p sheet. 

The p sheets have the usual twist, and when two such twisted p sheets are packed together, they form a barrel-like structure (Figure 5.1). Antiparallel P structures, therefore, in general have a core of hydrophobic side chains inside the barrel provided by residues in the P strands. The surface is formed by residues from the loop regions and from the strands. The aim of this chapter is to examine a number of antiparallel p structures and demonstrate how these rather complex structures can be separated into smaller comprehensible motifs. 

Figure 10.18 Side-chain interactions in the leucine zipper structure, (a) The hydrophobic side chains in spikes a and d (see Figure 10.17) form a hydrophobic core between the two coiled a helices, (b) Charged side chains in spikes and g can promote dimer formation by forming complementary charge interactions between the two a helices.

Naively, one might assume that it should be possible to scan the sequence and pick out regions with about 20 consecutive hydrophobic amino acids. However, no such regions occur in the reaction center proteins. Just as in soluble proteins there are hydrophobic side chains at the... 

In order to examine whether this sequence gave a fold similar to the template, the corresponding peptide was synthesized and its structure experimentally determined by NMR methods. The result is shown in Figure 17.15 and compared to the design target whose main chain conformation is identical to that of the Zif 268 template. The folds are remarkably similar even though there are some differences in the loop region between the two p strands. The core of the molecule, which comprises seven hydrophobic side chains, is well-ordered whereas the termini are disordered. The root mean square deviation of the main chain atoms are 2.0 A for residues 3 to 26 and 1.0 A for residues 8 to 26. 

The second major class of protein structures contains structures based around parallel or mixed j8-sheets. Parallel /3-sheet arrays, as previously discussed, distribute hydrophobic side chains on both sides of the sheet. This means that neither side of parallel /3-sheets can be exposed to solvent. Parallel /3-sheets are thus typically found as core structures in proteins, with little access to solvent. 

The pioneering work on amphiphilic polyelectrolytes goes back to 1951, when Strauss et al. [25] first synthesized amphiphilic polycations by quaternization of poly(2-vinylpyridine) with n-dodecyl bromide. They revealed that the long alkyl side chains attached to partially quaternized poly(vinylpyridine)s tended to aggregate in aqueous solution so that the polymers assumed a compact conformation when the mole fraction of the hydrophobic side chains exceeded a certain critical value. Thus, Strauss et al. became the first to show experimentally the intramolecular micellation of amphiphilic polymers and the existence of a critical content of hydrophobic residues which may be compared to the critical micelle concentration of ordinary surfactants. They called such amphiphilic polyelectrolytes polysoaps [25],... 

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