Nonpolar residues

Fig. 10. Sequences (see Table 1) of betabeUins. In each case, only one-half of the P-sandwich is shown. The dimer is formed from identical monomeric sets of four P-strands. In the pattern sequence, e is for end, p is for polar residue, n is for nonpolar residue, and t and r are for turn residues. Lower case f is iodophenyialanine lower case a, d, k, and p are the D-amino acid forms of alanine, aspartic acid, lysine, and proline, respectively B is P-alanine (2,53,60,61).

Hydrophobic bonds, or, more accurately, interactions, form because nonpolar side chains of amino acids and other nonpolar solutes prefer to cluster in a nonpolar environment rather than to intercalate in a polar solvent such as water. The forming of hydrophobic bonds minimizes the interaction of nonpolar residues with water and is therefore highly favorable. Such clustering is entropically driven. The side chains of the amino acids in the interior or core of the protein structure are almost exclusively hydrophobic. Polar amino acids are almost never found in the interior of a protein, but the protein surface may consist of both polar and nonpolar residues. 

In a typical a-helix of 12 (or n) residues, there are 8 (or w — 4) hydrogen bonds. As shown in Figure 6.9, the first 4 amide hydrogens and the last 4 carbonyl oxygens cannot participate in helix Fl-bonds. Also, nonpolar residues sit-... 

Less commonly, an a-helix can be completely buried in the protein interior or completely exposed to solvent. Citrate synthase is a dimeric protein in which a-helical segments form part of the subunit-subunit interface. As shown in Figure 6.24, one of these helices (residues 260 to 270) is highly hydrophobic and contains only two polar residues, as would befit a helix in the protein core. On the other hand. Figure 6.24 also shows the solvent-exposed helix (residues 74 to 87) of cahnodulln, which consists of 10 charged residues, 2 polar residues, and only 2 nonpolar residues. 

For polar side chains, AH hahi is positive and AHsoi, e , is negative. Because solvent molecules are ordered to some extent around polar groups, ASsoi, e , is small and positive. As shown in the figure, AGt t i for the polar groups of a protein is near zero. Comparison of all the terms considered here makes it clear that the single largest eontribution to the stability of a folded protein is for the nonpolar residues. 

The amino acid compositions and sequences of the /3-strands in porin proteins are novel. Polar and nonpolar residues alternate along the /3-strands, with polar residues facing the central pore or cavity of the barrel and nonpolar residues facing out from the barrel where they can interact with the hydrophobic lipid milieu of the membrane. The smallest diameter of the porin channel is about 5 A. Thus, a maltodextrin polymer (composed of two or more glucose units) must pass through the porin in an extended conformation (like a spaghetti strand). 

FIGURE 10.35 The amino acid sequences of several amphipathic peptide antibiotics, a-Helices formed from these peptides cluster polar residues on one face of the helix, with nonpolar residues at other positions. 

Imately 65 X 55 X 50 It Is composed of four polypeptide chains each resembling quite closely the myoglobin chain The three dimensional structure of the subunits Is held together by weak noncovalent bonds The polar amino acid side chains are In contact with the solvent, and the nonpolar residues are located In the Interior of the molecule or In regions which form the contacts between chains The heme group Is located In a pocket In each chain residues In contact with heme are Invariable ( e are the same In different mammalian hemoglobins) and the bonds between heme and chain are hydrophobic Interactions Contacts between like chains (a-a are... 

Fig. 14. Structural prediction and modeling of a fragment of FHA from B. pertussis containing Rl-repeats. (A) Successive stages in the modeling. From top to bottom identification of the consensus sequence repeat, generation of 2D template of the coil, and the modeled 3D structure. In the consensus sequence, letters indicate residues that are conserved at the level of >60% identity, x is any residue and filled circles represent bulky nonpolar residues. Apolar residues are in red glycine in green. In the 2D template, open circles denote any (but mainly polar) residues, while filled circles denote conserved, mainly nonpolar, residues. Circles inside the coil contour indicate side chains located inside the structure and circles outside the contour denote side chains facing the solvent. Arrows indicate /(-strands. (B) A fragment of the crystal structure of FHA (Clantin et al, 2004) (on the top, in green color) and the 3D model (bottom, in brown).

The cahnodulin-binding peptides assume random coil structures in solution, but in the presence of calmodulin they form amphipathic or amphiphilic (containing both polar and nonpolar residues) helices. All of these peptides have nanomolar (very high) affinities for calmodulin. Table 6.9 shows the primary amino acid sequence of some of the cahnoduUn-binding peptides, and it is informative to compare them as they are discussed in the following material. 

Methylene chloride-soluble residues. Methylene chloride-or chloroform-soluble C-labeled products were major residues in all of the plant tissues examined except peanut cell ciiltures (Figure 3). Chloroform-soluble C accounted for 59.2 of the radioactivity isolated from peanut roots 48 hr after treatment with [ C]PCNB. The radioactivity was in the form of PCNB (28.7 ), pentachloroaniline (22.5 ), pentachlorothiophenol (2.6 ) pentachlorothloanlsole (3.1 ) pentachlorothloanlsole sulfoxide (0.5 ) S-(pentachlorophenyl)-2-thioaoetic acid [(S-(PCP)ThioAcetate] (0.5 ) and S-(pentachlorophenyl)-3-thio-2-hydroxypropionic acid [S-(PCP)ThioLactate] (0.2 ) and S-(PCP)Cys (trace) (J), The structures of these compounds are shown in Figure 13. Based on TLC, the last three compounds in this list were classified as polar chloroform- or methylene chloride-soluble residues and the remaining compounds were classified as nonpolar residues. 

Trypsin, chymotrypsin, and elastase—three members of the serine protease family—catalyze the hydrolysis of proteins at internal peptide bonds adjacent to different types of amino acids. Trypsin prefers lysine or arginine residues chymotrypsin, aromatic side chains and elastase, small, nonpolar residues. Carboxypeptidases A and B, which are not serine proteases, cut the peptide bond at the carboxyl-terminal end of the chain. Carboxypeptidase A preferentially removes aromatic residues carboxypeptidase B, basic residues. (Illustration copyright by Irving Geis. Reprinted by permission.)... 

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