Polar 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).

ES Eluang, S Subbiah, M Levitt. Recognizing native folds by the airangements of hydrophobic and polar residues. J Mol Biol 252 709-720, 1995. 

The first sequence is from the enzyme citrate synthase, residues 260-270, which form a buried helix the second sequence is from the enzyme alcohol dehydrogenase, residues 355-365, which form a partially exposed helix and the third sequence is from troponin-C, residues 87-97, which form a completely exposed helix. Charged residues are colored red, polar residues ate blue, and hydrophobic residues are green. 

Residues 3, 5, 6, and 8 in the N-terminal arm lie in the minor groove and form contacts with either the edge of the bases or with the DNA backbone. Almost all homeodomains contain four conserved residues, Asn 51, Arg 53, Trp 48 and Phe 49, in the middle of the long recognition helix. The first two conserved polar residues interact with DNA. The second two are part of the hydrophobic core of the homeodomain, and are important for the accurate positioning of the recognition helix and the N-terminal arm with respect to... 

The helices are aligned according to approximate positions within the membrane and with respect to the photosynthetic pigments. LA is the first helix of subunit L, ME is the last helix of subunit M, HA is the only transmembrane helix of subunit H. Charged residues are eol-ored red, polar residues are blue, hydrophobic residues are green, and glycine is yellow. (From T.O. Yeates et al., Proc. Natl. Acad. Sci. USA 84 6438-6442, 1987.)... 

For each fold one searches for the best alignment of the target sequence that would be compatible with the fold the core should comprise hydrophobic residues and polar residues should be on the outside, predicted helical and strand regions should be aligned to corresponding secondary structure elements in the fold, and so on. In order to match a sequence alignment to a fold, Eisenberg developed a rapid method called the 3D profile method. The environment of each residue position in the known 3D structure is characterized on the basis of three properties (1) the area of the side chain that is buried by other protein atoms, (2) the fraction of side chain area that is covered by polar atoms, and (3) the secondary stmcture, which is classified in three states helix, sheet, and coil. The residue positions are rather arbitrarily divided into six classes by properties 1 and 2, which in combination with property 3 yields 18 environmental classes. This classification of environments enables a protein structure to be coded by a sequence in an 18-letter alphabet, in which each letter represents the environmental class of a residue position. 

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. 

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. 

The sialidase active site contains a relatively high number of charged amino acids and, in total, there are ten polar (Arg/Asp/Glu) and four non-polar residues that... 

Recently, peptoid-based mimics of both SP-C and SP-B have been designed to adopt helical secondary structures, and also mimic (to varying degrees) the sequence patterning of hydrophobic and polar residues found in the natural surfactant proteins. Peptoid-based SP-C mimics of up to 22 monomers in length, were synthesized and characterized by in vitro experimental methods [67, 68] (Fig. 1.8). The secondary structure of all molecules was assessed by circular dichroism and found to be helical. The surface activities of these peptoids, in comparison to the actual SP peptides described above, were characterized by surfactometry using... 

Resilin has a greater percentage of acidic residues than collagen, elastin, and silk fibroin and contains fewer non-polar residues (i.e., Gly, Ala, Val, He, Leu, Pro, Met, and Phe) than silk fibroin and elastin. The significant content of acidic residues might account for resilin s hydrophilicity as well as its low isoelectric point, as indicated through swelling experiments [141, 145]. Resilin contains little to no... 

SFE. SFE has been established as the extraction method of choice for solid samples. The usefulness of SFE for soil samples has been demonstrated for carbamate,organophosphorus and organochlorine pesticides. However, SFE is more effective in extracting nonpolar than polar residues. In order to obtain a greater extraction efficiency for the polar residues of imidacloprid, the addition of 20% methanol as modifier is required. Extraction at 276 bar and 80 °C with a solvent consisting of supercritical carbon dioxide modified with methanol (5%) for 40 min gives a recovery of 97% (RSD = 3.6%, n = 10). It is possible to use process-scale SFE to decontaminate pesticide residues from dust waste. ... 

Vila, J. A., Ripoll, D. R., and Scheraga, H. A. (2000). Physical reasons for the unusual a helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc. Natl. Acad. Sd. USA 97, 13075-13079. 

---