Amino acids polarity

With a knowledge of the methodology in hand, let s review the results of amino acid composition and sequence studies on proteins. Table 5.8 lists the relative frequencies of the amino acids in various proteins. It is very unusual for a globular protein to have an amino acid composition that deviates substantially from these values. Apparently, these abundances reflect a distribution of amino acid polarities that is optimal for protein stability in an aqueous milieu. Membrane proteins have relatively more hydrophobic and fewer ionic amino acids, a condition consistent with their location. Fibrous proteins may show compositions that are atypical with respect to these norms, indicating an underlying relationship between the composition and the structure of these proteins. 

Peppas et al. calculated the values for AH3 and AH by using Drago s acid-base coefficients of amino acid polar groups and of polymer surfaces [13, 18-20],... 

The best substrates for ophidian L-amino acid oxidases are aromatic or, most generally, hydrophobic amino acids, polar and basic amino acids being deami-nated at much lower rates Glu, Asp, and Pro are not oxidized by L-amino add oxidase. L-Amino add oxidase is also active on ring-substituted aromatic amino acids, as well as on seleno cysteinyl derivatives. The substrate specificity depends on the source of the enzyme (e.g. Ophiophagus hannah L-amino acid oxidase also oxidizes Lys and Om) and on the pH. The of the reaction of Crotalus adaman-... 

Amino acids Non-polar chain pi Amino acids Polar chain pi Amino acids Charged chain pi... 

Substituting a similar amino acid (polar, charged, or uncharged) in a polypeptide chain will have a much less drastic effect on the protein function than will the substitution of a much different amino acid. 

Water-soluble globular proteins usually have an interior composed almost entirely of non polar, hydrophobic amino acids such as phenylalanine, tryptophan, valine and leucine witl polar and charged amino acids such as lysine and arginine located on the surface of thi molecule. This packing of hydrophobic residues is a consequence of the hydrophobic effeci which is the most important factor that contributes to protein stability. The molecula basis for the hydrophobic effect continues to be the subject of some debate but is general considered to be entropic in origin. Moreover, it is the entropy change of the solvent that i... 

The most general methods for the syntheses of 1,2-difunctional molecules are based on the oxidation of carbon-carbon multiple bonds (p. 117) and the opening of oxiranes by hetero atoms (p. 123fl.). There exist, however, also a few useful reactions in which an a - and a d -synthon or two r -synthons are combined. The classical polar reaction is the addition of cyanide anion to carbonyl groups, which leads to a-hydroxynitriles (cyanohydrins). It is used, for example, in Strecker s synthesis of amino acids and in the homologization of monosaccharides. The ff-hydroxy group of a nitrile can be easily substituted by various nucleophiles, the nitrile can be solvolyzed or reduced. Therefore a large variety of terminal difunctional molecules with one additional carbon atom can be made. Equally versatile are a-methylsulfinyl ketones (H.G. Hauthal, 1971 T. Durst, 1979 O. DeLucchi, 1991), which are available from acid chlorides or esters and the dimsyl anion. Carbanions of these compounds can also be used for the synthesis of 1,4-dicarbonyl compounds (p. 65f.). 

Metal hydrides reduce preferably polar double bonds, whereas catalytic hydrogenation is somewhat selective for non-polar double bonds. Selective protection of amino groups in amino acids. 

Amino acids with polar hut nonionized side chains... 

The physical properties of a typical amino acid such as glycine suggest that it is a very polar substance much more polar than would be expected on the basis of its formula tion as H2NCH2CO2H Glycine is a crystalline solid it does not melt but on being heated It eventually decomposes at 233°C It is very soluble m water but practically insoluble m nonpolar organic solvents These properties are attributed to the fact that the stable form of glycine is a zwittenon, or inner salt... 

Hydrogen bonding stabilizes some protein molecules in helical forms, and disulfide cross-links stabilize some protein molecules in globular forms. We shall consider helical structures in Sec. 1.11 and shall learn more about ellipsoidal globular proteins in the chapters concerned with the solution properties of polymers, especially Chap. 9. Both secondary and tertiary levels of structure are also influenced by the distribution of polar and nonpolar amino acid molecules relative to the aqueous environment of the protein molecules. Nonpolar amino acids are designated in Table 1.3. 

Solubility. Solubility data of amino acids are given in Table 3. In all instances there are at least two polar groups, acting synergistically on the solubility in water. The solubility of amino acids having additional polar groups, eg, —OH, —SH, —COOH, —NH2, is even more enhanced. 

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).

The choice of a suitable immobilization method for a given enzyme and appHcation is based on a number of considerations including previous experience, new experiments, enzyme cost and productivity, process demands, chemical and physical stabiHty of the support, approval and safety issues regarding support, and chemicals used. Enzyme characteristics that greatly influence the approach include intra- or extraceUular location size surface properties, eg, charge/pl, lysine content, polarity, and carbohydrate and active site, eg, amino acids or cofactors. The size, charge, and polarity of the substrate should also be considered. 

Cosolvents ana Surfactants Many nonvolatile polar substances cannot be dissolved at moderate temperatures in nonpolar fluids such as CO9. Cosolvents (also called entrainers, modifiers, moderators) such as alcohols and acetone have been added to fluids to raise the solvent strength. The addition of only 2 mol % of the complexing agent tri-/i-butyl phosphate (TBP) to CO9 increases the solubility ofnydro-quinone by a factor of 250 due to Lewis acid-base interactions. Veiy recently, surfac tants have been used to form reverse micelles, microemulsions, and polymeric latexes in SCFs including CO9. These organized molecular assemblies can dissolve hydrophilic solutes and ionic species such as amino acids and even proteins. Examples of surfactant tails which interact favorably with CO9 include fluoroethers, fluoroacrylates, fluoroalkanes, propylene oxides, and siloxanes. 

A prior distribution for sequence profiles can be derived from mixtures of Dirichlet distributions [16,51-54]. The idea is simple Each position in a multiple alignment represents one of a limited number of possible distributions that reflect the important physical forces that determine protein structure and function. In certain core positions, we expect to get a distribution restricted to Val, He, Met, and Leu. Other core positions may include these amino acids plus the large hydrophobic aromatic amino acids Phe and Trp. There will also be positions that are completely conserved, including catalytic residues (often Lys, GIu, Asp, Arg, Ser, and other polar amino acids) and Gly and Pro residues that are important in achieving certain backbone conformations in coil regions. Cys residues that form disulfide bonds or coordinate metal ions are also usually well conserved. 

Reduce the size of the alphabet from 20 amino acids to a smaller alphabet of, say, six (aliphatic, aromatic, charged, polar, glycine, proline). 

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. 

Each amino acid has atoms in common, and these form the main chain of the protein. The remaining atoms form side chains that can be hydrophobic, polar, or charged. 

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