Hydrophobicity of amino acid residue

Many scales, either empirical or measured, have been proposed for the hydrophobicity of amino acid residues in proteins (Nakai and Li-Chan, 1988). The most extensive study on tlje hydrophobicity index of amino acids was published by Wilce et al. (1995). The authors derived four new scales of coefficients from the reversed-phase high-performance liquid chromatographic retention data of 1738 peptides and compared them with 12 previously published scales. 

G. D. Rose, A. R. Geselowitz, G. J. Lesser et al. Hydrophobicity of amino acid residues in globular proteins. Science, 229 (1985), 834 S. Miller, J. Janin, A. M. Lesk et al. Interior and surface of monomeric proteins. Journal of Molecular Biology, 196 (1987), 641 C. Lawrence, 1. Auger and C. Mannella. Distribution of accessible surfaces of amino acids in globular proteins. Proteins, 2 (1987), 153. 

Pacios, L.F. (2001) Distinct molecular surfaces and hydrophobicity of amino acid residues in proteins. J. Chem. Inf. Comput. Sci., 41, 1427—1435. 

Fig. 4. Alignment of amino acid residues surrounding the binding sites of iGluRl-7. Function lock, interdomain hydrogen bond Pkt, amphiphilic or hydrophobic residues bordering the pocket -NH3+, COO, and distal anion bind the respective charged moieties of glutamate Wat, binds to a binding-site water molecule in iGluR2.

Helical hydrophobic moment ratios, I , are evaluated for 34 polypeptides under conditions where the helix content is dictated solely by the short-range interactions operative in aqueous media. The mean-square helical hydrophobic moment is denoted by , and is the averaged of the squared hydrophoblcltles. This ratio would be one in absence of any correlation in the hydrophoblcltles of amino acid residues in helices. 

In the digestive system trypsin, chymotrypsin, and elastase work as a team. They are all endopeptidases, which means that they cleave protein chains at internal peptide bonds, but each preferentially hydrolyses bonds adjacent to a particular type of amino acid residue (fig. 8.4). Trypsin cuts just next to basic residues (lysine or arginine) chymotrypsin cuts next to aromatic residues (phenylalanine, tyrosine, or tryptophan) elastase is less discriminating but prefers small, hydrophobic residues such as alanine. 

Table 12. Hydrophobicity of side chains of amino acid residue adjacent to carboxyterminal bond to be split by the carboxypeptidase from A. saitoi...

The process through which a linear string of amino acid residues newly synthesized at a ribosome folds into a complex, three-dimensional, biologically active protein structure remains poorly understood. Consider how protein-folding contrasts with RNA-folding. Proteins have 20 distinct monomeric units, RNA only four. The amino acids include aromatic, hydrophobic, cationic, and anionic chemical properties compared to four comparable RNA nucleosides. Moreover, secondary and tertiary structures were fundamentally inter-linked in proteins, but are essentially distinct in RNA molecules. 

As with the majority of transmembrane proteins, the hydrophobic membrane-spanning region consists mainly of amino acid residues with hydrophobic side-chains that are folded in an a-helical conformation (see Topic B3). As each amino acid residue adds 0.15 nm to the length of an a-helix, a helix of 25 residues would have a length of 3.75 nm, just enough to span the hydrophobic core of the bilayer. The hydrophobic side-chains of the residues in the helix protrude outwards from the helix axis to interact via hydrophobic bonds with... 

Methods based on physicochemical properties of amino acid residues (Lim, 1974) such as volume, exposure, hydrophobicity/hydrophilicity, charge, hydrogen bonding potential, and so on. 

Figure 14. Hydrophobicity analysis of five P-type ATPases according to the Kyte-Doolittle method. A hydrophobicity value between -4.5 and +4.5 is assigned to each type of amino acid residue and mean values are successively calculated along the peptide sequence using a window of 18 residues. Segments corresponding to the transmembrane helices M1-M10 in the structural model in Figure 15 are shaded. Modified from Verma et al., 1988.

Natural thermostable enzymes are expected to be a good model for engineering stabilization of proteins. Study of thermostable enzymes from thermophilic microorganisms has revealed that the hydrophobicity of hydrophobic core inside the protein molecule and the electrostatic interactions of amino acid residues within the folded protein seem to be the cause of their stability. The enzymes from thermophilic microorganisms known so far do not contain the disulfide bond, but aqualysin I. Aqualysin I is an extracellular protease while the others are intracellular enzymes. 

They do this by completely spanning the bilayer (see Fig. 6-7). The parts that project on either side are polar, while the parts embedded in the bilayer consist of amino acid residues with hydrophobic... 

TABLE I Fundamental Properties of Amino Acid Residues in Terms of Occurrence in Proteins, Molecular Mass, Molecule Volume, Accessible Surface Area, Partial Specific Volume, pKa of Ionizing Side Chains, and Relative Hydrophobicity... 

Bitterness occurs as a defect in dairy products as a result of casein proteolysis by enzymes that produce bitter peptides. Bitter peptides are produced in cheese because of an undesirable pattern of hydrolysis of milk casein (Habibi-Najafi and Lee 1996). According to Ney (1979), bitterness in amino acids and peptides is related to hydrophobic-ity. Each amino acid has a hydrophobicity value (Af), which is defined as the free energy of transfer of the side chains and is based on solubility properties (Table 7-6). The average hydrophobicity of a peptide, Q, is obtained as the sum of the Af of component amino acids divided by the number of amino acid residues. Ney (1979) reported that bitterness is found only in peptides with molecular weights... 

The solubilisation of proteins and amino acids in organic solvents by reversed micelles provides a new method for the selective recovery, separation and concentration of bioproducts using liquid->liquid extraction techniques. Selectivity is affected by electrostatic interactions between the charged residues or moieties of the solute and the surfactant headgroups. These interactions are mediated by electrostatic screening as affected by solution ionic strength. The more hydrophobic the amino acid residue, the more favourable is the solubilisation of this residue in the partially structured water pool of the reversed micelle relative to the bulk, unstructured water phase. 

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