Amino acids hydrophobic character

Lesk and Chothia did find, however, that there is a striking preferential conservation of the hydrophobic character of the amino acids at the 59 buried positions, but that no such conservation occurs at positions exposed on the surface of the molecule. With a few exceptions on the surface, hydrophobic residues have replaced hydrophilic ones and vice versa. However, the case of sickle-cell hemoglobin, which is described below, shows that a charge balance must be preserved to avoid hydrophobic patches on the surface. In summary, the evolutionary divergence of these nine globins has been constrained primarily by an almost absolute conservation of the hydro-phobicity of the residues buried in the helix-to-helix and helix-to-heme contacts. 

The 20 natural amino acids differ from each other by the nature of their sidechains. Differences involve overall size, hydrophobic or hydrophilic character and, perhaps most importantly, ionization state. While the sidechains are normally written in terms of neutral structures, some may also exist in either protonated or deprotonated forms depending on pH. 

Fig. 3-10 The 20 protein amino acids divided by R group character as (a) hydrophobic, (b) hydrophilic, and (c) mixed. (Reprinted with permission from W. K. Purves and G. H. Orians, Life The Science of Biology," pp. 63-81, Copyright 1987 by Sinauer Associates, Inc., Sunderland, MA.)...

Polymers of amino acids, like polymers of nucleic acids, have both ionic and hydrophobic character. Unlike the polymers of nucleic acids, amino acid polymers may carry either a negative or a positive (or zero) net charge, are far more subject to irreversible denaturation and oxidation, and are labile to... 

In polar solvents, the structure of the acridine 13 involves some zwitterionic character 13 a [Eq. (7)] and the interior of the cleft becomes an intensely polar microenvironment. On the periphery of the molecule a heavy lipophilic coating is provided by the hydrocarbon skeleton and methyl groups. A third domain, the large, flat aromatic surface is exposed by the acridine spacer unit. This unusual combination of ionic, hydrophobic and stacking opportunities endows these molecules with the ability to interact with the zwitterionic forms of amino acids which exist at neutral pH 24). For example, the acridine diacids can extract zwitterionic phenylalanine from water into chloroform, andNMR evidence indicates the formation of 2 1 complexes 39 such as were previously described for other P-phenyl-ethylammonium salts. Similar behavior is seen with tryptophan 40 and tyrosine methyl ether 41. The structures lacking well-placed aromatics such as leucine or methionine are not extracted to measureable degrees under these conditions. 

The properties of the amino acid are determined by the residue R, which may, for example, confer hydrophilic or hydrophobic character. 

The cells of all contemporary living organisms are surrounded by cell membranes, which normally consist of a phospholipid bilayer, consisting of two layers of lipid molecules, into which various amounts of proteins are incorporated. The basis for the formation of mono- or bilayers is the physicochemical character of the molecules involved these are amphipathic (bifunctional) molecules, i.e., molecules which have both a polar and also a non-polar group of atoms. Examples are the amino acid phenylalanine (a) or the phospholipid phosphatidylcholine (b), which is important in membrane formation. In each case, the polar group leads to hydrophilic, and the non-polar group to hydrophobic character. 

These AChE forms differ in solubility and mode of membrane attachment rather than in catalytic activity. One class of molecular forms exists as homomeric assemblies of catalytic subunits that appear as monomers, dimers or tetramers (Fig. 11-7). These forms also differ in hydrophobicity, and their amphiphilic character arises from either exposure of an amphipathic helix or post-translational addition of a glycophospholipid on the carboxyl-terminal amino acid. The glycophospholipid allows the enzyme to be tethered on the external surface of the cell membrane. 

The binding domain for the hormone, or LBD, is situated in the carboxyl half of the receptor, the final portion of which is critical. For example, the deletion of 12 amino acids in the carboxyl end of the androgen receptor suppresses its capacity to bind hormone (O Malley et al. 1974). The LBD has an amino acid composition that confers upon it a net hydrophobic character, suitable for interacting with organic molecules of low molecular weight, such as steroids. 

Although the iron centers are coordinated by polar groups (aspartate, glutamate, histidine, tyrosinate, and thiolate side chains), the overall environment created by residues surrounding the iron-ligand center often has a hydrophobic character. Amino acids located in this second... 

Being highly hydrophobic but less lipophilic than their hydrocarbon analogs, fluoroalkyl amino acid side chains tend to interact with one another by fluorine-fluorine contacts. Therefore, even one single fluorinated amino acid can direct polypeptide folding due to strong character of fluorine-fluorine interactions (Section 3.3 and 3.4). 

Phosphohpase Cy and protein tyrosine phosphatase Syp possess an SH2 domain of class 3. Their substrate binding site has mostly hydrophobic character. The substrate is boimd in a stretched form in a flat pit where contacts are formed to a hydrophobic sequence section of the substrate, including 5—6 amino acids on the C-terminal side of the phosphotyrosine residue. 

A common trait in the synthesis of membrane glycoproteins is that they are formed on the intramembranous system of the cell. The first amino acids at the N-tenninus constitute a so-called leader sequence which, possibly due to its hydrophobic character, mediates the tunnelling of the nascent peptide chain to the lumen of the intra-membranous system215,216 (see Section 11,3). 

In the process of viral assembly, HIV PR specifically cleaves nine cleavage sites on GAG and GAG-POL polypeptides [21]. Examination of the amino acid composition of the recognized substrate sites (Table 1) indicates their hydrophobic character and significant sequence variability. The loose specificity of HIV PR most likely reflects its functions in a world of reduced complexity within the confines of the budding virion. The length of the viral protein precursors (approximately 1500 amino acids) reduces the number of potential sequences the protease must discriminate from in selecting its nine cleavage sites. Therefore,... 

A scale combining hydrophobicity and hydrophilicity of R groups it can be used to measure the tendency of an amino acid to seek an aqueous environment (- values) or a hydrophobic environment (+ values). See Chapter 11. From Kyte, J. Doolittle, R.F (1982) A simple method for displaying the hydropathic character of a protein. J. Mot. Biol. 157, 105-132. 

The main feature of the amino acid diagram is that A/a(js shows satisfactory linear correlation with A/part, with a slope of 1.22. Interfacial activity becomes stronger as the hydrophobicity of the amino acid residues increases. Since the amino acids have very hydrophilic amino and carboxyl groups, it may be said that the hydrophobicity increase enhances the amphiphilic character of the amino acids. 

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