Hydrophobic amino acid structure

Electrostatic effects have long been recognized in commercial HPLC columns for SEC of proteins (15,21,22). The usual remedy is to add 100 mM salt to the mobile phase. This works here too the Lys and Asp peaks collapse into the Gly peak with 100 mM salt (Eig. 8.8). High concentrations of sodium sulfate were added to determine the role played in SEC by hydrophobic interactions (sodium sulfate, a structure-forming salt, strengthens such interactions). Sodium sulfate increased the retention only of the most hydrophobic amino acids to any extent, and then only when the concentration approached 1 M. Clearly, hydrophobic interaction cannot account for the elution order of amino acids on PolyHEA. 

A leucine zipper is a structural motif present in a large class of transcription factors. These dimeric proteins contain two extended alpha helices that grip the DNA molecule much like a pair of scissors at adjacent major grooves. The coiled-coil dimerization domain contains precisely spaced leucine residues which are required for the interaction of the two monomers. Some DNA-binding proteins with this general motif contain other hydrophobic amino acids in these positions hence, this structural motif is generally called a basic zipper. 

Higher orders of protein structure are stabilized primarily—and often exclusively—by noncovalent interactions. Principal among these are hydrophobic interactions that drive most hydrophobic amino acid side chains into the interior of the protein, shielding them... 

The structures predicted for the fast and slow Ca -ATPase (Fig. 1) are 84 /o identical [8], There are 164 differences in the amino acid sequences between the two isoenzymes, 66 of which are conservative replacements, involving substitution of serine for threonine, aspartic for glutamic, lysine for arginine, or interchanges between aromatic or hydrophobic amino acids [8],... 

Loss of the native conformation of a protein generally exposes hydrophobic amino acid residues that are normally buried on the inside of the self-associated structure and are shielded from the aqueous environment. This leads to association between the exposed hydrophobic residues of neighboring proteins (aggregation) or between these exposed residues and hydrophobic surfaces that the protein may encounter either in the manufacturing process or in the primary package. 

The N-terminal peptide fragment of des-angiotensinogen Val-Ile-His-Asn contains two strongly hydrophobic amino acid residues on the N-terminal site of His-3. The potentiometric data have shown that the NiH.2L complex with this albumin-like sequence is more than two orders of magnitude more stable than the respective complex with Gly-Gly-His.1744 The NMR-based molecular structure has shown that the side chains of Val-1 and lie-2 form a well-ordered hydrophobic fence (Figure 21) shielding one side of the coordination plane from the bulk of... 

The structure of the major trimeric LHCII complex has been recently obtained at 2.72 A (Figure 7.3) (Liu et al., 2004). It was revealed that each 25kDa protein monomer contains three transmembrane and three amphiphilic a-helixes. In addition, each monomer binds 14 chlorophyll (8 Chi a and 6 Chi b) and 4 xanthophyll molecules 1 neoxanthin, 2 luteins, and 1 violaxanthin. The first three xanthophylls are situated close to the integral helixes and are tightly bound to some amino acids by hydrogen bonds to hydroxyl oxygen atoms and van der Waals interactions to chlorophylls, and hydrophobic amino acids such as tryptophan and phenylalanine. 

The enrichments and depletions displayed in Figure 1 are concordant with what would be expected if disorder were encoded by the sequence (Williams et al., 2001). Disordered regions are depleted in the hydrophobic amino acids, which tend to be buried, and enriched in the hydrophilic amino acids, which tend to be exposed. Such sequences would be expected to lack the ability to form the hydrophobic cores that stabilize ordered protein structure. Thus, these data strongly support the conjecture that intrinsic disorder is encoded by local amino acid sequence information, and not by a more complex code involving, for example, lack of suitable tertiary interactions. 

The partial structure of the adenovirus type 2 fiber shaft was the first /(-structured fibrous fold characterized at atomic detail. The shaft contains 15-residue sequence pseudo-repeats with an invariant glycine or proline and conserved hydrophobic amino acids (Fig. 3A Green et al., 1983). Unfolding studies led to the identification of a stable domain, consisting of amino acids 319-582, which was subcloned, expressed, and purified (Mitraki et al., 1999). Subsequently, it was crystallized, and its structure solved at 2.4-A resolution (van Raaij et al., 1999b). Its structure revealed a new fold, called the triple /(-spiral. ... 

Proteins represent another major group of membrane components. They play structural roles and/or are involved in many cellular processes, which are strictly coupled to membranes. Proteins can be either entirely embedded within the bilayer, or they might be firmly anchored (e.g. by a hydrophobic transmembrane segment composed of hydrophobic amino acid side-chains or as lipoprotein), or they can be just associated with the surface. 

The peptide chain in globular proteins is folded into fairly compact conformations. Water-soluble enzymes are typical globular proteins which have most of the hydrophobic amino acid residues located in the interior and the hydrophilic residues located mainly at the surface in contact with solvent water. The average radii are 20-40 A (Boyer, 1970). It is clear that there are common morphological features between surfactant micelles and enzyme molecules. This fact has prompted many chemists to use micelles as enzyme models. However, it must be emphasized that micelles exist in dynamic equilibria with monomeric surfactant and their hydrophobic core is quite fluid, whereas enzyme molecules have precisely fixed three-dimensional structures. 

A common feature of enzymes is the presence of a cleft or depression in the structure which is lined with mainly hydrophobic amino acid residues and into which the substrate fits. Certain amino acid residues which are concerned with either the orientation of the substrate, and hence the specificity of the enzyme, or are involved in the catalysis of the reaction, are located in this cleft. Those amino acid residues that are associated with the latter role form the active site of the enzyme and are often located towards the base of this cleft. In most cases they are ionic or reactive and include histidine, lysine, cysteine... 

We encountered the properties of hydrophilic and hydrophobic molecules in our thoughts about driving forces for formation of three-dimensional protein structures. Specifically, proteins fold in a way that puts most of the hydrophobic amino acid side chains into the molecular interior, where they can enjoy each other s company and avoid the dreaded aqueous environment. At the same time, they fold to get the hydrophilic amino acid side chains onto the molecular surface, where they happily interact with that enviromnent. The same ideas are important for the double-stranded helical structure of DNA. The hydrophobic bases are localized within the double hehx, where they interact with each other, and the strongly hydrophilic sugar and phosphate groups are exposed on the exterior of the double helix to the water environment. Now, we need to understand something more about structural features that control these properties. 

The native conformation of proteins is stabilized by a number of different interactions. Among these, only the disulfide bonds (B) represent covalent bonds. Hydrogen bonds, which can form inside secondary structures, as well as between more distant residues, are involved in all proteins (see p. 6). Many proteins are also stabilized by complex formation with metal ions (see pp. 76, 342, and 378, for example). The hydrophobic effect is particularly important for protein stability. In globular proteins, most hydrophobic amino acid residues are arranged in the interior of the structure in the native conformation, while the polar amino acids are mainly found on the surface (see pp. 28, 76). 

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