Amino acids hydrophilicity

The solubilization of amino acids in AOT-reversed micelles has been widely investigated showing the importance of the hydrophobic effect as a driving force in interfacial solubihzation [153-157]. Hydrophilic amino acids are solubilized in the aqueous micellar core through electrostatic interactions. The amino acids with strongly hydrophobic groups are incorporated mainly in the interfacial layer. The partition coefficient for tryptophan and micellar shape are affected by the loading ratio of tryptophan to AOT [158],... 

Among the common amino acids, eleven have side chains that contain polar functional groups that can form hydrogen bonds, such as —OH, —NH2, and — CO2 H. These hydrophilic amino acids are commonly found on the outside of a protein, where their interactions with water molecules increase the solubility of the protein. The other nine amino acids have nonpolar hydrophobic side chains containing mostly carbon and hydrogen atoms. These amino acids are often tucked into the inside of a protein, away from the aqueous environment of the cell. 

Amphipathic peptides contain amino acid sequences that allow them to adopt membrane active conformations [219]. Usually amphipathic peptides contain a sequence with both hydrophobic amino acids (e.g., isoleucine, valine) and hydrophilic amino acids (e.g., glutamic acid, aspartic acid). These sequences allow the peptide to interact with lipid bilayer. Depending on the peptide sequence these peptides may form a-helix or j6-sheet conformation [219]. They may also interact with different parts of the bilayer. Importantly, these interactions result in a leaky lipid bilayer and, therefore, these features are quite interesting for drug delivery application. Obviously, many of these peptides are toxic due to their strong membrane interactions. 

Using liposomes made from phospholipids as models of membrane barriers, Chakrabarti and Deamer [417] characterized the permeabilities of several amino acids and simple ions. Phosphate, sodium and potassium ions displayed effective permeabilities 0.1-1.0 x 10 12 cm/s. Hydrophilic amino acids permeated membranes with coefficients 5.1-5.7 x 10 12 cm/s. More lipophilic amino acids indicated values of 250 -10 x 10-12 cm/s. The investigators proposed that the extremely low permeability rates observed for the polar molecules must be controlled by bilayer fluctuations and transient defects, rather than normal partitioning behavior and Born energy barriers. More recently, similar magnitude values of permeabilities were measured for a series of enkephalin peptides [418]. 

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. 

Host defense peptide hydrophobicity (H) is defined as the proportion of hydrophobic amino acids within a peptide. Typically, these peptides are comprised of >30% hydrophobic residues and this governs the ability of a host defense peptide to partition into the lipid bilayer, an essential requirement for antimicrobial peptide-membrane interactions. Typically, the hydrophobic and hydrophilic amino acids of natural peptides are segregated to create specific regions or domains that allow for optimal interaction with microbial membranes. This likely represents evolutionary optimization to maximize the selectivity of these defense molecules. It has been established that increasing antimicrobial peptide hydrophobicity above a specific threshold correlates... 

Unnatural amino acids are added to the growth medium in most experiments. There are a large number of amino acid and amine transporters that are relatively nonspecific and which may help to transport the unnatural amino acids into cells. From measurements of cytoplasmic levels of amino acids, it is found that a large number of unnatural amino acids are efficiently transported to the E. coli cytoplasm in millimolar concentrations. Highly charged or hydrophilic amino acids may require derivatization (e.g., esterification, acylation) with groups that are hydrolyzed in the cytoplasm. Metabolically labile amino acids or analogues (e.g., a-hydroxy acids, A-methyl amino acids) may require strains in which specific metabolic enzymes are deleted. 

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. 

High distribution ratios and almost quantitative recovery were observed for all amino acids. In contrast to conventional solvents, the extraction of the most hydrophilic amino acids such as Gly is quantitative. Recovery of Trp, Leu, Ala, Gly, Lys, and Arg is 96, 93, 92, 95, 94, and 92%, respectively. Also, amino acids, including highly hydrophilic, can be extracted with high efficiency from the mixture. For example, the recovery of Trp, Val, Gly from their equimolar mixture is equal to 99, 94, and 93%, respectively. Extraction was performed by adding 3 mL of IL with crown ether concentration 0.10 mol L with a 3 mL aqueous solution of amino acids (5 10 mol/L each 1.8 pH) and shaking for 15 min. 

Enzymes, composed of various amino acids, constitute hydrophobic interior and hydrophilic exterior by arranging in space the appropriate amino acid residues. The hydrophobic receptor site is usually located inside and the hydrophilic amino acid residues located on the surface of enzyme are heavily solvated by water molecules in aqueous solution. Then, the supramolecular interactions with specific coenzymes, substrates, and inhibitors inevitably accompany extensive dehydration and conformational change of both enzyme and ligand. 

The transmembrane domain may be made up of one or many transmembrane elements. Generally, the transmembrane elements include 20-25 mostly hydrophobic amino acids. At the interface with aqueous medium, we often find hydrophilic amino acids in contact with the polar head groups of the phospholipids. In addition, they mediate distinct fixing of the transmembrane section in the phospholipid double layer. A sequence of 20-25 hydrophobic amino acids is seen as characteristic for membrane-spaiming elements. This property is used in analysis of protein sequences, to predict possible transmembrane elements in so-called hydropathy plots". 

In summary, the structural characteristics of peptides with high antioxidant activity are as follows a hydrogen bonding and hydrophilic amino acid residue in the position next to the C-terminus, a hydrophobic amino acid residue at the N-terminus, and an electronic amino acid residue at the C-terminus. 

Apolipoproteins ( apo designates the protein in its lipid-free form) combine with lipids to form several classes of lipoprotein particles, spherical complexes with hydrophobic lipids in the core and hydrophilic amino acid side chains at the surface (Fig. 21-39a). Different combinations of lipids and proteins produce particles of different densities, ranging from chylomicrons to high-density lipoproteins. These particles can be separated by ultracentrifugation (Table 21-2) and visualized by electron microscopy (Fig. 21-39b). 

A graphic representation of a three-dimensional model of the protein, cytochrome c. Amino acids with nonpolar, hydrophobic side chains (color) are found in the interior of the molecule, where they interact with one another. Polar, hydrophilic amino acid side chains (gray) are on the exterior of the molecule, where they interact with the polar aqueous solvent. (Illustration copyright by Irving Geis. Reprinted by permission.)... 

A model for the structure of bacteriorhodopsin, a membrane protein from Halobacterium halobium. The protein has seven membrane-spanning segments connected by shorter stretches of hydrophilic amino acid residues. 

Fig. S. Conformational modulation of a peptidic structure ( 6) controlled by a redox process [8], The hydrophilic amino acids are in bold face and the sulfoxide form of methionine is denoted by M°. On the left, the tr-helix axial projection on the right, the 0-sheet side-view representation...

In soluble globular proteins, hydrophilic amino acids tend to be on the exterior of the molecule whereas hydrophobic amino acids are packed in the interior [13]. To quantitatively describe the location of an amino acid in relation to the protein surface, different measures of solvent exposure have been developed. In the present context, the solvent exposure is modeled by the number s of protein atoms that are within a sphere of radius R centered at the position of atom c of amino acid a [5]. If the amino acid is buried in the protein interior, s is large because the surrounding volume is (almost) completely filled by protein atoms. On the other hand, if the amino acid is exposed, part of the volume is occupied by solvent molecules, which results in a smaller s (see Table 11.1 and Figure 11.3). Again, relative frequencies fac(s) and fc(s) are derived from the database and the net potential for solvent exposure is then... 

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