Protein hydrophobic-polar

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. 

Hydrophobic bonds, or, more accurately, interactions, form because nonpolar side chains of amino acids and other nonpolar solutes prefer to cluster in a nonpolar environment rather than to intercalate in a polar solvent such as water. The forming of hydrophobic bonds minimizes the interaction of nonpolar residues with water and is therefore highly favorable. Such clustering is entropically driven. The side chains of the amino acids in the interior or core of the protein structure are almost exclusively hydrophobic. Polar amino acids are almost never found in the interior of a protein, but the protein surface may consist of both polar and nonpolar residues. 

In most hydrophilic polymers, such as cellulose and proteins, each polar group interacts strongly with one water molecule only. In hydrophobic polymers such as polyolefins, on the other hand, Henry s law is obeyed over the complete range of relative pressures and only minute quantities of water are sorbed. 

In their native conformation, globular proteins have non-polar amino acid side chains oriented towards the interior of the protein and polar side chains oriented outwards, towards the solvent. The stability of the native conformation is determined by hydrophobic interactions within the interior of the molecule, and electrostatic interactions and hydrogen bond interactions at the protein-water interface. Disturbing these interactions can alter the balance between the intra- and intermole-cular interactions, which are responsible for maintaining the protein in soluble... 

Non-polm- and weakly polarizable molecules would be expected to interact mainly with the hydrophobic parts of the membrane lipids or proteins. Non-polar or weakly polar but highly polarizable anesthetics could interact with both hydrophobic and ionic or polar sites. 

The 20 amino acids capable of appearing in various microstructural combinations of sequence lengths, and total molecular lengths, allow assembly of an infinite number of distinct proteins [57]. The side chain R may be hydrophobic, polar, acidic, or basic. The structure of the amino acid is given in Fig. 5. 

The interactions between the amino acids and the solvent (electrostatic, hydrophilic, hydrophobic, S-S) determine the globular conformation. We can give some naive picture of the folded state in terms of a liquid-hydrocarbon model where the hydrophobic core stabilizes globular proteins. The hydrophilic (polar and charged) amino acids are exposed to the solvent and the hydrophobic (polar) amino acids are less exposed to the solvent and buried in the interior of the protein. 

Another characteristic of the secondary structure of protein includes the occurrence of hydrophobic amino acids clustered on the surface of globular proteins. It seems that hydrophobic amino acids occur regularly as the 20th amino acid in the primary structure of the peptide. These amino acids are rotated on an angle of 100° on the axis of the protein such that the globular proteins have all hydrophobic amino acids clustered to one side on the helical surface of protein, whereas the other end of the globular protein contains polar amino acids. Thus, it is possible to generate a wheel of amino acids in a protein in which the hydrophobic amino acids are clustered on one side of the helix, and the other side contains polar amino acids. 

To understand the structures and functions of proteins, you must be familiar with some of the distinctive properties of the amino acids, which are determined by their side chains. The side chains of different amino acids vary in size, shape, charge, hydrophoblclty, and reactivity. Amino acids can be classified into several broad categories based primarily on their solubility in water, which is influenced by the polarity of their side chains (Figure 2-13). Amino acids with polar side chains are hydrophilic and tend to be on the surfaces of proteins by interacting with water, they make proteins soluble in aqueous solutions and can form noncovalent interactions with other water-soluble molecules. In contrast, amino acids with nonpolar side chains are hydrophobic they avoid water and often aggregate to help form the water-insoluble cores of many proteins. The polarity of amino acid side chains thus Is responsible for shaping the final three-dimensional structure of proteins. 

The chemical differences arising from the differences in the primary structure are also very important because the balance of polar, nonpolar and charged amino acid side chains determines the surface activity of proteins in a particular system, i.e., the possibility and mode of their location at interfaces of different types. This amphi-pathic nature of the protein molecule allows it to bind with surfaces of different chemical nature. A very important property is the protein hydrophobicity [17]. It influences adsorption and orientation of proteins at interfaces and in many cases correlates with surface activity [2,21]. 

Atomic coordinates for both hen egg-white and human lysozymes were based on crystallographic structures determined by Blake etal. (32-36) and deposited in the Protein Data Bank (Brookhaven National Laboratory). The distribution of hydrophobic, polar, and charged atoms on the surface of the two proteins was analyzed by calculating... 

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