Hydrophobicity scales
Encyclopedia
Hydrophobicity scales are ranking lists for the relative hydrophobicity
of amino acid
residues. In general, the more positive the value, the more hydrophobic are the amino acids located in that region of the protein (while the more negative the value, the more hydrophillic those amino acids). These scales are commonly used to predict the transmembrane alpha-helices of membrane protein -- because as you measure the amino acid values consecutively along the protein, each time the values change from positive to negative (or vice versa) it is an indication that the amino acids are either attracted to (positive) or repelled from (negative) the hydrophobic region located inside the phospholipid membrane.
The hydrophobic effect represents the tendency of water to exclude non-polar molecules. The effect originates from the disruption of highly dynamic hydrogen bond
s between molecules of liquid water. Polar chemical groups, such as OH group in methanol
do not cause the hydrophobic effect. However, a pure hydrocarbon molecule, for example hexane
, cannot accept or donate hydrogen bonds to water. Introduction of hexane into water causes disruption of the hydrogen bonding network between water molecules. The hydrogen bonds are partially reconstructed by building a water "cage" around the hexane molecule, similar to that in clathrate hydrate
s formed at lower temperatures. The mobility of water molecules in the "cage" (or solvation shell
) is strongly restricted. This leads to significant losses in translational and rotational entropy
of water molecules and makes the process unfavorable in terms of free energy
of the system.
There are clear differences between the four scales shown in the table. Both the second and fourth scales place cysteine as the most hydrophobic residue, unlike the other two scales. This difference is due to the different methods used to measure hydrophobicity. The method used to obtain the Janin and Rose et al. scales was to examine proteins with known 3-D structures and define the hydrophobic character as the tendency for a residue to be found inside of a protein rather than on its surface. Since cysteine forms disulfide bonds that must occur inside a globular structure, cysteine is ranked as the most hydrophobic. The first and third scales are derived from the physiochemical properties of the amino acid side chains. These scales result mainly from inspection of the amino acid structures. Biswas et al., divided the scales based on the method used to obtain the scale in to five different categories.
(SDS) micelles. Also, amino acid side chain affinity for water was measured using vapor phases. Vapor phases represent the simplest non polar phases, because it has no interaction with the solute. The hydration potential and its correlation to the appearance of amino acids on the surface of proteins was studied by Wolfenden. Aqueous and polymer
phases were used in the development of a novel partitioning scale. Partitioning methods have many drawbacks. First, it is difficult to mimic the protein interior. In addition, the role of self solvation makes using free amino acids very difficult. Moreover, hydrogen bonds that are lost in the transfer to organic solvents are not reformed but often in the interior of protein.
The absolute values and relative rankings of hydrophobicity determined by chromatographic methods can be affected by a number of parameters. These parameters include the silica surface area and pore diameter, the choice and PH of aqueous buffer, temperature and the bonding density of stationary phase chains.
methods are based on the measurement of different physical properties. Examples include, partial molar heat capacity, transition temperature and surface tension. Physical methods are easy to use and flexible in terms of solute. The most popular hydrophobicity scale was developed by measuring surface tension values for the naturally occurring 20 amino acids in NaCl solution. The main drawbacks of surface tension measurements is that the broken hydrogen bonds and the neutalized charged groups remain at the solution air interface. Another physical property method involve measuring the solvation free energy. The solvation free energy is estimated as a product of an accessibility of an atom to the solvent and an tomic solvation parameter. Results indicate the solvation free energy lowers by an average of 1 Kcal/residue upon folding.
Hydrophobe
In chemistry, hydrophobicity is the physical property of a molecule that is repelled from a mass of water....
of amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
residues. In general, the more positive the value, the more hydrophobic are the amino acids located in that region of the protein (while the more negative the value, the more hydrophillic those amino acids). These scales are commonly used to predict the transmembrane alpha-helices of membrane protein -- because as you measure the amino acid values consecutively along the protein, each time the values change from positive to negative (or vice versa) it is an indication that the amino acids are either attracted to (positive) or repelled from (negative) the hydrophobic region located inside the phospholipid membrane.
Hydrophobicity and the hydrophobic effect
Hydrogen bond
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
s between molecules of liquid water. Polar chemical groups, such as OH group in methanol
Methanol
Methanol, also known as methyl alcohol, wood alcohol, wood naphtha or wood spirits, is a chemical with the formula CH3OH . It is the simplest alcohol, and is a light, volatile, colorless, flammable liquid with a distinctive odor very similar to, but slightly sweeter than, ethanol...
do not cause the hydrophobic effect. However, a pure hydrocarbon molecule, for example hexane
Hexane
Hexane is a hydrocarbon with the chemical formula C6H14; that is, an alkane with six carbon atoms.The term may refer to any of four other structural isomers with that formula, or to a mixture of them. In the IUPAC nomenclature, however, hexane is the unbranched isomer ; the other four structures...
, cannot accept or donate hydrogen bonds to water. Introduction of hexane into water causes disruption of the hydrogen bonding network between water molecules. The hydrogen bonds are partially reconstructed by building a water "cage" around the hexane molecule, similar to that in clathrate hydrate
Clathrate hydrate
Clathrate hydrates are crystalline water-based solids physically resembling ice, in which small non-polar molecules or polar molecules with large hydrophobic moieties are trapped inside "cages" of hydrogen bonded water molecules...
s formed at lower temperatures. The mobility of water molecules in the "cage" (or solvation shell
Solvation shell
A Solvation shell is a shell of any chemical species acting as a solvent, surrounding a solute species. When the solvent is water it is often referred to as a hydration shell or hydration sphere....
) is strongly restricted. This leads to significant losses in translational and rotational entropy
Entropy
Entropy is a thermodynamic property that can be used to determine the energy available for useful work in a thermodynamic process, such as in energy conversion devices, engines, or machines. Such devices can only be driven by convertible energy, and have a theoretical maximum efficiency when...
of water molecules and makes the process unfavorable in terms of free energy
Gibbs free energy
In thermodynamics, the Gibbs free energy is a thermodynamic potential that measures the "useful" or process-initiating work obtainable from a thermodynamic system at a constant temperature and pressure...
of the system.
Types of amino acid hydrophobicity scales
A number of different hydrophobicity scales have been developed.There are clear differences between the four scales shown in the table. Both the second and fourth scales place cysteine as the most hydrophobic residue, unlike the other two scales. This difference is due to the different methods used to measure hydrophobicity. The method used to obtain the Janin and Rose et al. scales was to examine proteins with known 3-D structures and define the hydrophobic character as the tendency for a residue to be found inside of a protein rather than on its surface. Since cysteine forms disulfide bonds that must occur inside a globular structure, cysteine is ranked as the most hydrophobic. The first and third scales are derived from the physiochemical properties of the amino acid side chains. These scales result mainly from inspection of the amino acid structures. Biswas et al., divided the scales based on the method used to obtain the scale in to five different categories.
Partitioning methods
The most common method of measuring amino acid hydrophobicity is partitioning between two immiscible liquid phases.Different Organic solvents are most widely used to mimic the protein interior. However, organic solvents are slightly miscible with water and the characteristics of both phases change making it difficult to obtain pure hydrophobicity scale. Nozaki and Tanford proposed the first major hydrophobicity scale for nine amino acids. Ethanol and dioxane are used as the organic solvents and the free energy of transfer of each amino acid was calculated. Non liquid phases can also be used with partitioning methods such as micellar phases and vapor phases. Two scales have been developed using micellar phases. Fendler et al. measured the partitioning of 14 radiolabeled amino acids using sodium dodecyl sulfateSodium dodecyl sulfate
Sodium dodecyl sulfate , sodium laurilsulfate or sodium lauryl sulfate is an organic compound with the formula CH311OSO3Na). It is an anionic surfactant used in many cleaning and hygiene products...
(SDS) micelles. Also, amino acid side chain affinity for water was measured using vapor phases. Vapor phases represent the simplest non polar phases, because it has no interaction with the solute. The hydration potential and its correlation to the appearance of amino acids on the surface of proteins was studied by Wolfenden. Aqueous and polymer
Polymer
A polymer is a large molecule composed of repeating structural units. These subunits are typically connected by covalent chemical bonds...
phases were used in the development of a novel partitioning scale. Partitioning methods have many drawbacks. First, it is difficult to mimic the protein interior. In addition, the role of self solvation makes using free amino acids very difficult. Moreover, hydrogen bonds that are lost in the transfer to organic solvents are not reformed but often in the interior of protein.
Accessible surface area methods
Hydrophobicity scales can also be obtained by calculating the solvent accessible surface areas for amino acid residues in the expended polypeptide chain or in alpha-helix and multiplying the surface areas by the empirical solvation parameters for the corresponding types of atoms.Chromatographic methods
Reversed phase liquid chromatography (RPLC) is the most important chromatographic method for measuring solute hydrophobicity. The non polar stationary phase mimics biological membranes. Peptide usage has many advantages because partition is not extended by the terminal charges in RPLC. Also, secondary structures formation is avoided by suing short sequence peptides. Derivatization of amino acids is necessary to ease its partition in to a C18 bonded phase. Another scale had been developed in 1971 and used peptide retention on hydrophillic gel. 1-butanol and pyridine were used as the mobile phase in this particular scale and glycine was used as the reference value. Pliska and his cowrkers used thin layer chromatography to relate mobility values of free amino acids to their hydrophobicities. About a decade ago, another hydrophilicity scale was published, this scale used normal phase liquid chromatography and showed the retention of 121 peptides on an amide-80 column.The absolute values and relative rankings of hydrophobicity determined by chromatographic methods can be affected by a number of parameters. These parameters include the silica surface area and pore diameter, the choice and PH of aqueous buffer, temperature and the bonding density of stationary phase chains.
Site-directed mutagenesis
This method use DNA recombinant technology and it gives an actual measurement of protein stability. In his detailed site directed mutagenesis studies, Utani and his coworkers substituted 19 amino acids at Trp49 of the tryptophan synthase and he measured the free energy of unfolding. Interestingly, they found that the increased stability is directly proportional to increase in hydrophobicity up to a certain size limit. The main disadvantage of site directed mutagenesis method is that not all the 20 naturally occurring amino acids can substitute a single residue in a protein. Moreover, these methods have cost problems and is useful only for measuring protein stability.Physical property methods
The hydrophobicity scales developed by physical propertyPhysical property
A physical property is any property that is measurable whose value describes a physical system's state. The changes in the physical properties of a system can be used to describe its transformations ....
methods are based on the measurement of different physical properties. Examples include, partial molar heat capacity, transition temperature and surface tension. Physical methods are easy to use and flexible in terms of solute. The most popular hydrophobicity scale was developed by measuring surface tension values for the naturally occurring 20 amino acids in NaCl solution. The main drawbacks of surface tension measurements is that the broken hydrogen bonds and the neutalized charged groups remain at the solution air interface. Another physical property method involve measuring the solvation free energy. The solvation free energy is estimated as a product of an accessibility of an atom to the solvent and an tomic solvation parameter. Results indicate the solvation free energy lowers by an average of 1 Kcal/residue upon folding.