Solvent exposure
Encyclopedia
The solvent exposure of an amino acid
in a protein
measures to what extent the
amino acid is accessible to the solvent
(usually water
) surrounding the protein. Generally speaking, hydrophobic amino acids will be buried inside the protein and thus shielded from the solvent, while hydrophilic amino acids will be close to the surface and thus exposed to the solvent. However, like with many biological rules exceptions are common and hydrophilic residues are frequently found to be buried in the native structure and vice versa.
Solvent exposure can be numerically described by several measures, the most popular measures being accessible surface area
and relative accessible surface area. Other measures are for example:
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...
in a protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
measures to what extent the
amino acid is accessible to the solvent
Solvent
A solvent is a liquid, solid, or gas that dissolves another solid, liquid, or gaseous solute, resulting in a solution that is soluble in a certain volume of solvent at a specified temperature...
(usually water
Water
Water is a chemical substance with the chemical formula H2O. A water molecule contains one oxygen and two hydrogen atoms connected by covalent bonds. Water is a liquid at ambient conditions, but it often co-exists on Earth with its solid state, ice, and gaseous state . Water also exists in a...
) surrounding the protein. Generally speaking, hydrophobic amino acids will be buried inside the protein and thus shielded from the solvent, while hydrophilic amino acids will be close to the surface and thus exposed to the solvent. However, like with many biological rules exceptions are common and hydrophilic residues are frequently found to be buried in the native structure and vice versa.
Solvent exposure can be numerically described by several measures, the most popular measures being accessible surface area
Accessible surface area
The accessible surface area is the surface area of a biomolecule that is accessible to a solvent. The ASA is usually quoted in square ångstrom . ASA was first described by Lee & Richards in 1971 and is sometimes called the Lee-Richards molecular surface...
and relative accessible surface area. Other measures are for example:
- Contact numberContact numberContact number is a simple solvent exposure measure that measures residue burial in proteins. The definition of CN varies between authors, but is generally defined as the number of either C\beta or C\alpha atoms with in a sphere around the C\beta or C\alpha atom of the residue. The radius of the...
: number of amino acid neighbors within a sphere around the amino acid. - Residue depthResidue depthResidue depth is a solvent exposure measure that describes to what extent a residue is buried in the protein structure space. It complements the information provided by conventional accessible surface area ....
: distance of the amino acid to the molecular surface. - Half sphere exposureHalf sphere exposureHalf Sphere Exposure is a protein solvent exposure measure that was first introduced by .Like all solvent exposure measures it measures how buried amino acid residues are in a protein. It is found by counting the number of amino acid neighbors within two half spheres of chosen radius around the...
: number of amino acid neighbors within two half spheres around the amino acid.