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Solvent Exposure
Solvent exposure occurs when a chemical, material, or person comes into contact with a solvent. Chemicals can be dissolved in solvents, materials such as polymers can be broken down chemically by solvents, and people can develop certain ailments from exposure to solvents both organic and inorganic. Some common solvents include acetone, methanol, tetrahydrofuran, dimethylsulfoxide, and water among countless others. In biology, 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, as 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 des ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical
A chemical substance is a form of matter having constant chemical composition and characteristic properties. Some references add that chemical substance cannot be separated into its constituent elements by physical separation methods, i.e., without breaking chemical bonds. Chemical substances can be simple substances (substances consisting of a single chemical element), chemical compounds, or alloys. Chemical substances are often called 'pure' to set them apart from mixtures. A common example of a chemical substance is pure water; it has the same properties and the same ratio of hydrogen to oxygen whether it is isolated from a river or made in a laboratory. Other chemical substances commonly encountered in pure form are diamond (carbon), gold, table salt (sodium chloride) and refined sugar (sucrose). However, in practice, no substance is entirely pure, and chemical purity is specified according to the intended use of the chemical. Chemical substances exist as solids, liquids, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residue ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acids
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha amino acids appear in the genetic code. Amino acids can be classified according to the locations of the core structural functional groups, as Alpha and beta carbon, alpha- , beta- , gamma- or delta- amino acids; other categories relate to Chemical polarity, polarity, ionization, and side chain group type (aliphatic, Open-chain compound, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid '' residues'' form the second-largest component (water being the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. It is thought that they played a key role in enabling lif ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Half Sphere Exposure
Half Sphere exposure (HSE) 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 Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo .... It is found by counting the number of amino acid neighbors within two half spheres of chosen radius around the amino acid. The calculation of HSE is found by dividing a contact number (CN) sphere in two halves by the plane perpendicular to the Cβ-Cα vector. This simple division of the CN sphere results in two strikingly different measures, HSE-up and HSE-down. HSE-up is defined as the number of Cα atoms in the upper half (containing the pseudo-Cβ atom) and analogously HSE-down is defined as the number of Cα atoms in the opposite sphere ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Residue Depth
Residue depth (RD) 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 (ASA). Currently, predictions in regards to whether a residue is exposed or buried are used in a wide variety of protein structure prediction engines. Such prediction can provide valuable information for protein fold recognition, functional residue prediction and protein drug design. Several biophysical properties of proteins have been shown to correlate with residue depth, including mutant protein stability, protein-protein interface hot-spot, H/D exchange rate of residue and residue conservation. Residue depth has also been utilized in predicting small molecule binding site on proteins, with accuracy statistically on par with other conventional methods. The method has the advantageous of being simple and intuitive. The method has been reported to detect unconventional flat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Contact Number
In chemistry, a contact number (CN) 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 within a sphere around the C\beta or C\alpha atom of the residue. The radius of the sphere is typically chosen to be between 8 and 14Å. See also * Kissing number In geometry, the kissing number of a mathematical space is defined as the greatest number of non-overlapping unit spheres that can be arranged in that space such that they each touch a common unit sphere. For a given sphere packing (arrangement of ..., a similar concept in mathematics References Solvents {{chemistry-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Relative Accessible Surface Area
Relative accessible surface area or relative solvent accessibility (RSA) of a protein residue is a measure of residue solvent exposure. It can be calculated by formula: \text = \text / \text where ASA is the solvent accessible surface area and MaxASA is the maximum possible solvent accessible surface area for the residue. Both ASA and MaxASA are commonly measured in ^2 . To measure the relative solvent accessibility of the residue side-chain only, one usually takes MaxASA values that have been obtained from Gly-X-Gly tripeptides, where X is the residue of interest. Several MaxASA scales have been published and are commonly used (see Table). In this table, the more recently published MaxASA values (from Tien et al. 2013) are systematically larger than the older values (from Miller et al. 1987 or Rose et al. 1985). This discrepancy can be traced back to the conformation in which the Gly-X-Gly tripeptides are evaluated to calculate MaxASA. The earlier works used t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Accessible Surface Area
The accessible surface area (ASA) or solvent-accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent. Measurement of ASA is usually described in units of square angstroms (a standard unit of measurement in molecular biology). ASA was first described by Lee & Richards in 1971 and is sometimes called the Lee-Richards molecular surface. ASA is typically calculated using the 'rolling ball' algorithm developed by Shrake & Rupley in 1973. This algorithm uses a sphere (of solvent) of a particular radius to 'probe' the surface of the molecule. Methods of calculating ASA Shrake–Rupley algorithm The Shrake–Rupley algorithm is a numerical method that draws a mesh of points equidistant from each atom of the molecule and uses the number of these points that are solvent accessible to determine the surface area. The points are drawn at a water molecule's estimated radius beyond the van der Waals radius, which is effectively similar to ‘rolling ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophilic
A hydrophile is a molecule or other molecular entity that is attracted to water molecules and tends to be dissolved by water.Liddell, H.G. & Scott, R. (1940). ''A Greek-English Lexicon'' Oxford: Clarendon Press. In contrast, hydrophobes are not attracted to water and may seem to be repelled by it. Hygroscopics ''are'' attracted to water, but are not dissolved by water. Molecules A hydrophilic molecule or portion of a molecule is one whose interactions with water and other polar substances are more thermodynamically favorable than their interactions with oil or other hydrophobic solvents. They are typically charge-polarized and capable of hydrogen bonding. This makes these molecules soluble not only in water but also in other polar solvents. Hydrophilic molecules (and portions of molecules) can be contrasted with hydrophobic molecules (and portions of molecules). In some cases, both hydrophilic and hydrophobic properties occur in a single molecule. An example of these amphiph ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophobic
In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, thus, prefer other neutral molecules and nonpolar solvents. Because water molecules are polar, hydrophobes do not dissolve well among them. Hydrophobic molecules in water often cluster together, forming micelles. Water on hydrophobic surfaces will exhibit a high contact angle. Examples of hydrophobic molecules include the alkanes, oils, fats, and greasy substances in general. Hydrophobic materials are used for oil removal from water, the management of oil spills, and chemical separation processes to remove non-polar substances from polar compounds. Hydrophobic is often used interchangeably with lipophilic, "fat-loving". However, the two terms are not synonymous. While hydrophobic substances are usually lipophilic, there are exceptions, suc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha amino acids appear in the genetic code. Amino acids can be classified according to the locations of the core structural functional groups, as Alpha and beta carbon, alpha- , beta- , gamma- or delta- amino acids; other categories relate to Chemical polarity, polarity, ionization, and side chain group type (aliphatic, Open-chain compound, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid '' residues'' form the second-largest component (water being the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. It is thought that they played a key role in enabling life ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Person
A person ( : people) is a being that has certain capacities or attributes such as reason, morality, consciousness or self-consciousness, and being a part of a culturally established form of social relations such as kinship, ownership of property, or legal responsibility. The defining features of personhood and, consequently, what makes a person count as a person, differ widely among cultures and contexts. In addition to the question of personhood, of what makes a being count as a person to begin with, there are further questions about personal identity and self: both about what makes any particular person that particular person instead of another, and about what makes a person at one time the same person as they were or will be at another time despite any intervening changes. The plural form "people" is often used to refer to an entire nation or ethnic group (as in "a people"), and this was the original meaning of the word; it subsequently acquired its use as a plural form of per ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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