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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] |
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] |
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] |
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] |
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] |
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] |
Protein Structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a ''residue'' indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
