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Hydrophobicity Scales
Hydrophobicity scales are values that define the relative hydrophobicity or hydrophilicity of amino acid residues. The more positive the value, the more hydrophobic are the amino acids located in that region of the protein. These scales are commonly used to predict the Transmembrane domain, transmembrane alpha-helices of membrane proteins. When consecutively measuring amino acids of a protein, changes in value indicate attraction of specific protein regions towards the hydrophobic region inside lipid bilayer. The hydrophobic or hydrophilic character of a compound or amino acid is its hydropathic character, hydropathicity, or hydropathy. Hydrophobicity and the hydrophobic effect The hydrophobic effect represents the tendency of water#Properties, water to exclude non-polar molecules. The effect originates from the disruption of highly dynamic hydrogen bonds between molecules of liquid water. Polar chemical groups, such as OH group in methanol do not cause the hydrophobic effect. Ho ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophobicity
In chemistry, hydrophobicity is the chemical property of a molecule (called a hydrophobe) that is seemingly intermolecular force, repelled from a mass of water. In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be chemical polarity#Nonpolar molecules, nonpolar and, thus, prefer other neutral molecules and nonpolar solvents. Because water molecules are polar, hydrophobes do not dissolution (chemistry), 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. The term ''hydrophobic''—which comes from the Ancient Greek (), "having a fear of water", constructed Liddell, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Entropy
Entropy is a scientific concept, most commonly associated with states of disorder, randomness, or uncertainty. The term and the concept are used in diverse fields, from classical thermodynamics, where it was first recognized, to the microscopic description of nature in statistical physics, and to the principles of information theory. It has found far-ranging applications in chemistry and physics, in biological systems and their relation to life, in cosmology, economics, sociology, weather science, climate change and information systems including the transmission of information in telecommunication. Entropy is central to the second law of thermodynamics, which states that the entropy of an isolated system left to spontaneous evolution cannot decrease with time. As a result, isolated systems evolve toward thermodynamic equilibrium, where the entropy is highest. A consequence of the second law of thermodynamics is that certain processes are irreversible. The thermodynami ... [...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 over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 appear in the genetic code of life. Amino acids can be classified according to the locations of the core structural functional groups ( alpha- , beta- , gamma- amino acids, etc.); other categories relate to polarity, ionization, and side-chain group type ( aliphatic, acyclic, aromatic, polar, 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 on Earth and its emergence. Amino acids are formally named by the IUPAC- IUBMB Joint Commi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Physical Property
A physical property is any property of a physical system that is measurable. The changes in the physical properties of a system can be used to describe its changes between momentary states. A quantifiable physical property is called ''physical quantity''. Measurable physical quantities are often referred to as '' observables''. Some physical properties are qualitative, such as shininess, brittleness, etc.; some general qualitative properties admit more specific related quantitative properties, such as in opacity, hardness, ductility, viscosity, etc. Physical properties are often characterized as intensive and extensive properties. An intensive property does not depend on the size or extent of the system, nor on the amount of matter in the object, while an extensive property shows an additive relationship. These classifications are in general only valid in cases when smaller subdivisions of the sample do not interact in some physical or chemical process when combined. P ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophobicity Scales2
In chemistry, hydrophobicity is the chemical property of a molecule (called a hydrophobe) that is seemingly repelled from a mass of water. 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. The term ''hydrophobic''—which comes from the Ancient Greek (), "having a fear of water", constructed Liddell, H.G. & Scott, R. (1940). ''A Greek-English Lexicon. revised and augmented througho ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Implicit Solvation
Implicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes. The implicit solvation model is justified in liquids, where the potential of mean force can be applied to approximate the averaged behavior of many highly dynamic solvent molecules. However, the interfaces and the interiors of biological membranes or proteins can also be considered as media with specific solvation or dielectric properties. These media are not necessarily uniform, since their properties c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alpha-helix
An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of local structure, and it is the local structure that is most easily predicted from a sequence of amino acids. The alpha helix has a right-handed helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid that is four residues earlier in the protein sequence. Other names The alpha helix is also commonly called a: * Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure) * 3.613-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen) Discovery In the early 1930s, William Astbury showed that there were d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Solvent 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] |
Polymer
A polymer () is a chemical substance, substance or material that consists of very large molecules, or macromolecules, that are constituted by many repeat unit, repeating subunits derived from one or more species of monomers. Due to their broad spectrum of properties, both synthetic and natural polymers play essential and ubiquitous roles in everyday life. Polymers range from familiar synthetic plastics such as polystyrene to natural biopolymers such as DNA and proteins that are fundamental to biological structure and function. Polymers, both natural and synthetic, are created via polymerization of many small molecules, known as monomers. Their consequently large molecular mass, relative to small molecule compound (chemistry), compounds, produces unique physical property, physical properties including toughness, high rubber elasticity, elasticity, viscoelasticity, and a tendency to form Amorphous solid, amorphous and crystallization of polymers, semicrystalline structures rath ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Micelles
A micelle () or micella () ( or micellae, respectively) is an aggregate (or supramolecular assembly) of surfactant amphipathic lipid molecules dispersed in a liquid, forming a colloidal suspension (also known as associated colloidal system). A typical micelle in water forms an aggregate, with the hydrophilic "head" regions in contact with surrounding solvent, sequestering the hydrophobic single-tail regions in the micelle centre. This phase is caused by the packing behavior of single-tail lipids in a bilayer. The difficulty in filling the volume of the interior of a bilayer, while accommodating the area per head group forced on the molecule by the hydration of the lipid head group, leads to the formation of the micelle. This type of micelle is known as a normal-phase micelle (or oil-in-water micelle). Inverse micelles have the head groups at the centre with the tails extending out (or water-in-oil micelle). Micelles are approximately spherical in shape. Other shapes, such ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sodium Dodecyl Sulfate
Sodium dodecyl sulfate (SDS) or sodium lauryl sulfate (SLS), sometimes written sodium laurilsulfate, is an organic compound with the formula and structure . It is an anionic surfactant used in many cleaning and hygiene products. This compound is the sodium salt of the 12-carbon organosulfate. Its hydrocarbon tail combined with a polar " headgroup" give the compound amphiphilic properties that make it useful as a detergent. SDS is also component of mixtures produced from inexpensive coconut and palm oils. SDS is a common component of many domestic cleaning, personal hygiene and cosmetic, pharmaceutical, and food products, as well as of industrial and commercial cleaning and product formulations. Physicochemical properties The critical micelle concentration (CMC) in water at 25 °C is 8.2 mM, and the aggregation number at this concentration is usually considered to be about 62. The micelle ionization fraction (α) is around 0.3 (or 30%). Applications Cleaning and hygie ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
