Irreversible processIn science, a process that is not reversible is called irreversible. This concept arises frequently in thermodynamics. All complex natural processes are irreversible, although a phase transition at the coexistence temperature (e.g. melting of ice cubes in water) is well approximated as reversible. In thermodynamics, a change in the thermodynamic state of a system and all of its surroundings cannot be precisely restored to its initial state by infinitesimal changes in some property of the system without expenditure of energy.
Enzyme inhibitorAn enzyme inhibitor is a molecule that binds to an enzyme and blocks its activity. Enzymes are proteins that speed up chemical reactions necessary for life, in which substrate molecules are converted into products. An enzyme facilitates a specific chemical reaction by binding the substrate to its active site, a specialized area on the enzyme that accelerates the most difficult step of the reaction.
Fusion proteinFusion proteins or chimeric (kī-ˈmir-ik) proteins (literally, made of parts from different sources) are proteins created through the joining of two or more genes that originally coded for separate proteins. Translation of this fusion gene results in a single or multiple polypeptides with functional properties derived from each of the original proteins. Recombinant fusion proteins are created artificially by recombinant DNA technology for use in biological research or therapeutics.
CysteineCysteine (symbol Cys or C; ˈsɪstɪiːn) is a semiessential proteinogenic amino acid with the formula . The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile. Cysteine is chiral, only L-cysteine is found in nature. The thiol is susceptible to oxidation to give the disulfide derivative cystine, which serves an important structural role in many proteins. In this case, the symbol Cyx is sometimes used. The deprotonated form can generally be described by the symbol Cym as well.
Benzyl groupIn organic chemistry, benzyl is the substituent or molecular fragment possessing the structure . Benzyl features a benzene ring () attached to a methylene group () group. In IUPAC nomenclature, the prefix benzyl refers to a substituent, for example benzyl chloride or benzyl benzoate. Benzyl is not to be confused with phenyl with the formula . The term benzylic is used to describe the position of the first carbon bonded to a benzene or other aromatic ring. For example, is referred to as a "benzylic" carbocation.
ChemoproteomicsChemoproteomics (also known as chemical proteomics) entails a broad array of techniques used to identify and interrogate protein-small molecule interactions. Chemoproteomics complements phenotypic drug discovery, a paradigm that aims to discover lead compounds on the basis of alleviating a disease phenotype, as opposed to target-based drug discovery (reverse pharmacology), in which lead compounds are designed to interact with predetermined disease-driving biological targets.
Alkyl groupIn organic chemistry, an alkyl group is an alkane missing one hydrogen. The term alkyl is intentionally unspecific to include many possible substitutions. An acyclic alkyl has the general formula of . A cycloalkyl group is derived from a cycloalkane by removal of a hydrogen atom from a ring and has the general formula . Typically an alkyl is a part of a larger molecule. In structural formulae, the symbol R is used to designate a generic (unspecified) alkyl group. The smallest alkyl group is methyl, with the formula .
DissipationIn thermodynamics, dissipation is the result of an irreversible process that affects a thermodynamic system. In a dissipative process, energy (internal, bulk flow kinetic, or system potential) transforms from an initial form to a final form, where the capacity of the final form to do thermodynamic work is less than that of the initial form. For example, transfer of energy as heat is dissipative because it is a transfer of energy other than by thermodynamic work or by transfer of matter, and spreads previously concentrated energy.
Catalytic triadA catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes. Catalytic triads are most commonly found in hydrolase and transferase enzymes (e.g. proteases, amidases, esterases, acylases, lipases and β-lactamases). An acid-base-nucleophile triad is a common motif for generating a nucleophilic residue for covalent catalysis. The residues form a charge-relay network to polarise and activate the nucleophile, which attacks the substrate, forming a covalent intermediate which is then hydrolysed to release the product and regenerate free enzyme.
Ligand (biochemistry)In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The etymology stems from Latin ligare, which means 'to bind'. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix.
Cystathionine gamma-lyaseThe enzyme cystathionine γ-lyase (EC 4.4.1.1, CTH or CSE; also cystathionase; systematic name L-cystathionine cysteine-lyase (deaminating; 2-oxobutanoate-forming)) breaks down cystathionine into cysteine, 2-oxobutanoate (α-ketobutyrate), and ammonia: L-cystathionine + H2O = L-cysteine + 2-oxobutanoate + NH3 (overall reaction) (1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate (1b) 2-aminobut-2-enoate = 2-iminobutanoate (spontaneous) (1c) 2-iminobutanoate + H2O = 2-oxobutanoate + NH3 (spontaneous) Pyridoxal phosphate is a prosthetic group of this enzyme.
Loschmidt's paradoxIn physics, Loschmidt's paradox (named for J.J. Loschmidt), also known as the reversibility paradox, irreversibility paradox, or Umkehreinwand (), is the objection that it should not be possible to deduce an irreversible process from time-symmetric dynamics. This puts the time reversal symmetry of (almost) all known low-level fundamental physical processes at odds with any attempt to infer from them the second law of thermodynamics which describes the behaviour of macroscopic systems.
Euler methodIn mathematics and computational science, the Euler method (also called the forward Euler method) is a first-order numerical procedure for solving ordinary differential equations (ODEs) with a given initial value. It is the most basic explicit method for numerical integration of ordinary differential equations and is the simplest Runge–Kutta method. The Euler method is named after Leonhard Euler, who first proposed it in his book Institutionum calculi integralis (published 1768–1870).
Chemical bondA chemical bond is a lasting attraction between atoms or ions that enables the formation of molecules, crystals, and other structures. The bond may result from the electrostatic force between oppositely charged ions as in ionic bonds, or through the sharing of electrons as in covalent bonds. The strength of chemical bonds varies considerably; there are "strong bonds" or "primary bonds" such as covalent, ionic and metallic bonds, and "weak bonds" or "secondary bonds" such as dipole–dipole interactions, the London dispersion force, and hydrogen bonding.
Fusion geneA fusion gene is a hybrid gene formed from two previously independent genes. It can occur as a result of translocation, interstitial deletion, or chromosomal inversion. Fusion genes have been found to be prevalent in all main types of human neoplasia. The identification of these fusion genes play a prominent role in being a diagnostic and prognostic marker. The first fusion gene was described in cancer cells in the early 1980s.
Formal chargeIn chemistry, a formal charge (F.C. or q*), in the covalent view of chemical bonding, is the hypothetical charge assigned to an atom in a molecule, assuming that electrons in all chemical bonds are shared equally between atoms, regardless of relative electronegativity. In simple terms, formal charge is the difference between the number of valence electrons of an atom in a neutral free state and the number assigned to that atom in a Lewis structure.
Iterative methodIn computational mathematics, an iterative method is a mathematical procedure that uses an initial value to generate a sequence of improving approximate solutions for a class of problems, in which the n-th approximation is derived from the previous ones. A specific implementation with termination criteria for a given iterative method like gradient descent, hill climbing, Newton's method, or quasi-Newton methods like BFGS, is an algorithm of the iterative method.
GlutathioneGlutathione (GSH, ˌɡluːtəˈθaɪəʊn) is an antioxidant in plants, animals, fungi, and some bacteria and archaea. Glutathione is capable of preventing damage to important cellular components caused by sources such as reactive oxygen species, free radicals, peroxides, lipid peroxides, and heavy metals. It is a tripeptide with a gamma peptide linkage between the carboxyl group of the glutamate side chain and cysteine. The carboxyl group of the cysteine residue is attached by normal peptide linkage to glycine.
Newton's methodIn numerical analysis, Newton's method, also known as the Newton–Raphson method, named after Isaac Newton and Joseph Raphson, is a root-finding algorithm which produces successively better approximations to the roots (or zeroes) of a real-valued function. The most basic version starts with a single-variable function f defined for a real variable x, the function's derivative f′, and an initial guess x0 for a root of f. If the function satisfies sufficient assumptions and the initial guess is close, then is a better approximation of the root than x0.
