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In chemistry, biochemistry, and pharmacology, a dissociation constant (KD) is a specific type of equilibrium constant that measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex falls apart into its component molecules, or when a salt splits up into its component ions. The dissociation constant is the inverse of the association constant. In the special case of salts, the dissociation constant can also be called an ionization constant. For a general reaction:
Enzymes are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and the field of pseudoenzyme analysis recognizes that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties.
In biochemistry, Michaelis–Menten kinetics, named after Leonor Michaelis and Maud Menten, is the simplest case of enzyme kinetics, applied to enzyme-catalysed reactions of one substrate and one product. It takes the form of a differential equation describing the reaction rate to , the concentration of the substrate A. Its formula is given by the Michaelis–Menten equation:
Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionized. ESI is different from other ionization processes since it may produce multiple-charged ions, effectively extending the mass range of the analyser to accommodate the kDa-MDa orders of magnitude observed in proteins and their associated polypeptide fragments.
Chemical specificity is the ability of binding site of a macromolecule to bind specific ligands. The fewer ligands a protein can bind, the greater its specificity.
In biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. The binding partner of the macromolecule is often referred to as a ligand. Ligands may include other proteins, enzyme substrates, second messengers, hormones, or allosteric modulators. The binding event is often, but not always, accompanied by a conformational change that alters the protein's function. Binding to protein binding sites is most often reversible, but can also be covalent reversible or irreversible.
In biochemistry, the Lineweaver–Burk plot is a graphical representation of the Michaelis–Menten equation of enzyme kinetics, described by Hans Lineweaver and Dean Burk in 1934.
In biochemistry, an Eadie–Hofstee plot is a graphical representation of the Michaelis–Menten equation in enzyme kinetics. It has been known by various different names, including Eadie plot, Hofstee plot and Augustinsson plot. Attribution to Woolf is often omitted, because although Haldane and Stern credited Woolf with the underlying equation, it was just one of the three linear transformations of the Michaelis–Menten equation that they initially introduced. However, Haldane indicated in 1957 that Woolf had indeed found the three linear forms:
In 1932, Dr. Kurt Stern published a German translation of my book Enzymes, with numerous additions to the English text. On pp. 119–120, I described some graphical methods, stating that they were due to my friend Dr. Barnett Woolf. [...] Woolf pointed out that linear graphs are obtained when is plotted against , against , or against , the first plot being most convenient unless inhibition is being studied.
In biochemistry, biotinylation is the process of covalently attaching biotin to a protein, nucleic acid or other molecule. Biotinylation is rapid, specific and is unlikely to disturb the natural function of the molecule due to the small size of biotin. Biotin binds to streptavidin and avidin with an extremely high affinity, fast on-rate, and high specificity, and these interactions are exploited in many areas of biotechnology to isolate biotinylated molecules of interest. Biotin-binding to streptavidin and avidin is resistant to extremes of heat, pH and proteolysis, making capture of biotinylated molecules possible in a wide variety of environments. Also, multiple biotin molecules can be conjugated to a protein of interest, which allows binding of multiple streptavidin, avidin or neutravidin protein molecules and increases the sensitivity of detection of the protein of interest. There is a large number of biotinylation reagents available that exploit the wide range of possible labelling methods. Due to the strong affinity between biotin and streptavidin, the purification of biotinylated proteins has been a widely used approach to identify protein-protein interactions and post-translational events such as ubiquitylation in molecular biology.
Streptavidin is a 52 kDa protein (tetramer) purified from the bacterium Streptomyces avidinii. Streptavidin homo-tetramers have an extraordinarily high affinity for biotin. With a dissociation constant (Kd) on the order of ≈10−14 mol/L, the binding of biotin to streptavidin is one of the strongest non-covalent interactions known in nature. Streptavidin is used extensively in molecular biology and bionanotechnology due to the streptavidin-biotin complex's resistance to organic solvents, denaturants, detergents, proteolytic enzymes, and extremes of temperature and pH.
Non-competitive inhibition is a type of enzyme inhibition where the inhibitor reduces the activity of the enzyme and binds equally well to the enzyme whether or not it has already bound the substrate. This is unlike competitive inhibition, where binding affinity for the substrate in the enzyme is decreased in the presence of an inhibitor.
Enzyme kinetics is the study of the rates of enzyme-catalysed chemical reactions. In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction are investigated. Studying an enzyme's kinetics in this way can reveal the catalytic mechanism of this enzyme, its role in metabolism, how its activity is controlled, and how a drug or a modifier might affect the rate.
Hydrogen–deuterium exchange is a chemical reaction in which a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa. It can be applied most easily to exchangeable protons and deuterons, where such a transformation occurs in the presence of a suitable deuterium source, without any catalyst. The use of acid, base or metal catalysts, coupled with conditions of increased temperature and pressure, can facilitate the exchange of non-exchangeable hydrogen atoms, so long as the substrate is robust to the conditions and reagents employed. This often results in perdeuteration: hydrogen-deuterium exchange of all non-exchangeable hydrogen atoms in a molecule.
An 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.
In the field of biochemistry, the specificity constant, is a measure of how efficiently an enzyme converts substrates into products. A comparison of specificity constants can also be used as a measure of the preference of an enzyme for different substrates. The higher the specificity constant, the more the enzyme "prefers" that substrate.
Molecular binding is an attractive interaction between two molecules that results in a stable association in which the molecules are in close proximity to each other. It is formed when atoms or molecules bind together by sharing of electrons. It often, but not always, involves some chemical bonding.
In biochemistry, a Hanes–Woolf plot, Hanes plot, or plot of against is a graphical representation of enzyme kinetics in which the ratio of the initial substrate concentration to the reaction velocity is plotted against . It is based on the rearrangement of the Michaelis–Menten equation shown below:
Victor Henri was a French-Russian physical chemist and physiologist. He was born in Marseilles as a son of Russian parents. He is known mainly as an early pioneer in enzyme kinetics. He published more than 500 papers in a variety of disciplines including biochemistry, physical chemistry, psychology, and physiology. Aleksey Krylov was his half-brother.
Chemoproteomics 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, in which lead compounds are designed to interact with predetermined disease-driving biological targets. As phenotypic drug discovery assays do not provide confirmation of a compound's mechanism of action, chemoproteomics provides valuable follow-up strategies to narrow down potential targets and eventually validate a molecule's mechanism of action. Chemoproteomics also attempts to address the inherent challenge of drug promiscuity in small molecule drug discovery by analyzing protein-small molecule interactions on a proteome-wide scale. A major goal of chemoproteomics is to characterize the interactome of drug candidates to gain insight into mechanisms of off-target toxicity and polypharmacology.
Competitive inhibition is interruption of a chemical pathway owing to one chemical substance inhibiting the effect of another by competing with it for binding or bonding. Any metabolic or chemical messenger system can potentially be affected by this principle, but several classes of competitive inhibition are especially important in biochemistry and medicine, including the competitive form of enzyme inhibition, the competitive form of receptor antagonism, the competitive form of antimetabolite activity, and the competitive form of poisoning.
References
- 1 2 Wanner K, Höfner G (27 June 2007). Mass Spectrometry in Medicinal Chemistry: Applications in Drug Discovery. John Wiley & Sons. pp. 142–156. ISBN 978-3-527-61091-4.
- 1 2 3 4 Berezhkovskii AM, Szabo A, Rotbart T, Urbakh M, Kolomeisky AB (April 2017). "Dependence of the Enzymatic Velocity on the Substrate Dissociation Rate". The Journal of Physical Chemistry B. 121 (15): 3437–3442. doi:10.1021/acs.jpcb.6b09055. PMC 5577799 . PMID 28423908.
- ↑ Reuveni S, Urbakh M, Klafter J (March 2014). "Role of substrate unbinding in Michaelis-Menten enzymatic reactions". Proceedings of the National Academy of Sciences of the United States of America. 111 (12): 4391–6. Bibcode:2014PNAS..111.4391R. doi: 10.1073/pnas.1318122111 . PMC 3970482 . PMID 24616494.
- ↑ Copeland RA (2000). Enzymes a practical introduction to structure, mechanism, and data analysis. Wiley Library Catalog: J. Wiley. pp. 76–81.
- ↑ Deng, Lu; Kitova, Elena N.; Klassen, John S. (2013-01-01). "Dissociation Kinetics of the Streptavidin–Biotin Interaction Measured Using Direct Electrospray Ionization Mass Spectrometry Analysis". Journal of the American Society for Mass Spectrometry. 24 (1): 49–56. Bibcode:2013JASMS..24...49D. doi:10.1007/s13361-012-0533-5. ISSN 1044-0305. PMID 23247970.
- ↑ Mereghetti, Paolo; Kokh, Daria; McCammon, J Andrew; Wade, Rebecca C (December 2011). "Diffusion and association processes in biological systems: theory, computation and experiment". BMC Biophysics. 4 (1): 2. doi: 10.1186/2046-1682-4-2 . ISSN 2046-1682. PMC 3093674 . PMID 21595997.