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Allosterically
In biochemistry, allosteric regulation (or allosteric control) is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site. The site to which the effector binds is termed the ''allosteric site'' or ''regulatory site''. Allosteric sites allow effectors to bind to the protein, often resulting in a conformational change and/or a change in protein dynamics. Effectors that enhance the protein's activity are referred to as ''allosteric activators'', whereas those that decrease the protein's activity are called ''allosteric inhibitors''. Allosteric regulations are a natural example of control loops, such as feedback from downstream products or feedforward from upstream substrates. Long-range allostery is especially important in cell signaling. Allosteric regulation is also particularly important in the cell's ability to adjust enzyme activity. The term ''allostery'' comes from the Ancient Greek ''allos'' (), "other", and ''stereos'' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Allosteric Regulation
In biochemistry, allosteric regulation (or allosteric control) is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site. The site to which the effector binds is termed the ''allosteric site'' or ''regulatory site''. Allosteric sites allow effectors to bind to the protein, often resulting in a conformational change and/or a change in protein dynamics. Effectors that enhance the protein's activity are referred to as ''allosteric activators'', whereas those that decrease the protein's activity are called ''allosteric inhibitors''. Allosteric regulations are a natural example of control loops, such as feedback from downstream products or feedforward from upstream substrates. Long-range allostery is especially important in cell signaling. Allosteric regulation is also particularly important in the cell's ability to adjust enzyme activity. The term ''allostery'' comes from the Ancient Greek ''allos'' (), "other", and ''stereos ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Dynamics
Proteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis. The study of protein dynamics is most directly concerned with the transitions between these states, but can also involve the nature and equilibrium populations of the states themselves. These two perspectives— kinetics and thermodynamics, respectively—can be conceptually synthesized in an "energy landscape" paradigm: highly populated states and the kinetics of transitions between them can be described by the depths of energy wells and the heights of energy barriers, respectively. Local flexibility: atoms and residues Portions of protein ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enzyme Model
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. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are catalytic RNA molecules, called ribozymes. Enzymes' specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the reaction rat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Daniel E
Daniel is a masculine given name and a surname of Hebrew origin. It means "God is my judge"Hanks, Hardcastle and Hodges, ''Oxford Dictionary of First Names'', Oxford University Press, 2nd edition, , p. 68. (cf. Gabriel—"God is my strength"), and derives from two early biblical figures, primary among them Daniel from the Book of Daniel. It is a common given name for males, and is also used as a surname. It is also the basis for various derived given names and surnames. Background The name evolved into over 100 different spellings in countries around the world. Nicknames (Dan, Danny) are common in both English and Hebrew; "Dan" may also be a complete given name rather than a nickname. The name "Daniil" (Даниил) is common in Russia. Feminine versions ( Danielle, Danièle, Daniela, Daniella, Dani, Danitza) are prevalent as well. It has been particularly well-used in Ireland. The Dutch names "Daan" and "Daniël" are also variations of Daniel. A related surname develo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Competitive Inhibition
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 (which can include any of the aforementioned types). Enzyme inhibition type In competitive inhibition of enzyme catalysis, binding of an inhibitor prevents binding of the target molecule of the enzyme, also known as the substrate. This is accomplished by blocking the binding site of the substrate – the active site – by some means. The Vmax indicates the maximum velocity of the reaction, while the Km is the amount of substrate needed to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Allosteric Modulation
In pharmacology and biochemistry, allosteric modulators are a group of substances that bind to a receptor to change that receptor's response to stimulus. Some of them, like benzodiazepines, are drugs. The site that an allosteric modulator binds to (i.e., an ''allosteric site'') is not the same one to which an endogenous agonist of the receptor would bind (i.e., an ''orthosteric site''). Modulators and agonists can both be called receptor ligands. Allosteric modulators can be 1 of 3 types either: positive, negative or neutral. Positive types increase the response of the receptor by increasing the probability that an agonist will bind to a receptor (i.e. affinity), increasing its ability to activate the receptor (i.e. efficacy), or both. Negative types decrease the agonist affinity and/or efficacy. Neutral types don't affect agonist activity but can stop other modulators from binding to an allosteric site. Some modulators also work as allosteric agonists. The term "allosteric" de ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative erro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Energy Functional
The energy functional is the total energy of a certain system, as a functional of the system's state. In the energy methods of simulating the dynamics of complex structures, a state of the system is often described as an element of an appropriate function space. To be in this state, the system pays a certain cost in terms of energy required by the state. This energy is a scalar quantity, a function of the state, hence the term ''functional''. The system tends to develop from the state with higher energy (higher cost) to the state with lower energy, thus local minima of this functional are usually related to the stable stationary states. Studying such states is part of the optimization problems, where the terms ''energy functional'' or ''cost functional'' are often used to describe the objective function. Examples * In Hamiltonian systems, the energy functional is given by the Hamiltonian. See also * Action (physics) * Density functional theory * Hamilton's principle * Histor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Statistical Ensemble
In physics, specifically statistical mechanics, an ensemble (also statistical ensemble) is an idealization consisting of a large number of virtual copies (sometimes infinitely many) of a system, considered all at once, each of which represents a possible state that the real system might be in. In other words, a statistical ensemble is a set of systems of particles used in statistical mechanics to describe a single system. The concept of an ensemble was introduced by J. Willard Gibbs in 1902. A thermodynamic ensemble is a specific variety of statistical ensemble that, among other properties, is in statistical equilibrium (defined below), and is used to derive the properties of thermodynamic systems from the laws of classical or quantum mechanics. Physical considerations The ensemble formalises the notion that an experimenter repeating an experiment again and again under the same macroscopic conditions, but unable to control the microscopic details, may expect to observe a ran ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Porphobilinogen Synthase
Aminolevulinic acid dehydratase (porphobilinogen synthase, or ALA dehydratase, or aminolevulinate dehydratase) is an enzyme () that in humans is encoded by the ''ALAD'' gene. Porphobilinogen synthase (or ALA dehydratase, or aminolevulinate dehydratase) synthesizes porphobilinogen through the asymmetric condensation of two molecules of aminolevulinic acid. All natural tetrapyrroles, including hemes, chlorophylls and vitamin B12, vitamin B12, share porphobilinogen as a common precursor. Porphobilinogen synthase is the prototype morpheein. Function It catalyzes the following reaction, the second step of the biosynthesis of porphyrin: :2 5-Aminolevulinic acid \rightleftharpoons porphobilinogen + 2 H2O It therefore catalyzes the condensation of 2 molecules of 5-aminolevulinate to form porphobilinogen (a precursor of heme, cytochromes and other hemoproteins). This reaction is the first common step in the biosynthesis of all biological tetrapyrroles. Zinc is essential for enzymati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Morpheein
Morpheeins are proteins that can form two or more different homo-oligomers (morpheein forms), but must come apart and change shape to convert between forms. The alternate shape may reassemble to a different oligomer. The shape of the subunit dictates which oligomer is formed. Each oligomer has a finite number of subunits (stoichiometry). Morpheeins can interconvert between forms under physiological conditions and can exist as an equilibrium of different oligomers. These oligomers are physiologically relevant and are not misfolded protein; this distinguishes morpheeins from prions and amyloid. The different oligomers have distinct functionality. Interconversion of morpheein forms can be a structural basis for allosteric regulation, an idea noted many years ago, and later revived. A mutation that shifts the normal equilibrium of morpheein forms can serve as the basis for a conformational disease. Features of morpheeins can be exploited for drug discovery. The dice image (F ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Induced Fit
Enzyme catalysis is the increase in the rate of a process by a biological molecule, an "enzyme". Most enzymes are proteins, and most such processes are chemical reactions. Within the enzyme, generally catalysis occurs at a localized site, called the active site. Most enzymes are made predominantly of proteins, either a single protein chain or many such chains in a multi-subunit complex. Enzymes often also incorporate non-protein components, such as metal ions or specialized organic molecules known as cofactor (e.g. adenosine triphosphate). Many cofactors are vitamins, and their role as vitamins is directly linked to their use in the catalysis of biological process within metabolism. Catalysis of biochemical reactions in the cell is vital since many but not all metabolically essential reactions have very low rates when uncatalysed. One driver of protein evolution is the optimization of such catalytic activities, although only the most crucial enzymes operate near catalytic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
