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Allostery
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 ''stere ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jean-Pierre Changeux
Jean-Pierre Changeux (; born 6 April 1936) is a French neuroscientist known for his research in several fields of biology, from the structure and function of proteins (with a focus on the allosteric proteins), to the early development of the nervous system up to cognitive functions. Although being famous in biological sciences for the MWC model, the identification and purification of the nicotinic acetylcholine receptor and the theory of epigenesis by synapse selection are also notable scientific achievements. Changeux is known by the non-scientific public for his ideas regarding the connection between mind and physical brain. As put forth in his book, ''Conversations on Mind, Matter and Mathematics'', Changeux strongly supports the view that the nervous system functions in a projective rather than reactive style and that interaction with the environment, rather than being instructive, results in the selection amongst a diversity of preexisting internal representations. Biograph ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MWC Model
In biochemistry, the Monod-Wyman-Changeux model (MWC model, also known as the symmetry model) describes allosteric transitions of proteins made up of identical subunits. It was proposed by Jean-Pierre Changeux in his PhD thesis, and described by Jacques Monod, Jeffries Wyman, and Jean-Pierre Changeux. It contrasts with the sequential model. The concept of two distinct symmetric states is the central postulate of the MWC model. The main idea is that regulated proteins, such as many enzymes and receptors, exist in different interconvertible states ''in the absence of any regulator''. The ratio of the different conformational states is determined by thermal equilibrium. This model is defined by the following rules: # An allosteric protein is an oligomer of protomers that are symmetrically related (for hemoglobin, we shall assume, for the sake of algebraic simplicity, that all four subunits are functionally identical). # Each protomer can exist in (at least) two conformational st ... [...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 ( ... [...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, 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 enzymatic activity. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequential Model
The sequential model (also known as the KNF model) is a theory that describes cooperativity of protein subunits. Koshland, D.E., Némethy, G. and Filmer, D. (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5, 365–385DOI: 10.1021/bi00865a047/ref> It postulates that a protein's conformation changes with each binding of a ligand, thus sequentially changing its affinity for the ligand at neighboring binding sites. It gives one explanation for cooperative binding. Overview This model for allosteric regulation of enzymes suggests that the subunits of multimeric proteins have two conformational states. The binding of the ligand causes conformational change in the other subunits of the multimeric protein. Although the subunits go through conformational changes independently (as opposed to in the MWC model), the switch of one subunit makes the other subunits more likely to change, by reducing the energy needed for subse ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 ''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. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure. Binding occurs by intermolecular forces, such as ionic bonds, hydrogen bonds and Van der Waals forces. The association or docking is actually reversible through dissociation. Measurably irreversible covalent bonding between a ligand and target molecule is atypical in biological systems. In contrast to the definition ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Subunit
In structural biology, a protein subunit is a polypeptide chain or single protein molecule that assembles (or "''coassembles''") with others to form a protein complex. Large assemblies of proteins such as viruses often use a small number of types of protein subunits as building blocks. A subunit is often named with a Greek or Roman letter, and the numbers of this type of subunit in a protein is indicated by a subscript. For example, ATP synthase has a type of subunit called α. Three of these are present in the ATP synthase molecule, leading to the designation α3. Larger groups of subunits can also be specified, like α3β3-hexamer and c-ring. Naturally-occurring proteins that have a relatively small number of subunits are referred to as oligomeric.Quote: ''Oligomer molecule: A molecule of intermediate relative molecular mass, the structure of which essentially comprises a small plurality of units derived, actually or conceptually, from molecules of lower relative molecula ... [...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 err ... [...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 * History ... [...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 ra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
