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Substrate Presentation
In molecular biology, substrate presentation is a biological process that activates a protein. The protein is sequestered away from its substrate and then activated by release and exposure to its substrate. A ''substrate'' is typically the substance on which an enzyme acts but can also be a protein surface to which a ligand binds. In the case of an interaction with an enzyme, the protein or organic substrate typically changes chemical form. Substrate presentation differs from allosteric regulation in that the enzyme need not change its conformation to begin catalysis. Substrate presentation is best described for domain partitioning at nanoscopic distances (<100 nm). Examples Amyloid precursor protein (APP) is cleaved by |
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Substrate Translocation
Substrate may refer to: Physical layers *Substrate (biology), the natural environment in which an organism lives, or the surface or medium on which an organism grows or is attached **Substrate (aquatic environment), the earthy material that exists in the bottom of an aquatic habitat, like dirt, rocks, sand, or gravel ** Substrate (vivarium), the material used in the bottom of a vivarium or terrarium **Substrate (aquarium), the material used in the bottom of an aquarium * Substrate (building), natural stone, masonry surface, ceramic and porcelain tiles *Substrate (chemistry), the reactant which is consumed during a catalytic or enzymatic reaction *Substrate (materials science), the material on which a process is conducted *Substrate (printing), the base material that images will be printed onto *Printed circuit board (PCB), or more specifically, the electrically insulating portion of a PCB structure, such as fiberglass bound together with epoxy cement * Substrate (geology), a strat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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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] |
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Enzyme Translocation
An enzyme () is a protein that acts as a biological catalyst 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 include catalytic RNA molecules, also called ribozymes. They are sometimes described as a ''type'' of enzyme rather than being ''like'' an enzyme, but even in the decades s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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PIP2 Domain
PIP2 domains (also called PIP2 clusters) are a type of cholesterol-independent lipid domain formed from phosphatidylinositol and positively charged proteins in the plasma membrane. They tend to inhibit lipid rafts, GM1 lipid raft function. Chemical properties Phosphatidylinositol 4,5-bisphosphate (PIP2) is an anionic signaling lipid. Its polyunsaturated acyl chains exclude it from GM1 lipid rafts. The multiple negative charges on PIP2 are thought to cluster proteins with positive charges residing in the plasma membrane leading to nanoscale clusters. PIP3 is also clustered away from PIP2 and away from GM1 lipid rafts. Biological function PIP2 domains inhibit GM1 domain function by attracting palmitoylated proteins away from GM1 lipid rafts. For this to occur, a protein must be both palmitoylated and bind PIP2. Presumably PIP2 could also antagonize PIP3 localization but this has not been shown directly. PLD2 PLD2, Phospholipase D2 (PLD2) binds PIP2 and localizes with lipid rafts. I ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Binding Domain
In molecular biology, binding domain is a protein domain which binds to a specific atom or molecule, such as calcium or DNA. A protein domain is a part of a protein sequence and a tertiary structure that can change or evolve, function, and live by itself independent of the rest of the protein chain. Upon binding, proteins may undergo a conformational change. Binding domains are essential for the function of many proteins. They are essential because they help splice, assemble, and translate proteins.Yong, J., T. J. Golembe, D. J. Battle, L. Pellizzoni, and G. Dreyfuss. "SnRNAs Contain Specific SMN-binding Domains That Are Essential for SnRNP Assembly". ''Molecular and Cellular Biology''. U.S. National Library of Medicine, April 2004. Retrieved April 2017. Examples of binding domains include the Zinc finger, which binds to DNA, and EF hand, which binds to calcium. See also *DNA-binding domain *Receptor (biochemistry) In biochemistry and pharmacology, receptors are chemical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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PIP2
Phosphatidylinositol 4,5-bisphosphate or PtdIns(4,5)''P''2, also known simply as PIP2 or PI(4,5)P2, is a minor phospholipid component of cell membranes. PtdIns(4,5)''P''2 is enriched at the plasma membrane where it is a substrate for a number of important signaling proteins. PIP2 also forms PIP2 domain, lipid clusters that sort proteins. PIP2 is formed primarily by the type I phosphatidylinositol 4-phosphate 5-kinases from Phosphatidylinositol 4-phosphate, PI(4)P. In metazoans, PIP2 can also be formed by type II phosphatidylinositol 5-phosphate 4-kinases from Phosphatidylinositol 5-phosphate, PI(5)P. The fatty acids of PIP2 are variable in different species and tissues, but the most common fatty acids are stearic acid, stearic in position 1 and arachidonic in 2. Signaling pathways PIP2 is a part of many cellular signaling pathways, including PI(4,5)P2 Cycle, PIP2 cycle, PI3K/AKT/mTOR pathway, PI3K signalling, and PI5P metabolism. Recently, it has been found in the Cell nucleu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Phosphatidylcholine
Phosphatidylcholines (PC) are a class of phospholipids that incorporate choline as a headgroup. They are a major component of biological membranes and can easily be obtained from a variety of readily available sources, such as egg yolk or soybeans, from which they are mechanically or chemically extracted using hexane. They are also a member of the lecithin group of yellow-brownish fatty substances occurring in animal and plant tissues. Dipalmitoylphosphatidylcholine (lecithin) is a major component of the pulmonary surfactant, and is often used in the lecithin–sphingomyelin ratio to calculate fetal lung maturity. While phosphatidylcholines are found in all plant and animal cells, they are absent in the membranes of most bacteria, including ''Escherichia coli ''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esch ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Phospholipase D
Phospholipase D (PLD) (EC 3.1.4.4; also known as lipophosphodiesterase II, lecithinase D, choline phosphatase; systematic name: phosphatidylcholine phosphatidohydrolase) is an anesthetic-sensitive and mechanosensitive enzyme of the phospholipase protein superfamily that catalyzes the hydrolysis of membrane phospholipids. The canonical reaction is: :\text + \text_2\text \rightarrow \text + \text Phospholipases occur widely across bacteria, yeast, plants, animals, and viruses. PLD's principal substrate is phosphatidylcholine, which it hydrolyzes to produce the membrane lipid phosphatidic acid (PA) and soluble choline in a cholesterol-dependent process termed substrate presentation. Plants encode numerous PLD isoenzymes, with molecular weights ranging from approximately 90 to 125 kilodalton, kDa. In mammals, six PLD isoenzymes (PLD1–PLD6) are expressed. PLD1 and PLD2 are the best characterized, responsible for classical phosphatidylcholine hydrolysis and PA signaling. Other is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Lipid Rafts
The plasma membranes of cells contain combinations of glycosphingolipids, cholesterol and protein receptors organized in glycolipoprotein lipid microdomains termed lipid rafts. Their existence in cellular membranes remains controversial. Indeed, Kervin and Overduin imply that lipid rafts are misconstrued protein islands, which they propose form through a proteolipid code. Nonetheless, it has been proposed that they are specialized membrane microdomains which compartmentalize cellular processes by serving as organising centers for the assembly of signaling molecules, allowing a closer interaction of protein receptors and their effectors to promote kinetically favorable interactions necessary for the signal transduction. Lipid rafts influence membrane fluidity and membrane protein trafficking, thereby regulating neurotransmission and receptor trafficking. Lipid rafts are more ordered and tightly packed than the surrounding bilayer, but float freely within the membrane bilayer. A ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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PLD2
Phospholipase D2 is an enzyme that in humans is encoded by the ''PLD2'' gene. Function Phosphatidylcholine (PC)-specific phospholipase D, phospholipases D (PLDs) catalyze the hydrolysis of PC to produce phosphatidic acid and choline. Activation of PC-specific PLDs occurs as a consequence of agonist stimulation of both tyrosine kinase and G protein-coupled receptors. PC-specific PLDs have been proposed to function in regulated secretion, cytoskeletal reorganization, transcriptional regulation, and cell cycle control.[supplied by OMIM] Mechanism of activation PLD2 is activated by substrate presentation. The enzyme is palmitoylated, which drives PLD2 to lipid rafts. PC substrate is polyunsaturated and resides in the membrane separately from lipid rafts near phosphatidylinositol 4,5-bisphosphate (PIP2). When PIP2 levels increase, PLD2 trafficks to PIP2 where it encounters its substrate PC. Scaffolding proteins that interact with PLD2 likely changes its preference of lipid rafts ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Spatial Biology
Spatial biology is the study of biomolecules and cells in their native three-dimensional context. Spatial biology encompasses different levels of cellular resolution including (1) subcellular localization of DNA, RNA, and proteins, (2) single-cell resolution and ''in situ'' communications like cell-cell interactions and cell signaling, (3) cellular neighborhoods, regions, or microenvironments, and (4) tissue architecture and organization in organs. Dysregulation of tissue organization is a common feature in human disease progression including tumorigenesis and neurodegeneration. Many fields within biology are studied for their individual contribution to spatial biology. Spatial transcriptomics Spatial transcriptomics measures mRNA transcript abundance and distribution ''in situ'' across a tissue. Spatial method for RNA ''in situ'' detection is first described in a 1969 landmark paper by Joseph G. Gall and Mary-Lou Pardue. Previous to spatial transcriptomics techniques, whol ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |