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PNGase F
Peptide:N-glycosidase F, commonly referred to as PNGase F, is an amidase of the peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase class. PNGase F works by cleaving between the innermost GlcNAc and asparagine residues of high mannose, hybrid, and complex oligosaccharides from N-linked glycoproteins and glycopeptides. This results in a deaminated protein or peptide and a free glycan. PNGase F has a molecular weight of 35,500 and consists of a polypeptide chain of 314 amino acids. The optimal pH for enzyme activity is 8.6. However, the activity is stable for a wide variety of conditions and reagents. PNGase F maintains 60% activity from pH 6.0 to pH 9.5. It is able to deglycosylate in the absence of denaturants, but needs extensive incubation and larger amounts of the enzyme to cleave native proteins.Anthony L. , Tarentino and Thomas H. Plummer Jr.. "Enzymatic deglycosylation of asparagine-linked glycans: Purification, properties, and specificity of oligosaccharide-cleaving ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amidase
In enzymology, an amidase (, ''acylamidase'', ''acylase (misleading)'', ''amidohydrolase (ambiguous)'', ''deaminase (ambiguous)'', ''fatty acylamidase'', ''N-acetylaminohydrolase (ambiguous)'') is an enzyme that catalyzes the hydrolysis of an amide: Thus, the two substrates of this enzyme are an amide and H2O, whereas its two products are monocarboxylate and NH3. This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amides. The systematic name of this enzyme class is acylamide amidohydrolase. Other names in common use include acylamidase, acylase, amidohydrolase, deaminase, fatty acylamidase, and N-acetylaminohydrolase. This enzyme participates in 6 metabolic pathways: urea cycle and metabolism of amino groups, phenylalanine metabolism, tryptophan metabolism, cyanoamino acid metabolism, benzoate degradation via coa ligation, and styrene degradation. Amidases contain a conserved stretch o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. In a typical MS procedure, a sample, which may be solid, liquid, or gaseous, is ionized, for example by bombarding it with a beam of electrons. This may cause some of the sample's molecules to break up into positively charged fragments or simply become positively charged without fragmenting. These ions (fragments) are then separated accordin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gel Electrophoresis
Gel electrophoresis is a method for separation and analysis of biomacromolecules ( DNA, RNA, proteins, etc.) and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size (IEF agarose, essentially size independent) and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge. Nucleic acid molecules are separated by applying an electric field to move the negatively charged molecules through a matrix of agarose or other substances. Shorter molecules move faster and migrate farther than longer ones because shorter molecules migrate more easily through the pores of the gel. This phenomenon is called sieving. Proteins are separated by the charge in agarose because the pores of the gel are too small to sieve proteins. Gel electrophoresis can also be used for the separation of nanoparticles. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Antibody
An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the pathogen, called an antigen. Each tip of the "Y" of an antibody contains a paratope (analogous to a lock) that is specific for one particular epitope (analogous to a key) on an antigen, allowing these two structures to bind together with precision. Using this binding mechanism, an antibody can ''tag'' a microbe or an infected cell for attack by other parts of the immune system, or can neutralize it directly (for example, by blocking a part of a virus that is essential for its invasion). To allow the immune system to recognize millions of different antigens, the antigen-binding sites at both tips of the antibody come in an equally wide variety. In contrast, the remainder of the antibody is relatively constant. It only occurs in a few varia ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lysosomal Storage Disease
Lysosomal storage diseases (LSDs; ) are a group of over 70 rare inherited metabolic disorders that result from defects in lysosomal function. Lysosomes are sacs of enzymes within cells that digest large molecules and pass the fragments on to other parts of the cell for recycling. This process requires several critical enzymes. If one of these enzymes is defective due to a mutation, the large molecules accumulate within the cell, eventually killing it. Lysosomal storage disorders are caused by lysosomal dysfunction usually as a consequence of deficiency of a single enzyme required for the metabolism of lipids, glycoproteins (sugar-containing proteins), or so-called mucopolysaccharides. Individually, lysosomal storage diseases occur with incidences of less than 1:100,000; however, as a group, the incidence is about 1:5,000 – 1:10,000. Most of these disorders are autosomal recessively inherited such as Niemann–Pick disease, type C, but a few are X-linked recessively inherited, su ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Glucanase
Glucanases are enzymes that break down large polysaccharides via hydrolysis. The product of the hydrolysis reaction is called a glucan, a linear polysaccharide made of up to 1200 glucose monomers, held together with glycosidic bonds. Glucans are abundant in the endosperm cell walls of cereals such as barley, rye, sorghum, rice, and wheat. Glucanases are also referred to as lichenases, hydrolases, glycosidases, glycosyl hydrolases, and/or laminarinases. Many types of glucanases share similar amino acid sequences but vastly different substrates. Of the known endo-glucanases, 1,3-1,4-β-glucanase is considered the most active. Structure β-glucanases The secondary and tertiary structures of β-glucanases involves the stacking of multiple β-sheets, each of which are made of several anti-parallel strands that bend and form a cleft crossing the active site of the enzyme. This type of structure has been called the "jelly roll fold." Some common β-glucanases * 1,3-β-glucana ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lectin
Lectins are carbohydrate-binding proteins that are highly specific for sugar groups that are part of other molecules, so cause agglutination of particular cells or precipitation of glycoconjugates and polysaccharides. Lectins have a role in recognition at the cellular and molecular level and play numerous roles in biological recognition phenomena involving cells, carbohydrates, and proteins. Lectins also mediate attachment and binding of bacteria, viruses, and fungi to their intended targets. Lectins are ubiquitous in nature and are found in many foods. Some foods, such as beans and grains, need to be cooked, fermented or sprouted to reduce lectin content. Some lectins are beneficial, such as CLEC11A, which promotes bone growth, while others may be powerful toxins such as ricin. Lectins may be disabled by specific mono- and oligosaccharides, which bind to ingested lectins from grains, legumes, nightshade plants, and dairy; binding can prevent their attachment to the carbohy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Barrel
In protein structures, a beta barrel is a beta sheet composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond). Beta-strands in many beta-barrels are arranged in an antiparallel fashion. Beta barrel structures are named for resemblance to the barrels used to contain liquids. Most of them are water-soluble proteins and frequently bind hydrophobic ligands in the barrel center, as in lipocalins. Others span cell membranes and are commonly found in porins. Porin-like barrel structures are encoded by as many as 2–3% of the genes in Gram-negative bacteria. It has been shown that more than 600 proteins with various function (e.g., oxidase, dismutase, amylase) contain the beta barrel structure. In many cases, the strands contain alternating polar and non-polar (hydrophilic and hydrophobic) amino acids, so that the hydrophobic residues are oriented into the interior of the barrel to form a hy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tetrahedral Carbonyl Addition Compound
A tetrahedral intermediate is a reaction intermediate in which the bond arrangement around an initially double-bonded carbon atom has been transformed from trigonal to tetrahedral. Tetrahedral intermediates result from nucleophilic addition to a carbonyl group. The stability of tetrahedral intermediate depends on the ability of the groups attached to the new tetrahedral carbon atom to leave with the negative charge. Tetrahedral intermediates are very significant in organic syntheses and biological systems as a key intermediate in esterification, transesterification, ester hydrolysis, formation and hydrolysis of amides and peptides, hydride reductions, and other chemical reactions. History One of the earliest accounts of the tetrahedral intermediate came from Rainer Ludwig Claisen in 1887. In the reaction of benzyl benzoate with sodium methoxide, and methyl benzoate with sodium benzyloxide, he observed a white precipitate which under acidic conditions yields benzyl benzoate, methyl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleophile
In chemistry, a nucleophile is a chemical species that forms bonds by donating an electron pair. All molecules and ions with a free pair of electrons or at least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they are Lewis bases. ''Nucleophilic'' describes the affinity of a nucleophile to bond with positively charged atomic nuclei. Nucleophilicity, sometimes referred to as nucleophile strength, refers to a substance's nucleophilic character and is often used to compare the affinity of atoms. Neutral nucleophilic reactions with solvents such as alcohols and water are named solvolysis. Nucleophiles may take part in nucleophilic substitution, whereby a nucleophile becomes attracted to a full or partial positive charge, and nucleophilic addition. Nucleophilicity is closely related to basicity. History The terms ''nucleophile'' and ''electrophile'' were introduced by Christopher Kelk Ingold in 1933, replacing the terms ''anionoid'' and ''cationoid' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Catalytic Triad
A 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. The nucleophile is most commonly a serine or cysteine amino acid, but occasionally threonine or even selenocysteine. The 3D structure of the enzyme brings together the triad residues in a precise orientation, even though they may be far apart in the sequence (primary structure). As well as divergent evolution of function (and even the triad's nucleophile), catalytic triads show some ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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