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HIV-1 Protease
A protease (also called a peptidase or proteinase) is an enzyme that performs proteolysis; protein catabolism by hydrolysis of peptide bonds. Proteases have evolved multiple times, and different classes of protease can perform the same reaction by completely different catalytic mechanisms
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TEV Protease
TEV protease
TEV protease
(EC 3.4.22.44, Tobacco Etch Virus nuclear-inclusion-a endopeptidase) is a highly sequence-specific cysteine protease from Tobacco Etch Virus (TEV).[1] It is a member of the PA clan of chymotrypsin-like proteases.[2] Due to its high sequence specificity it is frequently used for the controlled cleavage of fusion proteins in vitro and in vivo.[3]Contents1 Origin 2 Structure and function 3 Specificity 4 As a biochemical tool 5 References 6 External linksOrigin[edit] The tobacco etch virus encodes its entire genome as a single massive polyprotein (350 kDa). This is cleaved into functional units by the three proteases: P1 protease (1 cleavage site), helper-component protease (1 cleavage site) and TEV protease
TEV protease
(7 cleavage sites).[1] The native TEV protease
TEV protease
also contains an internal self-cleavage site
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Serine
Serine
Serine
(symbol Ser or S;[3][4] encoded by the codons UCU, UCC, UCA, UCG, AGU and AGC) is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH+ 3 form under biological conditions), a carboxyl group (which is in the deprotonated –COO− form in physiological conditions), and a side chain consisting of a hydroxymethyl group (see hydroxyl), classifying it as a polar amino acid
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Asparagine
Asparagine
Asparagine
(symbol Asn or N[2]), encoded by the codons AAU and AAC,[3] is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH+ 3 form under biological conditions), an α-carboxylic acid group (which is in the deprotonated −COO− form under biological conditions), and a side chain carboxamide, classifying it as a polar (at physiological pH), aliphatic amino acid. It is non-essential in humans, meaning the body can synthesize it. A reaction between asparagine and reducing sugars or other source of carbonyls produces acrylamide in food when heated to sufficient temperature
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Elimination Reaction
An elimination reaction is a type of organic reaction in which two substituents are removed from a molecule in either a one or two-step mechanism.[2] The one-step mechanism is known as the E2 reaction, and the two-step mechanism is known as the E1 reaction. The numbers do not have to do with the number of steps in the mechanism, but rather the kinetics of the reaction, bimolecular and unimolecular respectively. In rare cases, for molecules possessing particularly poor leaving groups, a third type of reaction, E1CB, exists
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Threonine
Threonine
Threonine
(symbol Thr or T[2]) is an amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH+ 3 form under biological conditions), a carboxyl group (which is in the deprotonated −COO− form under biological conditions), and a side chain containing a hydroxyl group, making it a polar, uncharged amino acid. It is essential in humans, meaning the body cannot synthesize it: it must be obtained from the diet. Threonine
Threonine
is synthesized from aspartate in bacteria such as E
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Glutamic Acid
Glutamic acid
Glutamic acid
(symbol Glu or E[4]) is an α-amino acid with formula C 5H 9O 4N. Its molecular structure could be idealized as HOOC-CH(NH 2)-(CH 2)2-COOH, with two carboxyl groups -COOH and one amino group -NH 2. However, in the solid state and mildly acid water solutions, the molecule assumes an electrically neutral zwitterion structure −OOC-CH(NH+ 3)-(CH 2)2-COOH. The acid can lose one proton from its second carboxyl group to form the conjugate base, the singly-negative anion glutamate −OOC-CH(NH+ 3)-(CH 2)2-COO−. This form of the compound is prevalent in neutral solutions. The glutamate neurotransmitter plays the principal role in neural activation.[5] This anion is also responsible for the savory flavor (umami) of certain foods, and used in glutamate flavorings such as MSG. In highly alkaline solutions the doubly negative anion −OOC-CH(NH 2)-(CH 2)2-COO− prevails
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Amino Acid
Amino acids
Amino acids
are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid.[1][2][3] The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids. About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways.[4] They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.)
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Cysteine
Cysteine
Cysteine
(symbol Cys or C)[3] (/ˈsɪstɪiːn/)[4] is a semi-essential[5] proteinogenic amino acid with the formula HO2CCH(NH2)CH2SH. It is encoded by the codons UGU and UGC. The thiol side chain in cysteine often participates in enzymatic reactions, as a nucleophile. The thiol is susceptible to oxidation to give the disulfide derivative cystine, which serves an important structural role in many proteins. When used as a food additive, it has the E number E920. Cysteine
Cysteine
has the same structure as serine, but with one of its oxygen atoms replaced by sulfur; replacing it with selenium gives selenocysteine. (Like other natural proteinogenic amino acids cysteine has (L) chirality in the older D/L notation based on homology to D and L glyceraldehyde
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Aspartic Acid
Aspartic acid
Aspartic acid
(symbol Asp or D;[3] encoded by the codons [GAU and GAC]), also known as aspartate, is an α-amino acid that is used in the biosynthesis of proteins.[4] Similar to all other amino acids it contains an amino group and a carboxylic acid
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Carboxyl
A carboxylic acid /ˌkɑːrbɒkˈsɪlɪk/ is an organic compound that contains a carboxyl group (C(=O)OH).[1] The general formula of a carboxylic acid is R–COOH, with R referring to the rest of the (possibly quite large) molecule. Carboxylic acids occur widely and include the amino acids (which make up proteins) and acetic acid (which is part of vinegar and occurs in metabolism). Salts and esters of carboxylic acids are called carboxylates. When a carboxyl group is deprotonated, its conjugate base forms a carboxylate anion. Carboxylate
Carboxylate
ions are resonance-stabilized, and this increased stability makes carboxylic acids more acidic than alcohols
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Catalytic Triad
A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes.[1][2] 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
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
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Histidine
Histidine
Histidine
(symbol His or H;[2] encoded by the codons CAU and CAC) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated –NH3+ form under biological conditions), a carboxylic acid group (which is in the deprotonated –COO− form under biological conditions), and an imidazole side chain (which is partially protonated), classifying it as a positively charged amino acid at physiological pH. Initially thought essential only for infants, longer-term studies have shown it is essential for adults also.[3] Histidine
Histidine
was first isolated by German physician Albrecht Kossel
Albrecht Kossel
and Sven Hedin in 1896.[4] It is also a precursor to histamine, a vital inflammatory agent in immune responses
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Protein Superfamily
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment[1] and mechanistic similarity, even if no sequence similarity is evident.[2] Sequence homology
Sequence homology
can then be deduced even if not apparent (due to low sequence similarity). Superfamilies typically contain several protein families which show sequence similarity within each family
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Zinc
Zinc
Zinc
is a chemical element with symbol Zn and atomic number 30. It is the first element in group 12 of the periodic table. In some respects zinc is chemically similar to magnesium: both elements exhibit only one normal oxidation state (+2), and the Zn2+ and Mg2+ ions are of similar size. Zinc
Zinc
is the 24th most abundant element in Earth's crust and has five stable isotopes. The most common zinc ore is sphalerite (zinc blende), a zinc sulfide mineral. The largest workable lodes are in Australia, Asia, and the United States
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PA Clan
A clan is a group of people united by actual or perceived kinship[1] and descent. Even if lineage details are unknown, clan members may be organized around a founding member or apical ancestor. Clans in indigenous societies tend to be exogamous, meaning that their members cannot marry one another. Clans preceded more centralized forms of community organization and government and are in every country. Members may identify with a coat of arms or other symbol to show they are an independent clan. The kinship-based bonds may be symbolic, whereby the clan shares a "stipulated" common ancestor that is a symbol of the clan's unity. When this "ancestor" is non-human, it is referred to as a totem, which is frequently an animal. The word clan is derived from the Gaelic clann[1] meaning "children" or "progeny"; it is not from the word for "family" in either Irish[2][3] or Scottish Gaelic
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