Amino from proteins

M.p. 207°C. The naturally occurring substance is dextrorotatory. Arginine is one of the essential amino-acids and one of the most widely distributed products of protein hydrolysis. It is obtained in particularly high concentration from proteins belonging to the prolamine and histone classes. It plays an important role in the production of urea as an excretory product. 

Henikoff S and J G Henikoff 1992. Amino Acid Substitution Matrices from Protein Blocks. Proceedir Hie National Academy of Sciences LISA 89 10915-10919. 

Biosynthesis. CRE is derived from a precursor of 196 amino acids (84,85). This gene contains one copy of CRE, which is flanked by double basic amino acids. The amino acid sequence of the CRE precursor suggests that it may arise from proteins related to POMC and neurophysins (31). The CRE precursor contains a cAMP responsive element which aHows stimulation of mRNA synthesis when intraceHular levels of cAMP are increased (86). 

In Parenteral and Enteral Nutrition. Amino acid transfusion has been widely used since early times to maintain basic nitrogen metaboHsm when proteinaceous food caimot be eaten. It was very difficult to prepare a pyrogen-free transfusion from protein hydrolysates. Since the advances in L-amino acid production, the crystalline L-amino acids have been used and the problem of pyrogen in transfusion has been solved. The formulation of amino acid transfusion has been extensively investigated, and a solution or mixture in which the ratio between essential and nonessential amino acid is 1 1, has been widespread clinically. Special amino acid mixtures (eg, branched chain amino acids-enriched solution) have been developed for the treatment of several diseases (93). 

The gel-like, bead nature of wet Sephadex enables small molecules such as inorganic salts to diffuse freely into it while, at the same time, protein molecules are unable to do so. Hence, passage through a Sephadex column can be used for complete removal of salts from protein solutions. Polysaccharides can be freed from monosaccharides and other small molecules because of their differential retardation. Similarly, amino acids can be separated from proteins and large peptides. 

Analysis and prediction of side-chain conformation have long been predicated on statistical analysis of data from protein structures. Early rotamer libraries [91-93] ignored backbone conformation and instead gave the proportions of side-chain rotamers for each of the 18 amino acids with side-chain dihedral degrees of freedom. In recent years, it has become possible to take account of the effect of the backbone conformation on the distribution of side-chain rotamers [28,94-96]. McGregor et al. [94] and Schrauber et al. [97] produced rotamer libraries based on secondary structure. Dunbrack and Karplus [95] instead examined the variation in rotamer distributions as a function of the backbone dihedrals ( ) and V /, later providing conformational analysis to justify this choice [96]. Dunbrack and Cohen [28] extended the analysis of protein side-chain conformation by using Bayesian statistics to derive the full backbone-dependent rotamer libraries at all... 

Figure 17.16 Ribbon diagram representations of the structures of domain B1 from protein G (blue) and the dimer of Rop (red). The fold of B1 has been converted to an a-helical protein like Rop by changing 50% of its amino acids sequence. (Adapted from S. Dalai et al.,...

Glycine is the simplest anino acid and the only one in Table 27.1 that is achiral. The a-carbon atom is a chirality center in all the others. Configurations in amino acids are normally specified by the d, l notational system. All the chiral amino acids obtained from proteins have the l configuration at their- a-carbon atom, meaning that the amine group is at the left when a Fischer projection is arianged so the carboxyl group is at the top. 

Although all the chiial amino acids obtained from proteins have the l configuration at then a carbon, that should not be taken to mean that D-amino acids are unknown. In fact, quite a number of D-anino acids occur naturally. D-Alanine, for example, is a constituent of bacterial cell walls and D-seiine occurs in brain tissue. The point is that D-fflnino acids are not constituents of proteins. 

One of the most useful applications of chiral derivatization chromatography is the quantification of free amino acid enantiomers. Using this indirect method, it is possible to quantify very small amounts of enantiomeric amino acids in parallel and in highly complex natural matrices. While direct determination of free amino acids is in itself not trivial, direct methods often fail completely when the enantiomeric ratio of amino acid from protein hydrolysis must be monitored in complex matrices. 

Amino acids isolated from protein hydrolysates. 

The importance of Heinrich Ritthausen s fundamental studies, 1862 to 1899, on analytical procedures for the determination of amino acids in proteins has been emphasized in the biographical sketches which have been presented by Osborne (210), Vickery (289), and Chibnall (47). It is of particular interest to note here the prediction made by Ritt-hausen about 1870 that the amino acid composition would prove to be the most adequate basis for the characterization of proteins. Ritthausen and Kreusler (230) were the first, in 1871, to determine amino acids derived from proteins, and some of the values which they found for aspartic and glutamic acids are given in Table III (cited by Chibnall, 47, and Vickery, 286). 

Animals, including humans, cannot synthesise all the different amino adds they need and thus require them in their diet. These amino adds are called the essential amino acids. Proteins in food are hydrolysed in the digestive tract and the resulting amino acids are reassembled into proteins within the animal s cells. All animals are ultimately dependent on plants for protein, as it is plants that create protein by combining inorganic nitrogen from the soil (as nitrate) with organic molecules derived from carbon from the atmosphere (as CO2). 

An interesting and important fact is that almost all amino acids isolated from proteins L-configuration have the L-configuration at the a-carbon, although some amino acids isolated from microbiological sources are the mirror image isomers, ie in the D-configuration. We shall consider amino add stereochemistry in more detail in section 8.3. 

An exopeptidase that sequentially releases an amino from the C-terminus of a protein or peptide. Carbox-ypeptidases are classified in Enzyme Nomenclature according to catalytic type and are included in subsubclasses 3.4.16-3.4.18. 

The human histamine Hi-receptor is a 487 amino acid protein that is widely distributed within the body. Histamine potently stimulates smooth muscle contraction via Hi-receptors in blood vessels, airways and in the gastrointestinal tract. In vascular endothelial cells, Hi-receptor activation increases vascular permeability and the synthesis and release of prostacyclin, plateletactivating factor, Von Willebrand factor and nitric oxide thus causing inflammation and the characteristic wheal response observed in the skin. Circulating histamine in the bloodstream (from, e.g. exposure to antigens or allergens) can, via the Hi-receptor, release sufficient nitric oxide from endothelial cells to cause a profound vasodilatation and drop in blood pressure (septic and anaphylactic shock). Activation of... 

Wilkins MR et al (1996) From proteins to proteomes large scale protein identification by two-dimensional electrophoresis and amino acid analysis. BioTechnol 14 61-65... 

Figure 10.4. Effect on apatite-collagen isotopic fractionation due to inhibition of amino acid production and preferred use of exogenous amino acids. Carnivore and herbivore, both based on C3 plants, have similar bulk isotopic composition of total edible tissues (T), leading to similar 5 C for apatite carbonate (AP). Collagen (CO) of carnivore is more enriched in Cthan that of herbivore, because of preferential utilization of amino acids derived from protein (P) of herbivore flesh in construction of carnivore s proteins. C ss = assimilated carbon.

Alternatively, one interesting drug delivery technique exploits the active transport of certain naturally-occurring and relatively small biomacromolecules across the cellular membrane. For instance, the nuclear transcription activator protein (Tat) from HIV type 1 (HlV-1) is a 101-amino acid protein that must interact with a 59-base RNA stem-loop structure, called the traus-activation region (Tar) at the 5 end of all nascent HlV-1 mRNA molecules, in order for the vims to replicate. HIV-Tat is actively transported across the cell membrane, and localizes to the nucleus [28]. It has been found that the arginine-rich Tar-binding region of the Tat protein, residues 49-57 (Tat+9 57), is primarily responsible for this translocation activity [29]. 

Many examples exist of using this protein motif to construct hydrogels from protein or peptide assembly. For example, Dong et al., reported elongated fibrils with diameters as small as 4 nm by incorporation of charged amino acids in the... 

The removal of released DA from the synaptic extracellular space to facilitate its intraneuronal metabolism is achieved by a membrane transporter that controls the synaptic concentration. This transporter has been shown to be a 619 amino-acid protein with 12 hydrophobic membrane spanning domains (see Giros and Caron 1993). Although it has similar amino-acid sequences to that of the NA (and GABA) transporter, there are sufficient differences for it to show some specificity. Thus DA terminals will not concentrate NA and the DA transporter is blocked by a drug such as nomifensine which has less effect on NA uptake. Despite this selectivity some compounds, e.g. amphetamine and 6-OHDA (but not MPTP), can be taken up by both neurons. The role of blocking DA uptake in the central actions of cocaine and amphetamine is considered later (Chapter 23). 

NS3 is a 631 amino acid protein, and its first 180 amino acids encode a serine protease of the chymotrypsin family (Figure 2.2A). It has a typical chymotrypsin-family fold consisting of two jS-barrels, with catalytic triad residues at the interface. His-57 and Asp-81 are contributed by the N-terminal jS-barrel and Ser-139 from the C-terminal jS-barrel. NS3 and closely related viral proteases are significantly smaller than other members of the chymotrypsin family, and many of the loops normally found between adjacent jS-strands in trypsin proteases are truncated in NS3 [31]. Probably... 

Gluconeogenesis Formation of glucose from precursors other than carbohydrates (especially by the liver and kidney) using amino acids from proteins, glycerol from fats, or lactate produced by muscle during anaerobic glycolysis. 

In the two equations above, notice that water is acting as an acid in one instance and as a base in the other. Substances like water that can act as an acid or a base depending on the circumstances are called amphoteric substances. The word comes from the Greek prefix ampho-, which means both. Water is the most common amphoteric substance, but amino acids, proteins, and some metal oxides—such as aluminum oxide (Al203) and zinc oxide (ZnO), for example—can also act as amphoteric substances. 

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