Branch-chained amino acids chemical structure

The sulfonylurea herbicides are a new family of chemical compounds, some of which are selectively toxic to weeds but not to crops. The selectivity of the sulfonylureas results from their metabolism to non-toxic compounds by particular crops, but not by weeds. In addition to efficient weed control, the sulfonylurea herbicides provide environmentally desirable properties such as field use rates as low as two grams/hectare and very low toxicity to mammals. The high specificity of the herbicides for their molecular target contributes to both of these properties. In addition, the low toxicity to mammals results from their lack of the target enzyme for the herbicides. Sulfonylureas inhibit the enzyme acetolactate synthase (ALS), also known as acetohydroxyacid synthase (AHAS), which catalyzes the first common step in the biosynthesis of the branched chain amino acids leucine, isoleucine and valine. In mammals these are three of the essential amino acids which must be obtained through dietary intake because the biosynthetic pathway for the branched chain amino acids is not present. The prototype structure of a sulfonylurea herbicide is shown in Figure 1. 

Dansylation of most amino acids (Fig. 2) is optimal in the pH range 9.5-11.0 pH values higher than 11.0 are associated with increased hydrolysis, and at values below 8.0, the unreacted (protonated) form of the ammo group predominates and reaction rates are slow (Seiler, 1970). The extent of dansylation of an ammo acid depends not only on the pH of the reaction mixture, but also on the chemical structure of the amino acid. Steric hindrance around the amino group, as is present in certain branched-chain amino acids, leads to decreased stability of the dansyl derivative. In addition, rates of dansylation depend on the excess quantity of dansyl chloride used, as well as on the reaction time and temperature. Since dansyl chloride is only slightly soluble in water,... 

Peptide Vaccines Peptide vaccines are chemically synthesized and normally consist of 8-24 amino acids. In comparison with protein molecules, peptide vaccines are relatively small. They are also known as peptidomimetic vaccines, as they mimic the epitopes. Complex structures of cyclic components, branched chains, or other configurations can be built into the peptide chain. In this way, they possess conformations similar to the epitopes and can be recognized by immune cells. An in silico vaccine design approach has been used to find potential epitopes. A critical aspect of peptide vaccines is to produce 3D structures similar to the native epitopes of the pathogen. 

This chapter focuses on computational techniques that allow for hiological discovery based on the protein sequence itself ov on their comparison to protein families. Unlike nucleotide sequences, which are composed of four bases that are chemically rather similar (yet distinct), the alphabet of 20 amino acids found in proteins allows for much greater diversity of structure and function, primarily because the differences in the chemical makeup of these residues are more pronounced. Each residue can influence the overall physical properties of the protein because these amino acids are basic or acidic, hydrophobic or hydrophilic, and have straight chains, branched chains, or are aromatic. Thus, each residue has certain propensities to form structures of different types in the context of a protein domain. These properties, of course, are the basis for one of the central tenets of biochemistry that sequence specifies conformation (Anflnsen et al., 1961). 

One of t ie frontiers in peptide science is the linear assembly of long peptides and small proteins, which requires that the accumulation of side reactions is minimized and that the hurdles posed by the so-called difficult sequences are overcome. In recent years precise and fast heating by microwave irradiation has emerged as a new parameter for further optimization of SPPS [ 1-8]. It has especially enabled the synthesis of long and difficult peptide sequences. During the synthesis of difficult sequences, the peptide chain most likely becomes partially inaccessible typically due to the formation of secondary structures, especially p-sheets [9]. In addition, steric hindrance caused by p-branched amino acids can be a problem. Several chemical methods to suppress intramolecular aggregation have been described and include pseudo-prolines [9], solvent composition [10], and chaotropic salts [11, 12], Heating is likely to... 

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