Protein substrate sites advantage

Multidomain proteins tend to occur more frequently in eukaryotes than in prokaryotes. Often the eukaryotic counterpart to a set of individual prokaryotic enzymes that catalyze successive reactions is a single, multidomain protein. The theoretical advantages proposed for such an arrangement include (1) a geometry for the direct transfer of substrates from one active site to another, in a process known as substrate channeling, in order to increase the overall flux of the pathway, (2) the protection of intermediates that may be unstable in aqueous environments or may be acted on inappropriately by other enzymes, (3) the facilitation of interactions between domains for purposes of allosteric regulatory functions, and (4) the establishment of a fixed stoichiometric ratio of the... 

The use of (3-casein as a test substrate presents, besides the importance of this protein in the food industry, advantages of releasing the hydrolysis from several structural limitations characteristic of many other potential native protein substrates. The use of this protein enabled a better understanding of the scope and validity of the results obtained with synthetic substrates. Additionally, the harnessing of mutated trypsins into the processing of (3-casein diversified the peptide products obtained. Most of the observed new cleavage sites were located in the hydrophobic portion of the protein. 

High reaction rates at ambient temperatures and near neutral pH values are necessary to design artificial proteases applicable to food industries, catalytic turnover in the peptide hydrolysis, and hydrolysis of a broad range of protein substrates at selected sites. In addition, easy separation of the catalysts from protein hydrolysates is required. Construction of catalytic centers directly on immobile supports is, therefore, advantageous to designing artificial proteases applicable to protein industries. 

On the other hand, in a minimal catalytic model system, the ribozymes have advantages over protein enzymes. Even short oligonucleotides can effectively use duplex formation to bind substrates and the known ribozymes are generally smaller than their protein counterparts. This substrate recognition through secondary structure is not a common feature of protein binding sites, where tertiary structural folds are necessary to optimize close packing of residues distant in primary sequence [42],... 

Vesicants, nerve agents, and phosgene are reactive electrophiles that react covalently with nucleophilic sites on macro molecules. Reactive nucleophilic sites exist on the bases and phosphate groups of DNA molecules. An advantage of DNA as a substrate is that it is present in all tissues of the body. A disadvantage is that repair mechanisms tend to excise the alkylated moiety, resulting in a much shorter lifetime compared to alkylated proteins (for a recent review of mass spectrometry for quantitation of DNA adducts, see Koc and Swen-berg <2>). 

The development of EPL has facilitated the production of large protein targets, but the requirement of specific N-terminal amino acids at the ligation site (cysteine [7], selenocysteine ]66J) reduces the general utilization of this method. Recently, we introduced a novel approach that we named expressed enzymatic ligation (EEL) for the semisynthesis of larger and chemically modified proteins that combines the advantages of the EPL with those of the substrate mimetic... 

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