Enzymatic fragmentation methods

Watanabe, M., Watanabe, J., Sonoyama, K., Tanabe, S. 2000. Novel method for producing hypoallergenic wheat flour by enzymatic fragmentation of the constituent allergens and its application to food processing. Biosci Biotechnol Biochem 64 2663-2667. 

Another application area in microwave technology is the use of microwave irradiation for the enzymatic digestion of proteins [106]. As discussed in the early part of this chapter, enzymatic cleavage to produce smaller peptide fragments of protein samples is an important step in structural characterization of proteins [24]. Traditional enzymatic digestion method usually takes several hours, whereas microwave-assisted digestion occurs in minutes. The initial... 

Real-time detection was also used for an isothermal amplification procedure termed nucleic acid sequence-based amplification, for the detection of artificial human papilloma virus sequences in SiHa cells. This method was not applied to real samples, but demonstrates the clinical applicability of additional microchip enzymatic amplification methods. Not all clinical microchip PCR amplifications looked for infectious agents, however. Cheng et al. showed a microchip PCR method for multiplex amplifications of dystrophin gene fragments for the detection of mutations associated with muscular dystrophy. 

Extrusion tripled the water solubility of sugar beet pulp fiber, primarily by reducing the molecular weight of pectin and hemicelluloses molecules (Ralet et ai, 1991). Ferulic acid, a phenolic acid normally associated with plant cell walls, was also recovered from the soluble sugar beet fraction. Smaller fragments may be soluble in aqueous ethanol, and thus discarded during the extraction steps common to enzymatic-gravimetric and enzymatic-chemical methods of fiber analysis. 

Whereas acid catalyzed hydrolysis of peptides cleaves amide bonds indiscriminately and eventually breaks all of them enzymatic hydrolysis is much more selective and is the method used to convert a peptide into smaller fragments... 

Determination of DNA Sequence Information. Almost all DNA sequence is determined by enzymatic methods (12) which exploit the properties of the enzyme DNA polymerase. Whereas a chemical method for DNA sequencing exists, its use has been supplanted for the most part in the initial deterrnination of a sequence. Chemical or Maxam-Gilbett sequencing (13) is mote often used for mapping functional sites on DNA fragments of known sequence. 

Another method that has been applied by our group to the study of enzymatic reactions is the Effective Fragment Potential (EFP) method [19]. The EFP method (developed at Mark Gordon s group at Iowa State University) allows the explicit inclusion of environment effects in quantum chemical calculations. The solvent, which may consist of discrete solvent molecules, protein fragments or other material, is treated explicitly using a model potential that incorporates electrostatics, polarization, and exchange repulsion effects. The solute, which can include some... 

This chapter reviewed some of our group s contributions to the development and application of QM/MM methods specifically as applied to enzymatic reactions, including the use of sequential MD/QM methods, the use of effective fragment potentials for reaction mechanisms, the development of the new QM/MM interface in Amber, as well as the implementation and optimization of the SCC-DFTB method in the Amber program. This last implementation allows the application of advanced MD and sampling techniques available in Amber to QM/MM problems, as exemplified by the potential and free energy surface surfaces for the reaction catalyzed by the Tripanosoma cruzi enzyme /ram-sialidasc shown here. 

The application of enzymes for the mild hydrolysis of esters has been well established as a convenient method, and hence can be regarded as a standard methodology in organic synthesis. Accordingly, the expectation is met that such enzymatic ester cleavage reactions are included in domino processes. In this context, a number of publications describe enzyme-initiated fragmentation reactions. 

When a colour layer of an artwork is analysed, a drop (5 10 pi) of this solution is localised on the sample surface. This method of enzymatic digestion can be, in principle, applied to all types of samples that occur in restoration practice fragments, cross-sections, microtome slices, etc. The samples are digested in closed microtubes to prevent evaporation of the solution. In the case of the cross-sections and microtome slices, it is essential to ensure the wetness of sample surface for the whole time of digestion. 

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