Protein fragmentation fragment identification

In the multistage approach, ToF-SIMS plays an important role and is first used to detect the presence of proteins in museum objects. Indeed, if blood is present in such a state of conservation that it can be recognized through chemical composition, proteins must be present. For this purpose, as described previously, low mass fragments are studied. Since samples are very complex and in order to ensure identification, two-dimensional images of all protein fragments are drawn and compared. Correlation between the different images confirms the presence of proteins. 

Libraries can also be made from naturally occurring peptides (e.g. melanocortin [30] and somatostatin [31]) and their variants, or be derived from protein-fragments. The former have been employed mainly for the identification of peptide variants with unproved characteristics, and the latter for the identification of antigenic determinants present on targets, for example by selecting for binders to monoclonal antibodies specific for an antigen-fragment peptide library. 

Bandemer considered the role of fuzzy set theory in analytical chemistry. The applications they described focused on pattern recognition problems, the calibration of analytical methods,quality control, and component identification and mixture evaluation. Gordon and Somorjai applied a fuzzy clustering technique to the detection of similarities among protein substructures. A molecular dynamics trajectory of a protein fragment was analyzed. In the following subsections, some applications based on the hierarchical fuzzy clustering techniques presented in this chapter are reviewed. 

The determination of the three-dimensional crystal structure of the 22-kDa fragment of apoE in 1991 represented a major milestone in the studies of the structure and function of apoE. With this structure, it is now possible to understand and interpret much of what was known previously about the protein. In addition, identification of the structures of the apoE2 and apoE4 variants provides new insight into how apoE interacts with the LDL receptor and how the preference for different lipoprotein classes might be influenced by structure. These structures represent the beginning of the next level of understanding of how... 

The first two methods are heavily constrained on the available structural data. The assignment of, at least, protein backbone resonances is clearly the prerequisite to be achieved prior to a chemical optimization series. Lacking an assignment, the information obtained by NMR-based fragment identification and by their corresponding binding affinities can be transferred to X-ray crystallography to reduce the number of trials. 

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