Overlapping fragments

The overall amino acid sequence of the protein is reconstructed from the sequences in overlapping fragments. 

An alternative approach to obtaining a starting model for the refinement that does not need NOE data is called molecular fragment replacement [71] and treats the protein of interest as overlapping fragments of 7 to 10 residues in length. A protein database is... 

In a further study, Taniuchi et al. (1977) have shown that in the association of overlapping fragments of staphylococcal nuclease, two different species of active enzyme are formed. On the basis of the products of limited proteolysis, structures for the two species were deduced. In one case a structure is proposed in which fragment 1-126 assumes native-like structure over the sequence 1-48, and all of fragment 50-149 assumes native-like structure. In the other case the structure is one in which fragment 1-126 assumes native-like structure over the sequence 1-110, while that part of fragment 50-149 in the sequence interval 111-149 assumes native-like structure. The interest of these results is enhanced by the finding that the two active species initially form in relative concentrations substantially different from their equilibrium concentrations. Thus, both a mobile equilibrium and substantial kinetic control of the early products are evident. Taniuchi et al. did not reach a clear-cut mechanistic conclusion from their studies. 

In this first formulation we have already established that it is most effective to scan the largest candidate fragments first. It is desirable to recognize overlapping fragments more distances are determined. However, it is inevitably the case that a substantial number of distances will be left undefined, particularly the longest distances which would not be incorporated into a fragment. 

One other approach is direct-inlet MS. A prerequisite for mass analysis is ionisation, a process that critically influences the sensitivity and selectivity of the experiment. Electron impact ionisation (El) causes considerable fragmentation. Because of overlapping fragment and parent ions, the molecular information is difficult to deconvolute, and little chemical information can be extracted. 

Lists of Bonding Fragment Pairs and Overlapping Fragment Pairs... 

Fig. 2. The use of overlapping fragments to determine the sequence of a peptide. The protein is first digested with trypsin and the resulting peptides separated and sequenced. The protein is separately digested with chymotrypsin and the resulting peptides again separated and sequenced. The order of the peptide fragments in the protein can be determined by comparing the sequences obtained.

I. Simon, L. Glasscr, and H. A. Schenga. Calculation tf protein cem forma [ion as an assembly of smbie overlapping fragments application io bovine poncremic tiypsin inhibitor. Proc. Natl Acad. Sci. USA 3661-3665(1991). 

---