Fragmentation of proteins

Sweeteners can be anything from simple sugars to fragments of proteins, such as aspartame, that trigger the sweet receptors on our tongues, sometimes up to two hundred times as strongly as sugar itself. 

Numerous studies of properties of individual organic molecules of biological interest were reported recently. They dealt with molecules which represented fragments of proteins, biological membranes, and nucleic acids, drugs, and drug analogs. Some results will be discussed below. 

Pande V. S. and Rokhsar D. S. Molecular dynamics simulations of unfolding and refolding of a p hairpin fragment of protein G. (1999) (preprint). 

Semisynthesis can be defined as the use of fragments of proteins, or intact proteins themselves, as ready-made intermediates in the chemical synthesis of proteins. Many modifications to the native structure of a protein can be expected to have profound effects, and produce materials of the greatest academic or practical value, but only involve a change of one or a few atoms out of the thousands that often go to make up the complete molecule. If a semisynthetic method can be found to incorporate, at the correct site, a small synthetic fragment carrying the wanted change, there is no need to go to the trouble of constructing the rest of the molecule when it has already been preformed for us biosynthetically. 

In recent years there has also been a trend toward designing stable protein ligands for CIP conditions. One such example is the ligand library based on ZZ-fragments of protein A.15... 

The protein identification or sequence determination of a protein can be achieved using two different approaches top-down [22, 23] and bottom-up [24], A top-down experiment involves high-resolution measurement of an intact molecular weight and direct fragmentation of protein ions by tandem mass spectrometry (MS/MS) [25], This approach surveys an entire protein sequence with 100% coverage. Post-translational modifications such as glyco-... 

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... 

It is important to note that effective and good biomarker can be a specific fragment of protein which is present in diseased state but not under normal conditions. Currently, existing biomarker of this type is Ap fragment of a-amyloid protein in Alzheimer s Disease (AD) (Olsson et al., 2003). 

In the latest years there has been a constant increase of the number of simulation studies concerning large molecules or even supermolecular aggregates, e.g. polymers, proteins or fragments of proteins, enzymes, membrane constituents, stimulated by the development of material science and biotechnology. 

Fig. 5. Representative configurations of the C-terminal fragment of protein G corresponding to different energy ranges...

B. Y. Ma, R. Nussinov (2000) Molecular dynamics simulations of a beta-hairpin fragment of protein G Balance between side-chain and backbone forces. J. Mol. Biol. 296, pp. 1091-1104... 

We previously showed that protein L induces proinflammatory mediator release from human basophils and mast cells, probably by interacting with FceRI-bound IgE [72, 79], We next evaluated whether protein L and a fragment of protein L denoted B1-B4 , which comprises four of the five immunoglobulinbinding repeats [73], induce cytokine (IL-4 and IL-13) synthesis and secretion from human basophils. Protein L and B,-B4 stimulated IL-4 release from basophils [80] and there was a significant correlation between IL-4 release induced by protein L and by B,-B4. These data demonstrate that protein L induces the secretion of IL-4 and IL-13, which are important for the polarization of Th2 cells [81], from basophils. 

Fragmentation of proteins as a result of treatment with the proteolytic enzyme trypsin. 

---