Protein fragmentation

Peptides derived from disnlfide-linked protein fragments... 

Fig. 35.2. Comparable fragments of different protein fragments, before (a) and after (b) matching.

Q-Sepharose was the separation medium chosen for preparative purification of plasmid pUC18.41 Cell proteins, fragments from RNase digestion of RNA, open coil plasmid and a denatured form of the plasmid were... 

Kniep R, Simon P (2007) Fluorapatite-Gelatine-Nanocomposites Self-Organized Morphogenesis, Real Structure and Relations to Natural Hard Materials. 270 73-125 Koenig BW (2007) Residual Dipolar Couplings Report on the Active Conformation of Rhodopsin-Bound Protein Fragments. 272 187-216 Kolusheva S, see Jelinek R (2007) 277 155-180... 

Detecting interactions by protein fragment complementation assays... 

Protein fragment complementation assays are based on an enzyme reassembly strategy whereby a protein-protein interaction promotes the efficient refolding and complementation of enzyme fragments to restore an active enzyme. The approach was initially developed using the reconstitution of ubiquitin as a sensor for protein-protein interactions (Johnsson and Varshavsky, 1994). Ubiquitin is a 76 amino acid protein that... 

Protein fragment complementation using dihydrofolate reductase... 

Remy, I., and Michnick, S. W. (1999). Clonal selection and in vivo quantitation of protein interactions with protein-fragment complementation assays. Proc. Natl. Acad. Sci. USA 96, 5394-5399. 

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... 

The low molecular weight mJz region of spectra derived from microorganism whole cells is generally comprised of mass spectral peaks derived from glycerides, phospholipids, glycolipids, and small protein fragments. This mass spectral information should be examined as a compliment to protein bio-... 

With advances in multidimensional NMR technology and the development of methods for uniform labeling of proteins with 15N and 13C, direct NMR studies on unfolded states of full-length proteins, rather than protein fragments, became possible. These studies were aided by the advent of high-field NMR spectrometers, which provide the necessary dispersion and sensitivity. High sensitivity is a critical factor in the study of unfolded and partly folded proteins, since NMR experiments must often be performed at very low concentrations to prevent aggregation. 

Soltes, L., Sebille, B. (1997). Reversible binding interactions between the tryptophan enantiomers and albumins of different animal species as determined by novel high performance liquid chromatographic methods an attempt to localize the d- and L-tryptophan binding sites on the human serum albumin polypeptide chain by using protein fragments. Chirality 9, 373-379. 

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. 

Analyze the cleaved proteins by SDS gel electrophoresis and Western blotting, followed by specific detection of the prey protein label. Comparison of prey protein fragments formed by chemical and enzymatic digestion can yield information as to the site of the resultant FeBABE-mediated cleavage. 

HOCl-mediated protein oxidation accelerates under pathophysiological conditions. Thus, proteins from extracellular matrix obtained from advanced human atherosclerotic lesions contained the enhanced levels of oxidized amino acids (DOPA and dityrosine) compared to healthy arterial tissue [44], It was also found that superoxide enhanced the prooxidant effect of hypochlorite in protein oxidation supposedly by the decomposition of chloramines and chlor-amides forming nitrogen-centered free radicals and increasing protein fragmentation [45], In addition to chlorination, hypochlorite is able to oxidize proteins. The most readily oxidized amino acid residue of protein is methionine. Methionine is reversibly oxidized by many oxidants including hypochlorite to methionine sulfide and irreversibly to methionine sulfone [46] ... 

The winter flounder antifreeze protein (AFP), characterized by Sicheri and Yang [42], consists of 37 residues of eight amino acids in an a-helix configuration. The AFP protein was synthesized by the conjoining of the Aa residues determined in the glycine mold, with the exception of the two residues at each of the termini, FIOOC-Asp Thr and Ala Arg-NP and the synthesized protein fragment is left with open amidic surfaces on the... 

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