Proteins and their Residues

Emphasis will be placed on recent structural and conformational studies of relatively large molecules, particularly those of biochemical importance. The 1 3 C nmr of carbohydrates, nucleic acids and their constituents, proteins and their residues, lipids and macromolecular model systems will be discussed in detail and attempts will be made to cover the literature exhaustively. This somewhat arbitrary selection is dictated by the availability of recent summaries on 13C spectroscopic measurements of steroids (Gray,... 

Phosphorylation is a common method of regulation. As described above, SH2 domains bind to phosphorylated tyrosine residues. Conversely, phosphorylation of serines and threonines proximal to SH3 and PDZ domains uncouples them from their target motifs. Therefore modulation of protein kinase activity in cells regulates interactions between adaptor proteins and their target proteins. 

The six major proteins of milk, asl-, o s2-, and /c-casein, jS-lactoglobulin, and a-lactalbumin, contain at least one tryptophan residue [57], the fluorescence of which allows the monitoring of the structural modifications of proteins and their physicochemical environment during the coagulation processes. Emission fluorescence spectra of the protein tryptophanyl residues were recorded for the milk coagulation kinetics induced by... 

Consider using quaternary ammonium compounds if the product is intended to be used at pH = 8-9 and in the absence of anionics, proteins, and milk residues. Their germicidal activity increases in the order of monomer = dimer < trimer < tetramer < polymer, with a peak of efficacy for C12 - C16 compounds [17],... 

An example of a noncovalent system has already been discussed in the case of ribonuclease A (see Section 5.1.6). 29 32 Thus, much information was gained from the relatively easy synthesis of many peptide analogues with sequences derived from either end of the 124-residue protein, and their combination with the protein segments RNase(21-124), RNase(l-118), or RNase(21-118) produced by selective enzymatic digestions. 

Figure 43. Solvation dynamics from MD simulations for isomer 2. (a) The linear-response calculated time-resolved Stokes shifts for indole-protein, indole-water, and their sum. (b) Direct nonequilibrium simulations of the time-resolved Stokes shifts for indole-water, indole-protein, and their sum. Note the lack of slow component in indole-water relaxation in both (a) and (b), which is opposite to isomer 1 in Fig. 42. Also shown is the indole-water (within 5 A of indole) with coupled long-time negative solvation, (c) Relaxation between indole-lys79 and indole-glu4. The interaction energy changes from these two residues nearly cancel each other, (d) The distance changes between the indole and two charged residues, but both residues move away from the indole ring.

The intrinsic fluorescence of the eight tryptophanyl residues in MBP can be used to measure its reversible unfolding/refolding reactions. When unfolded by incubation in a denaturant such as guanidinium hydrochloride, the side chains of the tryptophanyl residues are exposed to solvent and their fluorescence is quenched. On dilution of the denaturant, the subsequent refolding reaction can be monitored by the increase in fluorescence that results from burial of the side chains in the interior of the protein and their shielding from solvent (Liu et al., 1988, 1989). 

The identification of reactive or chemically modified residues of proteins is often extremely important for the characterization of proteins and their activity. Peptide mapping in conjunction with Edman sequencing and/or mass spectrophotometric analysis has been the method of choice to accomplish this characterization. However, this approach alone may not be sufficient or optimal for every situation as was the case when trying to identify the affinity ligand attachment sites on the B-chain of blocked ricin (Lambert et al., 1991a). 

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