Unspecific Protein Binding

Determination of unspecific binding reaction by competition of the RNA aptamers with cocaine 79 pi incubation buffer, 10 pi nAChR-enriched plasma membranes (800 pg/ml protein 1.6 pM receptor), 1 pi P-RNA dilution containing 10 mg/ml t-RNA anti-RNAse (40 U/pl), and 10 pi cocaine (10 mM). The percentage of binding of the ( P) RNA aptamers to the... 

Flavonoids, as food components or potential drugs, interact with a wide range of proteins by distinct mechanisms weak and rather unspecific binding of tannins to proline-rich or histi-dine-rich random coils leading to protein precipitation, specific enzyme inhibition, and... 

The structure of I19L was determined in aqueous solution at pH 6.8 by NMR [142]. Chemical shift values and the scarcity of cross-peaks in NOESY and ROESY spectra indicated that the peptide is mostly disordered in solution, although it has a helical propensity at residues 10-14 (Fig. 36). The bound conformation was investigated by means of tr-NOESY and STD experiments using a 30 1 excess of peptide relative to tubulin. The presence of intense, negative crosspeaks in the tr-NOESY spectrum proved that there is a fast binding equilibrium (Fig. 36). Unspecific binding was ruled out based on the absence of tr-NOE peaks in a control experiment where the protein was BSA instead of tubulin. The existence... 

Irreversible inhibitors have a major advantage over their reversible counterparts in that their action is sustained after systemic clearance. However, the pharmaceutical industry usually does not make use of irreversible inhibition principles, because unspecific binding to proteins other than the target enzyme may lead to considerable toxicity. Since most of the current cancer therapies are unspecific and very toxic, the irreversible kinase inhibition principle may well be applied in this research area, provided that an improved risk/benefit ratio is observed [4e],... 

The phenolic photoaffinity label azidodinoseb (Figure 4) binds less specifically than either azidoatrazine or azidotriazinone (14). In addition to other proteins, it labels predominantly the photosystem II reaction center proteins (spinach 43 and 47 kDa Chlamydomo-nas 47 and 51 kDa) (17). Because of the unspecific binding of azidodinoseb, this can best be seen in photosystem II preparations (17). Thus, the phenolic herbicides bind predominantly to the photosystem II reaction center, which might explain many of the differences observed between "DCMU-type" and phenolic herbicides (9). The photosystem II reaction center proteins and the 34 kDa herbicide binding protein must be located closely to and interact with each other in order to explain the mutual displacement of both types of herbicides (8,12,21). Furthermore, it should be noted that for phenolic herbicides, some effects at the donor side of photosystem II (22) and on carotenoid oxidation in the photosystem II reaction center have been found (23). 

The distribution of a compound in the human body can also be partially related to the absorption properties. There are specific transport systems that are expressed in certain tissues that can influence the distribution of the compound. For example, rosuvastatin, a new member of the statin family is transported by the OATP-C carrier system, which is selectively expressed in the liver, making this compound selectively distributed into this organ [27]. In general it is not possible to derive computational models for these selective transport systems since there is not yet enough experimental information and data to support the model building and validation. Nevertheless, there are three properties that are commonly used to describe the distribution of a compound in the human body the solubility, the unspecific binding of the compound to plasma proteins and the volume of distribution. 

Figure 11. Strategy for Affinity-Pulldown. Differentiation of true binding proteins and unspecific binding background by 0-labeling (for details cf text). Reprinted with permission from Mirgorodskaya et al. (2005b). Copyright 2005 American Chemical Society.

Since many proteins exhibit some unspecific binding to nucleic acids, it is crucial to include appropriate controls. In investigations of protein binding to immobilised RNA a control in which the RNA is replaced with an unrelated or mutated RNA is often used. 

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