Protein biological variability

Alterations in the protein pattern are immanent for mammalian body fluids or tissues. Differential expression profiles for the comparison of distinct samples are to be expected due to the biological variability related to patient age, gender or lifestyle. In order to distinguish disease-related features from false-positive differences the critical validation and assessment of putative markers is of fundamental importance (Zolg and Langen, 2004). 

Using the criteria that abimdances are altered by at least twofold, 12 proteins of interest were identified in the nucleus and 15 in the plasma membrane of mitoxantrone-resistant MCF-7 cells. These are listed in Tables 13.1 and 13.2. Experimental variation in Table 13.1 is based on isotope ratio determinations of peptides from at least three gels, each from three separate cultures, thus incorporating both biological variability and experimental uncertainty. Experimental variation in Table 13.2 is based on isotope ratios measured for multiple peptides for each protein, from three separate cultures. 

The proportion of a-helix in native proteins is variable and sometimes not very great. It is a mistake to over emphasize its role in interfacial structures, but where it is present its radial distribution of side chains means that its orientation in the interface will be governed by its over-all hydrophobicity. The presence of hydrophobic groups directed into the water is then possible as well as others contributing to cohesion between adjacent molecules as in the monolayers considered here. Those directed into the water may function as sites for the binding of other molecules in the aqueous phase. This is also a possibility for the p conformation but not for extended chain conformations where under pressure the hydrophobic side chains are directed away from the surface and the hydrophilic ones into the water. While this latter model has been accepted by surface chemists 37), the conformation appears unlikely both from a biological and a stereochemical standpoint. Indeed except where there is a regular alternation of hydrophobic and hydrophilic side chains, the conformation is probably not one acceptable within the usual criteria for polypeptide structures (5). 

Biological variability A correction factor of 25%, which was based on statistical considerations, was used to increase the calculated protein requirement to yield the RDA. The 25% correction results in a value for the requirement that would be expected to meet the needs of 97.5% of a normal population. With this correction, an RDA of 0.8 g protein/kg body weight for the adult was calculated (Food and Nutrition Board, 1989). 

Table 2.4 presents some, but probably not all, physical, chemical, and biological variables that may influence to a greater or lesser extent the crystallization of proteins. The difficulty in properly arriving at a just assignment of importance for each factor is substantial for several reasons. Every protein is different in its properties, and surprisingly perhaps, this applies even to proteins that differ by no more than one or just a few amino acids. There are even cases where the identical protein prepared by different procedures or at different times show significant variations. In addition each factor may differ considerably in importance for individual proteins. 

To evaluate assay performance, a set of VS prepared independently of the standards is used. At least five concentrations VS should be prepared, including the target LLOQ and ULOQ, low QC ( 3 times of the LLOQ), mid-QC, and high QC (—75 % of the ULOQ). Accuracy and precision can be evaluated from the total error (the sum of bias and precision) of VS data from the qualification runs in a similar way as for macromolecular protein drugs [17]. Given biological variability and other factors in biomarker research, more lenient acceptance criteria may be used for biomarker PD than for PK studies. Still, it should be recognized that accuracy and precision data of VS in buffer provide only a relative quantification, which may be quite different from measurements in the authentic matrix. 

CVp data taken from Kafonek SD, Derby CA, and Bachorik PS (1992) Biological variability of lipoproteins and apolipo-proteins in patients referred to a lipid clinic. Clinical Chemistry 38 864-872. 

Human hair is usually categorised ethnically into three major distinct groups Asian, Caucasian and African. Looking from the perspective of biological variability, environmental effects and diversity of fibre texture, it is remarkable how uniformly the amino acid makeup of protein components is across ethnic groups. The amino acid makeup of the protein components was reviewed by Wolfram and is depicted in Fig. 1 [1, 2, 18, 19]. 

Numerous quantitative structure-activity relationships have been derived for enzyme inhibitors, in some cases also for substrates. " Such in vitro data can be most easily correlated with physicochemical properties because binding or substrate behavior is not influenced by transport and other processes, such as absorption, distribution, metabolism, and/or elimination (the so-called ADME parameters). In addition, the precision and reproducibility of in vitro studies are much better than of animal studies because biological variability is eliminated. In some cases, the results of QSAR studies could be compared with protein 3D structures. " ... 

Abstract The entry of viruses into target cells involves a complex series of sequential steps, with opportunities for inhibition at every stage. Entry inhibitors exert their biological properties by inhibiting protein-protein interactions either within the viral envelope (Env) glycoproteins or between viral Env and host-cell receptors. The nature of resistance to entry inhibitors also differs from compounds inhibiting enzymatic targets due to their different modes of action and the relative variability in... 

The development of biological tools to support DDI studies has paralleled the development of bioanalytical techniques. To better understand in vitro-in vivo (IVIV) correlations, the effects of differences in enzyme preparations and incubation conditions must be understood. Differences between enzyme preparations include nonspecific binding, the ratio of accessory proteins (cytochrome b5 and reductase) to CYPs and genetic variability differences in incubation conditions include buffer strength, the presence of inorganic cations and solvent effects. Understanding how biology influences enzymatic activity is crucial to accurate and consistent prediction of the inhibition potential. 

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