Protein variations

Highton, R. and Peabody, R.B. (2000) Geographic protein variation and speciation in salamanders of the Plethodon jordani and Plethodon glutinosus complexes in the southern Appalachian Mountains with the descriptions of four new species. In R.C. Bruce, R.G. laeger, and L.D. Houck. (Eds.) The biology of plethodontid salamanders. Plenum, New York, pp. 31-94. 

Larson, A. and Highton, R. (1978) Geographic protein variation and divergence of the salamanders in the Plethodon welleri group (Amphibia Plethodontidae). Syst. Zool. 27, 431 —448. 

With the advent of protein sequencing, also in the 1950s, attempts were made to study protein variation directly on the primary structure. However, the method was very expensive and time-consuming and could not be applied to population genetics. It remained confined to evolutionary study of differences between species (applied to molecular phylogenetics) and to the demonstration of sequence mutation in important heritable diseases. 

The protein-to-protein variation in the amount of color produced with the BCA Protein Assay Reagent (CV = 15% for the group of 14 proteins at 1000 pg/ml in the standard tube protocol) is similar to that observed for the modified Lowry protein assay reagent. 

Each protein in a sample is unique and can demonstrate that individuality in protein assays as variation in the color response. Such protein-to-protein variation refers to differences in the amount of color (absorbance) that are obtained when the same mass (microgram or milligram) of various proteins are assayed concurrently (i.e., in the same run) by the same method. These differences in color response relate to differences among proteins due to amino acid sequence, isoelectric point (pi), secondary structure, and the presence of certain side chains or prosthetic groups. 

To analyze protein-to-protein variation for each method, a group of fourteen proteins was assayed in duplicate using the standard tube protocol in a single run. The net (blank corrected) average absorbance for each protein was calculated. To make it easier to interpret, the net absorbance for each protein was expressed as a ratio to the net absorbance for BSA. If a protein has a ratio of 0.80, it means that the protein produces -80% of the color that is obtained for an equivalent mass of BSA. 

Table B1.1.5 demonstrates the relative degree of protein-to-protein variation that can be expected with the different protein assay methods. This differential may be a consideration in selecting a protein assay method, especially if the relative color response ratio of the protein in the samples is unknown. As expected, the protein assay methods that share the same basic chemistry show similar protein-to-protein variation.

The protein-to-protein variation observed with the various protein assay methods makes it obvious why the largest source of error for protein assays is the choice of protein for the standard curve. If the sample contained IgG as the major protein and BSA was used for the standard curve, the estimated total protein concentration of the sample will be inaccurate. Whether the concentration was underestimated or overestimated depends upon which total protein assay method was used. If the Coomassie... 

The protein-to-protein variation in color response was measured at 1000 pg/ml for each protein in duplicate using the standard tube protocol. Within each assay, the average net or blank corrected absorbance was determined for each protein. The average net absorbance for each protein was divided by the average net absorbance obtained with BSA and expressed as a ratio. The standard deviation (SD) and the coefficient of variation (CV) is presented for the fourteen proteins assayed on the three methods. By comparing the CV s. the relative degree of protein-to-protein variation to be expected with the three methods can be assessed. 

While Table B1.1.5 is useful because it provides an estimate of the protein-to-protein variation in color response that can be expected with each method, it does not tell the whole story. Because the comparisons were done at a single protein concentration, it is not apparent that the color response ratio also varies with changes in protein concentration. 

A modified biuret reagent was formulated (sodium tartrate replaces sodium potassium tartrate, the sodium hydroxide concentration is reduced, and potassium iodide was deleted). When the modified biuret reagent was mixed with samples containing 2% detergent (SDS or sodium cholate or Triton X-I00), it resulted in less protein-to-protein variation among six proteins. 

Willett C. S. and Harrison R. G. (1999a) Insights into genome differentiation pheromonebinding protein variation and population history in the European com borer (Ostrinia nubilalis). Genetics 153, 1743-1751. 

Diferent proteins variation in the degree of phosphorylation, glycosylation, hydrophobicity and amphipathic structures. 

T4 and Ta circulate in the blood as equilibrium mixtures of free and protem-bound hormones. Thus changes in the concentration or affinity of TBG or other transport proteins profoundly affect the total hormone concentration in serum. Alternatively the steady-state concentration of the free hormone is independent of these binding protein variations and remains almost constant. 

Protein variations and analysis of synonymous and nonsynonymous base substitutions + ... 

Protein Variations, Codon, and Amino Acid Usage... 

It must be conceded that the concentration dependence given by this simple theory is very good, particularly at the higher concentrations. The excellent agreement of the numerical value of the derived and actual values of r indicate that the essence of the protein-protein interactions is contained in the theory the protein-protein interaction is dominated by hydrodynamic effects, rather than electrostatic interactions, for example. The latter can fall off more slowly with distance and may be responsible for the deviations of the model fit at low concentrations of protein. Variations in with protein charge (i.e., pH) for fixed concentration have been observed by NMRD (12) the effective interactions are maximum near the isoelectric point. It is here that the fluctuations in interprotein separation at fixed protein concentration are greatest protein molecules can approach more closely than when they are charged. Our simple model clearly does not include these second order effects. 

The expanding availability of information on genetic sequences, polymoiphisms, SNPs, protein variations and interactions, metabolic and phenotypical variants as well as the sensor technologies plus micro- and nanotechnologies in combination with the communication network spanning the globe will allow increasingly precise measurements of the ... 

Finally, the realization that gene-protein variations contribute to most common diseases leads to efforts of creating new drugs that act on these variants. 

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