, 2013) or SABIO-RK (Wittig et al., 2012) to obtain the appropriate references along with the functional enzyme data and to enter these data in a spread sheet. After the compilation of all relevant data you will make the
surprising discovery that the functional data is fragmented Navitoclax ic50 in such a way that for particular enzymes there are no published data at all, or that they exist but span an excessively broad range. For example, Km values from the literature (as stored, for example, in BRENDA) may have been measured at pH values from 3 to more than 10, and at temperatures from 0 to more than 100 °C. This is clearly not the fault of curators of these databases, but arises from the inadequacy of the data in the literature,
since the functional data were extracted from publications in primary biochemistry journals. Imagine another researcher who characterizes the ATP-coupled transport of ions across biological membranes. Usually these transporters are ion pumps that couple the transport of, for example, protons across the plasma membrane or intra-cellular membranes of compartments such as lysosomes or vacuoles against chemo-osmotic gradients to the hydrolysis of ATP. Among other issues regarding the catalytic properties of this enzyme, in particular, the thermodynamic coupling PF-02341066 in vitro ratio is the relationship of the number of ATP molecules hydrolyzed per number of ions transported in the focus of research (Rea and Sanders, 1987). This ratio is calculated as a function of ΔG
and both the transport of charges and equilibrium reaction of the hydrolysis of ATP (see for example Kettner et al., 2003). However, this calculation requires the value of the apparent equilibrium constant of the ATP hydrolysis, KATP, which depends on a number of parameters such as the pH and the concentrations of Mg2+, K+ and Ca2+ ( Alberty, 1968 and Rosing and Slater, 1972). When the calculations have been done our imaginary researcher wants to know whether his coupling ratios are consistent with those previously published with other organisms. However, he fails, despite finding coupling ratios in biochemical or biophysical papers, either because the calculations are not available or because they are insufficiently set out in the Materials and Methods section of the papers. Oxalosuccinic acid Thus, he can neither understand the published values nor compare his results with the published ones. These two following examples demonstrate the dilemma of protein functional data: Even though there are few projects that collect and organize functional and kinetic enzyme data such as the BRENDA database for enzyme functions and properties, SABIO-RK for biochemical reactions within metabolic pathways, KEGG, BioCyc (Caspi et al., 2010), and BioCarta for the representation of metabolic pathways, the availability of comparable functional enzyme data is limited or sometimes non-existent.