Biomedical subjects

I Knack

Publications and source records attributed to I Knack.

4 recordsLinked to original sources

PubMed1981

Microcomputers in enzymology. A versatile BASIC computer program for analyzing kinetic data.

Direct curve-fitting is uncontested as the method of choice for evaluating kinetic experiments. If carried out by computer, the numerical solution of such problems is superior to customary graphical procedures in any respect. However, most programs available to date, cannot be executed by small systems. We now describe a BASIC program for desk-top microcomputers that performs linear and non-linear regression analysis of kinetic data. It may be directly applied to a number of problems common in enzyme kinetics, and is easily modified to handle further ones. The performance of the program is illustrated by some typical applications; in addition, fundamental statistical methods are discussed that allow a critical examination of the results obtained.

Aminopeptidases↗

PubMed1980

The evaluation of non-hyperbolic ligand binding and substrate saturation data using variable Hill coefficients.

A fitting method for saturation curves is described that may be applied to any kind of ligand binding process, regardless of whether positive, negative or mixed cooperativity is involved. The procedure yields 'best values' of maximal saturation (or maximal velocity with enzymes); in addition, an empirical function is calculated that represents the concentration dependence of the Hill slope (i.e. the slope of the corresponding Hill plot). Since the method does not require the maximal saturation to be known in advance, it can be successfully applied to systems which, due to experimental limitations, may not be saturated with ligand. It is shown that in these cases values of maximal saturation are obtained that are considerably more reliable than those estimated by customary methods. Moreover, it is demonstrated that the concentration dependence of the Hill slope, the other main result of the proposed procedure, may offer useful evidence as to the molecular events leading to non-hyperbolicity and thus provide a rational basis for selecting more specific models to describe the properties of the system studied.

Humans↗

PubMed1978

Yeast dipeptidase: active site mapping by kinetic studies with substrates and substrate analogs.

In order to characterize the active site of yeast dipeptidase in more detail, kinetic studies with a variety of dipeptide substrates and substrate analogs were performed. To analyze kinetic data, computer programs were developed which first calculate initial velocities from progress curves and then evaluate the kinetic parameters by nonlinear regression analysis. A free carboxyl group is a prerequisite for binding of dipeptidase substrates; its position relative to the peptide bond must not deviate from the normal L-dipeptide conformation. The spatial arrangement of the terminal ammonium ion seems to be less crucial. The enzyme's substrate specificity clearly reflects the interactions of the substrate amino acid side chains with complementary dipeptidase subsites. The domain of the enzyme in contact with the C-terminal substrate side chain seems to be an open structure of moderately hydrophobic character. In contrast, the binding site for the amino-terminal side chain is a more strongly hydrophobic "pocket" of limited dimensions. The kinetics of inhibition by free amino acids points to an ordered release of products from the enzyme.

Amino Acids↗

PubMed1978

Studies of ligand binding to cholera toxin, III. Cooperativity of oligosaccharide binding.

Binding parameters for the interaction of cholera toxin and choleragenoid with monosialo-gangliotetraose, the oligosaccharide moiety of ganglioside II3 NeuAc-GgOse4-Cer, have been measured by equilibrium displacement dialysis. The experimental data were evaluated by a curve fitting computer program. The binding curves obtained at 6 degrees C reflected positive cooperativity with average Hill coefficients in the range of 1.16 to 1.25. The cholera toxin as well as its ganglioside-binding protomer B-protein bind 4 mol of monosialogangliotetraitol per mol of protein. The presence of disulfide-cleaving agents like 2-mercaptoethanol did not eliminate the cooperativity of the binding characteristics, but increased the Hill coefficient.

Cholera Toxin↗