Conformational flexibility of enzyme active sites

Effects of pH and KCl on the conformations of creatine kinase from rabbit muscle. Infrared, circular dichroic and fluorescence studies

The activity loss of creatine kinase (CK), observed at low pH (midpoint was 4.8) corresponded to the monomerization of the dimeric protein and was correlated with structural changes. The acid-induced unfolding was not complete at this pH, as probed by circular dichroic (CD) and fluorescence methods. Further decrease of pH, led to a second transition (midpoint was pH 3.5). The loss of activity was irreversible at pH 4.8 (< 20% native activity was recovered) while it was almost fully reversible (> 90% of native activity was recovered) for the enzyme incubated at pH 0.9-2.5. The amount of intermolecular beta-sheets (monitored with the 1620 cm-1 infrared component band) was maximal when the enzyme was incubated at pH 4.8, as a consequence of protein aggregation, while it was minimal at extremes of pH and at low ionic strength. Acid-induced and alkaline-induced denaturations promoted different structural changes, leading to distinct partially unfolded conformational states. The addition of KCl (from 0.05 M to 0.5 M) to an acidic solution of monomeric creatine kinase (pH 1.6) resulted in a highly cooperative transition from the partially unfolded conformation (UA) to the more compact conformation (A) with the properties of a molten globule, as probed by CD spectra and by fluorescence. The formation of intermolecular beta-sheets in the compact conformation was observed by infrared spectroscopy, indicating formation of unstable aggregates.

Activation of chicken liver dihydrofolate reductase in concentrated urea solutions

The activation and inactivation of dihydrofolate reductase from chicken liver during denaturation in a wide concentration range of urea are compared with changes in intrinsic fluorescence. At 2 M urea the enzyme is activated 3.6-fold and is stable up to 12 h in the activated form. At 4 M urea, the enzyme activity increases about 5-fold initially but the activated enzyme loses activity rapidly to a level well below that of the native enzyme. The activated enzyme is stabilized in presence of either DHF or NADPH. The Kd and Km of the enzyme for the substrates at various urea concentrations were determined and compared. In the presence of 3 M urea, the values of Kd for DHF and NADPH increase 4-fold and 10-fold, respectively, whereas the corresponding Km values increase 25-fold and 3-fold. A large increase in Vmax is mainly responsible for the activation. The inactivation and unfolding in urea are both biphasic processes. For the fast phase, the rate constant of inactivation is 10-fold greater than that of unfolding in 4 M urea. The effect of (NH4)2SO4 on the activation and unfolding of the enzyme was also studied. The results suggest that the active site of the enzyme is more easily perturbed by denaturants; and the activated enzyme appears to have a more open and flexible conformation at the active site, which is favorable for the full expression of the catalytic power of the enzyme. A scheme for the sequential activation and inactivation of DHFR accompanying its unfolding by increasing concentrations of urea is proposed.

Unfolding, conformational change of active sites and inactivation of creatine kinase in SDS solutions

It has been reported that inactivation occurs before noticeable conformational change can be detected during denaturation of creatine kinase (ATP: creatine N-phosphotransferase, EC 2.7.3.2) and other enzymes by guanidinium chloride or urea. Therefore, Tsou suggested that enzyme active sites may display more conformational flexibility than the enzyme molecules as a whole [Tsou (1986) Trends Biochem. Sci. 11, 427-429; Tsou (1993) Science 262, 380-381]. In this study, the conformational change of the active site, the unfolding of the whole molecule and the inactivation of creatine kinase in solutions of different concentrations of SDS are compared. The results show that, at low SDS concentrations, the conformational change of the active site and inactivation of the enzyme occur to nearly the same extent. However, both of these changes occur at much lower concentrations of SDS than required to significantly unfold the enzyme molecule. The rates of conformational changes of enzyme active sites are markedly faster than those of inactivation. However, at the same SDS concentration, both the inactivation rate and the rate of the active site conformational change are much faster than that of the unfolding of the enzyme molecule as a whole. The above results provide direct evidence of the flexibility of the active site of creatine kinase.

Inactivation and unfolding of aminoacylase during denaturation in sodium dodecyl sulfate solutions

During denaturation by sodium dodecyl sulfate (SDS), aminoacylase shows a rapid decrease in activity with increasing concentration of the detergent to reach complete inactivation at 1.0 mM SDS. The denatured minus native-enzyme difference spectrum showed two negative peaks at 287 and 295 nm. With the increase of concentration of SDS, both negative peaks increased in magnitude to reach maximal values at 5.0 mM SDS. The fluorescence emission intensity of the enzyme decreased, whereas there was no red shift of emission maximum in SDS solutions of increasing concentration. In the SDS concentration regions employed in the present study, no marked changes of secondary structure of the enzyme have been observed by following the changes in far-ultraviolet CD spectra. The inactivation of this enzyme has been followed and compared with the unfolding observed during denaturation in SDS solutions. A marked inactivation is already evident at low SDS concentration before significant conformational changes can be detected by ultraviolet absorbance and fluorescence changes. The inactivation rate constants of free enzyme and substrate-enzyme complex were determined by the kinetics method of the substrate reaction in the presence of inactivator previously described by Tsou [Tsou (1988), Adv. Enzymol. Related Areas Mol. Biol. 61, 381-436]. It was found that substrate protects against inactivation and at the same SDS concentrations, the inactivation rate of the free enzyme is much higher than the unfolding rate. The above results show that the active sites of metal enzyme containing Zn2+ are also situated in a limited and flexible region of the enzyme molecule that is more fragile to denaturants than the protein as a whole.

Comparison of inactivation and conformational changes of aminoacylase during guanidinium chloride denaturation

The inactivation and unfolding of aminoacylase (EC 3.5.1.14) during denaturation by different concentrations of guanidinium chloride (GuHCl) have been compared. A marked decrease in enzyme activity is already evident at low GuHCl concentrations before significant unfolding of the enzyme molecule, as monitored by fluorescence, ultraviolet difference absorption and CD measurement. The kinetic theory of the substrate reaction during irreversible inhibition of enzyme activity previously described by Tsou has been applied to a study on the kinetics of the course of inactivation of aminoacylase during denaturation by GuHCl. The inactivation rate constants of free enzyme and substrate-enzyme complex were determined by Tsou's method. The inactivation reaction kinetics were found to be a monophasic first-order reaction. The kinetics of the unfolding were a bisphasic process consisting of two first-order reactions. At lower GuHCl concentration (< 1.0 M), the enzyme activity was stripped at a high rate whereas its conformation was only slightly affected. At 1.0 M GuHCl, the inactivation rate of the enzyme was much faster than the unfolding rate. At higher GuHCl concentrations (> 1.0 M), the inactivation rate was too fast to be measured by conventional dynamic methods, whereas the unfolding remained as a bisphasic process with the fast reaction accruing very fast and the slow reaction occurring at a measurable rate. The results suggest that active sites of aminoacylase containing Zn2+ ions are situated in a limited region of the enzyme molecule that is more fragile to denaturants than the protein as a whole.

Inactivation during denaturation of ribonuclease A by guanidinium chloride is accompanied by unfolding at the active site

Inactivation of pancreatic RNAase A occurs in guanidinium chloride (GdmCl) at low concentrations before the unfolding of the molecule as a whole can be detected [Liu and Tsou (1987) Biochim. Biophys. Acta 916, 455-464]. We have now shown that the rate of digestion of the RNAase molecule by either trypsin or proteinase K increases significantly at low concentrations of GdmCl where the enzyme is largely inactivated, but fluorescence and absorption measurements reveal no conformational changes. N-Terminal sequence analysis of the peptide fragments generated shows that proteolysis occurs primarily at or near the active site. The decrease in activity of RNAase at low concentrations of GdmCl is therefore due to partial unfolding of the molecule, particularly at the active site and not to an inhibition by the denaturant.

Equilibrium unfolding studies of horse muscle acylphosphatase

The stability and equilibrium unfolding behaviour of horse muscle acylphosphatase have been studied by denaturing the protein under various conditions of temperature, pH, and urea concentration. Far-ultraviolet circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy indicate that this small monomeric protein unfolds reversibly and cooperatively. Thermodynamic parameters, the Gibbs free energy delta G and enthalpy delta H of unfolding, have been estimated for denaturation of the protein from NMR and CD data as 19 kJ mol-1 and 350 kJ mol-1, respectively. CD and 1H-NMR results suggest the presence of very little persistent residual structure in the denatured states studied under these different conditions. Furthermore, photo-chemically induced dynamic nuclear polarisation experiments show that in the denatured states aromatic residues are freely accessible to a flavin dye probe.

Inactivation precedes changes in allosteric properties and conformation of D-glyceraldehyde-3-phosphate dehydrogenase and fructose-1,6-bisphosphatase during denaturation by guanidinium chloride

It has been shown that inactivation of several enzymes precedes overall conformational changes of the enzyme molecules as a whole during denaturation [Tsou (1993) Science, 262, 380-381]. However, the relation between inactivation, loss of allosteric properties of oligomeric enzymes and unfolding of the enzyme molecule during denaturation remain little explored. These have now been compared for D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and fructose-1,6-bisphosphatase (FruP2ase) during denaturation by guanidinium chloride (GdmCl). GAPDH is completely inactivated at 0.3 M GdmCl but at this GdmCl concentration it still binds NAD+ with negative co-operativity. At 0.4 M GdmCl, inactivation of FruP2ase reaches completion whereas its allosteric properties, including the heterotropic effect of AMP inhibition and K+ activation with positive co-operativity, are only partially affected. Much higher GdmCl concentrations are required to bring about unfolding of the overall structures of both enzymes.