Small-angle X-ray scattering on malate synthase from baker's yeast. The native substrate-free enzyme and enzyme-substrate complexes

Enhanced Diffusion of Catalytically Active Enzymes

The past decade has seen an increasing number of investigations into enhanced diffusion of catalytically active enzymes. These studies suggested that enzymes are actively propelled as they catalyze reactions or bind with ligands (e.g., substrates or inhibitors). In this Outlook, we chronologically summarize and discuss the experimental observations and theoretical interpretations and emphasize the potential contradictions in these efforts. We point out that the existing multimeric forms of enzymes or isozymes may cause artifacts in measurements and that the conformational changes upon substrate binding are usually not sufficient to give rise to a diffusion enhancement greater than 30%. Therefore, more rigorous experiments and a more comprehensive theory are urgently needed to quantitatively validate and describe the enhanced enzyme diffusion.

Energy-dispersive small-angle X-ray scattering with cone collimation using X-ray capillary optics

Energy-dispersive small-angle X-ray scattering (ED-SAXS) with an innovative design of cone collimation based on an ellipsoidal single-bounce capillary (ESBC) and a polycapillary parallel X-ray lens (PPXRL) had been explored. Using this new cone collimation system, scattering angle 2θ has a theoretical minimum angle related to the mean half-opening angle of the hollow cone beam of 1.42 mrad, and with the usable X-ray energy ranging from 4 to 30 keV, the resulting observable scattering vector q is down to a minimum value of about 0.003 Å^-1 (or a Bragg spacing of about 2100 Å). However, the absorption of lower energies by X-ray capillary optics, sample transmission, and detector response function limits the application range to lower energy. Cone collimation ED-SAXS experiments carried out on pure water, Lupolen, and in situ temperature-dependent measurement of diacetylenic acid/melamine micelle solid were presented at three different scattering angles 2θ of 0.18°, 0.70° and 1.18° to illustrate the new opportunities offered by this technique as well as its limitations. Also, a comparison has been made by replacing the PPXRL with a pinhole, and the result shows that cone collimation ED-SAXS based on ESBC with PPXRL was helpful in improving the signal-to-noise ratio (i.e., reducing the parasitic background scattering) than ESBC with a pinhole. The cone collimation instrument based on X-ray capillary optics could be considered as a promising tool to perform SAXS experiments, especially cone collimation ED-SAXS has potential application for the in situ temperature-dependent studying on the kinetics of phase transitions.

Ligand binding on to maize (Zea mays) malate synthase: a structural study

A kinetic and ligand binding study on maize (Zea mays) malate synthase is presented. It is concluded from kinetic measurements that the enzyme proceeds through a ternary-complex mechanism. Michaelis constants (Km,glyoxylate and Km,acetyl-CoA) were determined to be 104 microM and 20 microM respectively. C.d. measurements in the near u.v.-region indicate that a conformational change is induced in the enzyme by its substrate, glyoxylate. From these studies we are able to calculate the affinity for the substrate (Kd,glyoxylate) as 100 microM. A number of inhibitors apparently trigger the same conformational change in the enzyme, i.e. pyruvate, glycollate and fluoroacetate. Another series of inhibitors bearing more bulky groups and/or an extra carboxylic acid also induce a conformational change, which is, however, clearly different from the former one. Limited proteolysis with trypsin results in cleavage of malate synthase into two fragments of respectively 45 and 19 kDa. Even when no more intact malate synthase chains are present, the final enzymic activity still amounts to 30% of the original activity. If trypsinolysis is performed in the presence of acetyl-CoA, the cleavage reaction is appreciably slowed down. The dissociation constant for acetyl-CoA (Kd,acetyl-CoA) was calculated to be 14.8 microM when the glyoxylate subsite is fully occupied by pyruvate and 950 microM (= 50 x Km) when the second subsite is empty. It is concluded that malate synthase follows a compulsory-order mechanism, glyoxylate being the first-binding substrate. Glyoxylate triggers a conformational change in the enzyme and, as a consequence, the correctly shaped binding site for acetyl-CoA is created. Demetallization of malate synthase has no effect on the c.d. spectrum in the near u.v.-region. Moreover, glyoxylate induces the same spectral change in the absence of Mg2+ as in its presence. Nevertheless, malate synthase shows no activity in the absence of the cation. We conclude that Mg2+ is essential for catalysis, rather than for the structure of the enzyme's catalytic site.

Primary and post-irradiation inactivation of the sulfhydryl enzyme malate synthase: correlation of protective effects of additives

The presence of additives during X-irradiation of malate synthase led to radioprotective effects against primary and post-irradiation inactivation. Pronounced effects were provided by typical scavengers, sulfhydryl reagents and specific ligands (substrates, products, analogues). The results show that scavenging and specific protection are responsible for the protective efficiency of additives. Scavengers delete noxious species formed during irradiation or post-radiationem. Sulfhydryl reagents may act as repair substances. Specific ligands protect the active site of the enzyme and the essential sulfhydryls; specific protection is more pronounced post-radiationem. Ligands and sulfhydryl reagents may additionally act as scavengers. A cumulative index for the protective power of additives against both sorts of inactivation was established.

Post-irradiation inactivation of the sulfhydryl enzyme malate synthase

The sulfhydryl enzyme malate synthase was inactivated in air-saturated aqueous solution by X-irradiation (2 kGy). Changes of activity were registered up to 60 h after irradiation. Effects of specific additives (formate, superoxide dismutase, catalase), added before and/or after irradiation, revealed the role of the deleterious radical and non-radical species responsible for the radiation damage: inactivation during irradiation is mainly due to the action of OH, to a minor extent to O(2) and H2O2; post-irradiation inactivation is mainly caused by H2O2. A partial restoration of enzyme activity by dithiothreitol, added after irradiation, was found for all systems investigated; repairs were significant even when they were initiated 60 h after irradiation.

Small-angle X-ray scattering study of adenosine triphosphatase from thermophilic bacterium PS3

Adenosine triphosphatase from the thermophilic bacterium PS3(TF1) has been studied by solution X-ray scattering. A structural change in TF1 caused by the binding of ADP was observed by examining the difference between the radii of gyration of the unligated and ligated forms. The radius of gyration of the unligated TF1 was found to be 49.5 +/- 0.3 A, and it decreased by approximately 3% after ligation with ADP. The positions and the amplitudes of a subsidiary maximum and a shoulder in the scattering profile showed subtle change on nucleotide binding. The lower limit of the maximum length of TF1 was determined to be 165 A for the unligated form and 150 A for the ligated form. The shape analysis of TF1 was performed by model calculations for simple triaxial bodies or their complexes. Among the various models tested, the one that gave the best fit with the experimental data consisted of seven ellipsoids of revolution; six identical ellipsoids with semi-axes: a = b = 18.5 A and c = 74 A. arranged hexagonally, and the other with a = b = 28 A and c = 45 A, located below the other six on the 6-fold axis. On the basis of this model it was suggested that there is a structural change on ligation with nucleotides, consisting of a shrinkage of the six long ellipsoids by 6% along their major axes.

Large-scale purification and some properties of malate synthase from baker's yeast

1. Malate synthase from baker's yeast (5 kg) was purified 400--500-fold to homogeneity. About 50--200 mg homogeneous enzyme were obtained within a week in a yield of 30% with reference to the total activity in cell-free crude extracts. The enzyme, pI = 7.5, was pure as judged from ultracentrifugal and gel electrophoretic studies. 2. Sedimentation and diffusion coefficients were determined: S 0 20,w = 8.26 +/- 0.05 S, D 0 20,w = 4.5 +/- 0.1 X 10(-7) cm2 s-1. The molecular weight of the synthase was found to be 175 000 +/- 10 000 and 180 000 +/- 10 000 by sedimentation/diffusion and by high-speed sedimentation equilibrium respectively. It was concluded from these and other results that malate synthase has a molecular mass of 180 000 +/- 10 000. 3. The synthase on sodium dodecylsulfate gel electrophoresis was dissociated to yield a single specimen of Mr about 66 000. The result indicates a composition of the native enzyme from three subunits of identical or nearly identical mass. 4. The binding of acetyl-coenzyme A to the synthase is independent of Mg2+ but that of glyoxylate is strictly dependent on the presence of Mg2+. Kinetic studies indicate that the malate synthase reaction follows a sequential random mechanism. 5. The intermolecular isotopic effect, kH:k2H = 1.4, was determined with acetyl-coenzyme A and [2H3]acetyl-coenzyme A under several different experimental conditions and was shown to reflect different maximal velocities of the two substrates. An enzymic procedure for the preparation of doubly labelled [3H, 14C]acetyl-coenzyme A is also presented.