A radiation target method for size determination of supercoiled plasmid DNA.

Supercoiled DNA plasmids were exposed in the frozen state to high-energy electrons. Surviving supercoiled molecules were separated from their degradation products (e.g., open circle and linear forms) by agarose gel electrophoresis and subsequently quantified by staining and image analysis. Complex survival curves were analyzed using radiation target theory, yielding the radiation-sensitive mass of each form. One of the irradiated plasmids was transfected into cells, permitting radiation analysis of gene expression. Loss of this function was associated with a mass much smaller than the entire plasmid molecule, indicating a lack of energy transfer in amounts sufficient to cause structural damage along the DNA polynucleotide. The method of radiation target analysis can be applied to study both structure and function of DNA.

Radiation inactivation of glutamate dehydrogenase hexamer: lack of energy transfer between subunits.

The effects of ionizing radiation on glutamate dehydrogenase and on fluorescein isothiocyanate--tagged glutamate dehydrogenase were analyzed by target theory. Enzymatic activity, fluorescence, and the survival of the 56,000-dalton monomer subunit were determined on frozen samples irradiated at -135 degrees C and on lyophilized samples irradiated at either -135 degrees C or +30 degrees C. The effects of temperature were the same for all three parameters. Enzymatic activity was lost after small doses of high-energy electrons, whereas fluorescence and monomer subunits survived much larger doses of radiation. Target analysis revealed that the functional unit size for enzymatic activity was the hexamer, confirming both the earlier radiation study and conventional biochemical analyses. Target sizes obtained from fluorescence and subunit structure measurements were close to that of the monomer. These results indicate that the primary ionization caused by electron bombardment results in damage to a single polypeptide strand and that there is no massive transfer of radiation energy to other units in the hexamer. The large target size observed for enzymatic activity appears to be a structural requirement for the simultaneous presence of six intact subunits rather than the result of the spread of energy from the initial site to adjacent chains with consequent damage to other subunits.

Amino acid coding in Sarcina lutea and Saccharomyces cerevisiae.

Aminoacyl-tRNA's from Sarcina lutea were tested for incorporation into protein in a heterologous system from Escherichia coli or for biniding in a homologous system from Sarcina lutea. Aminoacyl-tRNA's from Saccharomyces cerevisiae were tested for biniding in a homologous Saccharomyces cerevisiae system. Synthetic polyribonucleotides were used as messengers. The code which exists in Sarcina lutea and Saccharomyces cerevisiae is the same as in Escherichia coli.

Novel predictions from radiation target analysis.

The unusual technique of radiation inactivation has been used to determine the mass of many different macromolecules. Most of the radiation target sizes obtained agree with the known protein structures. However, in several cases the sizes obtained were not easily interpreted since they did not agree with values determined by more conventional methods. Subsequent studies have shown that many of these perplexing radiation target sizes were indeed correct, often revealing unanticipated details about the nature of the systems being studied.

Minimal functional unit for transport and enzyme activities of (Na+ + K+)-ATPase as determined by radiation inactivation.

Frozen aqueous suspensions of partially purified membrane-bound renal (Na+ + K+)-ATPase have been irradiated at -135 degrees C with high-energy electrons. (Na+ + K+)-ATPase and K+-phosphatase activities are inactivated exponentially with apparent target sizes of 184 +/- 4 kDa and 125 +/- 3 kDa, respectively. These values are significantly lower then found previously from irradiation of lyophilized membranes. After reconstitution of irradiated (Na+ + K+)-ATPase into phospholipid vesicles the following transport functions have been measured and target sizes calculated from the exponential inactivation curves: ATP-dependent Na+-K+ exchange, 201 +/- 4 kDa; (ATP + Pi)-activated Rb+-Rb+ exchange, 206 +/- 7 kDa and ATP-independent Rb+-Rb+ exchange, 117 +/- 4 kDa. The apparent size of the alpha-chain, judged by disappearance of Coomassie stain on SDS-gels, lies between 115 and 141 kDa. That for the beta-glycoprotein, though clearly smaller, could not be estimated. We draw the following conclusions: (1) The simplest interpretation of the results is that the minimal functional unit for (Na+ + K+)-ATPase is alpha beta. (2) The inactivation target size for (Na+ + K+)-dependent ATP hydrolysis is the same as for ATP-dependent pumping of Na+ and K+. (3) The target sizes, for K+-phosphatase (125 kDa) and ATP-independent Rb+-Rb+ exchange (117 kDa) are indistinguishable from that of the alpha-chain itself, suggesting that cation binding sites and transport pathways, and the p-nitrophenyl phosphate binding site are located exclusively on the alpha-chain. (4) ATP-dependent activities appear to depend on the integrity of an alpha beta complex.

Size of the catalytically active unit of rat hepatic carboxylester lipase in the presence and absence of bile salt.

Carboxylester lipase (CEL) catalyzes the hydrolysis of cholesteryl esters, retinyl esters, and triacylglycerols. CEL monomer has a MW of approximately 70000. Hydrolysis of these esters is stimulated by millimolar trihydroxy bile salts such as cholate, that also induce aggregation. Liver cytosols from 12 rats were frozen and irradiated at -135 degrees C with high energy electrons. In several experiments, paired samples of cytosol were adjusted to 20 mM cholate before irradiation. All samples were assayed for CEL using cholesteryl oleate as substrate. In untreated cytosols, CEL activity surviving radiation exposure could be fit to a single exponential function, the slope of which yielded a target size of 91 +/- 18 kDa. In a subset of these cytosols irradiated in the presence of cholate the calculated target size was 100 +/- 19 kDa, a value indistinguishable from that obtained for untreated cytosols. Some samples were also assayed using retinyl palmitate and triolein as substrates. With retinyl palmitate the mean target sizes were 96 and 108 kDa in the absence and presence of cholate, respectively, approximately the same as those observed when using cholesteryl oleate. When triolein was used as substrate the target sizes in the absence of cholate were smaller than for the other two esters (67 +/- 18 kDa) and closer to the known monomer molecular weight, but again cholate had no significant effect on this size. The structure responsible for CEL activity contains no more than one 70000 MW monomer and the results show that cholate-induced oligomerization is not required for catalytic activity.

Radiation inactivation studies of hepatic sinusoidal reduced glutathione transport system.

Sinusoidal transport of reduced glutathione (GSH) is a carrier-mediated process. Perfused liver and isolated hepatocyte models revealed a low-affinity transporter with sigmoidal kinetics (K(m) approximately 3.2-12 mM), while studies with sinusoidal membrane vesicles (SMV) revealed a high-affinity unit (K(m) approximately 0.34 mM) besides a low-affinity one (K(m) approximately 3.5-7 mM). However, in SMV, both the high- and low-affinity units manifested Michaelis-Menten kinetics of GSH transport. We have now established the sigmoidicity of the low-affinity unit (K(m) approximately 9) in SMV, consistent with other models, while the high-affinity unit has been retained intact with Michaelis-Menten kinetics (K(m) approximately 0.13 mM). We capitalized on the negligible cross-contributions of the two units to total transport at the low and high ends of GSH concentrations and investigated their characteristics separately, using radiation inactivation, as we did in canalicular GSH transport (Am. J. Physiol. 274 (1998) G923-G930). We studied the functional sizes of the proteins that mediate high- and low-affinity GSH transport in SMV by inactivation of transport at low (trace and 0.02 mM) and high (25 and 50 mM) concentrations of GSH. The low-affinity unit in SMV was much less affected by radiation than in canalicular membrane vesicles (CMV). The target size of the low-affinity sinusoidal GSH transporter appeared to be considerably smaller than both the canalicular low- and high-affinity transporters. The high-affinity unit in SMV was markedly inactivated upon irradiation, revealing a single protein structure with a functional size of approximately 70 kDa. This size is indistinguishable from that of the high-affinity GSH transporter in CMV reported earlier.

Radiation inactivation of binding sites for high-density lipoproteins in human liver membranes.

High-density lipoproteins (HDL) are involved in 'reverse cholesterol transport'. Whether or not cell-surface receptors for HDL exist and participate in this process remains controversial, and part of this controversy has centered on the nature of the HDL binding sites. We therefore used radiation inactivation to determine the molecular mass of the HDL binding sites in human liver membranes in situ. These binding sites, which shared all the characteristics of previously described putative HDL receptors, had a molecular mass of less than 10 kDa, indicating that they are probably not proteins. In addition, the binding of HDL to protein-free liposomes was characterized and was found to display the same affinity (KD = 5 micrograms protein/ml approximately 5.10(-8) M) as that to cell membranes, indicating that HDL binding to cell membranes may not require membrane proteins. These observations highlight an important application of radiation inactivation: the ability to demonstrate that something - in this case, a high-molecular-weight protein that accounts for the majority of the HDL binding activity in human liver membranes - is absent.

Movable lobes and flexible loops in proteins. Structural deformations that control biochemical activity.

Two classes of protein whose structure is modified by small ligands are reviewed. Proteins of one group contain two massive domains joined by a flexible link; in response to small molecules, the two lobes approach and enclose the ligand. In the other, a short segment of amino acids moves as a flexible loop over the ligand which often is trapped in a non-aqueous environment. Biochemical reaction rates are altered dramatically by these movements.

Radiation target analysis indicates that phenylalanine hydroxylase in rat liver extracts is a functional monomer.

The minimal enzymatically functional form of purified rat hepatic phenylalanine hydroxylase (PAH) is a dimer of identical subunits. Radiation target analysis of PAH revealed that the minimal enzymatically active form in crude extracts corresponds to the monomer. The 'negative regulation' properties of the tetrahydrobiopterin cofactor in both crude and pure samples implicates a large multimeric structure, minimally a tetramer of PAH subunits. Preincubation of the samples with phenylalanine prior to irradiation abolished this inhibition component without affecting the minimal functional unit target sizes of the enzyme in both preparations. The characteristics of rat hepatic PAH determined by studies of the purified enzyme in vitro may not completely represent the properties of PAH in vivo.

Structural studies of a human pi class glutathione S-transferase. Photoaffinity labeling of the active site and target size analysis.

The glutathione S-transferases (GSTs; EC 2.5.1.18) are a family of dimeric proteins that catalyze reactions between glutathione (GSH) and various electrophiles. A partial cDNA for human GST pi was obtained and the open reading frame completed. The completed cDNA was cloned, and GST pi protein was expressed in bacteria. Cloned enzyme was purified and had the same kinetic constants, molecular mass, pI value, and N-terminal sequence as placental GST pi except that some of the polypeptides had N-terminal methionines. A radiolabeled azido derivative of GSH, S-(p-azidophenacyl)-[3H]glutathione, was used to photoaffinity-label the active site of the cloned enzyme. Labeled enzyme did not bind to a GSH-agarose affinity column. Labeling was prevented in the presence of S-hexylglutathione, and noncovalently-bound azido affinity label was a competitive inhibitor towards 1-chloro-2,4-dinitrobenzene and GSH. These results suggest that the azido label was binding at the active site of the enzyme. Photoaffinity-labeled enzyme was trypsinized, and two labeled peptides were purified and sequenced. One peptide corresponded to residues 183-188, whereas the other corresponded to residues 183-186. These residues appear to form part of the hydrophobic (H-site) binding region of human GST pi that has not been shown previously. Cloned enzyme was subjected to radiation inactivation to assess the importance of subunit interactions in the maintenance of catalytic activity. The target size of enzymatic activity (23 kDa) was not significantly different from that of the protein monomer (24 kDa). Therefore, each subunit of human GST pi appears to be capable of independent catalytic activity.

Effects of high-energy electrons and gamma rays directly on protein molecules.

High-energy electrons and gamma rays ionize molecules at random along their trajectories. In each event, chemical bonds are ruptured, releasing radiolytic products that diffuse away. A solution of macromolecules is mostly water whose principal radiation products are H(+) and OH(-). These can diffuse to and react with macromolecules; this indirect action of radiation is responsible for 99.9% of the damage to proteins. In frozen samples, the ionizations still occur randomly and water is still the principle molecular target, but diffusion of radiation products is limited to only a very small distance. At very low temperatures, essentially all the radiation damage to macromolecules is due to primary ionizations occurring directly in those molecules. Therefore, proteins in frozen solutions are only 10(-3) to 10(-4) as sensitive to radiation as in the liquid state. Every molecule that suffered a direct ionization is destroyed; the only surviving molecules are those that escaped ionization. The survival of frozen proteins after irradiation is a direct measure of the mass of the active structures and independent of the presence of other proteins.

Direct Effects of Ionizing Radiation on Macromolecules.

In the dry or frozen states, macromolecules are damaged directly by interactions with ionizing radiation. Since γ-rays and high-energy electrons randomly ionize orbital electrons in their path, larger molecules are more likely to suffer an interaction with these radiations. In each interaction, energy is transferred to the struck molecule, resulting in irreversibly broken covalent bonds. There is an extensive literature describing these radiation modifications in both synthetic and biopolymers. Although many different properties are measured, there emerges a similar picture of the nature of radiation damage that is common to all macromolecules. The techniques used in study of one species may be used to resolve questions raised in the other class of macromolecules.