Biomedical subjects

S W Morrical

Publications and source records attributed to S W Morrical.

28 records · Page 2Linked to original sources

PubMed1990

Stabilization of recA protein-ssDNA complexes by the single-stranded DNA binding protein of Escherichia coli.

In vitro recombination reactions promoted by the recA protein of Escherichia coli are enhanced by the single-stranded DNA binding protein (SSB). SSB affects the assembly of the filamentous complexes between recA protein and ssDNA that are the active form of the recA protein. Here, we present evidence that SSB plays a complex role in maintaining the stability and activity of recA-ssDNA filaments. Results of ATPase, nuclease protection, and DNA strand exchange assays suggest that the continuous presence of SSB is required to maintain the stability of recA-ssDNA complexes under reaction conditions that support their recombination activity. We also report data that indicate that there is a functional distinction between the species of SSB present at 10 mM magnesium chloride, which enhances recA-ssDNA binding, and a species present at 1 mM magnesium chloride, which displaces recA protein from ssDNA. These results are discussed in the context of current models of SSB conformation and of SSB action in recombination activities of the recA protein.

Adenosine Triphosphate↗

PubMed1987

recA protein-promoted ATP hydrolysis occurs throughout recA nucleoprotein filaments.

When recA protein binds cooperatively to single-stranded DNA to form filamentous nucleoprotein complexes, it becomes competent to hydrolyze ATP. No correlation exists between the ends of such complexes and the rate of ATP hydrolysis. ATP hydrolysis is not, therefore, restricted to the terminal subunits on cooperatively bound recA oligomers, but occurs throughout the complex. Similarly, during recA protein-promoted branch migration (during DNA strand exchange), ATP hydrolysis is not restricted to recA protein monomers at the branch point. DNA cofactors of lengths varying from 16 bases to over 12,000 bases support ATP hydrolysis. The maximum value of kcat at infinite DNA concentration is about 29/min independent of the length of the DNA cofactor. The apparent dissociation constant, however, is a strong function of DNA length, providing evidence for a minimum site size of 30-50 bases for efficient binding of recA protein.

Adenosine Triphosphatases↗

PubMed1986

Continuous association of Escherichia coli single-stranded DNA binding protein with stable complexes of recA protein and single-stranded DNA.

The single-stranded DNA binding protein of Escherichia coli (SSB) stimulates recA protein promoted DNA strand exchange reactions by promoting and stabilizing the interaction between recA protein and single-stranded DNA (ssDNA). Utilizing the intrinsic tryptophan fluorescence of SSB, an ATP-dependent interaction has been detected between SSB and recA-ssDNA complexes. This interaction is continuous for periods exceeding 1 h under conditions that are optimal for DNA strand exchange. Our data suggest that this interaction does not involve significant displacement of recA protein in the complex by SSB when ATP is present. The properties of this interaction are consistent with the properties of SSB-stabilized recA-ssDNA complexes determined by other methods. The data are incompatible with models in which SSB is displaced after functioning transiently in the formation of recA-ssDNA complexes. A continuous association of SSB with recA-ssDNA complexes may therefore be an important feature of the mechanism by which SSB stimulates recA protein promoted reactions.

Adenosine Diphosphate↗

PubMed1985

Light scattering studies of the recA protein of Escherichia coli: relationship between free recA filaments and the recA X ssDNA complex.

Light scattering has been used to monitor and distinguish between two types of aggregation reactions observed with the recA protein of Escherichia coli. These are (1) the cooperative binding of recA protein to ssDNA in a pathway leading to DNA strand exchange and (2) the formation of free filaments by recA protein in the absence of DNA. Free filament formation requires Mg2+, is very sensitive to ionic strength, and occurs in the absence of single-stranded DNA and RNA. Turbidity measurements indicate that free recA filaments exhibit properties consistent with rigid rods which are 1 micron or more in length. A kinetically distinct nucleation step in free filament formation is observed under some conditions and becomes rate limiting at high pH. Ninety-degree light scattering was employed to measure binding of recA protein to ssDNA under conditions that either favor or block free filament formation. recA protein saturates ssDNA at a stoichiometric ratio of approximately four nucleotide residues per recA monomer. When free filament formation is blocked by various means, the apparent dissociation constant of the recA X ssDNA complex is approximately 10 nM. Under conditions in which free recA filaments form readily, however, the apparent dissociation constant increases to approximately 1 microM. This dramatic decrease in the observed affinity of recA protein for ssDNA under conditions that permit free filament formation does not reflect a change in the intrinsic affinity of recA protein for ssDNA. Instead, it provides evidence that free filament formation and ssDNA binding by recA protein are competing reactions.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA, Single-Stranded↗

PubMed1984

Variation of transition-state structure as a function of the nucleotide in reactions catalyzed by dehydrogenases. 2. Formate dehydrogenase.

Since hydride transfer is completely rate limiting for yeast formate dehydrogenase [Blanchard, J.S., & Cleland, W. W. (1980) Biochemistry 19, 3543], the intrinsic isotope effects on this reaction are fully expressed. Primary deuterium, 13C, and 18O isotope effects in formate and the alpha-secondary deuterium isotope effect at C-4 of the nucleotide have been measured for nucleotide substrates with redox potentials varying from -0.320 (NAD) to -0.258 V (acetylpyridine-NAD). As the redox potential gets more positive, the primary deuterium isotope effect increases from 2.2 to 3.1, the primary 13C isotope effect decreases from 1.042 to 1.036, the alpha-secondary deuterium isotope effect drops from 1.23 to 1.06, and Vmax decreases. The 18O isotope effects increase from 1.005 to 1.008 per single 18O substitution in formate (these values are dominated by the normal isotope effect on the dehydration of formate during binding; pyridinealdehyde-NAD gives an inverse value, possibly because it is not fully dehydrated during binding). These isotope effects suggest a progression toward earlier transition states as the redox potential of the nucleotide becomes more positive, with NAD having a late and acetyl-pyridine-NAD a nearly symmetrical transition state. By contrast, the I2 oxidation of formate in dimethyl sulfoxide has a very early transition state (13k = 1.0154; Dk = 2.2; 18k = 0.9938), which becomes later as the proportion of water in the solvent increases (13k = 1.0265 in 40% dimethyl sulfoxide and 1.0362 in water). alpha-secondary deuterium isotope effects with formate dehydrogenase are decreased halfway to the equilibrium isotope effect when deuterated formate is the substrate, showing that the bending motion of the secondary hydrogen is coupled to hydride transfer in the transition state and that tunneling of the two hydrogens is involved. The 15N isotope effect of 1.07 for NAD labeled at N-1 of the nicotinamide ring suggests that N-1 becomes pyramidal during the reaction. 18O fractionation factors for formate ion relative to aqueous solution are 1.0016 in sodium formate crystal, 1.0042 bound to Dowex-1, and 1.0040 as an ion pair (probably hydrated) in CHCl3. The CO2 analogue azide binds about 10(4) times better than the formate analogue nitrate to enzyme-nucleotide complexes (even though the Ki values for both and the affinity for formate vary by 2 orders of magnitude among the various nucleotides), but the ratio is not sensitive to the redox potential of the nucleotide. Thus, not the nature of the transition state but rather the shape of the initial binding pocket for formate is determining the relative affinity.(ABSTRACT TRUNCATED AT 400 WORDS)

Aldehyde Oxidoreductases↗

PubMed1984

SAMP lyase and AMP deaminase activity in rat parenchymal and kupffer cells in hepatocarcinogenesis.

SAMP lyase and AMP deaminase were determined in parenchymal and kupffer cells of rats fed either basal or carcinogen-enriched diets. Results were calculated on a U/mg protein and U/cell basis. Data indicated that although deaminase increased 1 1/2 to 2-fold in parenchymal cells on a U/mg protein and U/cell basis from rats fed carcinogen-enriched diets there was a greater increase in U/mg protein. In contrast, little to no increase was seen in kupffer cells. SAMP lyase, however, depicted a smaller increase in parenchymal cells of carcinogen-enriched diet fed rats, but a 4- to 5-fold elevation in kupffer cells regardless of whether the data were expressed in U/mg protein or U/cell. These data indicate that increased activity of AMP deaminase may be a result of resistance to degradation in parenchymal cells, whereas SAMP lyase elevations in kupffer cells may reflect an increase in enzyme concentration.

AMP Deaminase↗

PubMed1984

Unidirectional branch migration promoted by nucleoprotein filaments of RecA protein and DNA.

Described above are the initial results from a series of experiments designed to more carefully define the mechanism of RecA protein-promoted DNA strand exchange, and in particular, the branch migration phase of this reaction. We have also presented two general models for RecA protein-promoted branch migration. Although the data required to demonstrate a particular mechanism are presently unavailable, we believe these models will provide a useful framework to suggest future experiments. The models also suggest possible explanations for observations that are presently unexplained. In particular, it is possible to explain the observed inefficiency of ATP hydrolysis in this system without invoking the notion that much of the ATP hydrolysis observed is simply uncoupled. If the utilization of extensive filaments of RecA protein to carry out branch migration is inherently inefficient, why might such a mechanism be employed by the cell? The answer to this question may lie in the role of RecA protein-promoted branch migration in post-replication repair (West et al. 1981c). It might be expected that the branch points in a RecA protein-promoted branch migration reaction are susceptible to nuclease degradation. Such degradation would halt branch migration and prevent postreplication repair. One of the roles of the RecA nucleoprotein filament may be to protect the branch point from nuclease degradation and ensure formation of an extensive region of heteroduplex DNA. The apparent energetic cost of this reaction may be a relatively small price to pay to ensure the repair of a potentially lethal DNA lesion.

DNA, Bacterial↗

PubMed1983

Characterization studies of glucose dehydrogenase.

Porcine liver beta-D-glucose dehydrogenase has been isolated using Triton X-114 to release it from the endoplasmic reticulum. The purified enzyme contains a limited amount (1.7%) of lipid material, including cholesterol, fatty acids, mono and diglycerides, phosphatidylcholine, phosphatidylethanolamine, and cholesterol esters. This enzyme is a tetrameric protein containing an extensive number of hydrophobic residues. This form of glucose dehydrogenase is capable of turning over both beta-D-glucose and alpha-D-glucose-6-phosphate in vivo as indicated from a steady state kinetic analysis at 37 degrees C.

Amino Acids↗

PubMed1983

Guanidinium- and temperature-induced conformational changes in glucose dehydrogenase.

The conformational changes in glucose dehydrogenase are studied as a function of temperature and guanidinium chloride (GdmCl) concentration. The data were analyzed assuming a two-conformer model which gave similar results using either circular dichroism or enzyme activity. The free energy of denaturation was 0.94 kcal/mol from specific activity and 1.64 kcal/mol from circular dichroism measurements. The mid-point of the denaturation curve was 0.65 or 0.63 M GdmCl, as determined by specific activity or circular dichroism, respectively. The transition temperature, 6.4 degrees C, is close to that of a microsomal membrane phase change, a result that is consistent with the fact that glucose dehydrogenase contains lipid materials when isolated with a non-ionic detergent such as Triton X-114. As the temperature increased, the amount of beta-pleated sheet increased, and the alpha-helical content decreased, suggested that glucose dehydrogenase contains a stable core of beta-pleated sheet.

Animals↗

PubMed1982

A comparison of hepatic adenylosuccinate lyase from rats fed either a chow diet or a semisynthetic basal diet low in riboflavin.

1. AMPS Lyase which shows increased activity in both transplantable and primary hepatomas has been purified approximately 400-fold from both chow fed and basal fed rat liver. 2. The enzyme from basal fed rats shows subtle but significant differences from the enzyme from chow fed rats. Especially noted was the difference in effect of 100 mM Na+ on the enzyme from the two different sources after the whole liver had been frozen. 3. These differences may be related to the effects of starvation followed by refeeding or administration of either glucose or corn oil.

Adenylosuccinate Lyase↗