Some Seismic Profiles near the Western End of the Puerto Rico Trench

A cooperative program of seismic refraction profiling was completed in the vicinity of the Puerto Rico Trench by Hudson Laboratories, Woods Hole, Lamont, and Texas A. & M. Profiles completed near the western end of the Trench were analyzed at Hudson Laboratories. Five seismic layers are indicated below the water layer. The thickness/velocity relationships are as follows: 5.1 km of 1.5 km/sec. (water); 1 km of 1.7 km/sec. (sediment); 1.5 km of 3 km/sec. (metamorphics?); 2 km of 5.5 km/sec. (basement); and 2 km of 7.1 km/sec. (high speed basement). Below these, typical Moho velocities of 8.1 km/sec. were measured. Total depth to Moho ranges from 9 to 12 km below sea level, the greatest variation occurring in the basement layers. The least depth was measured 65 miles north of the Puerto Rico Trench.     

Factors Controlling the Production of Lysogenic Cultures of B. megatherium

(1) The proportion of infected B. megatherium cells which develop lysogenic colonies depends on the number and kind of infecting virus particles and on the culture medium in which the cells are growing. (2) Cells infected with 100 or more T virus particles (from megatherium 899) in yeast extract peptone disintegrate, produce very few virus particles, and less than one lysogenic colony per 10⁷ infected cells. Cells infected with one or a few particles produce 500 to 1000 virus particles each and about 30 lysogenic colonies per 10⁷ infected colonies. (3) T phage obtained from lysogenic magatherium KM cultures produces many more lysogenic cells than does the original megatherium 899 virus. (4) Cells infected with megatherium 899 T virus in peptone medium and then transferred to asparagine medium give rise to 10⁶ lysogenic colonies per 10⁷ infected cells and this transformation will occur even after the infected cells have been in peptone for 60 to 90 minutes and are beginning to produce virus particles. (5) Continued growth of KM strain with either C or T virus from megatherium 899 for several hundred generations in the steady state apparatus results in a lysogenic strain which produces several different types of virus.     

Calculations of intrinsic isotope effects and the detection of tunneling in enzyme-catalyzed reactions

The equation of Northrop [1975, Biochemistry, 14, 2644] for calculating intrinsic isotope effects from observed deuterium and tritium isotope effects of V/K, in which hydrogen is the reference isotope, has been extended to experimental designs using either deuterium or tritium as a reference. Partial derivatives of the intrinsic equations allow calculation of the relative precision of the three referenced isotope effects and these favor the order deuterium > tritium > hydrogen. In comparisons of observed and calculated isotope effects when hydrogen tunneling is present, both the precision and the magnitude of the difference was greater for intrinsic calculations than for exponentiations based upon a breakdown in the Swain-Schaad relationship.     

The low availability of dietary choline for the nutrition of the sheep.

1. Choline, which is present in the diet of the sheep either in the non-esterified form or combined in phospholipids, is rapidly degraded in the rumen. The ultimate product formed from the N-methyl groups is methane. 2. Analysis of the non-esterified choline and the phosphatidylcholine in ruminal and abomasal digesta indicate that the phospholipid is the main vehicle for the passage of choline to the lower digestive tract. 3. The concentration of phosphatidylcholine in abomasal digesta is lower than that of ruminal digesta, which is in line with a selective retention of protozoa in the rumen as observed by others. 4. On defaunation of the rumen to remove ciliated protozoa the concentration of phosphatidylcholine in ruminal digesta falls markedly and becomes lower than that in abomasal digesta. 5. Calculation shows that the adult sheep obtains at most only about 20--25 mg of effective choline per day from its diet (0.002--0.0025% of dietary total dry-weight intake). This is some fifty times less than the minimum required to avoid pathological lesions and death in other species investigated (0.1%+ of dietary dry-weight intake). 6. Sheep liver can synthesize choline from [14C]ethanolamine both in vitro and in vivo, but the synthesis of choline per kg body weight is many times less than it is in the rat. 7. The intact sheep oxidizes an injected dose of [1,2-14C]choline to CO2 at a rate that is several times less than that observed for the rat. This could help to explain the apparent minimal requirement of sheep for dietary choline.     

Effect of pressure on deuterium isotope effects of formate dehydrogenase

High pressure causes biphasic effects on the oxidation of formate by yeast formate dehydrogenase as expressed on the kinetic parameter V/K, which measures substrate capture. Moderate pressure increases capture by accelerating hydride transfer. The transition state for hydride transfer has a smaller volume than the free formate plus the capturing form of enzyme, with DeltaV(double dagger) = -9.7 +/- 1.0 mL/mol. Pressures above 1.5 kbar decrease capture, reminiscent of effects on the conformational change associated with the binding of nicotinamide adenine dinucleotide (NAD(+)) to yeast alcohol dehydrogenase [Northrop, D. B., and Y. K. Cho (2000) Biochemistry 39, 2406-2412]. The collision complex, E-NAD(+), has a smaller volume than the more tightly bound reactant-state complex, E-NAD(+), with DeltaV = +83.4 +/- 5.2 mL/mol. A comparison of the effects of pressure on the oxidation of normal and deuteroformate shows that the entire isotope effect on hydride transfer, 2.73 +/- 0.20, arises solely from transition-state phenomena, as was also observed previously with yeast alcohol dehydrogense. In contrast, normal primary isotope effects arise solely from different zero-point energies in reactant states, and those that express hydrogen tunneling arise from a mixture of both reactant-state and transition-state phenomena. Moreover, pressure increases the primary intrinsic deuterium isotope effect, the opposite of what was observed with yeast alcohol dehydrogense. The lack of a decrease in the isotope effect is also contrary to empirical precedents from chemical reactions suspected of tunneling and to theoretical constructs of vibrationally enhanced tunneling in enzymatic reactions. Hence, this new experimental design penetrates transition states of enzymatic catalysis as never before, reveals the presence of phenomena foreign to chemical kinetics, and calls for explanations of how enzymes work beyond the tenants of physical organic chemistry.     

Kinetic mechanism of the GCN5-related chromosomal aminoglycoside acetyltransferase AAC(6')-Ii from Enterococcus faecium: evidence of dimer subunit cooperativity

The aminoglycoside 6'-N-acetyltransferase AAC(6')-Ii from Enterococcus faecium is an important microbial resistance determinant and a member of the GCN5-related N-acetyltransferase (GNAT) superfamily. We report here the further characterization of this enzyme in terms of the kinetic mechanism of acetyl transfer and identification of rate-contributing step(s) in catalysis, as well as investigations into the binding of both acetyl-CoA and aminoglycoside substrates to the AAC(6')-Ii dimer. Product and dead-end inhibition studies revealed that AAC(6')-Ii follows an ordered bi-bi ternary complex mechanism with acetyl-CoA binding first followed by antibiotic. Solvent viscosity studies demonstrated that aminoglycoside binding and product release govern the rate of acetyl transfer, as evidenced by changes in both the k(cat)/K(b) for aminoglycoside and k(cat), respectively, with increasing solvent viscosity. Solvent isotope effects were consistent with our viscosity studies that diffusion-controlled processes and not the chemical step were rate-limiting in drug modification. The patterns of partial and mixed inhibition observed during our mechanistic studies were followed up by investigating the possibility of subunit cooperativity in the AAC(6')-Ii dimer. Through the use of AAC-Trp(164) --> Ala, an active mutant which exists as a monomer in solution, the partial nature of the competitive inhibition observed in wild-type dead-end inhibition studies was alleviated. Isothermal titration calorimetry studies also indicated two nonequivalent antibiotic binding sites for the AAC(6')-Ii dimer but only one binding site for the Trp(164) --> Ala mutant. Taken together, these results demonstrate subunit cooperativity in the AAC(6')-Ii dimer, with possible relevance to other oligomeric members of the GNAT superfamily.     

Quaking is essential for blood vessel development

For nearly 40 years functional studies of the mouse quaking gene (qkI) have focused on its role in the postnatal central nervous system during myelination. However, the homozygous lethality of a number of ENU-induced alleles reveals that quaking has a critical role in embryonic development prior to the start of myelination. In this article, we show that quaking has a previously unsuspected and essential role in blood vessel development. Interestingly, we found that quaking, a nonsecreted protein, is expressed in the yolk sac endoderm, adjacent to the mesodermal site of developing blood islands, where the differentiation of blood and endothelial cells first occurs. Antibodies against PE-CAM-1, TIE-2 and SM-alpha-actin reveal that embryos homozygous for the qk(k2) allele have defective yolk sac vascular remodeling and abnormal vessels in the embryo proper at midgestation, coinciding with the timing of embryonic death. However, these mutants exhibit normal expression of Nkx2.5 and alpha-sarcomeric actin, indicating that cardiac muscle differentiation was normal. Further, they had normal embryonic heart rates in culture, suggesting that cardiac function was not compromised at this stage of embryonic development. Together, these results suggest that quaking plays an essential role in vascular development and that the blood vessel defects are the cause of embryonic death.     

Effects of high pressure on enzymatic activity

Effects of high pressure on enzymatic reactions are poised to revolutionize enzyme kinetics. The reason for this is that experimental designs are at hand to separate effects on equilibria between reactant states from effects on catalytic transition states and both yield new information. The first of the former runs contrary to Pauling's hypothesis that substrates are bound more tightly in the transition state, while the latter penetrates the 'black box' of catalysis, the stabilized transition state itself, and returns a precise measure of a physical parameter, deltaV. This in turn opens the door to new forms of structure-activity relationships. The first of these has been described, the effect of pressure on isotope effects, with the surprising finding that the entire isotope effect comes from a transition state phenomenon such as quantum mechanical hydrogen tunneling.     

Crystal structure of the E1 component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex

The thiamine-dependent E1o component (EC 1.2.4.2) of the 2-oxoglutarate dehydrogenase complex catalyses a rate-limiting step of the tricarboxylic acid cycle (TCA) of aerobically respiring organisms. We describe the crystal structure of Escherichia coli E1o in its apo and holo forms at 2.6 A and 3.5 A resolution, respectively. The structures reveal the characteristic fold that binds thiamine diphosphate and resemble closely the alpha(2)beta(2) hetero-tetrameric E1 components of other 2-oxo acid dehydrogenase complexes, except that in E1o, the alpha and beta subunits are fused as a single polypeptide. The extended segment that links the alpha-like and beta-like domains forms a pocket occupied by AMP, which is recognised specifically. Also distinctive to E1o are N-terminal extensions to the core fold, and which may mediate interactions with other components of the 2-oxoglutarate dehydrogenase multienzyme complex. The active site pocket contains a group of three histidine residues and one serine that appear to confer substrate specificity and the capacity to accommodate the TCA metabolite oxaloacetate. Oxaloacetate inhibits E1o activity at physiological concentrations, and we suggest that the inhibition may allow coordinated activity within the TCA cycle. We discuss the implications for metabolic control in facultative anaerobes, and for energy homeostasis of the mammalian brain.