Enhanced Amino Acid Selection in Fully Evolved Tryptophanyl-tRNA Synthetase,Relative to Its Urzyme,Requires Domain Motion Sensed by the D1 Switch,a Remote Dynamic Packing Motif

We previously showed (Li, L., and Carter, C. W., Jr. (2013) J. Biol. Chem. 288, 34736–34745) that increased specificity for tryptophan versus tyrosine by contemporary Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) over that of TrpRS Urzyme results entirely from coupling between the anticodon-binding domain and an insertion into the Rossmann-fold known as Connecting Peptide 1. We show that this effect is closely related to a long range catalytic effect, in which side chain repacking in a region called the D1 Switch, accounts fully for the entire catalytic contribution of the catalytic Mg²⁺ ion. We report intrinsic and higher order interaction effects on the specificity ratio, (k_cat/K_m)_Trp/(k_cat/K_m)_Tyr, of 15 combinatorial mutants from a previous study (Weinreb, V., Li, L., and Carter, C. W., Jr. (2012) Structure 20, 128–138) of the catalytic role of the D1 Switch. Unexpectedly, the same four-way interaction both activates catalytic assist by Mg²⁺ ion and contributes −4.4 kcal/mol to the free energy of the specificity ratio. A minimum action path computed for the induced-fit and catalytic conformation changes shows that repacking of the four residues precedes a decrease in the volume of the tryptophan-binding pocket. We suggest that previous efforts to alter amino acid specificities of TrpRS and glutaminyl-tRNA synthetase (GlnRS) by mutagenesis without extensive, modular substitution failed because mutations were incompatible with interdomain motions required for catalysis.     

Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair

Eukaryotic DNA polymerase mu of the PolX family can promote the association of the two 3′‐protruding ends of a DNA double‐strand break (DSB) being repaired (DNA synapsis) even in the absence of the core non‐homologous end‐joining (NHEJ) machinery. Here, we show that terminal deoxynucleotidyltransferase (TdT), a closely related PolX involved in V(D)J recombination, has the same property. We solved its crystal structure with an annealed DNA synapsis containing one micro‐homology (MH) base pair and one nascent base pair. This structure reveals how the N‐terminal domain and Loop 1 of Tdt cooperate for bridging the two DNA ends, providing a templating base in trans and limiting the MH search region to only two base pairs. A network of ordered water molecules is proposed to assist the incorporation of any nucleotide independently of the in trans templating base. These data are consistent with a recent model that explains the statistics of sequences synthesized in vivo by Tdt based solely on this dinucleotide step. Site‐directed mutagenesis and functional tests suggest that this structural model is also valid for Pol mu during NHEJ.     

Role of prostaglandins in calcium-induced corticosteroid secretion by isolated frog interrenal gland

The role of prostaglandins (PGs) in calcium-induced corticosteroid secretion by frog adrenal (interrenal) gland examined using a perifusion technique. Increasing concentrations of CaCl₂ (4–10 mM) stimulated in a dose-dependent manner aldosterone, PGE₂ and 6-keto-PGF_1α production, whereas TXB₂ was not affected. The kinetics of the adrenal response to CaCl₂ indicated that the increase in PG output always preceded that of steroid. Administration of cobalt (4 mM), a calcium-channel inhibitor, blocked the calcium-induced stimulation of PGs and corticosteroids. Infusion of indomethacin (5 × 10⁻⁶M), a specific cyclooxygenase inhibitor, significantly decreased the basal production of PGs and steroids, and prevented the stimulatory effect of CaCl₂ (6 mM). Infusion of the calcium ionophore A 23187 (10⁻⁶ M), for 20 min, induced a marked stimulation of PG and steroid production. Taken together, these data support the notion that biosynthesis of prostaglandins is associated with calcium-induced corticosteroid secretion in frog adrenal cells.     

Open Lung Biopsy

Steady improvement in the diagnostic appraisal of obscure pulmonary and mediastinal disease has permitted more intelligent treatment, better prognosis, and where necessary more accurate assessment of compensability. Open lung biopsy is designed to obtain material for pathological study when there is no pleural, mediastinal, or airway lesion on which to base a working diagnosis.A study of 54 patients in whom lung biopsy was performed at the Toronto General Hospital and Weston Sanatorium is reported. A positive tissue diagnosis was obtained in approximately 75%. The procedure is considered relatively innocuous if sensible selection is exercised to exclude patients with terminal disease, particularly that associated with severe cardiorespiratory insufficiency. No major complications occurred in this series. It is concluded that open lung biopsy might reasonably receive much wider application than in the past in cases in which a definite diagnosis cannot otherwise be made.