Evaluation at atomic resolution of the role of strain in destabilizing the temperature‐sensitive T4 lysozyme mutant Arg 96 → His

Mutant R96H is a classic temperature‐sensitive mutant of bacteriophage T4 lysozyme. It was in fact the first variant of the protein to be characterized structurally. Subsequently, it has been studied extensively by a variety of experimental and computational techniques, but the reasons for the loss of stability of the mutant protein remain controversial. In the crystallographic refinement of the mutant structure at 1.9 Å resolution one of the bond angles at the site of substitution appeared to be distorted by about 11^°, and it was suggested that this steric strain was one of the major factors in destabilizing the mutant. Different computationally‐derived models of the mutant structure, however, did not show such distortion. To determine the geometry at the site of mutation more reliably, we have extended the resolution of the data and refined the wildtype (WT) and mutant structures to be better than 1.1 Å resolution. The high‐resolution refinement of the structure of R96H does not support the bond angle distortion seen in the 1.9 Å structure determination. At the same time, it does confirm other manifestations of strain seen previously including an unusual rotameric state for His96 with distorted hydrogen bonding. The rotamer strain has been estimated as about 0.8 kcal/mol, which is about 25% of the overall reduction in stability of the mutant. Because of concern that contacts from a neighboring molecule in the crystal might influence the geometry at the site of mutation we also constructed and analyzed supplemental mutant structures in which this crystal contact was eliminated. High‐resolution refinement shows that the crystal contacts have essentially no effect on the conformation of Arg96 in WT or on His96 in the R96H mutant.     

Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme

To try to resolve the loss of stability in the temperature‐sensitive mutant of T4 lysozyme, Arg 96 → His, all of the remaining 18 naturally occurring amino acids were substituted at site 96. Also, in response to suggestions that the charged residues Lys85 and Asp89, which are 5–8 Å away, may have important effects, each of these amino acids was replaced with alanine. Crystal structures were determined for many of the variants. With the exception of the tryptophan and valine mutants R96W and R96V, the crystallographic analysis shows that the substituted side chain following the path of Arg96 in wildtype (WT). The melting temperatures of the variants decrease by up to ～16°C with WT being most stable. There are two site 96 replacements, with lysine or glutamine, that leave the stability close to that of WT. The only element that the side chains of these residues have in common with the WT arginine is the set of three carbon atoms at the C^α, C^β, and C^γ positions. Although each side chain is long and flexible with a polar group at the distal position, the details of the hydrogen bonding to the rest of the protein differ in each case. Also, the glutamine replacement lacks a positive charge. This shows that there is some adaptability in achieving full stabilization at this site. At the other extreme, to be maximally destabilizing a mutation at site 96 must not only eliminate favorable interactions but also introduce an unfavorable element such as steric strain or a hydrogen‐bonding group that remains unsatisfied. Overall, the study highlights the essential need for atomic resolution site‐specific structural information to understand and to predict the stability of mutant proteins. It can be very misleading to simply assume that conservative amino acid substitutions cause small changes in stability, whereas large stability changes are associated with nonconservative replacements.     

Metabolic flux analysis and pharmaceutical production

Rational engineering of biological systems is an inherently complex process due to their evolved nature. Metabolic engineering emerged and developed over the past 20 years as a field in which methodologies for the rational engineering of biological systems is now being applied to specific industrial, medical, or scientific problems. Of considerable interest is the determination of metabolic fluxes within the cell itself, called metabolic flux analysis. This special issue and this review have a particular interest in the application of metabolic flux analysis for improving the pharmaceutical production process (for both small and large molecules). Though metabolic flux analysis has been somewhat limited in application towards pharmaceutical production, the overall goal is to: (1) have a better understanding of the organism and/or process in question, and (2) provide a rational basis to further engineer (on both metabolic and process scales) improved pharmaceutical production in these organisms. The focus of this review article is to present how experimental and computational methods of metabolic flux analysis have matured, mirroring the maturation of the metabolic engineering field itself, while highlighting some of the successful applications towards both small- and large-molecule pharmaceuticals.     

GH18 endo-β-N-acetylglucosaminidases use distinct mechanisms to process hybrid-type N-linked glycans

N-glycosylation is one of the most abundant posttranslational modifications of proteins, essential for many physiological processes, including protein folding, protein stability, oligomerization and aggregation, and molecular recognition events. Defects in the N-glycosylation pathway cause diseases that are classified as congenital disorders of glycosylation. The ability to manipulate protein N-glycosylation is critical not only to our fundamental understanding of biology but also for the development of new drugs for a wide range of human diseases. Chemoenzymatic synthesis using engineered endo-β-N-acetylglucosaminidases (ENGases) has been used extensively to modulate the chemistry of N-glycosylated proteins. However, defining the molecular mechanisms by which ENGases specifically recognize and process N-glycans remains a major challenge. Here we present the X-ray crystal structure of the ENGase EndoBT-3987 from Bacteroides thetaiotaomicron in complex with a hybrid-type glycan product. In combination with alanine scanning mutagenesis, molecular docking calculations and enzymatic activity measurements conducted on a chemically engineered monoclonal antibody substrate unveil two mechanisms for hybrid-type recognition and processing by paradigmatic ENGases. Altogether, the experimental data provide pivotal insight into the molecular mechanism of substrate recognition and specificity for GH18 ENGases and further advance our understanding of chemoenzymatic synthesis and remodeling of homogeneous N-glycan glycoproteins.     

Interactions between vesicular-arbuscular mycorrhizal fungi and asparagus

Summary The vesicular-arbuscular mycorrhizal (VAM) fungus,Glomus versiforme increased significantly the growth ofAsparagus officinalis under controlled conditions using Turface as the growth medium. The growth responses, including increases in root fresh weight, numbers of shoots, shoot dry weight, and shoot height follow a pattern similar to other mycorrhizal systems. Indigenous VAM fungi appeared to have negative effects on average shoot fresh and dry weight, number of shoots per pot and average shoot height on one year oldA. officinalis seedlings obtained from the field and grown under controlled conditions. These results may be due either to the high levels of soluble phosphate present in the soil or the ineffectiveness of the particular indigenous fungi as mycorrhizal fungi in asparagus. Indigenous mycorrhizal fungi overwinter in asparagus root crown as vesicles and as external and internal hyphae. Soil obtained from the same fields as the one year old crowns was a good source of mycorrhizal inoculum for sterile seedlings.     

Studies in eupatorium (Compositae), III. Apparent wind pollination

Eupatorium is a large, chiefly American genus in which some species have deviated from the usual reproductive methods of insect pollination and outcrossing. Apomixis and autogamy are two reproductive specializations which have been reported previously. A third, anemophily, is suspected inE. solidaginifolium, E. solidaginoides, E. monanthum, and several other species. Our assumptions are based upon morphological modifications of the inflorescence, anther appendages, style branches, and pollen. Wind pollination in the Compositae has heretofore been known only in the tribe Anthemideae and the subtribe Ambrosinae of the Heliantheae; its occurrence inEupatorium is an independent evolutionary event. The occurrence of apomixis, autogamy, and anemophily in members ofEupatorium from the same geographical region probably represents (at least in part) correlated responses to the same environmental stress, a scarcity of insect pollinators.     

Detection of Hepatitis B Antigen by Counter-Immunoelectrophoresis: Enhancing Role of Homologous Serum Diluents

Dilution of hyperimmune hepatitis type B antibody in undiluted homologous species normal serum has resulted in enhanced sensitivity for detecting hepatitis B antigen by a discontinuous counter-immunoelectrophoresis method compared to hepatitis type B antibody diluted in heterologous species normal serum or buffer solutions.     

Bacterial spore heat resistance correlated with water content, wet density, and protoplast/sporoplast volume ratio.

Five types of dormant Bacillus spores, between and within species, were selected representing a 600-fold range in moist-heat resistance determined as a D100 value. The wet and dry density and the solids and water content of the entire spore and isolated integument of each type were determined directly from gram masses of material, with correction for interstitial water. The ratio between the volume occupied by the protoplast (the structures bounded by the inner pericytoplasm membrane) and the volume occupied by the sporoplast (the structures bounded by the outer pericortex membrane) was calculated from measurements made on electron micrographs of medially thin-sectioned spores. Among the various spore types, an exponential increase in the heat resistance correlated directly with the wet density and inversely with the water content and with the protoplast/sporoplast volume ratio. Altogether with results supported a hypothesis that the extent of heat resistance is based in whole or in part on the extent of dehydration and diminution of the protoplast in the dormant spore, without implications about physiological mechanisms for attaining this state.     

Reversal of indomethacin-induced decreases in renal function by an isosterically-modified prostaglandin analog

A recently discovered isosterically-modified prostaglandin analog, 4-(3-[3-[2-(1-hydroxycyclohexyl)ethyl]-4-oxo-2-thiazolidinyl ] propyl) benzoic acid, was studied in conscious Na-deficient dogs to determine if this compound could reverse the deleterious renal effects induced by inhibition of renal cyclooxygenase. Indomethacin (2 mg/kg i.v.) reduced renal function significantly in all dogs studied: GFR decreased from 38 +/- 3 to 26 +/- 1 ml/min (P less than 0.01) and ERPF from 124 +/- 15 to 79 +/- 8 ml/min (P less than 0.01). On separate occasions, the six dogs used in this study were treated with a saline placebo intravenously or with the PG analog (0.1 mg/kg i.v.) 60 min after receiving indomethacin. After placebo treatments renal function remained suppressed for the duration of observation (2 hours). After treatment with PG analog, GFR was restored to pre-indomethacin levels within 1 hour (36 +/- 3 ml/min) and remained at this level or higher for the duration of the experiment. ERPF was restored to pre-indomethacin levels within 30 min of PG analog injection (140 +/- 7 ml/min) and subsequently rose ml/min) for the duration of the experiment. Urinary electrolyte excretion was suppressed by indomethacin and despite the large increase in ERPF, Na excretion was not augmented by PG analog. This study demonstrates that a synthetic, isosterically-modified prostaglandin analog can effectively reverse the hemodynamic effects of non-steroidal antiinflammatory drug treatment on renal function while not affecting renal Na excretion.