Miscibility of phosphatidylethanolamine-phosphatidylglycerol mixtures as a function of pH and acyl chain length

We have examined the mixing properties of phosphatidylethanolamine (PE) and phosphatidylglycerol (PG), the major components of many bacterial membranes. The phase transition behavior of dilute aqueous suspensions of PE:PG mixtures with different chain lengths (n = 14, 16) in 0.1 M NaCl at pH 7 and pH 2 was investigated by differential scanning calorimetry (DSC). The DSC curves were simulated using an approach which takes into account the broadening of the phase transition in addition to symmetric, non-ideal mixing in the gel and the liquid-crystalline phase. Based on the temperatures for onset and end of “melting” obtained by the simulations, the phase diagrams were constructed and then refined using a regular solution model with non-symmetric mixing in both phases. The mixing properties of PE:PG mixtures were analyzed as a function of pH and acyl chain length. In almost all cases, non-symmetric mixing behavior was observed, i.e. the non-ideality parameters are different for bilayers with low PG content compared to bilayers with high PG content. For equimolar mixtures at pH 7, when PG is negatively charged, the non-ideality parameters are negative for both phases, indicating preferential formation of mixed pairs. This mixed pair formation is more pronounced for the gel phase. At pH 2, when PG is partly protonated, the non-ideality parameter is less negative and the formation of mixed pairs is reduced compared to pH 7. The formation of PE:PG mixed pairs at pH 7 might be of benefit to a bacterial membrane, because it prevents demixing of lipid components with a concomitant destabilization of the membrane. Received: 3 August 1998 / Revised version: 4 October 1999 / Accepted: 12 October 1999     

High-pressure Sapphire Cell for Phase Equilibria Measurements of CO2/Organic/Water Systems

The high pressure sapphire cell apparatus was constructed to visually determine the composition of multiphase systems without physical sampling. Specifically, the sapphire cell enables visual data collection from multiple loadings to solve a set of material balances to precisely determine phase composition. Ternary phase diagrams can then be established to determine the proportion of each component in each phase at a given condition. In principle, any ternary system can be studied although ternary systems (gas-liquid-liquid) are the specific examples discussed herein. For instance, the ternary THF-Water-CO₂ system was studied at 25 and 40 °C and is described herein. Of key importance, this technique does not require sampling. Circumventing the possible disturbance of the system equilibrium upon sampling, inherent measurement errors, and technical difficulties of physically sampling under pressure is a significant benefit of this technique. Perhaps as important, the sapphire cell also enables the direct visual observation of the phase behavior. In fact, as the CO₂ pressure is increased, the homogeneous THF-Water solution phase splits at about 2 MPa. With this technique, it was possible to easily and clearly observe the cloud point and determine the composition of the newly formed phases as a function of pressure.The data acquired with the sapphire cell technique can be used for many applications. In our case, we measured swelling and composition for tunable solvents, like gas-expanded liquids, gas-expanded ionic liquids and Organic Aqueous Tunable Systems (OATS)^1-4. For the latest system, OATS, the high-pressure sapphire cell enabled the study of (1) phase behavior as a function of pressure and temperature, (2) composition of each phase (gas-liquid-liquid) as a function of pressure and temperature and (3) catalyst partitioning in the two liquid phases as a function of pressure and composition. Finally, the sapphire cell is an especially effective tool to gather accurate and reproducible measurements in a timely fashion.     

Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins

In this study, we carried out a comparative analysis between two classical methodologies to prospect residue contacts in proteins: the traditional cutoff dependent (CD) approach and cutoff free Delaunay tessellation (DT). In addition, two alternative coarse-grained forms to represent residues were tested: using alpha carbon (CA) and side chain geometric center (GC). A database was built, comprising three top classes: all alpha, all beta, and alpha/beta. We found that the cutoff value at about 7.0 A emerges as an important distance parameter. Up to 7.0 A, CD and DT properties are unified, which implies that at this distance all contacts are complete and legitimate (not occluded). We also have shown that DT has an intrinsic missing edges problem when mapping the first layer of neighbors. In proteins, it may produce systematic errors affecting mainly the contact network in beta chains with CA. The almost-Delaunay (AD) approach has been proposed to solve this DT problem. We found that even AD may not be an advantageous solution. As a consequence, in the strict range up to 7.0 A, the CD approach revealed to be a simpler, more complete, and reliable technique than DT or AD. Finally, we have shown that coarse-grained residue representations may introduce bias in the analysis of neighbors in cutoffs up to 6.8 A, with CA favoring alpha proteins and GC favoring beta proteins. This provides an additional argument pointing to the value of 7.0 A as an important lower bound cutoff to be used in contact analysis of proteins.     

Immobilization of urease within a thin channel ultrafiltration cell

Urease [urea amidohydrolase, EC 3.5.1.5] has been immobilized within a thin channel ultrafiltration cell. Loss of enzymic activity as a result of concentration polarization and other causes was minimized. The flow characteristics of the reactor were fully characterized by analysis of the distribution of residence times (using F diagrams) and kinetic data were also obtained for the immobilized enzyme. These data show that under certain conditions the thin channel ultrafiltration reactor can be considered to be an ideally mixed vessel. After almost 8 days of continuous operation it was found that 15% of the original enzyme activity remained.     

Expanding the viewpoint: Leveraging sequence information in enzymology

The use of protein sequence to inform enzymology in terms of structure, mechanism, and function has burgeoned over the past two decades. Referred to as genomic enzymology, the utilization of bioinformatic tools such as sequence similarity networks and phylogenetic analyses has allowed the identification of new substrates and metabolites, novel pathways, and unexpected reaction mechanisms. The holistic examination of superfamilies can yield insight into the origins and paths of evolution of enzymes and the range of their substrates and mechanisms. Herein, we highlight advances in the use of genomic enzymology to address problems which the in-depth analyses of a single enzyme alone could not enable.     

Seeing Patterns: Models, Visual Evidence and Pictorial Communication in the Work of Barbara McClintock

Barbara McClintock won the Nobel Prize in 1983 for her discovery of mobile genetic elements. Her Nobel work began in 1944, and by 1950 McClintock began presenting her work on “controlling elements.” McClintock performed her studies through the use of controlled breeding experiments with known mutant stocks, and read the action of controlling elements (transposons) in visible patterns of pigment and starch distribution. She taught close colleagues to “read” the patterns in her maize kernels, “seeing” pigment and starch genes turning on and off. McClintock illustrated her talks and papers on controlling elements or transposons with photographs of the spotted and streaked maize kernels which were both her evidence and the key to her explanations. Transposon action could be read in the patterns by the initiated, but those without step by step instruction by McClintock or experience in maize often found her presentations confusing. The photographs she displayed became both McClintock's means of communication, and a barrier to successful presentation of her results. The photographs also had a second and more subtle effect. As images of patterns arrived at through growth and development of the kernel, they highlight what McClintock believed to be the developmental consequences of transposition, which in McClintock's view was her central contribution, over the mechanism of transposition, for which she was eventually recognized by others. Scientific activities are extremely visual, both at the sites of investigation and in communication through drawings, photographs, and movies. Those visual messages deserve greater scrutiny by historians of science. This revised version was published online in July 2006 with corrections to the Cover Date.     

Physical–Chemical Properties of the Chiral Fungicide Fenamidone and Strategies for Enantioselective Crystallization

Thermodynamic and kinetic parameters are of prime importance for designing crystallization processes. In this article, Preferential Crystallization, as a special approach to carry out enantioselective crystallization, is described to resolve the enantiomers of the chiral fungicide fenamidone. In preliminary investigations the melting behavior and solid–liquid equilibria in the presence of solvents were quantified. The analyses revealed a stable solid phase behavior of fenamidone in the applied solvents. Based on the results obtained, a two–step crystallization route was designed and realized capable of providing highly pure enantiomers. An initial Preferential Crystallization of the racemate was performed prior to crystallizing the target enantiomer preferentially out of the enriched mother liquor. Chirality 28:514–520, 2016. © 2016 Wiley Periodicals, Inc.