Analysis of heregulin symmetry by weighted evolutionary tracing

Heregulins are members of the protein family of EGF-like growthand differentiation factors. The primary cell-surface targetsof heregulins are heterodimers of the EGF-receptor homolog HER2with either HER3 or HER4. We used a weighted evolutionary traceanalysis to identify structural features that distinguish theEGF-like domain (hrg) of heregulins from other members of theEGF family. In this analysis, each amino acid sequence is weightedaccording to its uniqueness and the variability in each positionis assigned by an amino acid substitution matrix. Conservedresidues in heregulin that are variable in other EGF-like domainsare considered possible specificity-conferring residues. Thisanalysis identifies two clusters of residues at the foot ofthe boot-shaped hrg domain. The residues in one cluster arerecruited from the N-terminus; those in the other are from the-loop region and show a weak sequence similarity to the N-terminalresidues at the opposite side of the boot. The remaining residueswith high conservation scores distribute themselves into thesetwo distinct surfaces on hrg. This pseudo-twofold symmetry andthe presence of two distinct interfaces may reflect the preferenceof hrg for heterodimeric versus homodimeric HER complexes.     

Miscibility behavior and coil overlap in ionic blends of phenylated polytriphenylene oxide and poly(methyl methacrylate)

Blends of sulfonated phenylated polytriphenylene oxide and poly(methyl methacrylate‐co‐4‐vinyl pyridine) were examined by dynamic mechanical, Fourier transform infrared, and NMR techniques. A high degree of miscibility was evident from a single drop in a plot of the storage modulus versus the temperature. The presence of ionic moieties due to proton transfer from sulfonic acid to 4‐vinyl pyridine was confirmed by both NMR and IR spectroscopy studies. The coils were found to be close to one another in dimethyl sulfoxide‐d₆ because the aromatic shielding effect of the phenyl rings of the phenylated polytriphenylene oxide units was observed from the upfield shift of most of the protons of poly(methyl methacrylate) in the NMR spectrum. However, the absence of cross peaks in the nuclear Overhauser and exchange spectroscopy experiments suggested that the intermolecular distance between the chains had to be larger than 4 Å. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 728–733, 2003     

Practical Design Model for Calculating Bubble Diffuser Contactor Ozone Transfer Efficiency

Ozone transfer to water or wastewater is necessary before desirable, effective ozone reactions occur. Several factors affect ozone transfer efficiency, including water quality characteristics, contactor configuration, and applied ozone characteristics. The design model presented in this paper addresses all factors affecting ozone transfer. The model was used to compare measured transfer efficiency with predicted transfer efficiency at four full-scale wastewater ozone disinfection facilities. A relatively good prediction was obtained at each plant.

The paper presents an example calculation of ozone transfer efficiency. Also, the effect of changes to some of the factors affecting transfer efficiency is presented, such as changes in diffuser depth, plant elevation, ozone concentration, water quality (i.e., ozone demand), pH, detention time, temperature, and acombination of factors. The design model may be used to evaluate the effect of changes in plant design on transfer efficiency, but cannot provide an absolute value for transfer efficiency until difficult-to-measure parameters, such as bubble diameter, are known.     

Glass transition relations in ionomeric “comb” polymers

The glass transition temperatures (T_g) and dynamic mechanical properties of random copolymers of styrene-4-vinylpyridine quaternized with iodoalkanes are presented for vinylpyridine contents up to ten percent and pendant alkyl chains up to ten carbons in length. Two linear relationships, between ion content and glass transition temperature and between pendant alkyl chain length and the T_g, are observed. An equation is presented that can be used to predict the T_g for such copolymers based on their ion contents and alkyl chain lengths.     

Microstructure and creep behavior in AE42 magnesium die-casting alloy

The micro structural analysis of die-cast AE42 reveals a correlation between micro structure and creep strength. A lamellar-phase Al₁₁RE₃, which dominates the interdendritic microstructure of the alloy, partly decomposes above 150‡C into Al₂RE and Al (forming Mg₁₇Al₁₂). The increased solubility of aluminum in magnesium at higher temperatures may also promote the decomposition of Al₁₁RE₃. The creep strength decreases sharply with these phase changes. A mechanism for the decrease in creep strength of AE42 is proposed whereby the reduced presence of lamellar Al1₁₁RE₃ and/or the presence of Mg₁₇Al₁₂ contribute to the observed poor creep strength at higher temperatures.     

Categories of quantum and classical channels

We introduce a construction that turns a category of pure state spaces and operators into a category of observable algebras and superoperators. For example, it turns the category of finite-dimensional Hilbert spaces into the category of finite-dimensional C*-algebras and completely positive maps. In particular, the new category contains both quantum and classical channels, providing elegant abstract notions of preparation and measurement. We also consider nonstandard models that can be used to investigate which notions from algebraic quantum information theory are operationally justifiable.     

Introduction: In-Use,In-Situ: Extending Field Research Methods—Part 2

This study used protocol analyses and user drawings of their models of the system to investigate the “getting lost” problem in hypertext navigation. The “getting lost” problem is viewed as occurring when routine expectations of naive users, concerning appropriate linear sequences, are violated. Several ways in which users persistently attempt to work within a linear model, despite its inapplicability, are examined. The transition to more hierarchical user models is described.     

Discovery of the ammonium substrate site on glutamine synthetase, a third cation binding site

Glutamine synthetase (GS) catalyzes the ATP-dependent condensation of ammonia and glutamate to yield glutamine, ADP, and inorganic phosphate in the presence of divalent cations. Bacterial GS is an enzyme of 12 identical subunits, arranged in two rings of 6, with the active site between each pair of subunits in a ring. In earlier work, we have reported the locations within the funnel-shaped active site of the substrates glutamate and ATP and of the two divalent cations, but the site for ammonia (or ammonium) has remained elusive. Here we report the discovery by X-ray crystallography of a binding site on GS for monovalent cations, Tl+ and Cs+, which is probably the binding site for the substrate ammonium ion. Fourier difference maps show the following. (1) Tl+ and Cs+ bind at essentially the same site, with ligands being Glu 212, Tyr 179, Asp 50', Ser 53' of the adjacent subunit, and the substrate glutamate. From its position adjacent to the substrate glutamate and the cofactor ADP, we propose that this monovalent cation site is the substrate ammonium ion binding site. This proposal is supported by enzyme kinetics. Our kinetic measurements show that Tl+, Cs+, and NH4+ are competitive inhibitors to NH2OH in the gamma-glutamyl transfer reaction. (2) GS is a trimetallic enzyme containing two divalent cation sites (n1, n2) and one monovalent cation site per subunit. These three closely spaced ions are all at the active site: the distance between n1 and n2 is 6 A, between n1 and Tl+ is 4 A, and between n2 and Tl+ is 7 A. Glu 212 and the substrate glutamate are bridging ligands for the n1 ion and Tl+. (3) The presence of a monovalent cation in this site may enhance the structural stability of GS, because of its effect of balancing the negative charges of the substrate glutamate and its ligands and because of strengthening the "side-to-side" intersubunit interaction through the cation-protein bonding. (4) The presence of the cofactor ADP increases the Tl+ binding to GS because ADP binding induces movement of Asp 50' toward this monovalent cation site, essentially forming the site. This observation supports a two-step mechanism with ordered substrate binding: ATP first binds to GS, then Glu binds and attacks ATP to form gamma-glutamyl phosphate and ADP, which complete the ammonium binding site. The third substrate, an ammonium ion, then binds to GS, and then loses a proton to form the more active species ammonia, which attacks the gamma-glutamyl phosphate to yield Gln. (5) Because the products (Glu or Gln) of the reactions catalyzed by GS are determined by the molecule (water or ammonium) attacking the intermediate gamma-glutamyl phosphate, this negatively charged ammonium binding pocket has been designed naturally for high affinity of ammonium to GS, permitting glutamine synthesis to proceed in aqueous solution.     

The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution

The dimer of bovine pancreatic ribonuclease A (RNase A) discovered by Crestfield, Stein, and Moore in 1962 has been crystallized and its structure determined and refined to a 2.1-A resolution. The dimer is 3D domain-swapped. The N-terminal helix (residues 1-15) of each subunit is swapped into the major domain (residues 23-124) of the other subunit. The dimer of bull seminal ribonuclease (BS-RNase) is also known to be domain-swapped, but the relationship of the subunits within the two dimers is strikingly different. In the RNase A dimer, the 3-stranded beta sheets of the two subunits are hydrogen-bonded at their edges to form a continuous 6-stranded sheet across the dimer interface; in the BS-RNase dimer, it is instead the two helices that abut. Whereas the BS-RNase dimer has 2-fold molecular symmetry, the two subunits of the RNase A dimer are related by a rotation of approximately 160 degrees. Taken together, these structures show that intersubunit adhesion comes mainly from the swapped helical domain binding to the other subunit in the "closed interface" but that the overall architecture of the domain-swapped oligomer depends on the interactions in the second type of interface, the "open interface." The RNase A dimer crystals take up the dye Congo Red, but the structure of a Congo Red-stained crystal reveals no bound dye molecule. Dimer formation is inhibited by excess amounts of the swapped helical domain. The possible implications for amyloid formation are discussed.     

Integrated diffractive andrefractive elements for spectrum shaping

Diffractive elements can be designed for spectrum shaping in the Fourier or Fresnel plane by iterative methods. It is necessary to use a Fourier lens and the wavelength for which the diffractive elements were designed to get the required spectrum shaping at the Fourier plane. Using a different wavelength will cause chromatic aberration. We deal with the combination of refractive and diffractive elements and two or more different diffractive elements on the same element to get appropriate beam shaping of light sources with a multiple spectral output. Simulations are preformed that transform the profile of a He-Ne laser with a Nd:YAG laser source, and shape the trapezoidal beam profile of an excimer laser into a Gaussian beam is also considered.