Investigations into the mechanism of orotidine 5'-monophosphate decarboxylase: Sources of substrate destabilization and transition state stabilization

Orotidine 5′-monophosphate decarboxylase (OMPDC) achieves a rarely paralleled rate acceleration, yet the catalytic basis prompting this enhancement have yet to be fully elucidated. To accomplish decarboxylation, OMPDC must overcome the high energy barrier due to the localized anionic charge of the intermediate. Mechanistic studies employing enzyme mutagenesis and product or intermediate analogues were used to investigate possible transition state stabilization by a carbene resonance structure. Viability of the carbene structure depends upon a key hydrogen bond between O4 of the substrate and the amide backbone of a conserved serine or threonine. Substitution of the conserved residue with Pro resulted in a kcat/KM of 1 M-1s-1; deletion of the FUMP O4 resulted in a product analogue that does not undergo H6 exchange or inhibit decarboxylation. Hence, indirect evidence reveals the O4-backbone interaction plays an important role for binding and catalysis. OMPDC likely has honed multiple mechanisms to attain its remarkable catalysis. The successful crystallizations of OMPDC a decade ago sparked hypotheses that structure and sequence conserved residues induced productive strain on the substrate-enzyme complex. Here, we demonstrate a new source of stress: a hydrophobic pocket adjacent to the OMP carboxylate that exhibits kinetic parameters characteristic of substrate destabilization. Substitution of these residues with hydrophilic side-chains, by providing hydrogen-bonding partners, decreased kcat by 10 to 10^4–fold. The same substitutions display very little change in the rate of product H6 exchange, supporting that this hydrophobic pocket affects the substrate-enzyme complex before the transition state. We also provide evidence that hydrophilic residues can insert water molecules into the pocket with detrimental effects to catalysis.

Molecular mechanism of stabilization of thin films for improved water evaporation protection

All-atom molecular dynamics simulations and experimental characterization have been used to examine the structure and dynamics of novel evaporation-suppressing films where the addition of a water-soluble polymer to an ethylene glycol monooctadecyl ether monolayer leads to improved water evaporation resistance. Simulations and Langmuir trough experiments demonstrate the surface activity of poly(vinyl pyrrolidone) (PVP). Subsequent MD simulations performed on the thin films supported by the PVP sublayer show that, at low surface pressures, the polymer tends to concentrate at the film/water interface. The simulated atomic concentration profiles, hydrogen bonding patterns, and mobility analyses of the water-polymer-monolayer interfaces reveal that the presence of PVP increases the atomic density near the monolayer film, improves the film stability, and reduces the mobility of interfacial waters. These observations explain the molecular basis of the improved efficacy of these monolayer/polymer systems for evaporation protection of water and can be used to guide future development of organic thin films for other applications.

The mechanism of breath aerosol formation

Background: Aerosol production during normal breathing is often attributed to turbulence in the respiratory tract. That mechanism is not consistent with a high degree of asymmetry between aerosol production during inhalation and exhalation. The objective was to investigate production symmetry during breathing. Methods: The aerosol size distribution in exhaled breath was examined for different breathing patterns including normal breathing, varied breath holding periods and contrasting inhalation and exhalation rates. The aerosol droplet size distribution measured in the exhaled breath was examined in real time using an aerodynamic particle sizer. Results and Conclusions: The dependence of the particle concentration decay rate on diameter during breath holding was consistent with gravitational settling in the alveolar spaces. Also, deep exhalation resulted in a 4 to 6 fold increase in concentration and rapid inhalation produced a further 2 to 3 fold increase in concentration. In contrast rapid exhalation had little effect on the measured concentration. A positive correlation of the breath aerosol concentration with subject age was observed. The results were consistent with the breath aerosol being produced through fluid film rupture in the respiratory bronchioles in the early stages of inhalation and the resulting aerosol being drawn into the alveoli and held before exhalation. The observed asymmetry of production in the breathing cycle with very little aerosol being produced during exhalation, is inconsistent with the widely assumed turbulence induced aerosolization mechanism.

Hydrogen bonding in the water stabilized structure of the modified unsymmetrically substituted viologen chromophore, N-ethyl-N'-(2-phosphonomethyl)-4,4'-bipyridylium dichloride

The crystal structure of the modified unsymmetrically N, N'-substituted viologen chromophore, N-ethyl- N'-(2-phosphonoethyl)-4, 4'-bipyridinium dichloride 0.75 hydrate. (1) has been determined. Crystals are triclinic, space group P-1 with Z = 2 in a cell with a = 7.2550(1), b = 13.2038(5), c = 18.5752(7) Å, α = 86.495(3), β = 83.527(2), γ = 88.921(2)o. The two independent but pseudo-symmetrically related cations in the asymmetric unit form one-dimensional hydrogen-bonded chains through short homomeric phosphonic acid O-H...O links [2.455(4), 2.464(4)A] while two of the chloride anions are similarly strongly linked to phosphonic acid groups [O-H…Cl, 2.889(4), 2.896(4)Å]. The other two chloride anions together with the two water molecules of solvation (one with partial occupancy) form unusual cyclic hydrogen-bonded bis(Cl...water) dianion units which lie between the layers of bipyridylium rings of the cation chain structures with which they are weakly associated.

The rate-limiting mechanism for the heterogeneous burning of cylindrical iron rods

This paper presents the findings of an investigation into the rate-limiting mechanism for the heterogeneous burning in oxygen under normal gravity and microgravity of cylindrical iron rods. The original objective of the work was to determine why the observed melting rate for burning 3.2-mm diameter iron rods is significantly higher in microgravity than in normal gravity. This work, however, also provided fundamental insight into the rate-limiting mechanism for heterogeneous burning. The paper includes a summary of normal-gravity and microgravity experimental results, heat transfer analysis and post-test microanalysis of quenched samples. These results are then used to show that heat transfer across the solid/liquid interface is the rate-limiting mechanism for melting and burning, limited by the interfacial surface area between the molten drop and solid rod. In normal gravity, the work improves the understanding of trends reported during standard flammability testing for metallic materials, such as variations in melting rates between test specimens with the same cross-sectional area but different crosssectional shape. The work also provides insight into the effects of configuration and orientation, leading to an improved application of standard test results in the design of oxygen system components. For microgravity applications, the work enables the development of improved methods for lower cost metallic material flammability testing programs. In these ways, the work provides fundamental insight into the heterogeneous burning process and contributes to improved fire safety for oxygen systems in applications involving both normal-gravity and microgravity environments.

Micro-family-owned business : transitory survival mechanism or long term wealth creator?

Principal Topic: Entrepreneurship is key to employment, innovation and growth (Acs & Mueller, 2008), and as such, has been the subject of tremendous research in both the economic and management literatures since Solow (1957), Schumpeter (1934, 1943), and Penrose (1959). The presence of entrepreneurs in the economy is a key factor in the success or failure of countries to grow (Audretsch and Thurik, 2001; Dejardin, 2001). Further studies focus on the conditions of existence of entrepreneurship, influential factors invoked are historical, cultural, social, institutional, or purely economic (North, 1997; Thurik 1996 & 1999). Of particular interest, beyond the reasons behind the existence of entrepreneurship, are entrepreneurial survival and good ''performance'' factors. Using cross-country firm data analysis, La Porta & Schleifer (2008) confirm that informal micro-businesses provide on average half of all economic activity in developing countries. They find that these are utterly unproductive compared to formal firms, and conclude that the informal sector serves as a social security net ''keep[ing] millions of people alive, but disappearing over time'' (abstract). Robison (1986), Hill (1996, 1997) posit that the Indonesian government under Suharto always pointed to the lack of indigenous entrepreneurship , thereby motivating the nationalisation of all industries. Furthermore, the same literature also points to the fact that small businesses were mostly left out of development programmes because they were supposed less productive and having less productivity potential than larger ones. Vial (2008) challenges this view and shows that small firms represent about 70% of firms, 12% of total output, but contribute to 25% of total factor productivity growth on average over the period 1975-94 in the industrial sector (Table 10, p.316). ---------- Methodology/Key Propositions: A review of the empirical literature points at several under-researched questions. Firstly, we assess whether there is, evidence of small family-business entrepreneurship in Indonesia. Secondly, we examine and present the characteristics of these enterprises, along with the size of the sector, and its dynamics. Thirdly, we study whether these enterprises underperform compared to the larger scale industrial sector, as it is suggested in the literature. We reconsider performance measurements for micro-family owned businesses. We suggest that, beside productivity measures, performance could be appraised by both the survival probability of the firm, and by the amount of household assets formation. We compare micro-family-owned and larger industrial firms' survival probabilities after the 1997 crisis, their capital productivity, then compare household assets of families involved in business with those who do not. Finally, we examine human and social capital as moderators of enterprises' performance. In particular, we assess whether a higher level of education and community participation have an effect on the likelihood of running a family business, and whether it has an impact on households' assets level. We use the IFLS database compiled and published by RAND Corporation. The data is a rich community, households, and individuals panel dataset in four waves: 1993, 1997, 2000, 2007. We now focus on the waves 1997 and 2000 in order to investigate entrepreneurship behaviours in turbulent times, i.e. the 1997 Asian crisis. We use aggregate individual data, and focus on households data in order to study micro-family-owned businesses. IFLS data covers roughly 7,600 households in 1997 and over 10,000 households in 2000, with about 95% of 1997 households re-interviewed in 2000. Households were interviewed in 13 of the 27 provinces as defined before 2001. Those 13 provinces were targeted because accounting for 83% of the population. A full description of the data is provided in Frankenberg and Thomas (2000), and Strauss et alii (2004). We deflate all monetary values in Rupiah with the World Development Indicators Consumer Price Index base 100 in 2000. ---------- Results and Implications: We find that in Indonesia, entrepreneurship is widespread and two thirds of households hold one or several family businesses. In rural areas, in 2000, 75% of households run one or several businesses. The proportion of households holding both a farm and a non farm business is higher in rural areas, underlining the reliance of rural households on self-employment, especially after the crisis. Those businesses come in various sizes from very small to larger ones. The median business production value represents less than the annual national minimum wage. Figures show that at least 75% of farm businesses produce less than the annual minimum wage, with non farm businesses being more numerous to produce the minimum wage. However, this is only one part of the story, as production is not the only ''output'' or effect of the business. We show that the survival rate of those businesses ranks between 70 and 82% after the 1997 crisis, which contrasts with the 67% survival rate for the formal industrial sector (Ter Wengel & Rodriguez, 2006). Micro Family Owned Businesses might be relatively small in terms of production, they also provide stability in times of crisis. For those businesses that provide business assets figures, we show that capital productivity is fairly high, with rates that are ten times higher for non farm businesses. Results show that households running a business have larger family assets, and households are better off in urban areas. We run a panel logit model in order to test the effect of human and social capital on the existence of businesses among households. We find that non farm businesses are more likely to appear in households with higher human and social capital situated in urban areas. Farm businesses are more likely to appear in lower human capital and rural contexts, while still being supported by community participation. The estimation of our panel data model confirm that households are more likely to have higher family assets if situated in urban area, the higher the education level, the larger the assets, and running a business increase the likelihood of having larger assets. This is especially true for non farm businesses that have a clearly larger and more significant effect on assets than farm businesses. Finally, social capital in the form of community participation also has a positive effect on assets. Those results confirm the existence of a strong entrepreneurship culture among Indonesian households. Investigating survival rates also shows that those businesses are quite stable, even in the face of a violent crisis such as the 1997 one, and as a result, can provide a safety net. Finally, considering household assets - the returns of business to the household, rather than profit or productivity - the returns of business to itself, shows that households running a business are better off. While we demonstrate that uman and social capital are key to business existence, survival and performance, those results open avenues for further research regarding the factors that could hamper growth of those businesses in terms of output and employment.

Structure of selected basic copper (II) sulphate minerals based upon spectroscopy : implications for hydrogen bonding

The application of near-infrared and infrared spectroscopy has been used for identification and distinction of basic Cu-sulphates that include devilline, chalcoalumite and caledonite. Near-infrared spectra of copper sulphate minerals confirm copper in divalent state. Jahn-Teller effect is more significant in chalcoalumite where 2B1g ® 2B2g transition band shows a larger splitting (490 cm-1) confirming more distorted octahedral coordination of Cu2+ ion. One symmetrical band at 5145 cm-1 with shoulder band 5715 cm-1 result from the absorbed molecular water in the copper complexes are the combinations of OH vibrations of H2O. One sharp band at around 3400 cm-1 in IR common to the three complexes is evidenced by Cu-OH vibrations. The strong absorptions observed at 1685 and 1620 cm-1 for water bending modes in two species confirm strong hydrogen bonding in devilline and chalcoalumite. The multiple bands in v3 and v4(SO4)2- stretching regions are attributed to the reduction of symmetry to the sulphate ion from Td to C2V. Chalcoalumite, the excellent IR absorber over the range 3800-500 cm-1 is treated as most efficient heat insulator among the Cu-sulphate complexes.

The ultra-low friction of the articular surface is pH-dependent and is built on a hydrophobic underlay including a hypothesis on joint lubrication mechanism

In this study, the influence of pH on interfacial energy distributed over the phospholipids-bilayer surface model and the effect of hydrophobicity on coefficient of friction (f) were investigated by using microelectrophoresis. An important clinical implication of deficiency in hydrophobicity is the loss of phospholipids that is readily observed in osteoarthritis joints. This paper establishes the influence of pH on interfacial energy upon an increase f, which might be associated with a decrease of hydrophobicity of the articular surface.

Spectroscopy of selected copper group minerals : chalcophyllite and chenevixite-implications for hydrogen bonding

NIR and IR spectroscopy has been applied for detection of chemical species and the nature of hydrogen bonding in arsenate complexes. The structure and spectral properties of copper(II) arsenate minerals chalcophyllite and chenevixite are compared with copper(II) sulphate minerals devilline, chalcoalumite and caledonite. Split NIR bands in the electronic spectrum of two ranges 11700-8500 cm-1 and 8500-7200 cm-1 confirm distortion of octahedral symmetry for Cu(II) in the arsenate complexes. The observed bands with maxima at 9860 and 7750 cm-1 are assigned to Cu(II) transitions 2B1g ® 2B2g and 2B1g ® 2A1g. Overlapping bands in the NIR region 4500-4000 cm-1 is the effect of multi anions OH-, (AsO4)3- and (SO4)2-. The observation of broad and diffuse bands in the range 3700-2900 cm-1 confirms strong hydrogen bonding in chalcophyllite relative to chenevixite. The position of the water bending vibrations indicates the water is strongly hydrogen bonded in the mineral structure. The strong absorption feature centred at 1644 cm-1 in chalcophyllite indicates water is strongly hydrogen bonded in the mineral structure. The H2O-bending vibrations shift to low wavenumbers in chenevixite and an additional band observed at 1390 cm-1 is related to carbonate impurity. The characterisation of IR spectra by ν3 antisymmetric stretching vibrations of (SO4)2- and (AsO4)3 ions near 1100 and 800 cm-1 respectively is the result of isomorphic substitution for arsenate by sulphate in both the minerals of chalcophyllite and chenevixite.