The crystal structure of free human hypoxanthineguanine phosphoribosyltransferase reveals extensive conformational plasticity throughout the catalytic cycle

Human hypoxanthine-guanine phosphoribosyltransferase (HGPRT) catalyses the synthesis of the purine nucleoside monophosphates, IMP and GMP, by the addition of a 6-oxopurine base, either hypoxanthine or guanine, to the 1-beta-position of 5-phospho-U-D-ribosyl-1-pyrophosphate (PRib-PP). The mechanism is sequential, with PRib-PP binding to the free enzyme prior to the base. After the covalent reaction, pyrophosphate is released followed by the nucleoside monophosphate. A number of snapshots of the structure of this enzyme along the reaction pathway have been captured. These include the structure in the presence of the inactive purine base analogue, 7-hydroxy [4,3-d] pyrazolo pyrimidine (HPP) and PRib-PP. Mg2+, and in complex with IMP or GMP. The third structure is that of the immucillinHP.Mg2+.PPi complex, a transition-state analogue. Here, the first crystal structure of free human HGPRT is reported to 1.9 angstrom resolution, showing that significant conformational changes have to occur for the substrate(s) to bind and for catalysis to proceed. Included in these changes are relative movement of subunits within the tetramer, rotation and extension of an active-site alpha-helix (D137-D153), reorientation of key active-site residues K68, D137 and K165, and the rearrangement of three active-site loops (100-128, 165-173 and 186-196). Toxoplasina gondii HGXPRT is the only other 6-oxopurine phosphoribosyltransferase structure solved in the absence of ligands. Comparison of this structure with human HGPRT reveals significant differences in the two active sites, including the structure of the flexible loop containing K68 (human) or K79 (T gondii). (c) 2005 Elsevier Ltd. All rights reserved.

A theoretical study of the origin of rotational barriers in push-pull ethylenes

Using the B3LYP/6-31G* ab initio method, we have studied the rotation about the C=C bonds in 15 push-pull ethylenes of the general formula (X,Y)C=C(CHO)(2) [X, Y = NH2, NHCH3, N(CH3)(2), OCH3, SCH3] in the gas phase. Two stationary points (minimum and transition state) were located for all compounds. The geometry, dipole moments, natural bond orbital atomic charges, as well as the rotational barriers were examined. The torsion angle 0 depends essentially on the presence or absence of intramolecular hydrogen bonds, and the barrier is a function of the torsion angle. (C) 2002 Elsevier Science B.V. All rights reserved.

Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase

Crystal structures have been determined for free Escherichia coli hypoxanthine phosphoribosyltransferase (HPRT) (2.9 Angstrom resolution) and for the enzyme in complex with the reaction products, inosine 5'-monophosphate (IMP) and guanosine 5-monophosphate (GMP) (2.8 Angstrom resolution). Of the known 6-oxopurine phosphoribosyltransferase (PRTase) structures, E. coli HPRT is most similar in structure to that of Tritrichomonas foetus HGXPRT, with a rmsd for 150 Calpha atoms of 1.0 Angstrom. Comparison of the free and product bound structures shows that the side chain of Phe156 and the polypeptide backbone in this vicinity move to bind IMP or GMP. A nonproline cis peptide bond, also found in some other 6-oxopurine PRTases, is observed between Leu46 and Arg47 in both the free and complexed structures. For catalysis to occur, the 6-oxopurine PRTases have a requirement for divalent metal ion, Usually Mg2+ in vivo. In the free structure, a Mg2+, is coordinated to the side chains of Glu103 and Asp104. This interaction may be important for stabilization of the enzyme before catalysis. E. coli HPRT is unique among the known 6-oxopurine PRTases in that it exhibits a marked preference for hypoxanthine as substrate over both xanthine and guanine. The structures suggest that its substrate specificity is due to the modes of binding of the bases. In E. coli HPRT, the carbonyl oxygen of Asp 163 would likely form a hydrogen bond with the 2-exocyclic nitrogen of guanine (in the HPRT-guanine-PRib-PP-Mg2+ complex). However, hypoxanthine does not have a 2-exocyclic atom and the HPRT-IMP structure suggests that hypoxanthine is likely to occupy a different position in the purine-binding pocket.

Molecular orbital theory calculations of the H2O-carbon reaction

Carbon gasification with steam to produce H-2 and CO is an important reaction widely used in industry for hydrogen generation. Although the literature is vast, the. mechanism for the formation of H-2 is still unclear. In particular, little has, been done to investigate the potential of molecular orbital theory to distinguish different mechanism possibilities. In this work, we used molecular orbital theory to demonstrate a favorable energetic pathway where H2O is first physically adsorbed on the virgin graphite surface with negligible change in molecular structure. Chemisorption occurs via O approaching the carbon edge site with one H atom stretching away from the O in the transition state. This is followed by a local minimum. state in which the stretching H is further disconnected from the O atoms and the remaining OH group is still on the carbon edge site. The disconnected H then pivot around the OH group to bond with the H of the OH group and forms H-2. The O atom remaining on the carbon edge site is subsequently desorbed as CO. The reverse occurs when H-2 reacts with the surface oxygen to produce H2O.

Thermodynamic non-ideality as an alternative source of the effect of sucrose on the thrombin-catalyzed hydrolysis of peptide p-nitroanalide substrates

The inhibitory effect of sucrose on the kinetics of thrombin-catalyzed hydrolysis of the chromogenic substrate S-2238 (D-phenylalanyl-pipecolyl-arginoyl-p-nitroanilide) is re-examined as a possible consequence of thermodynamic non-ideality-an inhibition originally attributed to the increased viscosity of reaction mixtures. However, those published results may also be rationalized in terms of the suppression of a substrate-induced isomerization of thrombin to a slightly more expanded (or more asymmetric) transition state prior to the irreversible kinetic steps that lead to substrate hydrolysis. This reinterpretation of the kinetic results solely in terms of molecular crowding does not signify the lack of an effect of viscosity on any reaction step(s) subject to diffusion control. Instead, it highlights the need for development of analytical procedures that can accommodate the concomitant operation of thermodynamic non-ideality and viscosity effects.

Back to (non)-Basics: Recent developments in neutral and charge-balanced glycosidase inhibitors

Certain glycosidase inhibitors possess potent antiviral, antitumour and antidiabetic properties. Glyconic acid lactones, the earliest glycosidase inhibitors identified, have planar anomeric carbons that mimic the transition state of glycoside hydrolysis. Other classes include lactams, glycals, epoxides, halides and sulfonium ions, the latter based on the natural product salacinol from an antidiabetic herb.

N-aminopyrroledione-hydrazonoketene-pyrazolium oxide-pyrazolone rearrangements and pyrazolone tautomerism

Flash vacuum thermolysis (FVT) of 1-(dimethylamino)pyrrole-2,3-diones 5 causes extrusion of CO with formation of transient hydrazonoketenes 7. The transient ketenes 7 are observable in the form of weak bands at 2130 (7a) or 2115 cm(-1) (7b) in the Ar matrix IR spectra resulting from either FVT or photolysis of either 5 or 1,1- dimethylpyrazolium-5- oxides 8, and these absorptions are in excellent agreement with B3LYP/6-31G* frequency calculations. Under FVT conditions the ketenes 7 cyclize to pyrazolium oxides 8, which undergo 1,4-migration of a methyl group to yield 1,4-dimethyl-3-phenylpyrazole-5(4H)-one 9a and 1,4,4-trimethyl-3-phenylpyrazole-5(4H)-one 9b. All three tautomers of 9a have been characterized, viz. the CH form 9a (most stable form in the gas phase, the solid state and solvents of low polarity), the OH form 9a' (metastable solid at room temperature) and the NH form 9a (stable in aprotic dipolar solvents). The isomeric 1,4-dimethyl-5-phenylpyrazole-3(2H)-one 12 tautomerizes to the 3-hydroxypyrazole 12'. The crystal structure of the hydrochloride 14 of 9a'/9a is reported, representing the first structurally characterised example of a protonated 5-hydroxypyrazole.

Development of an injectable grout for concrete repair and strengthening

This paper deals with the coupled effect of temperature and silica fume addition on rheological, mechanical behaviour and porosity of grouts based on CEMI 42.5R, proportioned with a polycarboxylate-based high range water reducer. Preliminary tests were conducted to focus on the grout best able to fill a fibrous network since the goal of this study was to develop an optimized grout able to be injected in a mat of steel fibers for concrete strengthening. The grout composition was developed based on criteria for fresh state and hardened state properties. For a CEMI 42.5R based grout different high range water reducer dosages (0%, 0.2%, 0.4%, 0.5%, 0.7%) and silica fume (SF) dosages (0%, 2%, 4%) were tested (as replacement of cement by mass). Rheological measurements were used to investigate the effect of polycarboxylates (PCEs) and SF dosage on grout properties, particularly its workability loss, as the mix was to be injected in a matrix of steel fibers for concrete jacketing. The workability behaviour was characterized by the rheological parameters yield stress and plastic viscosity (for different grout temperatures and resting times), as well as the procedures of mini slump cone and funnel flow time. Then, further development focused only on the best grout compositions. The cement substitution by 2% of SF exhibited the best overall behaviour and was considered as the most promising compared to the others compositions tested. Concerning the fresh state analysis, a significant workability loss was detected if grout temperature increased above 35 degrees C. Below this temperature the grout presented a self-levelling behaviour and a life time equal to 45 min. In the hardened state, silica fumes increased not only the grout's porosity but also the grout's compressive strength at later ages, since the pozzolanic contribution to the compressive strength does not occur until 28 d and beyond. (C) 2012 Elsevier Ltd. All rights reserved.

Sarcoplasmic reticulum calcium ATPase is inhibited by organic vanadium coordination compounds: pyridine-2,6-dicarboxylatodioxovanadium(V), BMOV, and an amavadine analogue

Inorg Chem. 2008 Jul 7;47(13):5677-84. doi: 10.1021/ic702405d

Dinámica y cinética de los procesos físicos y químicos del radical OH con compuestos orgánicos volátiles (COVs) de relevancia atmosférica. Dynamics and kinetics of the physical and chemical processes of OH radicals with atmospheric relevant volatile organic compounds (VOCs)

El objetivo del presente proyecto es estudiar los procesos físicos y químicos del radical OH con compuestos orgánicos volátiles (COVs), con los cuales sea factible la formación de agregados de van der Waals (vdW) responsables de la curvatura en los gráficos de Arrhenius, empleando técnicas modernas, complementarias entre si y novedosas en el país. El problema será abordado desde tres perspectivas complementarias: 1) estudios cinéticos, 2) estudios mecanísticos y de distribución de productos y 3) estudios de la dinámica de los procesos físicos y químicos. La finalidad es alcanzar una mejor comprensión de los mecanismos que intervienen en el comportamiento químico de especies presentes en la atmósfera y obtener datos cinéticos de alta calidad que puedan alimentar modelos computacionales capaces de describir la composición de la atmósfera, presente y futura. Los objetivos son estudiar: 1) mediante fotólisis láser pulsada con detección por fluorescencia inducida por láser (PLP-LIF), en reactores de flujo, la cinética de reacción del radical OH(v”=0) con COVs que presentan gráficos de Arrhenius curvos con energías de activación negativas, tales como alcoholes insaturados, alquenos halogenados, éteres halogenados, ésteres alifáticos; 2) en una cámara de simulación de condiciones atmosféricas de gran volumen (4500 L), la identidad y el rendimiento de productos de las reacciones mencionadas, a fines de evaluar su impacto atmosférico y dilucidar los mecanismos de reacción; 3) mediante haces moleculares y espectroscopía láser, la estructura y reactividad de complejos de vdW entre alcoholes insaturados o aromáticos (cresoles) y el radical OH, como modelo de los aductos propuestos como responsables de la desviación al comportamiento de Arrhenius de las reacciones mencionadas; 4) mediante PLP-LIF y expansiones supersónicas, las constantes específicas estado a estado (ksts) de relajación/reacción del radical OH(v”=1-4) vibracionalmente excitado con los COVs mencionados. Los resultados experimentales obtenidos serán contrastados con cálculos ab-initio de estructura electrónica, los cuales apoyarán las interpretaciones, permitirán proponer estructuras de estados de transición y aductos colisionales, como así también calcular las frecuencias de vibración de los complejos de vdW para su posterior asignación en los espectros LIF y REMPI. Asimismo, los mecanismos de reacción propuestos y los parámetros cinéticos medidos experimentalmente serán comparados con aquellos obtenidos por cálculos teóricos. The aim of this project is to study the physical and chemical processes of OH radicals with volatile organic compounds (VOCs) with which the formation of van der Waals (vdW) clusters, responsible for the observed curvature in the Arrhenius plots, might be feasible. The problem will be addressed as follow : 1) kinetic studies; 2) products distribution and mechanistic studies and 3) dynamical studies of the physical and chemical processes. The purpose is to obtain a better understanding of the mechanisms that govern the chemical behavior of species present in the atmosphere and to obtain high quality kinetic data to be used as input to computational models. We will study: 1) the reaction kinetics of OH (v”=0) radicals with VOCs such as unsaturated alcohols, halogenated alkenes, halogenated ethers, aliphatic esters, which show curved Arrhenius plots and negative activation energies, by PLP-LIF, in flow systems; 2) in a large volume (4500 L) atmospheric simulation chamber, reaction products yields in order to evaluate their atmospheric impact and reaction mechanisms; 3) using molecular beams and laser spectroscopy, the structure and reactivity of the vdW complexes formed between the unsaturated or aromatic alcohols and the OH radicals as a model of the adducts proposed as responsible for the non-Arrhenius behavior; 4) the specific state-to-state relaxation/reaction rate constants (ksts) of the vibrationally excited OH (v”=1-4) radical with the VOCs by PLP-LIF and supersonic expansions. Ab-initio calculations will be carried out to support the interpretation of the experimental results, to obtain the transition state and collisional adducts structures, as well as to calculate the vibrational frequencies of the vdW complexes to assign to the LIF and REMPI spectra. Also, the proposed reaction mechanisms and the experimentally measured kinetic parameters will be compared with those obtained from theoretical calculations.

Cis-configured aziridines are new pseudo-irreversible dual-mode inhibitors of Candida albicans secreted aspartic protease 2

A series of cis-configured epoxides and aziridines containing hydrophobic moieties and amino acid esters,were synthesized as new potential inhibitors of the secreted aspartic protease 2 (SAP2) of Candida albicans. Enzyme assays revealed the N- benzyl-3-phenyl-substituted aziridines 11 and 17 as the most potent inhibitors, with second-order inhibition, rate constants (k(2)) between 56000 and 12-1000 M-1 min(-1). The compounds were shown to be pseudo-irreversible dual-mode, inhibitors: the interm ediate esterified enzyme resulting from nucleophilic ring opening was hydrolyzed and yielded amino alcohols as transition state-mimetic reversible inhibitors. The results of docking studies with the ring-closed aziridine forms of the inhibitors suggest binding modes mainly dominated by hydrophobic interactions with the S1, S1' S2, and S2' subsites of the protease, and docking studies with the processed amino alcohol forms predict additional hydrogen bonds of the new hydroxy group to the active site Asp residues. C. albicans growth assays showed the compounds to decrease SAP2-dependent growth while not affecting SAP2-independent growth.

Myymäläketjun hankintatoiminnan mittarit, Case Tiimari Oyj

Työn tavoitteena oli kehittää yritykselle selkeä ja toimiva hankintatoiminnan suorituskykymittaristo, jonka avulla tietojärjestelmien tuottama tietosaadaan hyötykäyttöön. Tavoitteena oli myös selvittää yrityksen hankintatoiminnan nykytila. Selvitys auttoi sopivien mittareiden valinnassa. Teoriaosassa käsiteltiin suorituskyvyn mittaamista hankintatoiminnassa, mittariston suunnittelua ja käyttöönoton vaiheita sekä erilaisia malliratkaisuja hankintatoiminnan suorituskyvyn mittaamiselle. Empiirisessä osassa perehdyttiin yrityksen hankintatoiminnan nykytilaan sekä rakennettiin teorian, nykytila-analyysin ja hankintahenkilökunnan näkemysten pohjalta suorituskykymittaristo yrityksen osto-osastolle. Hankintatoiminnan nykytilanteen arvioinnissa korostuivat parhaillaan tapahtuvat suuret muutokset. Suorituskykymittaristo laadittiin siten, että se kattaa tärkeimmät osa-alueet myymäläketjun hankintatoiminnassa. Työn tuloksena kehitetty mittaristo koostuu toimittaja-, valikoima-, materiaalivirta- sekä varastomittareista.

Harmonisation of Inbound Logistics with Local Suppliers

Nokian Matkapuhelimien tuotantoprosessit on suunniteltu tukemaan massaräätälöintiä perustuen assembly-to-order tekniikkaan (ATO). Tämän työn tehtävänä oli kehittää toimitusmallit ATO-materiaaleille paikallisilta alihankkijoilta matkapuhelintehtaalle. Aluksi analysoitiin nykyiset toimintamallit perustun Nokia Komarom Kft:n työntekijöiden ja toimittajien haastatteluihin. Ongelmiksi havaittiin toimintatapojen monimuotoisuus, dokumentoinnin puute, puutteelliset laskut ja riittämätön toimitusseuranta.Malleille asetettavien joustavuusvaatimusten selvittämiseksi suoritettiin laajamittainen näkyvyysvälineiden ja tuotantokapasiteetin tutkimus. Vaatimukset tilauksesta toimitukseen läpimenoajoille ja kuljetustoiminnoille johdettiin joustavuusvaatimuksista. Työn lopussa muodostetaan toimitusmallit perustuen nykytilan analyysiin, havaittuihin ongelmiin ja malleille asetettuihin vaatimuksiin. Materiaalit jaetaan eri malleilla ohjattaviksi niiden ominaisuuksiin perustuen. Ensimmäinen malleista implementoidaan kahden pilottitoimittajan kanssa ja esitetään tulokset. Toista mallia hyödynnetään lähitulevaisuudessa Nokia Komarom Kft:n aloittaessa yhteistyön uusien paikallistoimittajien kanssa.

Informaation hallinta prosessiteollisuuden investointiprojektissa

Diplomityössä on tutkittu kohdeyrityksen, UPM-Kymmene Oyj Kymin tuotantoyksikön nykyisiä investointiprojektin tiedonhallinnan käytäntöjä. Nykytilan selvityksen ja haastatteluissa ilmenneiden tarpeiden perusteella on työssä esitelty uusi toimintamalli tulevia investointiprojekteja varten. Diplomityö perustuu aihepiirin kirjalliseen tarkasteluun ja yhteistyökumppaneiden haastatteluihin. Kirjallisuuden avulla on selvitetty dokumenttienhallinnan teoriaa ja tulevaisuuden näkymiä. Haastatteluilla on selvitetty Kymin tiedonhallinnan nykytilaa ja tulevia tarpeita. Haastatteluita on tehty Kymillä sisäisesti ja Kymin konsultti- ja laitetoimittajaosapuolten kanssa. Työssä käsitellään informaationhallintaa dokumenttienhallinnan ja erilaisten investointiprojektissa käsiteltävien dokumenttien pohjalta. Investointiprojektissa syntyvän talletettavan ja arkistoitavan dokumenttiaineiston lisäksi huomioidaan laitetietojen hallinta, mutta vain periaatteellisella tasolla. Investointiprojektin tiedonhallinnassa ehdotetaan siirryttävän perinteisestä eri projektiosapuolten keskinäisestä tiedonvaihdosta verkottuneeseen tiedonhallinnan malliin. Verkottuneessa tiedonhallinnassa toimitaan investointiprojektin osapuolten yhteisen tietovaraston avulla. Työn tuloksena syntynyt kohdeyrityksen toimintamalli koostuu useista eri osa-alueista, mikä mahdollistaa toimintamallin hyödyntämisen yksittäisiä osa-alueita kokonaisuudesta irrottamalla. Toimintamallia on mahdollista hyödyntää vastaavanlaisten tuotanto-laitosten investointiprojektien yhteydessä. Työssä toimintamallin käytännön sovellutus kohdeyrityksessä on esitetty käyttöönottoprojektina.

Classification and inventory management of abnormal demand items

The main objective of the study is to form a framework that provides tools to recognise and classify items whose demand is not smooth but varies highly on size and/or frequency. The framework will then be combined with two other classification methods in order to form a three-dimensional classification model. Forecasting and inventory control of these abnormal demand items is difficult. Therefore another object of this study is to find out which statistical forecasting method is most suitable for forecasting of abnormal demand items. The accuracy of different methods is measured by comparing the forecast to the actual demand. Moreover, the study also aims at finding proper alternatives to the inventory control of abnormal demand items. The study is quantitative and the methodology is a case study. The research methods consist of theory, numerical data, current state analysis and testing of the framework in case company. The results of the study show that the framework makes it possible to recognise and classify the abnormal demand items. It is also noticed that the inventory performance of abnormal demand items differs significantly from the performance of smoothly demanded items. This makes the recognition of abnormal demand items very important.