Probabilistic contact preferences in protein-ligand and protein-protein complexes

Modeller för intermolekulär växelvärkan utnyttjas brett inom biologin. Analys av kontakter mellan proteiner och läkemedelsforskning representerar typiska tillämpningsområden för dylika modeller. En modell som beskriver sådana molekylära växelverkningar kan utformas med hjälp av biofysisk teori, vilket tenderar att resultera i ytterst tung beräkningsbörda även för enkla tillämpningar. Ett alternativt sätt att formulera modeller är att utnyttja stora databaser som innehåller strukturmätningar gjorda med hjälp av till exempel röntgendiffraktion. Då man använder sig av empiriska mätdata direkt, möjliggör en statistisk modell att osäkerheten och inexaktheten i datat tas till hänsyn på ett adekvat sätt, samtidigt som beräkningsbördan håller sig på en rimligare nivå jämfört med kvantmekaniska metoder som i princip borde ge de optimala resultaten. I avhandlingen utvecklades en 3D modell för numerisk undersökning av intermolekulär växelverkan baserad på Bayesiansk statistik. Modellens syfte är att åstadkomma prognoser för det hurdana eller vilka molekylstrukturer prefereras i en given kontext, d.v.s. är mer sannolika inom ramen för interaktion. Modellen testades i essentiella molekyläromgivningar - en liten molekyl vid sin bindningsplats hos ett protein och en gränsyta mellan proteinerna i ett komplex. De erhållna numeriska resultaten motsvarar väl experimentella resultat som tidigare rapporterats i litteraturen, exempelvis kvalitativa bindningsaffiniteter och kemisk kännedom av vissa aminosyrors rumsliga förmågor att utgöra bindningar. I avhandlingen gjordes ytterligare preliminära tester av den statistiska ansatsen för modellering av den centrala molekylära strukturella anpassningsbarheten. I praktiken är den utvecklade modellen ämnad som ett led i en mer omfattande analysmetod, så som en s.k. farmakofor modell. Molekyylivuorovaikutusten mallintamista hyödynnetään laajasti biologisten kysymysten tarkastelussa. Tyypillisiä esimerkkejä sovelluskohteista ovat proteiinien väliset kontaktit ja lääkesuunnittelu. Vuorovaikutuksia kuvaavan mallin lähtökohta voi olla molekyyleihin liittyvä teoria, jolloin soveltamiseen liittyvä laskenta saattaa olla erityisen raskasta, tai suuri havaintojoukko joka on saatu aikaan esimerkiksi mittaamalla rakenteita röntgendiffraktio menetelmällä. Tilastollinen malli mahdollistaa havaintoaineistossa olevan epätarkkuuden ja epävarmuuden huomioimisen, samalla pitäen laskennallisen kuorman pienempänä verrattuna periaatteessa parhaan tuloksen antavaan kvanttimekaaniseen mallinnukseen. Väitöstyössä kehitettiin bayesiläiseen tilastotieteeseen perustuva 3D malli molekyylien välisten vuorovaikutusten laskennalliseen tarkasteluun. Mallin tehtävä on tuottaa ennusteita sen suhteen, minkä tai millaisten molekyylirakenteiden väliset kompleksit ovat etusijalla, toisin sanoen todennäköisempiä, vuorovaikutustilanteessa. Työssä kehitetyn menetelmän toimivuutta testattiin käyttötarkoituksen suhteen olennaisissa molekyyliympäristöissä - pieni molekyyli sitoutumiskohdassaan proteiinissa sekä rajapinta kahden proteiinin välilllä proteiinikompleksissa. Saadut laskennalliset tulokset vastasivat hyvin vertailuun käytettyjä kirjallisuudesta saatuja kokeellisia tuloksia, kuten laadullisia sitoutumisaffiniteetteja, sekä kemiallista tietoa esimerkiksi tiettyjen aminohappojen avaruudellisesta sidoksenmuodostuksesta. Väitöstyössä myös alustavasti testattiin tilastollista lähestymistapaa tärkeän molekyylien rakenteellisen mukautuvuuden mallintamiseen. Käytännössä malli on tarkoitettu osaksi jotakin laajempaa analyysimenetelmää, kuten farmakoforimallia.

Injúria potencial de herbicidas de solo ao girassol: IV - rendimento de aquênios e componentes do rendimento

Conduziu-se um ensaio em campo na Estação Experimental Agronômica da Universidade Federal do Rio Grande do Sul, em Eldorado do Sul, RS, em 1989/90. O objetivo foi determinar o efeito dos herbicidas clomazone, chlorimuronethyl, imazaquin e imazethaphyr, aplicados em três doses à superfície do solo (PRE) ou incorporados no mesmo (PPI), sobre o rendimento de aquênios de girassol e seus componentes. Os herbicidas de solo para controle de plantas daninhas na cultura da soja com maior potencial de dano ao girassol cultivado em sucessão, conforme indicado pelo rendimento de aquênios, foram os seguintes, em ordem decrescente: imazaquin > clomazone > imazethapyr> chlorimuron-ethyl. O efeito mais pronunciado dos herbicidas foi a redução da população de plantas. Este foi o fator que mais influenciou no rendimento do girassol.

Estudos anatômicos de folhas de espécies de plantas daninhas de grande ocorrência no Brasil: IV - Amaranthus deflexus, Amaranthus spinosus, Alternanthera tenella e Euphorbia heterophylla

Neste trabalho é apresentado um estudo da anatomia das folhas de espécies de plantas daninhas de grande ocorrência no Brasil: Amaranthus deflexus, Amaranthus spinosus, Alternanthera tenella e Euphorbia heterophylla, visando melhor compreensão das barreiras que cada espécie impõe à penetração dos herbicidas e outros compostos utilizados em aplicações foliares. As folhas completamente expandidas do terceiro ao quinto nó foram coletadas de plantas de ocorrência espontânea no campo. Das folhas de cada espécie foram obtidas três amostras da região mediana, com aproximadamente 1 cm², as quais foram utilizadas em estudos da estrutura, clarificação e em observações em microscópio eletrônico de varredura. Todas as espécies avaliadas são anfiestomáticas. As principais barreiras foliares potenciais à penetração de herbicidas observadas nas plantas daninhas A. deflexus e A. spinosus foram, respectivamente, grande espessura da cutícula da face adaxial e da cutícula das duas faces. Já em relação a A. tenella, grande espessura da cutícula das duas faces, elevado teor de cera epicuticular e alta densidade tricomática foram os principais obstáculos potenciais detectados. E. heterophylla apresentou como possíveis principais barreiras foliares à penetração de agroquímicos o alto teor de cera epicuticular, a elevada densidade de laticíferos e a grande espessura da cutícula da face adaxial.

Structural studies and in vivo characterisation of Oct4:PORE and Oct4/Sox2:UTF1 complexes

Monikykyiset kantasolut pystyvät erilaistumaan alkion kehityksen aikana miksi tahansa kehittyvän eläimen kudokseksi. Alkion kehitystä on tutkittu vuosikymmeniä ja ensimmäisen kerran kantasoluja viljeltiin 1980-luvulla. Noin vuosikymmen myöhemmin kloonattiin ensimmäinen nisäkäs, Dolly-lammas, mikä oli läpimurto perimän kloonauksessa. Vajaa kymmenen vuotta sitten japanilaiset tutkijat pystyivät ensimmäisen kerran tuottamaan indusoituja monikykyisiä kantasoluja. Nämä kantasolut tuotettiin ilmentämällä neljää geeniä, jotka uudelleenohjelmoivat erilaistuneet solut takaisin kantasoluiksi. Geenien ilmentymistä säätelevä ja DNA:han sitoutuvan proteiinin Oct4:n on todettu olevan tärkeä tekijä uudelleenohjelmissa. Oct4 kuuluu transkriptiotekijäperheeseen, joka säätelee geenien ilmentymistä kantasoluissa. Tässä työssä kiteytin Oct4-proteiinin sen kohde-DNA:n kanssa sekä tutkin sen sitoutumista ja atomitason rakennetta röntgensädekristallografian avulla. Tutkimuksessamme paljastui useita Oct4:n atomitason rakenteellisia ominaisuuksia, jotka selittävät sen säätelymekanismeja kantasoluissa.

Libri Armeniaci Bibliothecae Universitatis Helsingiensis: catalogum ordine litterarum, IV

Supplementum-osassa paljon tyhjiä välilehtiä.

Espécies de Parmotrema (Parmeliaceae, Ascomycota) do litoral Centro-Sul do Estado de São Paulo IV.: grupo químico protocetrárico

O levantamento das espécies pertencentes aos gêneros de grandes parmélias do litoral Centro-Sul do Estado de São Paulo revelou a ocorrência de onze espécies de Parmotrema sensu stricto (talos foliosos de lobos arredondados em geral com mais de 0,5 cm de largura com margens inferiores não rizinadas) contendo ácido protocetrárico como principal constituinte químico medular. São apresentados uma chave de identificação, descrições, comentários e ilustrações.

Kertomuksia Suomen historiasta - IV - Ensimmäinen osa, Ruotsin mahtawuuden aikakausi, Kustaa Aadolfin ja Kristiinan hallitus

Nimiösivulla myös: Warustettu 19:llä kuwalla.

Geographiske chartor öfwer Swerige med hans maj. konung Gustaf IV Adolphs allernådigste tillstånd utgifne af friherre S. G. Hermelin. [Kartta-aineisto] Andra Afdelningen, Storfurstendömet Finland.

Karttalehdet: Charta öfwer Swerige med tilgränsande länder ; Charta öfwer Storfurstendömet Finland ; Charta öfver Åbo och Björneborgs höfdingedöme ; Charta öfver Wasa höfdingedöme ; Charta öfver Uleåborgs höfdingedöme ; Charta öfver Savolax och Karelens eller Kuopio höfdingedöme ; Charta öfver Nylands och Tavastehus samt Kymmenegårds höfdingedömen. Nimiösivun kuva: Utsigt ifrån Wermasvuori åt sjöarne Jokijärvi och Ilmolanselkä uti Hauho sockn i Nylands och Tavastehus höfdingedöme / ritad af C. P. Hällström ; graverad af J. F. Martin.

Gallia IV : nova tabula : Francia

Julkaisussa: Geographia universalis, vetus et nova, complectens Claudii Ptolemaei Alexandrini enarrationis libros VIII

Tabulae Peutingerianae segmentum III : a Marcomannis ad Sarmatas usque ; Segmentum IV : a Sarmatis usque ad Hamaxobios

Julkaisussa: Accuratissima orbis antiqui delineatio, sive, geographia vetus, sacra & profana

Precipitated immune complexes of IgM induce the generation of reactive oxygen species by rabbit polymorphonuclear leucocytes

We report that immune complexes of IgM (ICIgM) antibodies and ovalbumin in the form of a precipitate from the equivalence zone induce the generation of reactive oxygen species by rabbit blood polymorphonuclear leucocytes (PMN), as measured by the chemiluminescence (CL) production in the presence of luminol. The kinetics of CL generation induced by ICIgM is quite different from that induced by precipitated immune complexes of IgG (ICIgG): the maximum rate of CL production for ICIgM occurs around 14 min, whereas for ICIgG it occurs about 5 min after incubation with the cells. Also the triggering of the process requires a higher concentration of ICIgM than of ICIgG. Evidence is presented that these effects are not mediated by interaction of the antigen (ovalbumin) with the cell, since immune precipitates of ovalbumin and the F(ab')2 fragment had no effect. Our observations that precipitated ICIgM can also be an effective stimulus for CL generation and thus for O2- production reveal a new functional capability of PMN. These results may have implications for the understanding of the participation of ICIgM (as well as of ICIgG) in inflammatory reactions mediated by PMN in immune complex diseases, and in the mechanisms of defense against microbes and other non-self agents.

Breviarium Fratrum Praedicatorum (MS C.IV.10)

Two probably originally distinct but roughly contemporary books (I-II, copied by three scribes, A-C): A psalter and a Dominican breviary. Complete critical and codicological description of the book and its contents available in the Codices Fennici -database.

Contents: I: Psalter: Fols. 7r–76va, Psalter, with additional hymns, concluding with Te Deum; Fols. 76vb–77vb, the Athanasian Creed; Fols. 77vb–80v, litany and other prayers. II: Dominican breviary: Fols. 1r–6v, English Dominican calendar (Jan.–Dec.); Fols. 81r–242v, 276r–312r, proprium de tempore (defect), from the First Advent to the First Sunday after Trinity, and from septuagesima in mensis Augusti to the 25th Sunday after Trinity; Fols. 313ra–318v, Office for the dedication of a church; Fols. 243r–275v, 319r–334v, 353r–v, 335r–352v, 354r–371r, proprium de sanctis (defect), from the beginning up to the office of Mary Magdalene, with a misplaced leaf, fol. 353, at translatio B. Dominici, and, after several missing gatherings, the end of commune sanctorum; Fol. 371v, originally empty, with office for St Ursula added in a saec. XIV hand.

The brain decade in debate: IV. Chronobiology

The present article is the adapted version of an electronic symposium organized by the Brazilian Society of Neuroscience and Behavior (SBNeC) which took place on June 14, 2000. The text is divided into three sections: I. The main issues, II. Chronodrugs, and III. Methods. The first section is dedicated to the perspectives of chronobiology for the next decade, with opinions about the trends of future research being emitted and discussed. The second section deals mostly with drugs acting or potentially acting on the organism's timing systems. In the third section there are considerations about relevant methodological issues concerning data analysis.

Sec61alpha synthesis is enhanced during translocation of nascent chains of collagen type IV in F9 teratocarcinoma cells after retinoic acid treatment

Nascent procollagen peptides and other secretory proteins are transported across the endoplasmic reticulum (ER) membrane through a protein-conducting channel called translocon. Sec61alpha, a multispanning membrane translocon protein, has been implicated as being essential for translocation of polypeptide chains into the cisterns of the ER. Sec61alpha forms a protein complex with collagen and Hsp47, an ER-resident heat shock protein that binds specifically to collagen. However, it is not known whether Sec61alpha is ubiquitously produced in collagen-producing F9 teratocarcinoma cells or under heat shock treatment. Furthermore, the production and utilization of Sec61alpha may depend on the stage of cell differentiation. Cultured F9 teratocarcinoma cells are capable of differentiation in response to low concentrations of retinoic acid. This differentiation results in loss of tumorigenicity. Mouse F9 cells were grown in culture medium at 37ºC and 43ºC (heat shock treatment) treated or not with retinoic acid, and labeled in certain instances with 35S-methionine. Membrane-bound polysomes of procollagen IV were then isolated. Immunoprecipitation and Western blot analysis were performed using polyclonal antibodies against collagen IV, Hsp47 and Sec61alpha. Under retinoic acid-untreated conditions, F9 cells produced undetectable amounts of Sec61alpha. Sec61alpha, Hsp47 and type IV collagen levels were increased after retinoic acid treatment. Heat shock treatment did not alter Sec61alpha levels, suggesting that Sec61alpha production is probably not affected by heat shock. These data indicate that the enhanced production of Sec61alpha in retinoic acid-induced F9 teratocarcinoma cells parallels the increased synthesis of Hsp47 and collagen type IV.

Dipeptidyl peptidase IV (CD26) activity in the hematopoietic system: differences between the membrane-anchored and the released enzyme activity

Dipeptidyl peptidase IV (DPP-IV; CD26) (EC 3.4.14.5) is a membrane-anchored ectoenzyme with N-terminal exopeptidase activity that preferentially cleaves X-Pro-dipeptides. It can also be spontaneously released to act in the extracellular environment or associated with the extracellular matrix. Many hematopoietic cytokines and chemokines contain DPP-IV-susceptible N-terminal sequences. We monitored DPP-IV expression and activity in murine bone marrow and liver stroma cells which sustain hematopoiesis, myeloid precursors, skin fibroblasts, and myoblasts. RT-PCR analysis showed that all these cells produced mRNA for DPP-IV. Partially purified protein reacted with a commercial antibody to CD26. The K M values for Gly-Pro-p-nitroanilide ranged from 0.43 to 0.98 mM for the membrane-associated enzyme of connective tissue stromas, and from 6.76 to 8.86 mM for the enzyme released from the membrane, corresponding to a ten-fold difference, but only a two-fold difference in K M was found in myoblasts. K M of the released soluble enzyme decreased in the presence of glycosaminoglycans, nonsulfated polysaccharide polymers (0.8-10 µg/ml) or simple sugars (320-350 µg/ml). Purified membrane lipid rafts contained nearly 3/4 of the total cell enzyme activity, whose K M was three-fold decreased as compared to the total cell membrane pool, indicating that, in the hematopoietic environment, DPP-IV activity is essentially located in the lipid rafts. This is compatible with membrane-associated events and direct cell-cell interactions, whilst the long-range activity depending upon soluble enzyme is less probable in view of the low affinity of this form.