Modes of binding of guanosine monophosphates to ribonuclease T1 - A computer modelling study

Computer-modelling studies on the modes of binding of the three guanosine monophosphate inhibitors 2'-GMP, 3'-GMP, and 5'-GMP to ribonuclease (RNase) T1 have been carried out by energy minimization in Cartesian-coordinate space. The inhibitory power was found to decrease in the order 2'-GMP > 3'-GMP > 5'-GMP in agreement with the experimental observations. The ribose moiety was found to form hydrogen bonds with the protein in all the enzyme-inhibitor complexes, indicating that it contributes to the binding energy and does not merely act as a spacer between the base and the phosphate moieties as suggested earlier. 2'-GMP and 5'-GMP bind to RNase T1 in either of the two ribose puckered forms (with C3'-endo more favoured over the C2'-endo) and 3'-GMP binds to RNase T1 predominantly in C3'-endo form. The catalytically important residue His-92 was found to form hydrogen bond with the phosphate moiety in all the enzyme-inhibitor complexes, indicating that this residue may serve as a general acid group during catalysis. Such an interaction was not found in either X-ray or two-dimensional NMR studies.

Die mündliche Sprachkompetenz finnischer Deutschlernender aus Sicht der grammatikalischen Korrektheit : Eine Fehleranalyse im Rahmen des HY-TALK-Projekts

Tutkielman päätavoitteena on analysoida suomalaisten, saksaa opiskelevien lukiolaisten suullisen testin suorituksia kielen oikeellisuuden näkökulmasta virheanalyysin avulla. Aineistona on osa Helsingin yliopiston HY-TALK-hankkeen saksan kielen tutkimusaineistosta: videoinnit suullisen kielitaidon testeistä sekä asiantuntijaraadin arvioinnit suorituksista. Koska aineisto on suullinen, tutkielmassa tarkastellaan aluksi suullisen kielen piirteitä. Virheanalyysin pohjana ovat muun muassa Corderin, Nickelin, Kleppinin ja Jamesin esittämät teoriat. Tutkielmassa analysoidaan kolmentoista, selkeästi joko A1.3- tai A2.2-taitotasolle arvioidun opiskelijan suoritukset. Virheanalyysin tavoitteena on saada selville kielioppivirheiden määrät, kullekin taitotasolle tyypilliset kielioppivirheet sekä selvittää tasojen välisiä eroja. Virheanalyysissä ei huomioida leksikaalisia eikä ääntämisvirheitä, vaan keskitytään morfologisiin ja syntaktisiin virheisiin. Virheet jaotellaan eri virheluokkiin (nominaalilausekkeiden deklinaatio, pronomini, taipumattomat sanaluokat, kysymyssanat, kieltoilmaukset, verbit ja lauserakenne) ja ne tilastoidaan taulukoihin. Lisäksi pohditaan virheiden syitä sekä virheiden vaikutusta kielen ymmärrettävyyteen. Jälkimmäistä selvitetään saksaa äidinkielenään puhuvan, kolmihenkisen raadin avulla. Raadin sekä numeeriset että verbaaliset arvioinnit ovat myös osa tutkielman aineistoa. Toinen tutkielman päätavoite on opetussuunnitelman taitotasoasteikon validointi. Tarkoituksena on selvittää oikeellisuuden taitotasokuvausten toimivuutta arvioinnissa A1.3- ja A2.2-tasojen osalta. Tätä tavoitetta varten selvitetään myös kielitaidon arvioinnin taustalla olevia teorioita. HY-TALK-asiantuntijaraadin arviointeja verrataan virheanalyysin tuloksiin korrelaatiokertoimen ja regressiosuoran avulla. Virheanalyysin perusteella voidaan todeta, että molemmilla tasoilla olevat opiskelijat tekevät eniten virheitä nominaalilausekkeiden deklinaatiossa (A2.2-tasolla 60,0 prosenttia kaikista virheistä ja A1.3-tasolla 42,2 prosenttia). A1.3-tasolle arvioidut opiskelijat tekevät paljon virheitä myös verbeissä ja lauserakenteissa, kun taas A2.2-tason opiskelijat hallitsevat nämä rakenteet paremmin. A1.3-tasolle arvioidut opiskelijat tekevät enemmän virheitä (22,10 virhettä sataa sanaa kohden) kuin A2.2-tasolle arvioidut (9,80 virhettä sataa sanaa kohden). Virheiden syitä ovat muun muassa testitilanne, puhekumppanin vaikutus ja interferenssi. Kielen ymmärrettävyyteen vaikuttavat saksalaisen raadin mukaan kielioppivirheiden lisäksi muun muassa puheen sujuvuus ja leksikaaliset ongelmat. Vakavimpina virheinä pidetään virheitä lauserakenteessa, sillä ne haittaavat usein ymmärrettävyyttä. Deklinaatiovirheitä puolestaan ei yleensä pidetä vakavina virheinä. Taitotasokuvaukset toimivat A1.3- ja A2.2-tasojen osalta hyvin, sillä virheanalyysin virhemäärät ja HY-TALK-raadin arvioinnit korreloivat keskenään, kun otetaan huomioon molemmat tasot A1.3 ja A2.2. Kielioppivirheiden määrä siis vaikuttaa kielen oikeellisuuden arviointiin. Taitotasokuvauksia olisi kuitenkin joiltain osin syytä tarkentaa ja yhtenäistää esimerkiksi konkreettisten esimerkkien avulla (esim. mikä on peruskielioppivirhe?) ja kuvaamalla myös kielen ymmärrettävyyttä joka tasolla.

Assignment of Fundamental Vibrations of Hydrazo Derivatives. Carbohydrazide and Diprotonated Carbohydrazide

The Infrared spectra of carbohydrazide, diprotonated carbohydrazide and their deuterated compounds have been measured in the solid state. From the results on thio- and selenocarbohydrazides and other related molecules and normal coordinate analyses using a Urey-Bradley force field assignments of the fundamental vibrational frequencies and a description of the normal modes of carbohydrazide, diprotonated carbohydrazide and their deuterated species are given.

Solvation dynamics in liquid water. A novel interplay between librational and diffusive modes

A microscopic calculation of the solvation dynamics of an ion in liquid water is presented. The calculated solvation time correlation function shows an ultrafast Gaussian decay which carries about 70%–90% of the strength followed by a biexponential decay with time constants equal to 250 fs and 1 ps. These results are in excellent agreement with the computer simulations of Maroncelli and Fleming and also with the experimental findings of Barbara and Jarzeba. In addition, we find that both the rotational librations and the intermolecular translational vibrational modes of water contribute significantly to the initial Gaussian decay.

Immune responses to hemagglutinin-neuraminidase protein of peste des petits ruminants virus expressed in transgenic peanut plants in sheep

Peste des petits ruminants (PPR) is an acute, highly contagious disease of small ruminants caused by a morbillivirus, Peste des petits ruminants virus (PPRV). The disease is prevalent in equatorial Africa, the Middle East, and the Indian subcontinent. A live attenuated vaccine is in use in some of the countries and has been shown to provide protection for at least three years against PPR. However, the live attenuated vaccine is not robust in terms of thermotolerance. As a step towards development of a heat stable subunit vaccine, we have expressed a hemagglutinin-neuraminidase (HN) protein of PPRV in peanut plants (Arachis hypogea) in a biologically active form, possessing neuraminidase activity. Importantly. HN protein expressed in peanut plants retained its immunodominant epitopes in their natural conformation. The immunogenicity of the plant derived HN protein was analyzed in sheep upon oral immunization. Virus neutralizing antibody responses were elicited upon oral immunization of sheep in the absence of any mucosal adjuvant. In addition, anti-PPRV-HN specific cell-mediated immune responses were also detected in mucosally immunized sheep. (C) 2010 Elsevier B.V. All rights reserved.

Electron transfer reaction in the marcus inverted region: role of high frequency vibrational modes

A theoretical study of the dynamics of photo-electron transfer reactions in the Marcus inverted regime is presented. This study is motivated partly by the recent proposal of Barbara et al. (J. Phys. Chem. 96, 3728, 1991) that a minimal model of an electron transfer reaction should consist of a polar solvent mode (X), a low frequency vibrational mode (Q) and one high frequency mode (q). Interplay between these modes may be responsible for the crossover observed in the dynamics from a solvent controlled to a vibrational controlled electron transfer. The following results have been obtained. (i) In the case of slowly relaxing solvents, the proximity of the point of excitation to an effective sink on the excited surface is critical in determining the decay of the reactant population. This is because the Franck-Condon overlap between the reactant ground and the product excited states decreases rapidly with increase in the quantum number of the product vibrational state. (ii) Non-exponential solvation dynamics has an important effect in determining the rates of electron transfer. Especially, a biphasic solvation and a large coupling between the reactant and the product states both may be needed to explain the experimental results. ©1996 American Institute of Physics

Modes of binding of 2'-AMP to RNase T1. A computer modeling study

The modes of binding of adenosine 2'-monophosphate (2'-AMP) to the enzyme ribonuclease (RNase) T1 were determined by computer modelling studies. The phosphate moiety of 2'-AMP binds at the primary phosphate binding site. However, adenine can occupy two distinct sites--(1) The primary base binding site where the guanine of 2'-GMP binds and (2) The subsite close to the N1 subsite for the base on the 3'-side of guanine in a guanyl dinucleotide. The minimum energy conformers corresponding to the two modes of binding of 2'-AMP to RNase T1 were found to be of nearly the same energy implying that in solution 2'-AMP binds to the enzyme in both modes. The conformation of the inhibitor and the predicted hydrogen bonding scheme for the RNase T1-2'-AMP complex in the second binding mode (S) agrees well with the reported x-ray crystallographic study. The existence of the first mode of binding explains the experimental observations that RNase T1 catalyses the hydrolysis of phosphodiester bonds adjacent to adenosine at high enzyme concentrations. A comparison of the interactions of 2'-AMP and 2'-GMP with RNase T1 reveals that Glu58 and Asn98 at the phosphate binding site and Glu46 at the base binding site preferentially stabilise the enzyme-2'-GMP complex.

Modes of binding of α(1–2) linked manno-oligosaccharides to concanavalin A

Three-dimensional structures of the complexes of concanavalin A (ConA) with alpha(1-2) linked mannobiose, triose and tetraose have been generated with the X-ray crystal structure data on native ConA using the CCEM (contact criteria and energy minimization) method. All the constituting mannose residues of the oligosaccharide can reach the primary binding site of ConA (where methyl-alpha-D-mannopyranose binds). However, in all the energetically favoured complexes, either the non-reducing end or middle mannose residues of the oligosaccharide occupy the primary binding site. The middle mannose residues have marginally higher preference over the non-reducing end residue. The sugar binding site of ConA is extended and accommodates at least three alpha(1-2) linked mannose residues. Based on the present calculations two mechanisms have been proposed for the binding of alpha(1-2) linked mannotriose and tetraose to ConA.