16 research outputs found
Lymen borrelioosin epidemiologinen seuranta : Ohje kliinisen mikrobiologian laboratorioille seurantatiedon yhtenÀistÀmiseksi
Asymmetric Switching in a Homodimeric ABC Transporter: A Simulation Study
ABC transporters are a large family of membrane proteins involved in a variety of cellular processes, including multidrug and tumor resistance and ion channel regulation. Advances in the structural and functional understanding of ABC transporters have revealed that hydrolysis at the two canonical nucleotide-binding sites (NBSs) is co-operative and non-simultaneous. A conserved core architecture of bacterial and eukaryotic ABC exporters has been established, as exemplified by the crystal structure of the homodimeric multidrug exporter Sav1866. Currently, it is unclear how sequential ATP hydrolysis arises in a symmetric homodimeric transporter, since it implies at least transient asymmetry at the NBSs. We show by molecular dynamics simulation that the initially symmetric structure of Sav1866 readily undergoes asymmetric transitions at its NBSs in a pre-hydrolytic nucleotide configuration. MgATP-binding residues and a network of charged residues at the dimer interface are shown to form a sequence of putative molecular switches that allow ATP hydrolysis only at one NBS. We extend our findings to eukaryotic ABC exporters which often consist of two non-identical half-transporters, frequently with degeneracy substitutions at one of their two NBSs. Interestingly, many residues involved in asymmetric conformational switching in Sav1866 are substituted in degenerate eukaryotic NBS. This finding strengthens recent suggestions that the interplay of a consensus and a degenerate NBS in eukaroytic ABC proteins pre-determines the sequence of hydrolysis at the two NBSs
Vanha teollisuusrakennus asuinympÀristössÀ - asuntoalue Jokelan vanutehtaan tontille
Diplomityö kÀsittelee Tuusulan kunnan Jokelassa sijaitsevan vanhan teollisuusmiljöön sopeuttamista osaksi ympÀrille kasvavaa asuinaluetta.
TyössÀ on kaksi osaa: kohdetontilla sijaitsevan 1920- ja 1950-luvuilla rakennetun 2-kerroksisen vanhan vanutehtaan sopeuttaminen uuteen tilanteeseen sekÀ tontilla kÀyttÀmÀttÀ olevan rakennusoikeuden hyödyntÀminen alueella meneillÀÀn olevan kaavoitustyön hengen mukaisesti.
VANUTEHDAS Vanutehtaan tulevaisuutta tutkivassa osassa rakennus on suunniteltu vaihtoehtoisesti joko asuinaluetta palvelevaksi rakennukseksi tai asuintaloksi.
NÀistÀ pÀÀpaino on jÀlkimmÀisessÀ.
Asuintaloratkaisussa vanutehtaan uudempi osa on esitetty osittain purettavaksi.
Purku rajautuu talon pilarilinjoihin ja avaa massan keskelle suojaisan sisÀpihan.
Tehtaaseen sijoitetut asunnot on pÀÀosin suunniteltu useampikerroksisiksi huoneistoiksi, joihin kuljetaan suoraan piha-alueelta.
Ratkaisun perusteena on osaltaan rakennuksen korkea huonekorkeus, joka sallii asuntojen sisÀiset parviratkaisut.
Toisaalta koska kohde sijaitsee maaseututaajamassa, on suunnittelussa haluttu vÀlttÀÀ puhtaasti kerrostalomaisia asuntoratkaisuja.
Jokelan vanutehtaan kerrosala on esitetyssÀ asuintalomuodossa 2420 m[2] ja huoneistoala 1980 m[2].
PARI- JA RIVITALOALUE Jokelan vanutehtaan tontti on kooltaan 21320 m[2].
Tuusulan kunnan alueelle suositteleman tehokkuuden puitteissa on kÀyttÀmÀtön rakennusoikeus hyödynnetty suunnittelemalla tontille pari- ja rivitaloja.
Rakennusten suunnittelussa on lÀhtökohtana ollut maaseudun työlÀisasuntojen arkkitehtuurin perinne sekÀ ympÀröivÀ teollinen miljöö.
Taloissa toistuva perusasunto muodostuu kaksikerroksisesta asuinosasta sekÀ sisÀpihan ympÀrille kiertyvÀstÀ yksikerroksisesta huolto- ja pesutilojen ketjusta.
SisÀpiha rajautuu aidalla rakennusmassojen vÀlissÀ kulkevaan kotikujaan.
Peilautuessaan kotikujan suhteen pari- ja rivitalot muodostavat tontilla hallitsevana olevan vanutehtaan mittakaavaan sopeutettuja suorakaiteenmuotoisia kortteleita.
NÀiden ulkokehÀn muodostavat talojen sisÀÀnkÀyntijulkisivut ovat yleisilmeeltÀÀn valkoiseksi rapattuja.
Kortteleita halkovia kotikujia reunustavat rakennukset ovat puisia.
Asuntojen pohjaratkaisut on suunniteltu elinkaariasumisen periaatteita noudattaen.
Perusasuntotyypin muodostavaa 168 m[2] asuntokokonaisuutta voidaan jakaa usealla eri tavalla pienempiin itsenÀisiin huoneistoihin erottamalla porrashuone ja tuulikaappi vÀliseinÀllÀ alakerran asunnosta.
Perusjaon muodostavat alakerta, ylÀkerta ja tarvittaessa suoraan tuulikaappiin avautuva sivuasunto.
Rivi- ja paritalojen yhteenlaskettu kerrosala on 3370 m[2] ja huoneistoala 2688 m[2].
Koko asuinalueen kerrosala on 5990 m[2], joka kohdetontilla johtaa tehokkuuteen e= 0,28
Kolesterolin ja fosfolipidien spesifiset vuorovaikutukset
Kolesterolilla on moninaisia vaikutuksia fosfolipidikaksoiskerroksiin, mm. rasvahappoketjujen jÀrjestÀmiseen, lipidien tiivistymiseen kaksoiskerroksen tasossa, sekÀ jÀrjestyneiden faasien rakentumiseen.
TÀmÀn tyyppisten vaikutusten voimakkuus riippuu kaksoiskerroksen fosfolipideistÀ ja niiden molekulaarisista vuorovaikutuksista kolesterolin kanssa.
Kolesterolin tiedetÀÀn esimerkiksi vuorovaikuttavan suotuisammin sfingomyeliinin kuin fosfatidyylikoliinin kanssa, mikÀ tietyissÀ olosuhteissa johtaa jÀrjestyneiden lateraalisten lipidialueiden muodostumiseen.
TÀllaiset lipidialueet (tai -lautat) voivat organisoida kalvoproteiineja ja siten osallistua membraanien biologisiin toimintoihin Spesifisten kolesterolifosfolipidi -vuorovaikutusten mekanismit ovat kuitenkin pÀÀosin tuntemattomia.
TÀssÀ diplomityössÀ tutkitaan kolesterolin, palmitoyyli-sfingomyeliinin (SM) ja palmitoyyli-oleoyyli-fosfatidyylikoliinin (POPC) vuorovaikutuksia lipidikaksoiskerroksessa laajoilla molekyylidynamiikkasimulaatioilla.
Tutkitussa systeemissÀ kÀytetÀÀn ongelmaan sovitettua lipidikonfiguraatiota: yksittÀisiÀ SM- ja kolesteroli-monomeerejÀ sekÀ SM-kolesterolidimeerejÀ upotettuna POPC-kaksoiskerrokseen nestefaasissa.
TÀmÀ systeemi sallii dimeerisen ja monomeerisen SM:n ja kolesterolin suoran vertailun, mikÀ mahdollistaa nÀiden molekyylien spesifiseen vuorovaikutukseen johtavien ominaisuuksien identifioinnin.
TÀmÀ tutkimus osoittaa, ettÀ suorilla SM-kolesteroli -vetysidoksilla ei ole merkittÀvÀÀ vaikutusta lipidilauttojen muodostumisen alkuvaiheissa.
Sen sijaan nÀiden lipidien vuorovaikutusten "spesifisyys" on hienovaraisempaa: heikommat vetysidokset kompensoidaan elektrostaattisilla vuorovaikutuksilla SM:n pÀÀryhmÀn ja kolesterolin hapen vÀlillÀ sekÀ parannetuilla hydrofobisilla ja van-der-Waals vuorovaikutuksilla.
Toisin kuin suorat vetysidokset, nÀmÀ vuorovaikutukset hyötyvÀt alhaisemmasta kolesterolin kallistumasta kaksoiskerroksessa
ABC proteins : from bacterial structures to human disease
EThOS - Electronic Theses Online ServiceGBUnited Kingdo
Tilt : major factor in sterols' ordering capability in membranes
Using extensive atomistic simulations, we show that there is a single experimentally accessible parameterthe sterol tiltthat can be used to determine a sterol's capability to induce order, and thus to promote, e.g., formation of lipid rafts. The observations also facilitate designing new effective sterols
SUR1: a unique ATP-binding cassette protein that functions as an ion channel regulator
SUR1 is an ATP-binding cassette (ABC) transporter with a novel function. In contrast to other ABC proteins, it serves as the regulatory subunit of an ion channel. The ATP-sensitive (KATP) channel is an octameric complex of four pore-forming Kir6.2 subunits and four regulatory SUR1 subunits, and it links cell metabolism to electrical activity in many cell types. ATPase activity at the nucleotide-binding domains of SUR results in an increase in KATP channel open probability. Conversely, ATP binding to Kir6.2 closes the channel. Metabolic regulation is achieved by the balance between these two opposing effects. Precisely how SUR1 talks to Kir6.2 remains unclear, but recent studies have identified some residues and domains that are involved in both physical and functional interactions between the two proteins. The importance of these interactions is exemplified by the fact that impaired regulation of Kir6.2 by SUR1 results in human disease, with loss-of-function SUR1 mutations causing congenital hyperinsulinism and gain-of-function SUR1 mutations leading to neonatal diabetes. This paper reviews recent data on the regulation of Kir6.2 by SUR1 and considers the molecular mechanisms by which SUR1 mutations produce disease
Plasma soluble urokinase-type plasminogen activator receptor (P-suPAR) in the diagnostics between malignant and non-malignant pancreatic lesions
Background: Soluble urokinase-type plasminogen activator receptor (suPAR) is a biomarker elevated in several inflammatory conditions and cancers. It has recently been shown to be elevated in pancreatic ductal adenocarcinoma (PDAC). Plasma suPAR (P-suPAR) predicts the severity of the disease in first acute alcohol-induced pancreatitis (AAP) and ten-year mortality after recovery from first AAP. According to our previous results, P-suPAR is not elevated in chronic pancreatitis (CP) and could possibly be used in distinguishing pancreatic cancer (PC) from CP. When imaging creates a suspicion of a pancreatic lesion, the distinction between malignant and non-malignant disease is crucial. Additional tools are needed, and we still lack a sufficiently sensitive and specific biomarker. Our aim was to further investigate whether preoperatively measured P-suPAR is beneficial in distinguishing between malignant and non-malignant pancreatic lesions. Methods: One hundred and seventy-six patients evaluated in Tampere University Hospital for pancreatic surgery for suspected malignant pancreatic lesion were recruited for the study. The final study group consisted of 113 patients. P-suPAR and other covariates were measured before the planned operation. Results: P-suPAR was significantly higher in patients with pancreatic cancer (PC) [median 4.1 (IQR 3.3â5.1) ng/mL] than in patients with non-malignant [3.3 (2.9â4.4) ng/mL; p = 0.012] histology. ROC curve analysis resulted in an AUC of 0.65 (95% CI 0.55â0.76); p = 0.007 and a cutoff value of 3.2 ng/mL. Crosstabulation yielded sensitivity of 82% and specificity of 43%. A combination of positive P-suPAR and elevated plasma carbohydrate antigen 19â9 (P-CA19-9) tests did not improve sensitivity but elevated specificity up to 86â88%. Conclusions: Preoperative P-suPAR is elevated in patients with PC compared to patients with a non-malignant pancreatic lesion. Combining P-suPAR with P-CA19â9 may improve diagnostic accuracy.Peer reviewe
Isotropic Bicelles Stabilize the Juxtamembrane Region of the Influenza M2 Protein for Solution NMR Studies
The
protein M2 from influenza is a tetrameric membrane protein
with several roles in the viral life cycle. The transmembrane helix
(TMH) of M2 has proton channel activity that is required for unpackaging
the viral genome. Additionally a C-terminal juxtamembrane region includes
an amphipathic helix (APH) important for virus budding and scission.
The APH interacts with membranes and is required for M2 localization
to the site of viral budding. As a step toward obtaining high resolution
information on the structure and lipid interactions of the M2 APH,
we sought to develop a fast tumbling bicelle system, which would make
studies of M2 in a membrane-like environment by solution NMR possible.
Since M2 is highly sensitive to the solubilizing environment, an M2
construct containing the APH was studied under micelle and bicelle
conditions while maintaining the same detergent and lipid headgroup
chemistry to facilitate interpretation of the spectroscopic results.
The sequence from a human H1N1 âswine fluâ isolate was
used to design an M2 construct (swM2) similar in amino acid sequence
to currently circulating viruses. Comparison of swM2 solubilized in
either the diacyl detergent 1,2-dihexanoyl-<i>sn</i>-glycero-3-phosphocholine
(DHPC) or a mixture of DHPC and the lipid 1,2-dipalmitoyl-<i>sn</i>-glycero-3-phosphocholine (DPPC) (<i>q</i> =
0.4) indicated that the largest changes were a decrease in helicity
at the N-terminus of the TMH and a decrease in dynamics for the juxtamembrane
linker residues connecting the TMH and the APH. Whereas the linker
region is very dynamic and the amide protons are rapidly exchanged
with water protons in micelles, the dynamics and water exchange are
largely suppressed in the presence of lipid. Chemical shift changes
and relaxation measurements were consistent with an overall stabilization
of the linker region, with only modest changes in conformation or
environment of the APH itself. Such changes are consistent with differences
observed in structures of M2 in lipid bilayers and detergent micelles,
indicating that the bicelle system provides a more membrane-like environment