Browsing by Subject "MECHANISM"

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  • Raivola, Juuli; Haikarainen, Teemu; Silvennoinen, Olli (2020)
    The Janus kinase-signal transducer and activator of transcription protein (JAK-STAT) pathway mediates essential biological functions from immune responses to haematopoiesis. Deregulated JAK-STAT signaling causes myeloproliferative neoplasms, leukaemia, and lymphomas, as well as autoimmune diseases. Thereby JAKs have gained significant relevance as therapeutic targets. However, there is still a clinical need for better JAK inhibitors and novel strategies targeting regions outside the conserved kinase domain have gained interest. In-depth knowledge about the molecular details of JAK activation is required. For example, whether the function and regulation between receptors is conserved remains an open question. We used JAK-deficient cell-lines and structure-based mutagenesis to study the function of JAK1 and its pseudokinase domain (JH2) in cytokine signaling pathways that employ JAK1 with different JAK heterodimerization partner. In interleukin-2 (IL-2)-induced STAT5 activation JAK1 was dominant over JAK3 but in interferon-gamma (IFN gamma) and interferon-alpha (IFN alpha) signaling both JAK1 and heteromeric partner JAK2 or TYK2 were both indispensable for STAT1 activation. Moreover, IL-2 signaling was strictly dependent on both JAK1 JH1 and JH2 but in IFN gamma signaling JAK1 JH2 rather than kinase activity was required for STAT1 activation. To investigate the regulatory function, we focused on two allosteric regions in JAK1 JH2, the ATP-binding pocket and the alpha C-helix. Mutating L633 at the alpha C reduced basal and cytokine induced activation of STAT in both JAK1 wild-type (WT) and constitutively activated mutant backgrounds. Moreover, biochemical characterization and comparison of JH2s let us depict differences in the JH2 ATP-binding and strengthen the hypothesis that de-stabilization of the domain disturbs the regulatory JH1-JH2 interaction. Collectively, our results bring mechanistic understanding about the function of JAK1 in different receptor complexes that likely have relevance for the design of specific JAK modulators.
  • Fewer, David P.; Jokela, Jouni; Heinila, Lassi; Aesoy, Reidun; Sivonen, Kaarina; Galica, Tomas; Hrouzek, Pavel; Herfindal, Lars (2021)
    Cyanobacteria produce a variety of chemically diverse cyclic lipopeptides with potent antifungal activities. These cyclic lipopeptides have an amphipathic structure comprised of a polar peptide cycle and hydrophobic fatty acid side chain. Many have antibiotic activity against a range of human and plant fungal pathogens. This review article aims to summarize the present knowledge on the chemical diversity and cellular effects of cyanobacterial cyclic lipopeptides that display antifungal activity. Cyclic antifungal lipopeptides from cyanobacteria commonly fall into four structural classes; hassallidins, puwainaphycins, laxaphycins, and anabaenolysins. Many of these antifungal cyclic lipopeptides act through cholesterol and ergosterol-dependent disruption of membranes. In many cases, the cyclic lipopeptides also exert cytotoxicity in human cells, and a more extensive examination of their biological activity and structure-activity relationship is warranted. The hassallidin, puwainaphycin, laxaphycin, and anabaenolysin structural classes are unified through shared complex biosynthetic pathways that encode a variety of unusual lipoinitiation mechanisms and branched biosynthesis that promote their chemical diversity. However, the biosynthetic origins of some cyanobacterial cyclic lipopeptides and the mechanisms, which drive their structural diversification in general, remain poorly understood. The strong functional convergence of differently organized chemical structures suggests that the production of lipopeptide confers benefits for their producer. Whether these benefits originate from their antifungal activity or some other physiological function remains to be answered in the future. However, it is clear that cyanobacteria encode a wealth of new cyclic lipopeptides with novel biotechnological and therapeutic applications.
  • Seifert, Tina; Malo, Marcus; Kokkola, Tarja; Engen, Karin; Friden-Saxin, Maria; Wallen, Erik A. A.; Lahtela-Kakkonen, Maija; Jarho, Elina M.; Luthman, Kristina (2014)
  • Vegh, Russell B.; Bravaya, Ksenia B.; Bloch, Dmitry A.; Bommarius, Andreas S.; Tolbert, Laren M.; Verkhovsky, Michael; Krylov, Anna I.; Solntsev, Kyril M. (2014)
  • Prisle, Nonne L.; Lin, Jack J.; Purdue, Sara; Lin, Haisheng; Meredith, J. Carson; Nenes, Athanasios (2019)
    The role of surfactants in governing water interactions of atmospheric aerosols has been a recurring topic in cloud microphysics for more than two decades. Studies of detailed surface thermodynamics are limited by the availability of aerosol samples for experimental analysis and incomplete validation of various proposed Kohler model frameworks for complex mixtures representative of atmospheric aerosol. Pollenkitt is a viscous material that coats grains of pollen and plays important roles in pollen dispersion and plant reproduction. Previous work suggests that it may also be an important contributor to pollen water uptake and cloud condensation nuclei (CCN) activity. The chemical composition of pollenkitt varies between species but has been found to comprise complex organic mixtures including oxygenated, lipid, and aliphatic functionalities. This mix of functionalities suggests that pollenkitt may display aqueous surface activity, which could significantly impact pollen interactions with atmospheric water. Here, we study the surface activity of pollenkitt from six different species and its influence on pollenkitt hygroscopicity. We measure cloud droplet activation and concentration-dependent surface tension of pollenkitt and its mixtures with ammonium sulfate salt. Experiments are compared to predictions from several thermodynamic models, taking aqueous surface tension reduction and surfactant surface partitioning into account in various ways. We find a clear reduction of surface tension by pollenkitt in aqueous solution and evidence for impact of both surface tension and surface partitioning mechanisms on cloud droplet activation potential and hygroscopicity of pollenkitt particles. In addition, we find indications of complex nonideal solution effects in a systematic and consistent dependency of pollenkitt hygroscopicity on particle size. The impact of pollenkitt surface activity on cloud microphysics is different from what is observed in previous work for simple atmospheric surfactants and more resembles recent observations for complex primary and secondary organic aerosol, adding new insight to our understanding of the multifaceted role of surfactants in governing aerosol-water interactions. We illustrate how the explicit characterization of pollenkitt contributions provides the basis for modeling water uptake and cloud formation of pollen and their fragments over a wide range of atmospheric conditions.
  • Gupta, Govind; Gliga, Anda; Hedberg, Jonas; Serra, Angela; Greco, Dario; Odnevall Wallinder, Inger; Fadeel, Bengt (2020)
    Abstract The neurotoxicity of hard metal-based nanoparticles (NPs) remains poorly understood. Here, we deployed the human neuroblastoma cell line SH-SY5Y differentiated or not into dopaminergic- and cholinergic-like neurons to study the impact of tungsten carbide (WC) NPs, WC NPs sintered with cobalt (Co), or Co NPs versus soluble CoCl2. Co NPs and Co salt triggered a dose-dependent cytotoxicity with an increase in cytosolic calcium, lipid peroxidation, and depletion of glutathione (GSH). Co NPs and Co salt also suppressed glutathione peroxidase 4 (GPX4) mRNA and protein expression. Co-exposed cells were rescued by N-acetylcysteine (NAC), a precursor of GSH, and partially by liproxstatin-1, an inhibitor of lipid peroxidation. Furthermore, in silico analyses predicted a significant correlation, based on similarities in gene expression profiles, between Co-containing NPs and Parkinson's disease, and changes in the expression of selected genes were validated by RT-PCR. Finally, experiments using primary human dopaminergic neurons demonstrated cytotoxicity and GSH depletion in response to Co NPs and CoCl2 with loss of axonal integrity. Overall, these data point to a marked neurotoxic potential of Co-based but not WC NPs and show that neuronal cell death may occur through a ferroptosis-like mechanism.
  • Akhavan-Tafti, M.; Palmroth, M.; Slavin, J. A.; Battarbee, M.; Ganse, U.; Grandin, M.; Le, G.; Gershman, D. J.; Eastwood, J. P.; Stawarz, J. E. (2020)
    The Vlasiator hybrid-Vlasov code was developed to investigate global magnetospheric dynamics at ion-kinetic scales. Here we focus on the role of magnetic reconnection in the formation and evolution of magnetic islands at the low-latitude magnetopause, under southward interplanetary magnetic field conditions. The simulation results indicate that (1) the magnetic reconnection ion kinetics, including the Earthward pointing Larmor electric field on the magnetospheric side of an X-point and anisotropic ion distributions, are well-captured by Vlasiator, thus enabling the study of reconnection-driven magnetic island evolution processes, (2) magnetic islands evolve due to continuous reconnection at adjacent X-points, "coalescence" which refers to the merging of neighboring islands to create a larger island, "erosion" during which an island loses magnetic flux due to reconnection, and "division" which involves the splitting of an island into smaller islands, and (3) continuous reconnection at adjacent X-points is the dominant source of magnetic flux and plasma to the outer layers of magnetic islands resulting in cross-sectional growth rates up to + 0.3 R-E(2)/min. The simulation results are compared to the Magnetospheric Multiscale (MMS) measurements of a chain of ion-scale flux transfer events (FTEs) sandwiched between two dominant X-lines. The MMS measurements similarly reveal (1) anisotropic ion populations and (2) normalized reconnection rate similar to 0.18, in agreement with theory and the Vlasiator predictions. Based on the simulation results and the MMS measurements, it is estimated that the observed ion-scale FTEs may grow Earth-sized within similar to 10 min, which is comparable to the average transport time for FTEs formed in the subsolar region to the high-latitude magnetopause. Future simulations shall revisit reconnection-driven island evolution processes with improved spatial resolutions.
  • Hasan, Galib; Salo, Vili-Taneli; Valiev, Rashid; Kubecka, Jakub; Kurten, Theo (2020)
    Organic peroxy radicals (RO2) are key intermediates in the chemistry of the atmosphere. One of the main sink reactions of RO2 is the recombination reaction RO2 + R'O-2, which has three main channels (all with O-2 as a coproduct): (1) R-H=O + R'OH, (2) RO + R'O, and (3) ROOR'. The RO + R'O "alkoxy" channel promotes radical and oxidant recycling, while the ROOR' "dimer" channel leads to low-volatility products relevant to aerosol processes. The ROOR' channel has only recently been discovered to play a role in the gas phase. Recent computational studies indicate that all of these channels first go through an intermediate complex( 1)(RO center dot center dot center dot O-3(2)center dot center dot center dot OR'). Here, O-3(2) is very weakly bound and will likely evaporate from the system, giving a triplet cluster of two alkoxy radicals: (3)(RO center dot center dot center dot OR'). In this study, we systematically investigate the three reaction channels for an atmospherically representative set of RO + R'O radicals formed in the corresponding RO2+ R'O-2 reaction. First, we systematically sample the possible conformations of the RO center dot center dot center dot OR' clusters on the triplet potential energy surface. Next, we compute energetic parameters and attempt to estimate reaction rate coefficients for the three channels: evaporation/dissociation to RO + R'O, a hydrogen shift leading to the formation of R'(-H)=O + ROH, and "spin-flip" (intersystem crossing) leading to, or at least allowing, the formation of ROOR' dimers. While large uncertainties in the computed energetics prevent a quantitative comparison of reaction rates, all three channels were found to be very fast (with typical rates greater than 10 6 s(-1)). This qualitatively demonstrates that the computationally proposed novel RO2 + R'O-2 reaction mechanism is compatible with experimental data showing non-negligible branching ratios for all three channels, at least for sufficiently complex RO2.
  • Khan, Suleiman A.; Faisal, Ali; Mpindi, John Patrick; Parkkinen, Juuso A.; Kalliokoski, Tuomo; Poso, Antti; Kallioniemi, Olli P.; Wennerberg, Krister; Kaski, Samuel (2012)
  • Wang, Yonghong; Gao, Wenkang; Wang, Shuai; Song, Tao; Gong, Zhengyu; Ji, Dongsheng; Wang, Lili; Liu, Zirui; Tang, Guiqian; Huo, Yanfeng; Tian, Shili; Li, Jiayun; Li, Mingge; Yang, Yuan; Chu, Biwu; Petäjä, Tuukka; Kerminen, Veli-Matti; He, Hong; Hao, Jiming; Kulmala, Markku; Wang, Yuesi; Zhang, Yuanhang (2020)
    Although much attention has been paid to investigating and controlling air pollution in China, the trends of air-pollutant concentrations on a national scale have remained unclear. Here, we quantitatively investigated the variation of air pollutants in China using long-term comprehensive data sets from 2013 to 2017, during which Chinese government made major efforts to reduce anthropogenic emission in polluted regions. Our results show a significant decreasing trend in the PM2.5 concentration in heavily polluted regions of eastern China, with an annual decrease of similar to 7% compared with measurements in 2013. The measured decreased concentrations of SO2, NO2 and CO (a proxy for anthropogenic volatile organic compounds) could explain a large fraction of the decreased PM2.5 concentrations in different regions. As a consequence, the heavily polluted days decreased significantly in corresponding regions. Concentrations of organic aerosol, nitrate, sulfate, ammonium and chloride measured in urban Beijing revealed a remarkable reduction from 2013 to 2017, connecting the decreases in aerosol precursors with corresponding chemical components closely. However, surface-ozone concentrations showed increasing trends in most urban stations from 2013 to 2017, which indicates stronger photochemical pollution. The boundary-layer height in capital cities of eastern China showed no significant trends over the Beijing-Tianjin-Hebei, Yangtze River Delta and Pearl River Delta regions from 2013 to 2017, which confirmed the reduction in anthropogenic emissions. Our results demonstrated that the Chinese government was successful in the reduction of particulate matter in urban areas from 2013 to 2017, although the ozone concentration has increased significantly, suggesting a more complex mechanism of improving Chinese air quality in the future.
  • Gulumkar, Vijay; Äärelä, Antti; Moisio, Olli; Rahkila, Jani; Tähtinen, Ville; Leimu, Laura; Korsoff, Niko; Korhonen, Heidi; Poijärvi-Virta, Päivi; Mikkola, Satu; Nesati, Victor; Vuorimaa-Laukkanen, Elina; Viitala, Tapani; Yliperttula, Marjo; Roivainen, Anne; Virta, Pasi (2021)
    An azide-functionalized 12-armed Buckminster fullerene has been monosubstituted in organic media with a substoichiometric amount of cyclooctyne-modified oligonucleo-tides. Exposing the intermediate products then to the same reaction (i. e., strain-promoted alkyne-azide cycloaddition, SPAAC) with an excess of slightly different oligonucleotide constituents in an aqueous medium yields molecularly defined monofunctionalized spherical nucleic acids (SNAs). This procedure offers a controlled synthesis scheme in which one oligonucleotide arm can be functionalized with labels or other conjugate groups (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid, DOTA, and Alexa-488 demonstrated), whereas the rest of the 11 arms can be left unmodified or modified by other conjugate groups in order to decorate the SNAs' outer sphere. Extra attention has been paid to the homogeneity and authenticity of the C60-azide scaffold used for the assembly of full-armed SNAs.
  • Haapanen, Outi; Reidelbach, Marco; Sharma, Vivek (2020)
    Respiratory complex I (NADH:quinone oxidoreductase) plays a central role in generating the proton electrochemical gradient in mitochondrial and bacterial membranes, which is needed to generate ATP. Several high-resolution structures of complex I have been determined, revealing its intricate architecture and complementing the biochemical and biophysical studies. However, the molecular mechanism of long-range coupling between ubiquinone (Q) reduction and proton pumping is not known. Computer simulations have been applied to decipher the dynamics of Q molecule in the similar to 30 angstrom long Q tunnel. In this short report, we discuss the binding and dynamics of Q at computationally predicted Q binding sites, many of which are supported by structural data on complex I. We suggest that the binding of Q at these sites is coupled to proton pumping by means of conformational rearrangements in the conserved loops of core subunits.
  • Mkrtchyan, Satenik; Jakubczyk, Michal; Lanka, Suneel; Pittelkow, Michael; Iaroshenko, Viktor O. (2021)
    We describe a mechanism-guided discovery of a synthetic methodology that enables the preparation of aromatic amides from 2-bromo-2,2-difluoroacetamides utilizing a copper-catalyzed direct arylation. Readily available and structurally simple aryl precursors such as aryl boronic acids, aryl trialkoxysilanes and dimethyl-aryl-sulfonium salts were used as the source for the aryl substituents. The scope of the reactions was tested, and the reactions were insensitive to the electronic nature of the aryl groups, as both electron-rich and electron-deficient aryls were successfully introduced. A wide range of 2-bromo-2,2-difluoroacetamides as either aliphatic or aromatic secondary or tertiary amides were also reactive under the developed conditions. The described synthetic protocols displayed excellent efficiency and were successfully utilized for the expeditious preparation of diverse aromatic amides in good-to-excellent yields. The reactions were scaled up to gram quantities.
  • Colis, Laureen; Ernst, Glen; Sanders, Sara; Liu, Hester; Sirajuddin, Paul; Peltonen, Karita; DePasquale, Michael; Barrow, James C.; Laiho, Marikki (2014)
    RNA polymerase I (Pol I) is a dedicated polymerase that transcribes the 45S ribosomal (r) RNA precursor. The 45S rRNA precursor is subsequently processed into the mature 5.8S, 18S, and 28S rRNAs and assembled into ribosomes in the nucleolus. Pol I activity is commonly deregulated in human cancers. On the basis of the discovery of lead molecule BMH-21, a series of pyridoquinazolinecarboxamides have been evaluated as inhibitors of Pol I and activators of the destruction of RPA194, the Poll large catalytic subunit protein. Structure-activity relationships in assays of nucleolar stress and cell viability demonstrate key pharmacophores and their physicochemical properties required for potent activation of Pol I stress and cytotoxidty. This work identifies a set of bioactive compounds that potently cause RPA194 degradation that function in a tightly constrained chemical space. This work has yielded novel derivatives that contribute to the development of Pol I inhibitory cancer therapeutic strategies.
  • Pradhan, Barun; Cajuso, Tatiana; Katainen, Riku; Sulo, Paivi; Tanskanen, Tomas; Kilpivaara, Outi; Pitkanen, Esa; Aaltonen, Lauri A.; Kauppi, Liisa; Palin, Kimmo (2017)
    Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3' transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches. We developed a long-distance inverse PCR (LDI-PCR) based approach to monitor the mobility of active L1 elements based on their 3' transduction activity. LDI-PCR requires no prior knowledge of the insertion target region. By applying LDI-PCR in conjunction with Nanopore sequencing (Oxford Nanopore Technologies) on one L1 reported to be particularly active in human cancer genomes, we detected 14 out of 15 3' transductions previously identified by whole genome sequencing in two different colorectal tumour samples. In addition we discovered 25 novel highly subclonal insertions. Furthermore, the long sequencing reads produced by LDI-PCR/Nanopore sequencing enabled the identification of both the 5' and 3' junctions and revealed detailed insertion sequence information.
  • Karhu, Lasse; Magarkar, Aniket; Bunker, Alex; Xhaard, Henri (2019)
    We assess the stability of two previously suggested binding modes for the neuropeptide orexin-A in the OX2 receptor through extensive molecular dynamics simulations. As the activation determinants of the receptor remain unknown, we simulated an unliganded receptor and two small-molecular ligands, the antagonist suvorexant and the agonist Nag26 for comparison. Each system was simulated in pure POPC membrane as well as in the 25% cholesterol–POPC membrane. In total, we carried out 36 μs of simulations. Through this set of simulations, we report a stable binding mode for the C-terminus of orexin-A. In addition, we suggest interactions that would promote orexin receptor activation, as well as others that would stabilize the inactive state.
  • Das, Biswanath; Al-Hunaiti, Afnan; Sanchez-Eguia, Brenda N.; Zeglio, Erica; Demeshko, Serhiy; Dechert, Sebastian; Braunger, Steffen; Haukka, Matti; Repo, Timo; Castillo, Ivan; Nordlander, Ebbe (2019)
    The new di- and tetranuclear Fe(III) mu-oxido complexes [Fe-4(mu-O)(4) (PTEBIA)(4)]CF3SO3)(4)(CH3CN)(2)] (1a) , [Fe-2(mu-O)Cl-2(PTEBIA)(2)(CF3SO3)(2) (1b), and [Fe-2(mu-O)(HCOO)(2)(PTEBIA)(2)](ClO4)(2) (MeOH) (2) were prepared from the sulfur-containing ligand (2-((2,4-dimethylphenyl)thiO)-N,N-bis ((1-methyl-benzimidazol-2-yl)methyl)ethanamine (PTEBIA). The tetrairon complex 1a features four mu-oxido bridges, while in dinuclear 1b, the sulfur moiety of the ligand occupies one of the six coordination sites of each Fe(III) ion with a long Fe-S distance of 2.814(6) angstrom . In 2, two Fe(III) centers are bridged by one oxido and two formate units, the latter likely formed by methanol oxidation. Complexes 1a and 1 b show broad sulfur-toiron charge transfer bands around 400-430 nm at room temperature, consistent with mononuclear structures featuring Fe-S interactions. In contrast, acetonitrile solutions of 2 display a sulfur-to-iron charge transfer band only at low temperature (228 K) upon addition of H2O2/CH3COOH, with an absorption maximum at 410 nm. Homogeneous oxidative catalytic activity was observed for 1a and 1b using H2O2 as oxidant, but with low product selectivity. High valent iron-oxo intermediates could not be detected by UV-vis spectroscopy or ESI mass spectrometry. Rather, evidence suggest preferential ligand oxidation, in line with the relatively low selectivity and catalytic activity observed in the reactions.
  • Lihavainen, Heikki; Asmi, Eija; Aaltonen, Veijo; Makkonen, Ulla; Kerminen, Veli-Matti (2015)
    We used more than five years of continuous aerosol measurements to estimate the direct radiative feedback parameter associated with the formation of biogenic secondary organic aerosol (BSOA) at a remote continental site at the edge of the boreal forest zone in Northern Finland. Our upper-limit estimate for this feedback parameter during the summer period (ambient temperatures above 10 degrees C) was -97 +/- 66 mWm(-2) K-1 (mean +/- STD) when using measurements of the aerosol optical depth (f(AOD)) and -63 +/- 40 mWm(-2) K-1 when using measurements of the 'dry' aerosol scattering coefficient at the ground level (f(sigma)). Here STD represents the variability in f caused by the observed variability in the quantities used to derive the value of f. Compared with our measurement site, the magnitude of the direct radiative feedback associated with BSOA is expected to be larger in warmer continental regions with more abundant biogenic emissions, and even larger in regions where biogenic emissions are mixed with anthropogenic pollution.
  • Spruit, Cindy; Wicklund, Anu; Wan, Xing; Skurnik, Mikael; Pajunen, Maria (2020)
    The lytic phage, fHe-Kpn01 was isolated from sewage water using an extended-spectrum beta-lactamase-producing strain of Klebsiella pneumoniae as a host. The genome is 43,329 bp in size and contains direct terminal repeats of 222 bp. The genome contains 56 predicted genes, of which proteomics analysis detected 29 different proteins in purified phage particles. Comparison of fHe-Kpn01 to other phages, both morphologically and genetically, indicated that the phage belongs to the family Podoviridae and genus Drulisvirus. Because fHe-Kpn01 is strictly lytic and does not carry any known resistance or virulence genes, it is suitable for phage therapy. It has, however, a narrow host range since it infected only three of the 72 tested K. pneumoniae strains, two of which were of capsule type KL62. After annotation of the predicted genes based on the similarity to genes of known function and proteomics results on the virion-associated proteins, 22 gene products remained annotated as hypothetical proteins of unknown function (HPUF). These fHe-Kpn01 HPUFs were screened for their toxicity in Escherichia coli. Three of the HPUFs, encoded by the genes g10, g22, and g38, were confirmed to be toxic.