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  • 1. Barrefelt, Asa
    et al.
    Zhao, Ying
    Larsson, Malin K.
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Egri, Gabriella
    Kuiper, Raoul V.
    Hamm, Jorg
    Saghafian, Maryam
    Caidahl, Kenneth
    Brismar, Torkel B.
    Aspelin, Peter
    Heuchel, Rainer
    Muhammed, Mamoun
    Dahne, Lars
    Hassan, Moustapha
    Fluorescence labeled microbubbles for multimodal imaging2015In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 464, no 3, p. 737-742Article in journal (Refereed)
    Abstract [en]

    Air-filled polyvinyl alcohol microbubbles (PVA-MBs) were recently introduced as a contrast agent for ultrasound imaging. In the present study, we explore the possibility of extending their application in multimodal imaging by labeling them with a near infrared (NIR) fluorophore, VivoTag-680. PVA-MBs were injected intravenously into FVB/N female mice and their dynamic biodistribution over 24 h was determined by 3D-fluorescence imaging co-registered with 3D-mu CT imaging, to verify the anatomic location. To further confirm the biodistribution results from in vivo imaging, organs were removed and examined histologically using bright field and fluorescence microscopy. Fluorescence imaging detected PVA-MB accumulation in the lungs within the first 30 min post-injection. Redistribution to a low extent was observed in liver and kidneys at 4 h, and to a high extent mainly in the liver and spleen at 24 h. Histology confirmed PVA-MB localization in lung capillaries and macrophages. In the liver, they were associated with Kupffer cells; in the spleen, they were located mostly within the marginal-zone. Occasional MBs were observed in the kidney glomeruli and interstitium. The potential application of PVA-MBs as a contrast agent was also studied using ultrasound (US) imaging in subcutaneous and orthotopic pancreatic cancer mouse models, to visualize blood flow within the tumor mass. In conclusion, this study showed that PVA-MBs are useful as a contrast agent for multimodal imaging. (C) 2015 Elsevier Inc. All rights reserved.

  • 2. Cai, Yixiao
    et al.
    Lendel, Christofer
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Österlund, Lars
    Kasrayan, Alex
    Lannfelt, Lars
    Ingelsson, Martin
    Nikolajeff, Fredrik
    Karlsson, Mikael
    Bergstrom, Joakim
    Changes in secondary structure of alpha-synuclein during oligomerization induced by reactive aldehydes2015In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 464, no 1, p. 336-341Article in journal (Refereed)
    Abstract [en]

    The oxidative stress-related reactive aldehydes 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE) have been shown to promote formation of alpha-synuclein oligomers in vitro. However, the changes in secondary structure of alpha-synuclein and the kinetics of the oligomerization process are not known and were the focus of this study. Size exclusion chromatography showed that after 1 h of incubation, HNE induced the formation of an oligomeric alpha-synuclein peak with a molecular weight of about similar to 2000 kDa, which coincided with a decreasing similar to 50 kDa monomeric peak. With prolonged incubation (up to 24 h) the oligomeric peak became the dominating molecular species. In contrast, in the presence of ONE, a similar to 2000 oligomeric peak was exclusively observed after 15 min of incubation and this peak remained constant with prolonged incubation. Western blot analysis of HNE-induced alpha-synuclein oligomers showed the presence of monomers (15 kDa), SDS-resistant low molecular (30-160 kDa) and high molecular weight oligomers (>= 260 kDa), indicating that the oligomers consisted of both covalent and non-covalent protein. In contrast, ONE-induced alpha-synuclein oligomers only migrated as covalent cross-linked high molecular-weight material (>= 300 kDa). Both circular dichroism (CD) and Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy showed that the formation of HNE- and ONE-induced oligomers coincided with a spectral change from random coil to beta-sheet. However, ONE-induced alpha-synuclein oligomers exhibited a slightly higher degree of beta-sheet. Taken together, our results indicate that both HNE and ONE induce a change from random coil to beta-sheet structure that coincides with the formation of alpha-synuclein oligomers; albeit through different kinetic pathways depending on the degree of cross-linking. (C) 2015 Elsevier Inc. All rights reserved.

  • 3.
    Edholm, Olle
    et al.
    KTH, Superseded Departments, Physics.
    Nordlander, P.
    Chen, W.
    Ohlsson, P. I.
    Smith, M. L.
    Paul, J.
    The effect of water on the Fe3+/Fe2+ reduction potential of heme2000In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 268, no 3, p. 683-687Article in journal (Refereed)
    Abstract [en]

    Hemeproteins can act as catalysts, oxygen carriers or electron conductors. The ferric/ferrous reduction potential E-m7 of iron in the center of the prosthetic group ranges from negative values for peroxidases to an extreme positive value for cytochrome a, with Hb and Mb in the middle [1]. Proteins exercise their influence on E-m7 in several ways: via substituents at the periphery of the chelate structure, via the proximal ligand, and via interaction with the surrounding medium, amino acid side chains, or polar solvents. Work on recombined proteins and ap-substituted free hemes documented that the first two effects are additive [2]. For the third effect, models of the dielectric media on a molecular level have been successfully applied [3-5]. E-m7 has also been empirically correlated to the degree of heme exposure to water [6-8]. The apoprotein/porphyrin and water/porphyrin interfaces are complementary since water molecules fill any empty space in the crevice and surround any pertinent part of heme outside the protein boundary. The present work links to this idea by a combination of statistical mechanics simulations and quantum mechanical calculations comparing heme in water with heme in an apolar environment. Our results show that polarization of the porphyrin pi-electron cloud by the held from water dipoles influences E-m7 The dominant effect of this and other determinates of iron electron availability is perturbations of delocalized electron density in the porphyrin chelate, reproduced by a model where the prosthetic group is treated as a disc of uniform electron density. The present work is also of interest since the interfacial energy constitutes the main barrier for heme-protein Separation [9-11].

  • 4. El-Sayed, R.
    et al.
    Ye, F.
    Asem, Heba
    KTH, School of Engineering Sciences (SCI), Applied Physics, Functional Materials, FNM.
    Ashour, Radwa
    KTH, School of Engineering Sciences (SCI), Applied Physics, Functional Materials, FNM.
    Zheng, W.
    Muhammed, Mamoun
    KTH, School of Engineering Sciences (SCI), Applied Physics, Functional Materials, FNM. Alexandria University, Egypt.
    Hassan, M.
    Importance of the surface chemistry of nanoparticles on peroxidase-like activity2017In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 491, no 1, p. 15-18Article in journal (Refereed)
    Abstract [en]

    We report the studies on origin of peroxidase-like activity for gold nanoparticles, as well as the impact from morphology and surface charge of nanoparticles. For this purpose, we have synthesized hollow gold nanospheres (HAuNS) and gold nanorods (AuNR) with different morphology and surface chemistry to investigate their influence on the catalytic activity. We found that citrate-capped HAuNS show catalyzing efficiency in oxidation reaction of 3,3′,5,5′-tetramethylbenzidine (TMB) by hydrogen peroxide (H2O2) and it is superior to that of cetyltrimethylammonium bromide (CTAB)-capped AuNR. The kinetics of catalytic activities from HAuNS and AuNR were respectively studied under varied temperatures. The results indicated that surface chemistry rather than morphology of nanoparticles plays an important role in the catalytic reaction of substrate. Furthermore, influencing factors such as pH, amount of nanoparticle and H2O2 concentration were also investigated on HAuNS-catalyzed system. The great impact of nanoparticle surface properties on catalytic reactions makes a paradigm in constructing nanozymes as peroxidase mimic for sensing application.

  • 5. Ermund, Anna
    et al.
    Meiss, Lauren N.
    Rodriguez-Pineiro, Ana M.
    Baehr, Andrea
    Nilsson, Harriet E.
    KTH, School of Technology and Health (STH), Medical Engineering. Department of Medical Biochemistry, University of Gothenburg, SE-405 30 Gothenburg, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, and School of Technology and Health, KTH Royal Institute of Technology, Novum, SE-141 57 Huddinge, Sweden.
    Trillo-Muyo, Sergio
    Ridley, Caroline
    Thornton, David J.
    Wine, Jeffrey J.
    Hebert, Hans
    KTH, School of Technology and Health (STH), Medical Engineering, Structural Biotechnology. Department of Biosciences and Nutrition, Karolinska Institutet, and School of Technology and Health, KTH Royal Institute of Technology, Novum, SE-141 57 Huddinge, Sweden.
    Klymiuk, Nikolai
    Hansson, Gunnar C.
    The normal trachea is cleaned by MUC5B mucin bundles from the submucosal glands coated with the MUC5AC mucin2017In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 492, no 3, p. 331-337Article in journal (Refereed)
    Abstract [en]

    To understand the mucociliary clearance system, mucins were visualized by light, confocal and electron microscopy, and mucus was stained by Alcian blue and tracked by video microscopy on tracheal explants of newborn piglets. We observed long linear mucus bundles that appeared at the submucosal gland openings and were transported cephalically. The mucus bundles were shown by mass spectrometry and immunostaining to have a core made of MUC5B mucin and were coated with MUC5AC mucin produced by surface goblet cells. The transport speed of the bundles was slower than the airway surface liquid flow. We suggest that the goblet cell MUC5AC mucin anchors the mucus bundles and thus controls their transport. Normal clearance of the respiratory tree of pigs and humans, both rich in submucosal glands, is performed by thick and long mucus bundles. 

  • 6. Fadeel, B.
    et al.
    Fornara, A.
    Toprak, Muhammet S.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Functional Materials, FNM.
    Bhattacharya, K.
    Keeping it real: The importance of material characterization in nanotoxicology2015In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 468, no 3, p. 498-503Article in journal (Refereed)
    Abstract [en]

    Nanomaterials are small and the small size and corresponding large surface area of nanomaterials confers specific properties, making these materials desirable for various applications, not least in medicine. However, it is pertinent to ask whether size is the only property that matters for the desirable or detrimental effects of nanomaterials? Indeed, it is important to know not only what the material looks like, but also what it is made of, as well as how the material interacts with its biological surroundings. It has been suggested that guidelines should be implemented on the types of information required in terms of physicochemical characterization of nanomaterials for toxicological studies in order to improve the quality and relevance of the published results. This is certainly a key issue, but it is important to keep in mind that material characterization should be fit-for-purpose, that is, the information gathered should be relevant for the end-points being studied.

  • 7.
    Fugelstad, Johanna
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Brown, Christian
    KTH, School of Biotechnology (BIO), Glycoscience.
    Hukasova, Elvira
    Sundqvist, Gustav
    KTH, School of Biotechnology (BIO), Glycoscience.
    Lindqvist, Arne
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Functional characterization of the pleckstrin homology domain of a cellulose synthase from the Oomycete Saprolegnia monoica2012In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 417, no 4, p. 1248-1253Article in journal (Refereed)
    Abstract [en]

    Some oomycetes, for instance Saprolegnia parasitica, are severe fish pathogens that cause important economic losses worldwide. Cellulose biosynthesis is a vital process for this class of microorganisms, but the corresponding molecular mechanisms are poorly understood. Of all cellulose synthesizing enzymes known, only some oomycete cellulose synthases contain a pleckstrin homology (PH) domain. Some human PH domains bind specifically to phosphoinositides, but most PH domains bind phospholipids in a non-specific manner. In addition, some PH domains interact with various proteins. Here we have investigated the function of the PH domain of cellulose synthase 2 from the oomycete Saprolegnia monoica (SmCesA2), a species closely related to S. parasitica. The SmCesA2 PH domain is similar to the C-terminal PH domain of the human protein TAPP1. It binds in vitro to phosphoinositides, F-actin and microtubules, and co-localizes with F-actin in vivo. Our results suggest a role of the SmCesA2 PH domain in the regulation, trafficking and/or targeting of the cell wall synthesizing enzyme.

  • 8.
    Hasmats, Johanna
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gréen, Henrik
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Solnestam, Beata Werne
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Zajac, Pawel
    Huss, Mikael
    Orear, Cedric
    Validire, Pierre
    Bjursell, Magnus
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Validation of whole genome amplification for analysis of the p53 tumor suppressor gene in limited amounts of tumor samples2012In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 425, no 2, p. 379-383Article in journal (Refereed)
    Abstract [en]

    Personalized cancer treatment requires molecular characterization of individual tumor biopsies. These samples are frequently only available in limited quantities hampering genomic analysis. Several whole genome amplification (WGA) protocols have been developed with reported varying representation of genomic regions post amplification. In this study we investigate region dropout using a 929 polymerase based WGA approach. DNA from 123 lung cancers specimens and corresponding normal tissue were used and evaluated by Sanger sequencing of the p53 exons 5-8. To enable comparative analysis of this scarce material, WGA samples were compared with unamplified material using a pooling strategy of the 123 samples. In addition, a more detailed analysis of exon 7 amplicons were performed followed by extensive cloning and Sanger sequencing. Interestingly, by comparing data from the pooled samples to the individually sequenced exon 7, we demonstrate that mutations are more easily recovered from WGA pools and this was also supported by simulations of different sequencing coverage. Overall this data indicate a limited random loss of genomic regions supporting the use of whole genome amplification for genomic analysis.

  • 9. Johansson, Daniel X.
    et al.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Persson, Mats A. A.
    Fluorescent protein pair emit intracellular FRET signal suitable for FACS screening2007In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 352, no 2, p. 449-455Article in journal (Refereed)
    Abstract [en]

    The fluorescent proteins ECFP and HcRed were shown to give an easily resolved FRET-signal when expressed as a fusion inside mammalian cells. HeLa-tat cells expressing ECFP, pHcRed, or the fusion protein pHcRed-ECFP were analyzed by flow cytometry after excitation of ECFP. Cells expressing HcRed-ECFP, or ECFP and HcRed, were mixed and FACS-sorted for FRET positive cells: HcRed-ECFP cells were greatly enriched (72 times). Next, cloned human antibodies were fused with ECFP and expressed anchored to the ER membrane. Their cognate antigens (HIV-1 gp120 or gp41) were fused to HcRed and co-expressed in the ER. An increase of 13.5 +/- 1.5% (mean +/- SEM) and 8.0 +/- 10.7% in ECFP fluorescence for the specific antibodies reacting with gp 120 or gp41, respectively, was noted after photobleaching. A positive control (HcRed-ECFP) gave a 14.8 +/- 2.6% increase. Surprisingly, the unspecific antibody (anti-TT) showed 12.1 +/- 1.1% increase, possibly because overexpression in the limited ER compartment gave false FRET signals.

  • 10. Kim, D.
    et al.
    Lee, J.
    Lee, Sunjae
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, South Korea.
    Park, J.
    Lee, D.
    Predicting unintended effects of drugs based on off-target tissue effects2016In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 469, no 3, p. 399-404Article in journal (Refereed)
    Abstract [en]

    Unintended effects of drugs can be caused by various mechanisms. Conventional analysis of unintended effects has focused on the target proteins of drugs. However, an interaction with off-target tissues of a drug might be one of the unintended effect-related mechanisms. We propose two processes to predict a drug’s unintended effects by off-target tissue effects: 1) identification of a drug’s off-target tissue and; 2) tissue protein - symptom relation identification (tissue protein - symptom matrix). Using this method, we predicted that 1,177 (10.7%) side-effects were related to off-target tissue effects in 11,041 known side-effects. Off-target tissues and unintended effects of successful repositioning drugs were also predicted. The effectiveness of relations of the proposed tissue protein - symptom matrix were evaluated by using the literature mining method. We predicted unintended effects of drugs as well as those effect-related off-target tissues. By using our prediction, we are able to reduce drug side-effects on off-target tissues and provide a chance to identify new indications of drugs of interest.

  • 11.
    Kuttuva, Gunaratna R.
    et al.
    KTH, Superseded Departments, Biotechnology.
    Nekhotiaeva, N.
    Good, L.
    The signal peptide NPFSD fused to ricin A chain enhances cell uptake and cytotoxicity in Candida albicans2003In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 301, no 2, p. 529-534Article in journal (Refereed)
    Abstract [en]

    Microorganisms possess stringent cell membranes which limit the cellular uptake of antimicrobials. One strategy to overcome these barriers is to attach drugs or research reagents to carrier peptides that enter cells by passive permeation or active uptake. Here the short endocytosis signal peptide NPFSD was found to efficiently deliver both FITC and GFP,into Saccharomyces cerevisiae and Candida albicans with uptake into the majority of cells in a population. The NPFSD signal is itself non-toxic, but when fused to the ricin A chain toxin (RTA) the peptide enhanced both cell uptake and toxicity against C albicans, which like other yeasts is resistant to naked RTA. Cell entry required at least 1 h incubation, temperatures above 4degreesC, and an energy source, and uptake was outcompeted with free peptide. Therefore, the NPFSD peptide can carry a range of compounds into yeasts and this delivery route holds promise to enhance the activity of antifungals.

  • 12. Nasman, J.
    et al.
    Jolkkonen, Mikael
    Ammoun, S.
    Karlsson, E.
    Akerman, K. E. O.
    Recombinant expression of a selective blocker of M-1 muscarinic receptors2000In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 271, no 2, p. 435-439Article in journal (Refereed)
    Abstract [en]

    Mamba venoms contain peptides with high selectivity for muscarinic receptors, Due to the limited availability of the M-1 muscarinic receptor-selective MT7 or ml-toxin 1, the peptide was expressed in Sf9 cells using a synthetic cDNA and purified, The isolated peptide had over four orders of magnitude higher affinity for the M-1 compared to M-2-M-5 muscarinic receptors, The peptide strongly inhibited Ca2+ mobilisation ;through recombinant and endogenously expressed M-1 receptors, having no effect on the function of the other subtypes. The MT7 peptide provides a unique tool for identification and functional characterisation of M-1 receptors in cells and tissues,

  • 13. Rosok, O.
    et al.
    Pedeutour, F.
    Odeberg, Jacob
    KTH, Superseded Departments, Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Aasheim, H. C.
    The C1orf9 gene encodes a putative transmembrane member of a novel protein family2000In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 267, no 3, p. 855-862Article in journal (Refereed)
    Abstract [en]

    Here we report the characterization of a human mRNA encoding a novel protein denoted C1orf9 (chromosome 1 open reading frame 9). The cDNA sequence, derived from a testis cDNA library, contains 5700 bp which encodes an open reading frame of 1254 amino acids, The deduced protein contains a putative N-terminal signal peptide and one putative transmembrane region, indicating membrane localization. No significant homology was found with known characterized proteins. However, a 150 amino acid region has significant homology to deduced protein sequences from other organisms, including Caenorhabditis elegans (43% identity), Saccharomyces cerevisiae (47% identity), Schizosaccharomyces pombe (48% identity), and two proteins from Arabidopsis thaliana (42% and 40% identity), suggesting a novel family of conserved domains. The Clorf9 gene was assigned to chromosome 1q24. The gene spans approximately 78.7 kb and is organized into at least 24 exons. Expression analysis revealed a single Clorf9 mRNA species of approximately 6.0 kb with a predominant expression in pancreas and testis, and only low levels of expression in other tissues examined.

  • 14.
    Winzell, Anders
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO), Glycoscience.
    Wang, Yucheng
    KTH, School of Biotechnology (BIO), Glycoscience.
    Ezcurra, Ines
    KTH, School of Biotechnology (BIO), Glycoscience.
    Conserved CA-rich motifs in gene promoters of Pt x tMYB021-responsive secondary cell wall carbohydrate-active enzymes in Populus2010In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 394, no 3, p. 848-853Article in journal (Refereed)
    Abstract [en]

    In order to understand gene regulation during wood formation, we cloned a MYB46-like gene in hybrid aspen. Populus tremula x tremuloides, called PtxtMYB021 Phylogenetic and paired identity analysis of MYB46-like genes in Populus and Arabidopsis reveals relationships between paralogous pairs of Populus MYB46-like proteins and their Arabidopsis counterparts MYB46 and MYB83, and suggest that PtxtMYB021 is the ortholog of MYB46 Ptxt-MYB021 is expressed mainly in xylem tissues, and transiently expressed PtxtMYB46 transactivates gene promoters of xylan-active CAZymes GT43A, GT43B and Xyn10A Analysis of conserved motifs within these promoters identify the sequence CCACCAAC, called ACTYP, which is similar to the AC elements mediating transactivation by MYB transcription factors during lignin biosynthesis Further analysis by Motif Finder identifies four 6 bp CA-rich motifs overlapping ACTYP, and we show that these motifs are enriched in xylem-specific promoters We propose that AC-type regulatory elements mediate xylem-specific MYB46-dependent expression of secondary cell wall carbohydrate-active enzymes (CAZymes), besides activating gene expression of lignin biosynthesis enzymes.

  • 15. Yu, Meijuan
    et al.
    Yang, Feifei
    Chu, Wangsheng
    Wang, Yu
    Zhao, Haifeng
    Gao, Bin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhao, Wei
    Sun, Jianping
    Wu, Fangming
    Zhang, Xiaowei
    Shi, Yunyu
    Wu, Ziyu
    3D local structure around Zn in Kti11p as a representative Zn-(Cys)4 motif as obtained by MXAN2008In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 374, no 1, p. 28-32Article in journal (Refereed)
    Abstract [en]

    Zinc is an important component of many proteins that play key roles in transcription, translation, and catalysis. Kti11p, DESR1, both belonging to a protein family characterized by a CSL zinc finger domain, and the co-catalytic zinc-protein PML containing a Zn2+ binding domain called RING or C3HC4 finger are all structurally determined by NMR although the zinc sites are silent to this spectroscopical method. The comparison of X-ray absorption near-edge spectroscopy (XANES) data for the three proteins demonstrates that fingerprints effect is a reliable method for a primary characterization of ligand species. Ab initio full MS Calculations performed by MAN are applied to obtain chemical and stereo structural information around the Zn ion in Kti11p. For the first time this high-spatial resolution technique confirms the formation of a stable Zn tetrahedral configuration with four sulfur ligands, and returns extremely accurate bond angle information between ligands.

  • 16. Zhu, Chaoyong
    et al.
    Odeberg, Jacob
    KTH, School of Biotechnology (BIO), Gene Technology.
    Hamsten, Anders
    Eriksson, Per
    Allele-specific MMP-3 transcription under in vivo conditions2006In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 348, no 3, p. 1150-1156Article in journal (Refereed)
    Abstract [en]

    A common matrix metalloproteinases-3 (MMP-3) -1612 5A/6A promoter polymorphism is associated with risk for cardiovascular disease, rheumatoid arthritis, and other diseases. Here we used the haplotype chromatin immunoprecipitation method to study allele-specific MMP-3 expression under in vivo conditions in heterozygous THP-1 cells. Pyrosequencing was used to analyse the ratio of 5A-allele to 6A-allele after chromatin immunoprecipitation using an antibody against phosphorylated active RNA polymerase II. There was no allele-specific difference in transcriptional activity during basal conditions, i.e., in unstimulated monocytic THP-1 cells. However, after stimulation of MMP-3 expression by monocyte differentiation or incubation with IL-1 beta, the haplotype containing the 5A-allete was associated with higher transcriptional activity compared with the 6A-containing haplotype. Electromobility shift assay demonstrated increased binding of nuclear proteins to the 5A-allele after monocyte differentiation. In conclusion, the common MMP-3 5A/6A promoter polymorphism appears to be functional only during specific environmental conditions involving inflammation.

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