12 results on '"Berntsson, R."'
Search Results
2. Beyond the membrane: Characterization of the oligopeptide binding protein from Escherichia coli: C4.13
- Author
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Klepsch, M., Berntsson, R., de Gier, J.-W., and Slotboom, D.-J.
- Published
- 2010
3. A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family
- Author
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Carreras-Puigvert, J., Zitnik, M., Jemth, A. -S, Carter, M., Unterlass, J. E., Hallström, Björn M., Loseva, O., Karem, Z., Calderón-Montanõ, J. M., Lindskog, C., Edqvist, P. -H, Matuszewski, D. J., Ait Blal, Hammou, Berntsson, R. P. A., Häggblad, M., Martens, U., Studham, M., Lundgren, B., Wählby, C., Sonnhammer, E. L. L., Lundberg, Emma, Stenmark, P., Zupan, B., Helleday, T., Carreras-Puigvert, J., Zitnik, M., Jemth, A. -S, Carter, M., Unterlass, J. E., Hallström, Björn M., Loseva, O., Karem, Z., Calderón-Montanõ, J. M., Lindskog, C., Edqvist, P. -H, Matuszewski, D. J., Ait Blal, Hammou, Berntsson, R. P. A., Häggblad, M., Martens, U., Studham, M., Lundgren, B., Wählby, C., Sonnhammer, E. L. L., Lundberg, Emma, Stenmark, P., Zupan, B., and Helleday, T.
- Abstract
The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes. To a certain extent, their substrate preference redundancies correlate with structural classes, thus linking structure and activity relationships. To elucidate interdependence among the NUDIX hydrolases, we pairwise deplete them generating an epistatic interaction map, evaluate cell cycle perturbations upon knockdown in normal and cancer cells, and analyse their protein and mRNA expression in normal and cancer tissues. Using a novel FUSION algorithm, we integrate all data creating a comprehensive NUDIX enzyme profile map, which will prove fundamental to understanding their biological functionality., QC 20180503
- Published
- 2017
- Full Text
- View/download PDF
4. Escherichia coli Peptide Binding Protein OppA Has a Preference for Positively Charged Peptides
- Author
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Klepsch, M. M., Kovermann, M., Löw, C., Balbach, J., Permentier, H. P., Fusetti, F., de Gier, J. W., Gier, Jan-Willem de, Slotboom, D. J., Berntsson, R. P. -A., Analytical Biochemistry, Medicinal Chemistry and Bioanalysis (MCB), Groningen Biomolecular Sciences and Biotechnology, and Zernike Institute for Advanced Materials
- Subjects
Models, Molecular ,Salmonella typhimurium ,STRUCTURAL BASIS ,Protein Conformation ,Lipoproteins ,Immunoblotting ,Peptide binding ,Tripeptide ,Plasma protein binding ,Crystallography, X-Ray ,peptide binding protein, oligopeptide transporter, ABC transporter, Escherichia coli, substrate binding protein ,Substrate Specificity ,Protein structure ,ABC TRANSPORTERS ,Structural Biology ,Escherichia coli ,Binding site ,Molecular Biology ,SPECIFICITY ,chemistry.chemical_classification ,Oligopeptide ,Binding Sites ,OLIGOPEPTIDE PERMEASE ,COMPLEX ,Chemistry ,MEMBRANE-PROTEINS ,Escherichia coli Proteins ,oligopeptide transporter ,SALMONELLA-TYPHIMURIUM ,Isothermal titration calorimetry ,Biological Transport ,substrate binding protein ,Amino acid ,MODEL ,peptide binding protein ,Biochemistry ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,ddc:540 ,LIGAND-BINDING ,ABC transporter ,Carrier Proteins ,Oligopeptides ,Protein Binding - Abstract
The Escherichia coli peptide binding protein OppA is an essential component of the oligopeptide transporter Opp. Based on studies on its orthologue from Salmonella typhimurium, it has been proposed that OppA binds peptides between two and five amino acids long, with no apparent sequence selectivity. Here, we studied peptide binding to E. coli OppA directly and show that the protein has an unexpected preference for basic peptides. OppA was expressed in the periplasm, where it bound to available peptides. The protein was purified in complex with tightly bound peptides. The crystal structure (up to 2.0 angstrom) of OppA liganded with the peptides indicated that the protein has a preference for peptides containing a lysine. Mass spectrometry analysis of the bound peptides showed that peptides between two and five amino acids long bind to the protein and indeed hinted at a preference for positively charged peptides. The preference of OppA for peptides with basic residues, in particular lysines, was corroborated by binding studies with peptides of defined sequence using isothermal titration calorimetry and intrinsic protein fluorescence titration. The protein bound tripeptides and tetrapeptides containing positively charged residues with high affinity, whereas related peptides without lysines/arginines were bound with low affinity. A structure of OppA in an open conformation in the absence of ligands was also determined to 2.0 angstrom, revealing that the initial binding site displays a negative surface charge, consistent with the observed preference for positively charged peptides. Taken together, E. coli OppA appears to have a preference for basic peptides. (C) 2011 Elsevier Ltd. All rights reserved.
- Published
- 2011
5. Importance of a Hydrophobic Pocket for Peptide Binding in Lactococcal OppA▿
- Author
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Berntsson, R. P.- A., Thunnissen, A.-M. W. H., Poolman, B., and Slotboom, D.-J.
- Published
- 2011
- Full Text
- View/download PDF
6. Escherichia coli Peptide Binding Protein OppA Has a Preference for Positively Charged Peptides
- Author
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Klepsch, Mirjam, Kovermann, M., Low, C., Balbach, J., Permentier, H. P., Fusetti, F., de Gier, Jan-Willem, Slotboom, D. J., Berntsson, R. P. -A, Klepsch, Mirjam, Kovermann, M., Low, C., Balbach, J., Permentier, H. P., Fusetti, F., de Gier, Jan-Willem, Slotboom, D. J., and Berntsson, R. P. -A
- Abstract
The Escherichia coli peptide binding protein OppA is an essential component of the oligopeptide transporter Opp. Based on studies on its orthologue from Salmonella typhimurium, it has been proposed that OppA binds peptides between two and five amino acids long, with no apparent sequence selectivity. Here, we studied peptide binding to E. coli OppA directly and show that the protein has an unexpected preference for basic peptides. OppA was expressed in the periplasm, where it bound to available peptides. The protein was purified in complex with tightly bound peptides. The crystal structure (up to 2.0 angstrom) of OppA liganded with the peptides indicated that the protein has a preference for peptides containing a lysine. Mass spectrometry analysis of the bound peptides showed that peptides between two and five amino acids long bind to the protein and indeed hinted at a preference for positively charged peptides. The preference of OppA for peptides with basic residues, in particular lysines, was corroborated by binding studies with peptides of defined sequence using isothermal titration calorimetry and intrinsic protein fluorescence titration. The protein bound tripeptides and tetrapeptides containing positively charged residues with high affinity, whereas related peptides without lysines/arginines were bound with low affinity. A structure of OppA in an open conformation in the absence of ligands was also determined to 2.0 angstrom, revealing that the initial binding site displays a negative surface charge, consistent with the observed preference for positively charged peptides. Taken together, E. coli OppA appears to have a preference for basic peptides., authorCount :9
- Published
- 2011
- Full Text
- View/download PDF
7. Optimized in vitro and in vivo expression of proteorhodopsin: a seven-transmembrane proton pump
- Author
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Gourdon, P., Alfredsson, A., Pedersen, A., Malmerberg, E., Nyblom, M., Widell, M., Berntsson, R., Pinhassi, Jarone, Braiman, M., Hansson, Ö., Bonander, N., Karlsson, G., Neutze, R., Gourdon, P., Alfredsson, A., Pedersen, A., Malmerberg, E., Nyblom, M., Widell, M., Berntsson, R., Pinhassi, Jarone, Braiman, M., Hansson, Ö., Bonander, N., Karlsson, G., and Neutze, R.
- Published
- 2008
8. Developing an Enterprise Specific Application Portfolio Assessment Method: From Architectural Principles to Measures.
- Author
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Lindstrom, A. and Berntsson, R.
- Published
- 2006
- Full Text
- View/download PDF
9. Systematic screens for fertility genes essential for malaria parasite transmission reveal conserved aspects of sex in a divergent eukaryote.
- Author
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Sayers C, Pandey V, Balakrishnan A, Michie K, Svedberg D, Hunziker M, Pardo M, Choudhary J, Berntsson R, and Billker O
- Subjects
- Animals, Male, Female, Mice, Protozoan Proteins genetics, Protozoan Proteins metabolism, Plasmodium berghei genetics, Malaria transmission, Malaria genetics, Fertility genetics
- Abstract
Sexual reproduction in malaria parasites is essential for their transmission to mosquitoes and offers a divergent eukaryote model to understand the evolution of sex. Through a panel of genetic screens in Plasmodium berghei, we identify 348 sex and transmission-related genes and define roles for unstudied genes as putative targets for transmission-blocking interventions. The functional data provide a deeper understanding of female metabolic reprogramming, meiosis, and the axoneme. We identify a complex of a SUN domain protein (SUN1) and a putative allantoicase (ALLC1) that is essential for male fertility by linking the microtubule organizing center to the nuclear envelope and enabling mitotic spindle formation during male gametogenesis. Both proteins have orthologs in mouse testis, and the data raise the possibility of an ancient role for atypical SUN domain proteins in coupling the nucleus and axoneme. Altogether, our data provide an unbiased picture of the molecular processes that underpin malaria parasite transmission. A record of this paper's transparent peer review process is included in the supplemental information., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
10. Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.
- Author
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Verma A, Åberg-Zingmark E, Sparrman T, Mushtaq AU, Rogne P, Grundström C, Berntsson R, Sauer UH, Backman L, Nam K, Sauer-Eriksson E, and Wolf-Watz M
- Subjects
- Humans, Catalysis, Catalytic Domain, Archaea genetics, Adenylate Kinase chemistry
- Abstract
Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while
19 F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.- Published
- 2022
- Full Text
- View/download PDF
11. Suicide, guns, and buyback programs: An epidemiologic analysis of firearm-related deaths in Connecticut.
- Author
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Baumann L, Clinton H, Berntsson R, Williams SS, Rovella JC, Shapiro D, Thaker S, Borrup K, Lapidus G, and Campbell BT
- Subjects
- Adult, Connecticut epidemiology, Female, Firearms statistics & numerical data, Homicide legislation & jurisprudence, Humans, Incidence, Male, Middle Aged, Retrospective Studies, Suicide legislation & jurisprudence, Survival Rate trends, Wounds, Gunshot prevention & control, Firearms legislation & jurisprudence, Homicide prevention & control, Police, Violence legislation & jurisprudence, Violence prevention & control, Wounds, Gunshot epidemiology, Suicide Prevention
- Abstract
Background: Gun buyback programs aim to remove unwanted firearms from the community with the goal of preventing firearm injury and death. Buyback programs are held in many communities, but evidence demonstrating their effectiveness is lacking. The purpose of this study is to compare firearms collected at buyback events to crime guns and firearms used in homicides and suicides., Methods: Detailed firearm and case data were obtained from the Hartford Police Department and the Office of the Chief Medical Examiner from January through December of 2015. Information was reviewed for guns collected at buyback events, crime guns confiscated by police, and for weapons associated with firearm fatalities. Detailed firearm data included type, manufacturer, model, and caliber (small, ≤ 0.32 caliber; medium, 0.357 caliber to 9 mm; large, ≥ 0.40 caliber). χ analyses were used for comparisons between groups., Results: In 2015, 224 crime guns were seized by the Hartford Police, 169 guns were collected at four community buyback events, and there were 187 firearm-related deaths statewide (105 suicides, 81 homicides, 1 legal intervention). Comparisons between buyback, crime, and fatality-related firearms are shown in the table below. Medium caliber handguns account for the majority of crime guns and fatalities, and buyback programs collected smaller caliber handguns. The demographics of individuals who turn in guns at buyback events and commit suicide are similar: age (buyback, 63 ± 11; suicide, 52 ± 18; homicide, 34 ± 12 years), sex (buyback, 81%; suicide, 91%; homicide, 84% men), and race (buyback, 80%; suicide, 97%; homicide, 47% white)., Conclusion: Handguns account for the majority of crime guns and firearm-related fatalities in Connecticut. Buyback programs are both an opportunity to remove unwanted handguns from the community and to remove firearms from the homes of individuals at increased risk of suicide., Level of Evidence: Epidemiologic/therapeutic study, level IV.
- Published
- 2017
- Full Text
- View/download PDF
12. Optimized in vitro and in vivo expression of proteorhodopsin: a seven-transmembrane proton pump.
- Author
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Gourdon P, Alfredsson A, Pedersen A, Malmerberg E, Nyblom M, Widell M, Berntsson R, Pinhassi J, Braiman M, Hansson O, Bonander N, Karlsson G, and Neutze R
- Subjects
- Bioreactors, Cloning, Molecular, Gammaproteobacteria genetics, Gammaproteobacteria metabolism, Gene Expression, Nuclear Magnetic Resonance, Biomolecular, Protein Sorting Signals, Proton Pumps, Rhodopsins, Microbial, Rhodopsin biosynthesis, Rhodopsin chemistry, Rhodopsin genetics, Rhodopsin isolation & purification
- Abstract
Proteorhodopsin is an integral membrane light-harvesting proton pump that is found in bacteria distributed throughout global surface waters. Here, we present a protocol for functional in vitro production of pR using a commercial cell-free synthesis system yielding 1.0mg purified protein per milliliter of cell lysate. We also present an optimized protocol for in vivo over-expression of pR in Escherichia coli, and a two-step purification yielding 5mg of essentially pure functional protein per liter of culture. Both approaches are straightforward, rapid, and easily scalable. Thus either may facilitate the exploitation of pR for commercial biotechnological applications. Finally, the implications of some observations of the in vitro synthesis behavior, as well as preliminary results towards a structural determination of pR are discussed.
- Published
- 2008
- Full Text
- View/download PDF
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