Browsing Bergen Open Research Archive by Author "Reuter, Nathalie"

Now showing items 1-20 of 32

    • The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection 

      Dobrovolska, Olena; Brilkov, Maxim; Madeleine, Noëlly; Ødegaard-Fougner, Øyvind; Strømland, Øyvind; Martin, Stephen R.; De Marco, Valeria; Christodoulou, Evangelos; Teigen, Knut; Isaksson, Johan; Underhaug, Jarl; Reuter, Nathalie; Aalen, Reidunn B.; Aasland, Rein; Halskau, Øyvind (Journal article; Peer reviewed, 2020)
      Chromatin post‐translational modifications are thought to be important for epigenetic effects on gene expression. Methylation of histone N‐terminal tail lysine residues constitutes one of many such modifications, executed ...

    • Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects 

      Myklebust, Line Merethe; Van Damme, Petra; Støve, Svein Isungset; Dörfel, Max J; Abboud, Angèle; Kalvik, Thomas Vikestad; Grauffel, Cédric; Jonckheere, Veronique; Wu, Yiyang; Swensen, Jeffrey; Kaasa, Hanna; Liszczak, Glen; Marmorstein, Ronen; Reuter, Nathalie; Lyon, Gholson J; Gevaert, Kris; Arnesen, Thomas (Peer reviewed; Journal article, 2014-12-03)
      The X-linked lethal Ogden syndrome was the first reported human genetic disorder associated with a mutation in an N-terminal acetyltransferase (NAT) gene. The affected males harbor an Ser37Pro (S37P) mutation in the gene ...

    • Cation‐π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field 

      Khan, Hanif Muhammad; MacKerell, Alexander D.; Reuter, Nathalie (Peer reviewed; Journal article, 2019)
      Cation-π interactions between tryptophan and choline or trimethylated lysines are vital for many biological processes. The performance of the additive CHARMM36 force field against target quantum mechanical data is shown ...

    • Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases 

      Krtenic, Bojan; Drazic, Adrian; Arnesen, Thomas; Reuter, Nathalie (Journal article; Peer reviewed, 2020)
      The enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily count more than 870 000 members through all kingdoms of life and share the same structural fold. GNAT enzymes transfer an acyl moiety from acyl coenzyme ...

    • Comparing the intrinsic dynamics of multiple protein structures using elastic network models 

      Fuglebakk, Edvin; Tiwari, Sandhya Premnath; Reuter, Nathalie (Peer reviewed; Journal article, 2015-05)
      Background: Elastic network models (ENMs) are based on the simple idea that a protein can be described as a set of particles connected by springs, which can then be used to describe its intrinsic flexibility using, for ...

    • Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations 

      Skjærven, Lars; Grant, Barry; Muga, Arturo; Teigen, Knut; McCammon, J. Andrew; Reuter, Nathalie; Martinez, Aurora (Peer reviewed; Journal article, 2011-03-10)
      GroEL is an ATP dependent molecular chaperone that promotes the folding of a large number of substrate proteins in E. coli. Large-scale conformational transitions occurring during the reaction cycle have been characterized ...

    • Dissecting peripheral protein-membrane interfaces 

      Tubiana, Thibault Michel Joseph; Sillitoe, Ian; Orengo, Christine; Reuter, Nathalie (Journal article; Peer reviewed, 2022-12-14)
      Peripheral membrane proteins (PMPs) include a wide variety of proteins that have in common to bind transiently to the chemically complex interfacial region of membranes through their interfacial binding site (IBS). In ...

    • Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases 

      Abboud, Angèle; Bedoucha, Pierre; Byska, Jan; Arnesen, Thomas; Reuter, Nathalie (Journal article; Peer reviewed, 2020)
      N-terminal acetyltransferases (NATs) belong to the superfamily of acetyltransferases. They are enzymes catalysing the transfer of an acetyl group from acetyl coenzyme A to the N-terminus of polypeptide chains. N-terminal ...

    • Expression and purification of human neutrophil proteinase 3 from insect cells and characterization of ligand binding 

      Khorsand, Fahimeh; Haug, Bengt Erik; Kursula, Inari Talvikki; Reuter, Nathalie; Brenk, Ruth (Journal article; Peer reviewed, 2024)
      Neutrophil proteinase 3 (PR3) is an important drug target for inflammatory lung diseases such as chronic obstructive pulmonary disease and cystic fibrosis. Drug discovery efforts targeting PR3 require active enzyme for in ...

    • Interfacial Aromatics Mediating Cation-π Interactions with Choline-Containing Lipids Can Contribute as Much to Peripheral Protein Affinity for Membranes as Aromatics Inserted below the Phosphates 

      Waheed, Qaiser; Khan, Hanif Muhammad; He, Tao; Roberts, Mary F.; Gershenson, Anne; Reuter, Nathalie (Peer reviewed; Journal article, 2019)
      Membrane-binding interfaces of peripheral proteins are restricted to a small part of their exposed surface, so the ability to engage in strong selective interactions with membrane lipids at various depths in the interface, ...

    • Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3 

      Gartan, Parveen; Khorsand, Fahimeh; Mizar, Pushpak; Vahokoski, Juha; Cervantes, Luis F.; Haug, Bengt Erik; Brenk, Ruth; Brooks, Charles L.; Reuter, Nathalie (Journal article; Peer reviewed, 2024)
      Using a combination of multisite λ−dynamics (MSλD) together with in vitro IC50 assays, we evaluated the polypharmacological potential of a scaffold currently in clinical trials for inhibition of human neutrophil elastase ...

    • Membrane models for molecular simulations of peripheral membrane proteins 

      Moqadam, Mahmoud; Tubiana, Thibault Michel Joseph; Moutoussamy, Emmanuel Edouard; Reuter, Nathalie (Journal article; Peer reviewed, 2021)
      Peripheral membrane proteins (PMPs) bind temporarily to the surface of biological membranes. They also exist in a soluble form and their tertiary structure is often known. Yet, their membrane-bound form and their ...

    • Membrane specificity of the human cholesterol transfer protein STARD4 

      Talandashti, Reza; van Ek, Larissa; Gehin, Charlotte; Xue, Dandan; Moqadam, Mahmoud; Gavin, Anne-Claude; Reuter, Nathalie (Journal article; Peer reviewed, 2024)
      STARD4 regulates cholesterol homeostasis by transferring cholesterol between the plasma membrane and endoplasmic reticulum. The STARD4 structure features a helix-grip fold surrounding a large hydrophobic cavity holding the ...

    • A Membrane-Assisted Mechanism for the Release of Ceramide from the CERT START Domain 

      Moqadam, Mahmoud; Gartan, Parveen; Talandashti, Reza; Chiapparino, Antonella; Titeca, Kevin; Gavin, Anne-Claude; Reuter, Nathalie (Journal article; Peer reviewed, 2024)
      Ceramide transfer protein CERT is the mediator of nonvesicular transfer of ceramide from the ER to Golgi. In CERT, START is the domain responsible for the binding and transport of ceramide. A wealth of structural data has ...

    • A model for hydrophobic protrusions on peripheral membrane proteins 

      Fuglebakk, Edvin; Reuter, Nathalie (Peer reviewed; Journal article, 2018-07-26)
      With remarkable spatial and temporal specificities, peripheral membrane proteins bind to biological membranes. They do this without compromising solubility of the protein, and their binding sites are not easily distinguished. ...

    • Model Mechanism for Lipid Uptake by the Human STARD2/PC-TP Phosphatidylcholine Transfer Protein 

      Talandashti, Reza; Moqadam, Mahmoud; Reuter, Nathalie (Journal article; Peer reviewed, 2024)
      The human StAR-related lipid transfer domain protein 2 (STARD2), also known as phosphatidylcholine (PC) transfer protein, is a single-domain lipid transfer protein thought to transfer PC lipids between intracellular ...

    • Overlay databank unlocks data-driven analyses of biomolecules for all 

      Kiirikki, Anne M.; Antila, Hanne Susanna; Bort, Lara S.; Buslaev, Pavel; Favela-Rosales, Fernando; Ferreira, Tiago Mendes; Fuchs, Patrick F J; Garcia-Fandino, Rebeca; Gushchin, Ivan; Kav, Batuhan; Kučerka, Norbert; Kula, Patrik; Kurki, Milla; Kuzmin, Alexander; Lalitha, Anusha; Lolicato, Fabio; Madsen, Jesper J.; Miettinen, Markus Sakari; Mingham, Cedric; Monticelli, Luca; Nencini, Ricky; Nesterenko, Alexey; Piggot, Thomas J.; Piñeiro, Ángel; Reuter, Nathalie; Samantray, Suman; Suárez-Lestón, Fabián; Talandashti, Reza; Ollila, O H Samuli (Journal article; Peer reviewed, 2024)
      Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose ...

    • PDBe-KB: collaboratively defining the biological context of structural data 

      Varadi, Mihaly; Anyango, Stephen; Armstrong, David; Berrisford, John; Choudhary, Preeti; Deshpande, Mandar; Nadzirin, Nurul; Nair, Sreenath S.; Pravda, Lukas; Tanweer, Ahsan; Al-Lazikani, Bissan; Andreini, Claudia; Barton, Geoffrey J.; Bednar, David; Berka, Karel; Blundell, Tom; Brock, Kelly P.; Carazo, Jose Maria; Damborsky, Jiri; David, Alessia; Dey, Sucharita; Dunbrack, Roland; Recio, Juan Fernandez; Fraternali, Franca; Gibson, Toby; Helmer-Citterich, Manuela; Hoksza, David; Hopf, Thomas; Jakubec, David; Kannan, Natarajan; Krivak, Radoslav; Kumar, Manjeet; Levy, Emmanuel D.; London, Nir; Macias, Jose Ramon; Srivatsan, Madhusudhan M.; Marks, Debora S.; Martens, Lennart; McGowan, Stuart A.; McGreig, Jake E.; Modi, Vivek; Parra, R. Gonzalo; Pepe, Gerardo; Piovesan, Damiano; Prilusky, Jaime; Putignano, Valeria; Radusky, Leandro G.; Ramasamy, Pathmanaban; Rausch, Atilio O.; Reuter, Nathalie; Rodriguez, Luis A.; Rollins, Nathan J.; Rosato, Antonio; Rubach, Paweł; Serrano, Luis; Singh, Gulzar; Skoda, Petr; Sorzano, Carlos Oscar S.; Stourac, Jan; Sulkowska, Joanna I.; Svobodova, Radka; Tichshenko, Natalia; Tosatto, Silvio C.E.; Vranken, Wim; Wass, Mark N.; Xue, Dandan; Zaidman, Daniel; Thornton, Janet; Sternberg, Michael; Orengo, Christine; Velankar, Sameer (Journal article; Peer reviewed, 2022)
      The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or ...

    • Peptidomimetic inhibitors targeting the membrane-binding site of the neutrophil proteinase 3 

      Maximova, Ksenia; Reuter, Nathalie; Trylska, Joanna (Peer reviewed; Journal article, 2019)
      Proteinase 3 (PR3), together with other serine proteases, such as neutrophil elastase (NE) and cathepsin G (CG), regulates inflammatory and immune responses. However, in comparison with NE and CG, there is increasing ...

    • Phosphatidylcholine Cation—Tyrosine π Complexes: Motifs for Membrane Binding by a Bacterial Phospholipase C 

      Roberts, Mary F.; Gershenson, Anne; Reuter, Nathalie (Journal article; Peer reviewed, 2022-09-21)
      Phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes are a virulence factor in many Gram-positive organisms. The specific activity of the Bacillus thuringiensis PI-PLC is significantly increased by adding ...