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

Now showing items 1-20 of 26

    • 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 ...

    • 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 ...

    • 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. ...

    • 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 ...

    • A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding 

      Khan, Hanif Muhammad; He, Tao; Fuglebakk, Edvin; Grauffel, Cédric; Yang, Boqian; Roberts, Mary F.; Gershenson, Anne; Reuter, Nathalie (Peer reviewed; Journal article, 2016-03)
      Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) is a secreted virulence factor that binds specifically to phosphatidylcholine (PC) bilayers containing negatively charged phospholipids. ...

    • Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes 

      Tiwari, Sandhya Premnath; Reuter, Nathalie (Peer reviewed; Journal article, 2016-03-25)
      The conservation of the intrinsic dynamics of proteins emerges as we attempt to understand the relationship between sequence, structure and functional conservation. We characterise the conservation of such dynamics in a ...

    • Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases 

      Grauffel, Cédric; Abboud, Angèle; Liszczak, Glen; Marmorstein, Ronen; Arnesen, Thomas; Reuter, Nathalie (Peer reviewed; Journal article, 2012-12-28)
      Nt-acetylation is among the most common protein modifications in eukaryotes. Although thought for a long time to protect proteins from degradation, the role of Nt-acetylation is still debated. It is catalyzed by enzymes ...

    • Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage 

      Moutoussamy, Emmanuel Edouard; Waheed, Qaiser; Binford, Greta J.; Khan, Hanif Muhammad; Moran, Shane M.; Eitel, Anna R.; Cordes, Matthew H.J.; Reuter, Nathalie (Journal article; Peer reviewed, 2022)
      Spider venom GDPD-like phospholipases D (SicTox) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the β clade. Most α clade toxins present ...

    • Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C 

      Moutoussamy, Emmanuel Edouard; Khan, Hanif Muhammad; Roberts, Mary B; Gershenson, Anne; Chipot, Christophe; Reuter, Nathalie (Journal article; Peer reviewed, 2022)
      Peripheral membrane proteins (PMPs) bind temporarily to cellular membranes and play important roles in signaling, lipid metabolism, and membrane trafficking. Obtaining accurate membrane-PMP affinities using experimental ...