Browsing Bergen Open Research Archive by Author "Skjærven, Lars"

Now showing items 1-10 of 10

    • 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 ...

    • Conformational stabilization as a strategy to prevent nucleophosmin mislocalization in leukemia 

      Urbaneja, María A.; Skjærven, Lars; Aubi Catevilla, Oscar; Underhaug, Jarl; López, David J.; Arregi, Igor; Alonso-Mariño, Marián; Cuevas, Andoni; Rodríguez, José A.; Martinez, Aurora; Bañuelos, Sonia (Peer reviewed; Journal article, 2017-10-24)
      Nucleophosmin (NPM) is a nucleolar protein involved in ribosome assembly and cell homeostasis. Mutations in the C-terminal domain of NPM that impair native folding and localization are associated with acute myeloid leukemia ...

    • Integrating protein structural dynamics and evolutionary analysis with Bio3D 

      Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J. (Peer reviewed; Journal article, 2014-12-10)
      Background: Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how ...

    • Online interactive analysis of protein structure ensembles with Bio3D-web 

      Skjærven, Lars; Jariwala, Shashank; Yao, Xin-Qiu; Grant, Barry J. (Peer reviewed; Journal article, 2016-11)
      Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. Major functionality is provided for identifying protein structure sets for analysis, their ...

    • The Peripheral Binding of 14-3-3γ to Membranes Involves Isoform-Specific Histidine Residues 

      Bustad, Helene J.; Skjærven, Lars; Ying, Ming; Halskau, Øyvind; Baumann, Anne; Rodriguez-Larrea, David; Costas, Miguel; Underhaug, Jarl; Sanchez-Ruiz, Jose M.; Martinez, Aurora (Peer reviewed; Journal article, 2012-11-26)
      Mammalian 14-3-3 protein scaffolds include seven conserved isoforms that bind numerous phosphorylated protein partners and regulate many cellular processes. Some 14-3-3-isoforms, notably γ, have elevated affinity for ...

    • A Pharmacological Chaperone Therapy for Acute Intermittent Porphyria 

      Bustad, Helene J.; Toska, Karen; Schmitt, Caroline; Vorland, Marta; Skjærven, Lars; Kallio, Juha Pekka; Simonin, Sylvie; Lettéron, Philippe; Underhaug, Jarl; Sandberg, Sverre; Martinez, Aurora (Peer reviewed; Journal article, 2019-12-03)
      Mutations in hydroxymethylbilane synthase (HMBS) cause acute intermittent porphyria (AIP), an autosomal dominant disease where typically only one HMBS allele is mutated. In AIP, the accumulation of porphyrin precursors ...

    • Stable preparations of tyrosine hydroxylase provide the solution structure of the full-length enzyme 

      Bezem, Maria Teresa; Baumann, Anne; Skjærven, Lars; Meyer, Romain; Kursula, Petri; Martinez, Aurora; Flydal, Marte Innselset (Peer reviewed; Journal article, 2016-07-27)
      Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the biosynthesis of catecholamine neurotransmitters. TH is a highly complex enzyme at mechanistic, structural, and regulatory levels, and the preparation of ...

    • TMM@: a web application for the analysis of transmembrane helix mobility 

      Skjærven, Lars; Jonassen, Inge; Reuter, Nathalie (Peer reviewed; Journal article, 2007-07-02)
      Background: To understand the mechanism by which a protein transmits a signal through the cell membrane, an understanding of the flexibility of its transmembrane (TM) region is essential. Normal Mode Analysis (NMA) has ...

    • Towards Responsible Media Recommendation 

      Elahi, Mehdi; Jannach, Dietmar; Skjærven, Lars; Knudsen, Erik; Sjøvaag, Helle; Tolonen, Kristian; Holmstad, Øyvind; Pipkin, Igor; Throndsen, Eivind; Stenbom, Agnes; Fiskerud, Eivind; Oesch, Adrian; Vredenberg, Loek; Trattner, Christoph (Journal article; Peer reviewed, 2021)
      Reading or viewing recommendations are a common feature on modern media sites. What is shown to consumers as recommendations is nowadays often automatically determined by AI algorithms, typically with the goal of helping ...

    • WEBnm@ v2.0: Web server and services for comparing protein flexibility 

      Tiwari, Sandhya Premnath; Fuglebakk, Edvin; Hollup, Siv Midtun; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn Helge; Tekle, Kidane M; Reuter, Nathalie (Peer reviewed; Journal article, 2014-12-30)
      Background: Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the ...