Browsing Bergen Open Research Archive by Author "Reuter, Nathalie"
Now showing items 1-19 of 19
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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 ... -
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, ... -
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. ... -
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 ... -
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 ... -
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 ... -
Two homologous neutrophil serine proteases bind to POPC vesicles with different affinities: When aromatic amino acids matter
Schillinger, Anne-Sophie; Grauffel, Cédric; Khan, Hanif Muhammad; Halskau, Øyvind; Reuter, Nathalie (Peer reviewed; Journal article, 2014-12)Neutrophil serine proteases Proteinase 3 (PR3) and human neutrophil elastase (HNE) are homologous antibiotic serine proteases of the polymorphonuclear neutrophils. Despite sharing a 56% sequence identity they have been ... -
Visual Cavity Analysis in Molecular Simulations
Parulek, Julius; Turkay, Cagatay; Reuter, Nathalie; Viola, Ivan (Peer reviewed; Journal article, 2013-11-12)Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel technique, which ... -
Visual exploration of large normal mode spaces to study protein flexibility
Bedoucha, Pierre; Reuter, Nathalie; Hauser, Helwig; Byska, Jan (Journal article; Peer reviewed, 2020-05-22)When studying the function of proteins, biochemists utilize normal mode decomposition to enable the analysis of structural changes on time scales that are too long for molecular dynamics simulation. Such a decomposition ... -
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 ... -
WEBnm@: a web application for normal mode analyses of proteins
Hollup, Siv Midtun; Sælensminde, Gisle; Reuter, Nathalie (Peer reviewed; Journal article, 2005-12-30)Background: Normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channels ...