Blar i Bergen Open Research Archive på forfatter "Mitternacht, Simon"

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    • Binding Leverage as a Molecular Basis for Allosteric Regulation 

      Mitternacht, Simon; Berezovsky, Igor N. (Peer reviewed; Journal article, 2011-09-15)
      Allosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures the ...

    • Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication 

      Mitternacht, Simon; Berezovsky, Igor N. (Peer reviewed; Journal article, 2011-12-08)
      Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are visited ...

    • FreeSASA: An open source C library for solvent accessible surface area calculations 

      Mitternacht, Simon (Peer reviewed; Journal article, 2016-02-29)
      Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools ...

    • A geometry-based generic predictor for catalytic and allosteric sites 

      Mitternacht, Simon; Berezovsky, Igor N. (Peer reviewed; Journal article, 2011)
      An important aspect of understanding protein allostery, and of artificial effector design, is the characterization and prediction of substrate- and effector-binding sites. To find binding sites in allosteric enzymes, many ...

    • Mechanical resistance in unstructured proteins 

      Jónsson, Sigurður Ægir; Mitternacht, Simon; Irbäck, Anders (Peer reviewed; Journal article, 2013-06-18)
      Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of ...

    • Monte Carlo Study of the Formation and Conformational Properties of Dimers of Aβ42 Variants 

      Mitternacht, Simon; Staneva, Iskra; Härd, Torleif; Irbäck, Anders (Peer reviewed; Journal article, 2011)
      Small soluble oligomers, and dimers in particular, of the amyloid β-peptide (Aβ) are believed to play an important pathological role in Alzheimer's disease. Here, we investigate the spontaneous dimerization of Aβ42, with ...

    • SPACER: server for predicting allosteric communication and effects of regulation 

      Goncearenco, Alexander; Mitternacht, Simon; Yong, Taipang; Eisenhaber, Birgit; Eisenhaber, Frank; Berezovsky, Igor (Peer reviewed; Journal article, 2013-06-03)
      The SPACER server provides an interactive framework for exploring allosteric communication in proteins with different sizes, degrees of oligomerization and function. SPACER uses recently developed theoretical concepts based ...