• Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations 

      Wilkins, Ryan Scott; Lund, Bjarte Aarmo; Isaksen, Geir Villy; Åqvist, Johan Lennart Gösta; Brandsdal, Bjørn Olav (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-12-19)
      Chorismate mutase (CM) enzymes have long served as model systems for benchmarking new methods and tools in computational chemistry. Despite the enzymes’ prominence in the literature, the extent of the roles that activation enthalpy and entropy play in catalyzing the conversion of chorismate to prephenate is still subject to debate. Knowledge of these parameters is a key piece in fully understanding ...
    • A comparative study of cold-and warmadapted Endonucleases A using sequence analyses and molecular Dynamics simulations 

      Michetti, Davide; Brandsdal, Bjørn Olav; Bon, Davide; Isaksen, Geir Villy; Tiberti, Matteo; Papaleo, Elena (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-02-13)
      The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics ...
    • Computational design of the temperature optimum of an enzyme reaction 

      van der Ent, Florian; Skagseth, Susann; Lund, Bjarte Aarmo; Sočan, Jaka; Griese, Julia J.; Brandsdal, Bjørn Olav; Åqvist, Johan Lennart Gösta (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-06-28)
      Cold-adapted enzymes are characterized both by a higher catalytic activity at low temperatures and by having their temperature optimum down-shifted, compared to mesophilic orthologs. In several cases, the optimum does not coincide with the onset of protein melting but reflects some other type of inactivation. In the psychrophilic α-amylase from an Antarctic bacterium, the inactivation is thought to ...
    • Entropy and Enzyme Catalysis 

      Åqvist, Johan; Kazemi, Masoud; Isaksen, Geir Villy; Brandsdal, Bjørn Olav (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-02-07)
      The role played by entropy for the enormous rate enhancement achieved by enzymes has been debated for many decades. There are, for example, several confirmed cases where the activation free energy is reduced by around 10 kcal/mol due to entropic effects, corresponding to a rate enhancement of ∼107 compared to the uncatalyzed reaction. However, despite substantial efforts from both the experimental ...
    • Protein surface softness is the origin of enzyme cold-adaptation of trypsin 

      Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Bjørn Olav (Journal article; Tidsskriftartikkel; Peer reviewed, 2014)
    • QresFEP: An Automated Protocol for Free Energy Calculations of Protein Mutations in Q 

      Jespers, Willem; Isaksen, Geir Villy; Andberg, Tor Arne Heim; Vasile, Silvana; van Veen, Amber; Åqvist, Johan; Brandsdal, Bjørn Olav; Gutiérrez-de-Terán, Hugo (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-08-22)
      Predicting the effect of single-point mutations on protein stability or protein−ligand binding is a major challenge in computational biology. Free energy calculations constitute the most rigorous approach to this problem, though the estimation of converged values for amino acid mutations remains challenging. To overcome this limitation, we developed tailored protocols to calculate free energy ...
    • Structure and Mechanism of a Cold-Adapted Bacterial Lipase 

      van der Ent, Florian; Lund, Bjarte Aarmo; Svalberg, Linn; Purg, Miha; Chukwu, Ghislean; Widersten, Mikael; Isaksen, Geir Villy; Brandsdal, Bjørn Olav; Åqvist, Johan Lennart Gösta (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-05-03)
      The structural origin of enzyme cold-adaptation has been the subject of considerable research efforts in recent years. Comparative studies of orthologous mesophilic–psychrophilic enzyme pairs found in nature are an obvious strategy for solving this problem, but they often suffer from relatively low sequence identity of the enzyme pairs. Small bacterial lipases adapted to distinctly different ...
    • Synthetic cationic antimicrobial peptides bind with their hydrophobic parts to drug site II of human serum albumin 

      Sivertsen, Annfrid; Isaksson, Johan; Leiros, Hanna-Kirsti S.; Svenson, Johan; Svendsen, John Sigurd; Brandsdal, Bjørn Olav (Journal article; Tidsskriftartikkel; Peer reviewed, 2014)
    • ThermoSlope: A Software for Determining Thermodynamic Parameters from Single Steady-State Experiments 

      Lund, Bjarte Aarmo; Brandsdal, Bjørn Olav (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-11-26)
      The determination of the temperature dependence of enzyme catalysis has traditionally been a labourious undertaking. We have developed a new approach to the classical Arrhenius parameter estimation by fitting the change in velocity under a gradual change in temperature. The evaluation with a simulated dataset shows that the approach is valid. The approach is demonstrated as a useful tool by ...
    • Towards Rational Computational Engineering of Psychrophilic Enzymes 

      Socan, Jaka; Isaksen, Geir Villy; Brandsdal, Bjørn Olav; Åqvist, Johan Lennart Gösta (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-12-16)
      Cold-adapted enzymes from psychrophilic species achieve their high catalytic efficiency at low temperature by a different partitioning of the activation free energy into its enthalpic and entropic components, compared to orthologous mesophilic enzymes. Their lower activation enthalpy, partly compensated by an increased entropic penalty, has been suggested to originate from changes in flexibility of ...