Johannes Kästner

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Epidermal growth factor receptor (EGFR; ErbB1, HER1 in humans) is a receptor tyrosine kinase triggering signals across the plasma membranes of cells to determine cell fate. We have used molecular dynamics simulations to investigate structural models of ErbB1 ectodomains. We show that, with minor rearrangements, the ErbB1 back-to-back dimer can align almost(More)
Algorithmic improvements of the dimer method [G. Henkelman and H. Jonsson, J. Chem. Phys. 111, 7010 (1999)] are described in this paper. Using the limited memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) optimizer for the dimer translation greatly improves the convergence compared to the previously used conjugate gradient algorithm. It also saves one energy(More)
Herein, we test and compare different techniques to obtain averaged reaction barriers from quantum mechanics/molecular mechanics (QM/MM) simulations based on snapshots taken from molecular dynamics. Reasonable values can be obtained from a fairly small sample of well-chosen snapshots if an exponential averaging, also called Boltzmann averaging, is used.(More)
We used the free-energy perturbation (FEP) method in quantum mechanics/molecular mechanics (QM/MM) calculations to compute the free-energy profile of the hydroxylation reaction in the enzyme p-hydroxybenzoate hydroxylase (PHBH). k statistics were employed to analyze the FEP sampling including estimation of the sampling error. Various approximations of the(More)
We present a method to analyze biased molecular-dynamics and Monte Carlo simulations, also known as umbrella sampling. In the limiting case of a strong bias, this method is equivalent to thermodynamic integration. It employs only quantities with easily controllable equilibration and greatly reduces the statistical errors compared to the standard weighted(More)
The radical mechanism of the conversion of glutamate to methylaspartate catalyzed by glutamate mutase is studied with quantum mechanical/molecular mechanical (QM/MM) simulations based on density functional theory (DFT/MM). The hydrogen transfer between the substrate and the cofactor is found to be rate limiting with a barrier of 101.1 kJ mol(-1). A careful(More)
The calculation of free-energy differences is one of the main challenges in computational biology and biochemistry. Umbrella sampling, biased molecular dynamics (MD), is one of the methods that provide free energy along a reaction coordinate. Here, the method is derived in a historic overview and is compared with related methods like thermodynamic(More)
The flavoenzyme monoamine oxidase (MAO) is essential for the enzymatic decomposition of neurotransmitters. While it is commonly accepted that the rate limiting step of the reaction is the stereoselective abstraction of a hydrogen from the substrate, the precise mechanism is unknown. We modeled the reaction of human MAO-B with benzylamine by means of QM/MM(More)
We present a microiterative adiabatic scheme for quantum mechanical/molecular mechanical (QM/MM) energy minimization that fully optimizes the MM part in each QM macroiteration. This scheme is applicable not only to mechanical embedding but also to electrostatic and polarized embedding. The electrostatic QM/MM interactions in the microiterations are(More)
The flavin-containing enzyme monoamine oxidase (MAO) is essential for the enzymatic decomposition of amine neurotransmitters. The exact mechanism of the oxidative deamination of amines to aldehydes by the enzyme has not yet been fully understood despite extensive research on the area. The rate limiting step is the reductive half-reaction where the Hα(More)