Chris Oostenbrink

Summary

Affiliation: University of Natural Resources and Applied Life Sciences
Country: Austria

Publications

  1. pmc Molecular dynamics simulations give insight into D-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase
    Michael M H Graf
    Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences BOKU, Muthgasse 18, 1190, Vienna, Austria
    J Comput Aided Mol Des 27:295-304. 2013
  2. pmc Rationalization of stereospecific binding of propranolol to cytochrome P450 2D6 by free energy calculations
    Gabor Nagy
    Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
    Eur Biophys J 41:1065-76. 2012
  3. ncbi request reprint Malleability and versatility of cytochrome P450 active sites studied by molecular simulations
    Chris Oostenbrink
    Leiden Amsterdam Centre for Drug Research, Division of Molecular and Computational Toxicology, The Netherlands
    Curr Drug Metab 13:190-6. 2012
  4. doi request reprint Free energy calculations from one-step perturbations
    Chris Oostenbrink
    Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
    Methods Mol Biol 819:487-99. 2012
  5. ncbi request reprint Free energy calculations of protein-ligand interactions
    Anita de Ruiter
    Institute for Molecular Modeling and Simulation, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
    Curr Opin Chem Biol 15:547-52. 2011
  6. doi request reprint Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered cytochrome P450 BM3 mutants
    Stephanie B A de Beer
    Leiden Amsterdam Center for Drug Research, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
    J Chem Inf Model 52:2139-48. 2012
  7. ncbi request reprint Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450
    Eva Stjernschantz
    Vrije Universiteit Amsterdam, Leiden Amsterdam Centre for Drug Research, Division of Molecular Toxicology, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
    Expert Opin Drug Metab Toxicol 4:513-27. 2008
  8. doi request reprint Efficient free energy calculations on small molecule host-guest systems - a combined linear interaction energy/one-step perturbation approach
    Chris Oostenbrink
    Division of Molecular Toxicology, Vrije Universiteit Amsterdam, Leiden Amsterdam Centre for Drug Research, De Boelelaan 1083, NL 1081 HV, Amsterdam, The Netherlands
    J Comput Chem 30:212-21. 2009
  9. doi request reprint Cytochrome P450 3A4 inhibition by ketoconazole: tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations
    Urban Bren
    Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, AT 1190 Vienna, Austria
    J Chem Inf Model 52:1573-82. 2012
  10. doi request reprint Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies
    Anita de Ruiter
    Institute for Molecular Modeling and Simulation, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
    J Comput Chem 34:1024-34. 2013

Collaborators

Detail Information

Publications23

  1. pmc Molecular dynamics simulations give insight into D-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase
    Michael M H Graf
    Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences BOKU, Muthgasse 18, 1190, Vienna, Austria
    J Comput Aided Mol Des 27:295-304. 2013
    ..Our findings corroborate and rationalize the experimentally observed dioxidation of GLC by PDH and its promiscuity towards different sugars...
  2. pmc Rationalization of stereospecific binding of propranolol to cytochrome P450 2D6 by free energy calculations
    Gabor Nagy
    Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
    Eur Biophys J 41:1065-76. 2012
    ..Finally we rationalize the results at a molecular level and compare data with experimental findings and previously estimated free energies...
  3. ncbi request reprint Malleability and versatility of cytochrome P450 active sites studied by molecular simulations
    Chris Oostenbrink
    Leiden Amsterdam Centre for Drug Research, Division of Molecular and Computational Toxicology, The Netherlands
    Curr Drug Metab 13:190-6. 2012
    ..A high level of active site flexibility does not only allow for the binding of a large variety of substrates and inhibitors, but also appears to be important to facilitate ligand binding and unbinding...
  4. doi request reprint Free energy calculations from one-step perturbations
    Chris Oostenbrink
    Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
    Methods Mol Biol 819:487-99. 2012
    ..The method may be applied using many different simulation programs. Here, analyses are exemplified at the hand of the GROMOS simulation package...
  5. ncbi request reprint Free energy calculations of protein-ligand interactions
    Anita de Ruiter
    Institute for Molecular Modeling and Simulation, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
    Curr Opin Chem Biol 15:547-52. 2011
    ....
  6. doi request reprint Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered cytochrome P450 BM3 mutants
    Stephanie B A de Beer
    Leiden Amsterdam Center for Drug Research, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
    J Chem Inf Model 52:2139-48. 2012
    ..Marcus theory is subsequently used to relate the thermodynamic stability to transition state energies and rates of formation...
  7. ncbi request reprint Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450
    Eva Stjernschantz
    Vrije Universiteit Amsterdam, Leiden Amsterdam Centre for Drug Research, Division of Molecular Toxicology, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
    Expert Opin Drug Metab Toxicol 4:513-27. 2008
    ..Simultaneously, many computational drug-design methods have been developed, and are being applied to study the interactions between drug candidates and cytochrome P450 enzymes (P450s)...
  8. doi request reprint Efficient free energy calculations on small molecule host-guest systems - a combined linear interaction energy/one-step perturbation approach
    Chris Oostenbrink
    Division of Molecular Toxicology, Vrije Universiteit Amsterdam, Leiden Amsterdam Centre for Drug Research, De Boelelaan 1083, NL 1081 HV, Amsterdam, The Netherlands
    J Comput Chem 30:212-21. 2009
    ....
  9. doi request reprint Cytochrome P450 3A4 inhibition by ketoconazole: tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations
    Urban Bren
    Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, AT 1190 Vienna, Austria
    J Chem Inf Model 52:1573-82. 2012
    ..This confirms the general applicability of rapid free-energy methods to study challenging biomolecular systems like cytochromes P450, which are characterized by a large flexibility and malleability of their active sites...
  10. doi request reprint Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies
    Anita de Ruiter
    Institute for Molecular Modeling and Simulation, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
    J Comput Chem 34:1024-34. 2013
    ..It is also the least dependent on the choice of the intermediate states, making it more robust than TI...
  11. doi request reprint Lipid A from lipopolysaccharide recognition: structure, dynamics and cooperativity by molecular dynamics simulations
    José Antonio Garate
    Department of Medical Sciences and Process Engineering, Institute of Molecular Modelling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
    Proteins 81:658-74. 2013
    ..The MD2/Lipid A-TLR4 complex simulations show that the presence of the ligand energetically stabilizes the complex relative to the ligand-free structures, indicating cooperativity in the binding process...
  12. pmc Entropic and enthalpic contributions to stereospecific ligand binding from enhanced sampling methods
    Balder Lai
    Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation at BOKU University of Natural Resources and Life Sciences, Muthgasse 18, A 1190 Vienna, Austria
    J Chem Inf Model 54:151-8. 2014
    ....
  13. ncbi request reprint Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3
    Eva Stjernschantz
    Leiden Amsterdam Centre for Drug Research, Division of Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
    Proteins 71:336-52. 2008
    ..This allows for an orientation of the substrates favorable for formation of the major metabolite by P450 BM3...
  14. pmc A systematic framework for molecular dynamics simulations of protein post-translational modifications
    Drazen Petrov
    Max F Perutz Laboratories, University of Vienna, Campus Vienna Biocenter, Vienna, Austria
    PLoS Comput Biol 9:e1003154. 2013
    ....
  15. ncbi request reprint Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation
    Maria M Reif
    Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Wien, Austria
    J Comput Chem 35:227-43. 2014
    ....
  16. pmc Dihedral-based segment identification and classification of biopolymers II: polynucleotides
    Gabor Nagy
    University of Natural Resources and Life Sciences, Institute for Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
    J Chem Inf Model 54:278-88. 2014
    ..While the detailed classification of DISICL adds sensitivity to a structure analysis, it can be readily reduced to eight simplified classes providing a more general overview of the secondary structure in polynucleotides...
  17. pmc Dihedral-based segment identification and classification of biopolymers I: proteins
    Gabor Nagy
    University of Natural Resources and Life Sciences, Institute for Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
    J Chem Inf Model 54:266-77. 2014
    ..J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400542n), the analysis of polynucleotides is described and applied. Overall, DISICL represents a potentially useful tool to analyze biopolymer structures at a high level of detail. ..
  18. pmc Expression and glycoengineering of functionally active heteromultimeric IgM in plants
    Andreas Loos
    Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
    Proc Natl Acad Sci U S A 111:6263-8. 2014
    ..Moreover, the generation of IgMs with a controlled glycosylation pattern allows the study of the so far unknown contribution of sugar moieties to the function of IgMs. ..
  19. pmc Conformationally constrained lipid A mimetics for exploration of structural basis of TLR4/MD-2 activation by lipopolysaccharide
    Daniel Artner
    Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A 1190 Vienna, Austria
    ACS Chem Biol 8:2423-32. 2013
    ..Our findings suggest that besides the chemical structure, also the three-dimensional arrangement of the diglucosamine backbone of MD-2-bound Lipid A determines endotoxic effects on TLR4. ..
  20. doi request reprint Free-energy differences between states with different conformational ensembles
    José Antonio Garate
    Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
    J Comput Chem 34:1398-408. 2013
    ..Additionally, a coupled OSP with LE/US was carried out, allowing the calculation of conformational and alchemical free energies of GTP and 8-substituted GTP analogs...
  21. doi request reprint Molecular insight into propeptide-protein interactions in cathepsins L and O
    Maria M Reif
    Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
    Biochemistry 51:8636-53. 2012
    ....