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@article{721208, author = {Negri, A. and Marco, E. and Damborský, Jiří and Gago, Frederico}, article_number = {3}, keywords = {Stepwise Dissection; Visualization; Catalytic Mechanism; Haloalkane Dehalogenase LinB; Molecular Dynamics Simulations; Computer Graphics}, language = {eng}, issn = {1093-3263}, journal = {JOURNAL OF MOLECULAR GRAPHICS AND MODELLING}, title = {Stepwise Dissection and Visualization of the Catalytic Mechanism of Haloalkane Dehalogenase LinB using Molecular Dynamics Simulations and Computer Graphics}, url = {http://loschmidt.chemi.muni.cz/peg/abstracts/jmgm07.html}, volume = {26}, year = {2007} }
TY - JOUR ID - 721208 AU - Negri, A. - Marco, E. - Damborský, Jiří - Gago, Frederico PY - 2007 TI - Stepwise Dissection and Visualization of the Catalytic Mechanism of Haloalkane Dehalogenase LinB using Molecular Dynamics Simulations and Computer Graphics JF - JOURNAL OF MOLECULAR GRAPHICS AND MODELLING VL - 26 IS - 3 SP - 643-651 EP - 643-651 SN - 10933263 KW - Stepwise Dissection KW - Visualization KW - Catalytic Mechanism KW - Haloalkane Dehalogenase LinB KW - Molecular Dynamics Simulations KW - Computer Graphics UR - http://loschmidt.chemi.muni.cz/peg/abstracts/jmgm07.html N2 - The different steps of the dehalogenation reaction carried out by LinB on three different substrates have been characterized using a combination of quantum mechanical calculations and molecular dynamics simulations. This has allowed us to obtain information in atomic detail about each step of the reaction mechanism, that is, substrate entrance and achievement of the near-attack conformation, transition state stabilization within the active site, halide stabilization, water molecule activation and subsequent hydrolytic attack on the ester intermediate with formation of alcohol, and finally product release. Importantly, no bias or external forces were applied during the whole procedure so that both intermediates and products were completely free to sample configuration space in order to adapt to the plasticity of the active site and/or search for an exit. Differences in substrate reactivity were found to be correlated with the ease of adopting the near-attack conformation and two different exit pathways were found for product release that do not interfere with substrate entrance. Additional support for the different entry and exit pathways was independently obtained from an examination of the enzyme's normal modes. ER -
NEGRI, A., E. MARCO, Jiří DAMBORSKÝ a Frederico GAGO. Stepwise Dissection and Visualization of the Catalytic Mechanism of Haloalkane Dehalogenase LinB using Molecular Dynamics Simulations and Computer Graphics. \textit{JOURNAL OF MOLECULAR GRAPHICS AND MODELLING}. 2007, roč.~26, č.~3, s.~643-651. ISSN~1093-3263.
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