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Main Title: | Probing the Structure of [NiFeSe] Hydrogenase with QM/MM Computations |
Author(s): | Moubarak, Samah Elghobashi-Meinhardt, Nadia Said Tombolelli, Daria Mroginski, Maria Andrea |
Type: | Article |
Language Code: | en |
Abstract: | The geometry and vibrational behavior of selenocysteine [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough have been investigated using a hybrid quantum mechanical (QM)/ molecular mechanical (MM) approach. Structural models have been built based on the three conformers identified in the recent crystal structure resolved at 1.3 Å from X-ray crystallography. In the models, a diamagnetic Ni2+ atom was modeled in combination with both Fe2+ and Fe3+ to investigate the effect of iron oxidation on geometry and vibrational frequency of the nonproteic ligands, CO and CN-, coordinated to the Fe atom. Overall, the QM/MM optimized geometries are in good agreement with the experimentally resolved geometries. Analysis of computed vibrational frequencies, in comparison with experimental Fourier-transform infrared (FTIR) frequencies, suggests that a mixture of conformers as well as Fe2+ and Fe3+ oxidation states may be responsible for the acquired vibrational spectra. |
URI: | https://depositonce.tu-berlin.de/handle/11303/11011 http://dx.doi.org/10.14279/depositonce-9903 |
Issue Date: | 22-Jan-2020 |
Date Available: | 24-Apr-2020 |
DDC Class: | 540 Chemie und zugeordnete Wissenschaften |
Subject(s): | NiFeSe hydrogenase quantum mechanics QM molecular mechanics MM geometry optimizations vibrational frequency analyses Fourier transform infrared frequencies FTIR |
Sponsor/Funder: | DFG, 390540038, EXC 2008: UniSysCat DFG, 414044773, Open Access Publizieren 2019 - 2020 / Technische Universität Berlin EC/H2020/810856/EU/Twin to Illuminate Metals in Biology and Biocatalysis through Biospectroscopy/TIMB3 |
License: | https://creativecommons.org/licenses/by/4.0/ |
Journal Title: | Applied Sciences |
Publisher: | MDPI |
Publisher Place: | Basel |
Volume: | 10 |
Issue: | 3 |
Article Number: | 781 |
Publisher DOI: | 10.3390/app10030781 |
EISSN: | 2076-3417 |
Appears in Collections: | FG Modellierung biomolekularer Systeme » Publications |
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