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Article

Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential

Institute of Basic Biological Problems of the Russian Academy of Sciences—A Separate Subdivision of PSCBR RAS (IBBP RAS), Institutskaya str., 2, Pushchino, 142290 Moscow, Russia
Int. J. Mol. Sci. 2020, 21(1), 366; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21010366
Received: 29 November 2019 / Revised: 26 December 2019 / Accepted: 1 January 2020 / Published: 6 January 2020
Three-dimensional structures of six closely related hydrogenases from purple bacteria were modeled by combining the template-based and ab initio modeling approach. The results led to the conclusion that there should be a 4Fe3S cluster in the structure of these enzymes. Thus, these hydrogenases could draw interest for exploring their oxygen tolerance and practical applicability in hydrogen fuel cells. Analysis of the 4Fe3S cluster’s microenvironment showed intragroup heterogeneity. A possible function of the C-terminal part of the small subunit in membrane binding is discussed. Comparison of the built models with existing hydrogenases of the same subgroup (membrane-bound oxygen-tolerant hydrogenases) was carried out. Analysis of intramolecular interactions in the large subunits showed statistically reliable differences in the number of hydrophobic interactions and ionic interactions. Molecular tunnels were mapped in the models and compared with structures from the PDB. Protein–protein docking showed that these enzymes could exchange electrons in an oligomeric state, which is important for oxygen-tolerant hydrogenases. Molecular docking with model electrode compounds showed mostly the same results as with hydrogenases from E. coli, H. marinus, R. eutropha, and S. enterica; some interesting results were shown in case of HupSL from Rba. sphaeroides and Rvi. gelatinosus. View Full-Text
Keywords: hydrogenases; hydrogen fuel cells; homology modeling; FeS clusters; transmembrane helices; molecular docking; molecular tunnels hydrogenases; hydrogen fuel cells; homology modeling; FeS clusters; transmembrane helices; molecular docking; molecular tunnels
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MDPI and ACS Style

Abdullatypov, A.V. Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential. Int. J. Mol. Sci. 2020, 21, 366. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21010366

AMA Style

Abdullatypov AV. Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential. International Journal of Molecular Sciences. 2020; 21(1):366. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21010366

Chicago/Turabian Style

Abdullatypov, Azat V. 2020. "Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential" International Journal of Molecular Sciences 21, no. 1: 366. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21010366

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