Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport |
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Authors: | Mattia Falconi Francesco Oteri Francesco Di Palma Saurabh Pandey Andrea Battistoni Alessandro Desideri |
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Affiliation: | (1) Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica, 00133 Rome, Italy;(2) CIBB, Center of Biostatistics and Bioinformatics, Via della Ricerca Scientifica, 00133 Rome, Italy;(3) Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Rome, Italy |
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Abstract: | Comparative homology modelling techniques have been used to model the protein ZnuA from Salmonella enterica serovar Typhimurium using the 3D structure of the homologous protein from Escherichia coli. These two-domain proteins bind one Zn2+ atom, with high affinity, in the inter-domain cleft and possess a histidine-rich loop in the N-terminal domain. Alternative structures of the ZnuA histidine-rich loop, never resolved by the X-ray diffraction method, have been modelled. A model of the apo form, one with the histidine-rich loop deleted and two alternative structures with a second zinc ion bound to the histidine-rich loop, have been generated. In all the modelled proteins, investigated through molecular dynamics simulation, the histidine-rich loop is highly mobile and its fluctuations are correlated to the ligand stability observed in the zinc sites. Based on the plasticity of the histidine-rich loop and its significant effects on protein mobility a possible role in the capture and/or transfer of the zinc ions has been suggested. |
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