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Molecules 2015, 20(8), 14265-14292; doi:10.3390/molecules200814265

Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria

Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna I-40127, Italy
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Academic Editor: Rino Ragno
Received: 28 April 2015 / Revised: 23 July 2015 / Accepted: 28 July 2015 / Published: 5 August 2015
(This article belongs to the Special Issue Molecular Docking in Drug Design)
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Abstract

The interaction between macromolecules is a fundamental aspect of most biological processes. The computational techniques used to study protein-protein and protein-nucleic acid interactions have evolved in the last few years because of the development of new algorithms that allow the a priori incorporation, in the docking process, of experimentally derived information, together with the possibility of accounting for the flexibility of the interacting molecules. Here we review the results and the evolution of the techniques used to study the interaction between metallo-proteins and DNA operators, all involved in the nickel and iron metabolism of pathogenic bacteria, focusing in particular on Helicobacter pylori (Hp). In the first part of the article we discuss the methods used to calculate the structure of complexes of proteins involved in the activation of the nickel-dependent enzyme urease. In the second part of the article, we concentrate on two applications of protein-DNA docking conducted on the transcription factors HpFur (ferric uptake regulator) and HpNikR (nickel regulator). In both cases we discuss the technical expedients used to take into account the conformational variability of the multi-domain proteins involved in the calculations. View Full-Text
Keywords: macromolecular docking; urease; urease metallocenter biosynthesis; NikR; Fur; Helicobacter pylori macromolecular docking; urease; urease metallocenter biosynthesis; NikR; Fur; Helicobacter pylori
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Musiani, F.; Ciurli, S. Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria. Molecules 2015, 20, 14265-14292.

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