I chose a target molecule that I chose from an Original molecule.

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Question Description

Target molecule is attached and Original Molecule is attached within its own Article so it helps you start from there.

This assignment is the first stage of the proposal writing process you will do over the next few weeks. This is probably the most intensive and difficult step of the process. In this stage you will provide a statement of relevance (literature background), target molecule, and comprehensive annotated bibliography for your proposed molecule. In this section your goal is to highlight your molecule’s importance and relevance to the literature.

The statement of relevance should contain the following key aspects in a sufficient level of detail, but not be limited to:

  • a big picture analysis of the relevance of your system in the context of the biological/medicinal/biochemical literature.
    • Pressing questions still unanswered from the biochemical, biological perspective
  • Biomimetic previous approaches to solving some of these pressing questions. This is where you give context to how biomimetic complexes have helped develop answers for this system.
  • Proposed compound and description as to how this particular structure you chose will help answer key questions about your system. Here you have to be specific about the structural properties proposed and the potential for this compound to help answer the pressing questions proposed earlier. this step requires that you read a lot of literature, synthesize it, and justify the importance of your work.

this stage will be graded using a SPECIFICATIONS based four-point rubric using the criteria below

D Level• Paper is turned in on time and contains all three major components: a. Statement of relevance (literature background) max four pages but no minimum as long as you cover the basics page. b. Target molecule: Clear diagrams indicating the target molecule using professional drawing tools. Structure is chemically sound. c. A SEPARATE DOCUMENT where you must describe the process you have followed to write their submission. d. Comprehensive annotated bibliography. Contains at least 2 paragraphs describing the relevance of the paper, attaches (to student folder) ALL annotated papers. The total number of references of this stage and stage 2 must equal 20 minimum. A D level needs at least 5 references.

C Level (D level +...)a. Statement of relevance is written mostly in student’s own words. Potential contributions to the literature are stated at a basic level and could be interpreted as ambiguous. Details are missing. b. Target molecule diagram is exceptional and demonstrates key features of the target compound. There is no ambiguity about target. c. Bibliography was extensively researched and ALL citations are PROPERLY annotated for their potential contribution to the paper and to the overall synthetic project. An additional 5 references are added.

B Level (C level +...)a. Student has clearly written this work in their own words and shows an appropriate dominance of the background literature. Contributions to the literature are stated with a medium level of sophistication. No ambiguity from the writing.

A level (B level +...)a) The writing reflects a deep level of understanding of the background literature. It shows a high level of sophistication with the understanding of the topic. Relevance and importance of the work engages the reader and justifies the work’s ability to be published.

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Inorganic Chemistry Communications 89 (2018) 37–40 Contents lists available at ScienceDirect Inorganic Chemistry Communications journal homepage: www.elsevier.com/locate/inoche Short communication The first structural model for the resting state of the active site of nickel acireductone dioxygenase (Ni-ARD) Denisa A. Ivan a, Alexander J. Gremillion a, Anthony Sanchez a, Servando Sanchez a, Vincent M. Lynch b, Santiago A. Toledo a,⁎ a b Department of Chemistry, St. Edward's University, 3001 S. Congress Ave. Austin, TX 78704, USA Department of Chemistry, The University of Texas at Austin, 120 Inner Campus Dr Stop G2500, Austin, TX 78712, USA a r t i c l e i n f o Article history: Received 19 December 2017 Received in revised form 14 January 2018 Accepted 16 January 2018 Available online 31 January 2018 a b s t r a c t The synthesis and preliminary biomimetic reactivity of the first structural analogue for the resting state of the active site of the nickel oxygenase nickel acireductone dioxyegenase (Ni-ARD), is presented. Compound 1 ([NiII (OPhN4(6-H-DPEN)(H2O))](OTf)) is only the second model complex for Ni-ARD. The N4O ligand motif, mimics the contributions of the glutamate and histidines enzymatic residues, and opens up the possibility for systematic structural modification studies that will lead to a greater understanding of the role that structure plays in function for ARD. Early reactivity studies with 1 suggest that it might capable of carbon-carbon bond cleavage of a ketone presumably via dioxygenase type chemistry in line with the reactivity of the enzyme. © 2018 Elsevier B.V. All rights reserved. 1. Introduction Oxygenases are metalloenzymes that catalyze a wide-variety of transformations including aromatic and aliphatic oxidative carboncarbon bond cleavage and hydroxylation reactions [1–4]. Unlike the prominence of iron [1,5] and copper oxygenases [6–8] in nature, there is only one known nickel dioxygenase, nickel acireductone dioxygenase (Ni-ARD) [9,10]. Ni-ARD plays a key role in the ubiquitous methionine salvage pathway in plants and bacteria. Ni-ARD catalyzes the transformation of acireductone into 3 (methylthio) propionate, formate and carbon monoxide [11]. When iron is bound to ARD (Fe-ARD’), a distinct set of products results making this enzyme the only known example of a pair of metalloenzymes whose function differs only by the identity of the metal ion. A mammalian analogue of Ni-ARD (MmARD) was crystallographically characterized at high resolution [13], and the human analogue of ARD (HsARD) is now available albeit at low resolution [14]. In-vitro studies have shown that both of these mammalian analogues perform the same metal dependent chemistry as that observed in the bacterial ARD and are capable of reactivity when bound to Ni+2, Fe+2, Co+2 and Mn+2 [13,15]. However, there is no known role of NiARD in humans [10]. Recent in-vitro studies have shown that HsARD might play an intracellular regulatory role in brain tumors [16], and genetic studies have shown that the gene coding for HsARD is ⁎ Corresponding author. E-mail address: stoledoc@stedwards.edu (S.A. Toledo). https://doi.org/10.1016/j.inoche.2018.01.014 1387-7003/© 2018 Elsevier B.V. All rights reserved. downregulated in human and rat prostate, gastrocarcinoma and fibrosarcoma cells [17,18]. The metal promiscuity shown in binding studies by Ringe et al. indicated that MmARD displays “off-pathway” chemistry producing carbon monoxide when bound to Mn2+ or Co2+ [13]. CO has sparked recent interest as a signaling neurotransmitter molecule in mammals [12]. It is hypothesized that production of CO, a known antiapoptotic signaling molecule [19,20], could lead to cancerous cells displaying antiapoptotic behavior. Many questions remain about NiARD and its role in disease. Those studying ARD are in agreement that fundamental questions about the exact mechanism and the role of different metals in directing the chemistry of ARD are yet to be answered [10,13,21,22,24]. Biochemical work by Pochapsky and Ringe [13,23], computational work by Alexandrova [22], and biomimetic modeling work by Berreau [21], have shed light on key mechanistic aspects of this enzyme's function. Berreau's work with a NiIIN4 complex coordinated to a bulky ARD substrate analogue ([(6–Ph2TPA)Ni(PhC(O)C(OH)C(O) Ph]+), is the only known Ni-ARD functional model [25–26]. This compound was important in helping understand the role that water might play in promoting Ni-ARD vs. Fe-ARD chemistry [21,27]. In spite of it being a functional model, this complex has an N4 chelating ligand set and does not mimic the coordination environment of the enzyme's active site (Fig. 1-left), specifically the contribution of the oxygen donor of the glutamate residue in ARD. To add to this body of work, the synthesis and preliminary biomimetic reactivity of the first structural analogue for the resting state of active site of Ni-ARD, [NiII(OPhN4(6H-DPEN)(H2O))](OTf) 1 (Fig. 1-right) is presented here. This compound 38 D.A. Ivan et al. / Inorganic Chemistry Communications 89 (2018) 37–40 Fig. 1. Skeletal structure of the primary coordination sphere of the active site of Ni-ARD (left) and the structural drawing of [NiII(OPhN4(6-H-DPEN)(H2O))]+ (1-right). is only the second biomimetic model of ARD. Furthermore, the ligand structure (an N4O chelate) attempts to mimic the enzyme's O-donor while providing structural flexibility for further modifications and for studying the mechanism of substrate activation (vide infra). Early reactivity studies suggest this compound might be capable of carbon-carbon bond cleavage of a ketone possibly via dioxygenase type chemistry in line with the reactivity of the enzyme. Nickel complex 1 was isolated as an air-stable purple powder from the in-situ condensation between salicylaldehyde and ligand precursor (N,N Bis(2 pyridilmethyl)ethane 1,2 diamine; 6-H-DPEN) (Scheme 1). Purple crystals of this compound were obtained from the slow vapor diffusion of diethyl ether into a saturated 2-butanone solution of the powder and its structure and identity was unambiguously confirmed by single-crystal X-ray diffraction analysis and elemental analysis (ESM Fig. S4). The ORTEP representation of 1 is shown in Fig. 2. 1 is an octahedral complex coordinated by a penta-coordinate chelating N4O ligand and a water molecule on the sixth site. While this model compound has an additional N-donor in comparison to the enzyme's active site, it attempts to model the electronic contribution of the glutamate donor in the enzyme by introduction of a phenolate oxygen. Compound 1 and its coordination to water models the resting state of Ni-ARD. This feature will help further probe questions about the influence of water in the enzyme's mechanism [10,21,24]. Unlike the enzyme, this pentadentate coordination leaves only one potential site for substrate coordination via displacement of water, however, the ligand should be flexible enough to probe bidentate coordination and activation of acireductone diketone type analogues since pyridine type ligands like those of 1 have been shown to be labile and capable of being displaced by substrates Fig. 2. Molecular structure of [NiII(OPhN4(6-H-DPEN)(H2O))](OTf) 1. Hydrogen atoms and counter ion have been omitted for clarity. Thermal ellipsoids are drawn at the 50% probability level.1 1CCDC 1577098 contains the supplementary crystallographic data for this article. These data can be obtained free of charge via http://wwwccdc.cam.ac.uk/ data_request/cif, or by emailing data_request@ccdc.cam.ac.uk, or by contacting the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB@1EZ, UK; Fax: +44-1223-336033. [32–34]. This added flexibility opens up the opportunity to study how coordination of substrate mono vs. bi-dentate might affect the mechanism of oxidation. We argue that this ligand coordination adds flexibility and does not take away from its ability to serve as an ARD biomimetic complex. Table 1 gives structural comparisons between the active site of mammalian ARD from Mus musculus (MmARD, PDB ID: 5I91) [13] and compound 1. The average Ni-Nitrogen bonds for the complex and that of the active site are in good agreement (Ave. Ni-N(Comp.1) = 2.102, Ave. Ni-N(enzyme) = 2.1). The Ni-O(Phenolate) is slightly shorter than the Ni-OGlu bond while the NiO2(H2O) bond length is similar to the Ni-O(H2O) average bond length from the enzyme (Table 1). The model complex binds tighter to the oxygen donors in comparison to the enzyme. This is likely due to the differences in donation ability between a phenolic donor in the model and the glutamate O-donor in the active site. To highlight the similarities between the model and the active site of the enzyme we rendered an overlay between the structure of 1 and the Scheme 1. Synthetic route of metal complex 1. D.A. Ivan et al. / Inorganic Chemistry Communications 89 (2018) 37–40 39 Table 1 Selected bond distances in Å for MmARDa and complex 1. Ni-MmARD Ni-O(E94) Ni-N(H88) Ni-N(H90) Ni-N(H133) Ni-O(H2O)b a b 2.1 2.1 2.1 2.1 2.15 1 Ni-O1 (O-Ph) Ni-O2 (H2O) Ni-N1 Ni-N2 Ni-N3 Ni-N4 2.024 (2) 2.075 (2) 2.12 (3) 2.001 (3) 2.104 (3) 2.184 (3) From Ni-MmARD 1.7 Å resolution [13]. Average Ni-O(H2O) bond length for the two coordinated waters. active site of MmARD (Fig. 3).1 The resulting root mean square deviation was 0.24 Å and was calculated for all Ni ligand atoms in our model relative to the corresponding ligand atoms in PDB entry 5I91, which included Glu94 and two crystallographic water molecules, in addition to the histidines. The UV–Visible spectrum of complex 1 (ESM Fig. S2) shows two bands in the ultraviolet region at 239 nm (ε = 18,050 L/mol·cm) and 372 nm (ε = 4226 L/mol·cm) and two in the visible region at 535 nm (ε = 18 L/mol·cm) and another at ~870 nm (ε = 16 L/mol·cm). The UV bands can be attributed by comparison to similar examples in the literature to ligand based charge transfer transitions [21,28] while the visible bands are typical of high spin Ni2+ pyridine based compounds from the literature [26,29]. During our synthetic optimization experiments, in an attempt to maximize the yield of compound 1, we attempted its synthesis in the presence of triethylamine. This auxiliary base was added to aid in the deprotonation of the phenol proton from salicylaldehyde to form an anionic chelating ligand and encourage ligand coordination to the metal. After following the work-up and crystallization procedures as those used in 1, purple crystal rods were isolated. Single crystal x-ray analysis revealed the structure of an octahedral, acetic acid bound Ni2+ complex ([NiII(OPhN4(6-H-DPEN)(HOAc))](OTf) 2) (Fig. 4). The structure and identity of 2 has been confirmed unambiguously by X-ray crystallography, and elemental analysis (ESM Fig. S6), confirming it is the bulk of the material isolated. The bound acetic acid in 2 forms a six-member ring structure through a strong hydrogen bond between the phenolate oxygen and the hydrogen from acetic acid (O1\\H-O2 = 1.547 Å; O1\\O2 = 2.435 Å). These distances are associated with a hydrogen bond with strong covalent character [30], and are similar to examples of acetic acid bound Ni2+ complexes [31]. The isolation of compound 2 was an unexpected result since our goal was to maximize the yield of 1. The source of acetic acid bound in 2 is unknown. Control experiments suggest it does not come from contaminations of the starting ligand or 2-butanone solvent. These negative controls led us to infer that a possible source of acetic acid could be the oxidation of solvent used for crystallization, 2-butanone. Acetic acid could form from the base mediated carbon-carbon cleavage and dioxygenation of the 2,3 bond of butanone to give acetic acid as one of the products. This oxygenation type reactivity would be similar to that of the Ni-ARD enzyme. The base mediated, oxidative cleavage of a carbon-carbon bond for cyclic and benzylic ketones, cyclic diones, and aliphatic aldehydes is well documented using copper compounds [35]. Ni-ARD biomimetic work in the Berrau lab, showed that the aforementioned N4 ligated complex of Ni2+ and Fe2+ bound to a bulky acireductone analogue can do carbon-carbon oxidative cleavage of the bound substrate [21]. To our knowledge, the carbon-carbon cleavage and oxidation of an aliphatic ketone (e.g. 2-butanone) mediated by a nickel compound such as 1, is unprecedented. While no mechanistic evidence has been gathered so far for the formation of 2, the literature precedent for copper mediated carbon-carbon cleavage of ketones, and the 1 Superimposition were done using the MODELER protocol as implemented in the Discovery Studio program suite, where the nitrogen ligand atoms of our model were tethered to the N3 atom of the imidazole ring of the His88, His90 and His133 residues. Fig. 3. Overlay of the active site of MmARD (PDB ID: 5I91) [13] and compound 1 (skeletal structure). lack of experimental evidence for an alternative path to forming 2, lead us to the preliminary conclusion that oxidative carbon-carbon bond cleavage could be occurring. Understanding the mechanism of oxygenation for the observed reactivity of 1, will help answer questions about the influence of structure in promoting carbon-carbon oxidative bond cleavage of ketones mediated by nickel. Mechanistic studies to understand the presumed dioxygenation reactivity are underway. A family of biomimetic models structurally related to 1 is now being synthesized to greatly expand the current limited availability of Ni-ARD models. Preliminary studies with these new complexes suggest the N4O motif of the ligand in 1 appears to display this biomimetic reactivity more broadly. These compounds open up the possibility of systematic structure-function studies that will enhance the understanding of the mechanism of action in Ni-ARD. Future work involves structural, reactivity, and mechanistic comparisons across the family of complexes with different first row transition metals relevant ARD's role in disease. This family will greatly contribute to Fig. 4. Molecular Structure of ([NiII(OPhN4(6-H-DPEN)(HOAc))](OTf) 2. Hydrogen atoms and counterion have been omitted for clarity. Thermal ellipsoids are drawn at the 50% probability level.2 2CCDC 1577112 contains the supplementary crystallographic data for this article. These data can be obtained free of charge via http://wwwccdc.cam.ac.uk/ data_request/cif, or by emailing data_request@ccdc.cam.ac.uk, or by contacting the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB@1EZ, UK; Fax: +44-1223-336033. 40 D.A. Ivan et al. / Inorganic Chemistry Communications 89 (2018) 37–40 questions that still remain about Ni-ARD, its mechanism of action and the role of metal in product formation. Acknowledgements We thank the Welch Foundation (BH-0018), NSF-STEP (0969153), NSF-IUSE (1525490), DOE-McNair Post-Baccalaureate Achievement Program (P217A170002) and the St. Edward's University Presidential Faculty award for faculty and undergraduate student support. We also thank Professor Eamonn Healy at St. Edward's University for his contribution with the enzyme-complex overlay. We also would like to thank the University of Texas Mass Spectrometry Facility for high-resolution ESI-MS of samples. Appendix A. Supplementary material Experimental details for the synthesis and characterization of compounds 1 and 2 as well as summarized crystallographic data is available through the supplementary material, which is available to authorized users. Supplementary data associated with this article can be found in the online version, at doi: https://doi.org/10.1016/j.inoche.2018.01.014. References [1] T.D.H. Bugg, S. Ramaswamy, Curr. Opin. Chem. Biol. 2 (1998) 159–172. [2] G.D. Stanganz, A. Glieder, L. Brecker, D.W. Ribbons, W. Steiner, Biochem. J. 369 (2003) 573–581. [3] D.J. Hopper, A. Kaderbhai, Biochem. J. 344 (1999) 397–402. [4] R.M. Cicchillo, H. Zhang, J.A. Blodgett, J.T. Whitteck, G. Li, S.K. Nair, W.A. Van Der Donk, W.W. Metcalf, Nature 459 (2009) 871–874. [5] M.M. Abu-Omar, A. Loaiza, N. Hontzeas, Chem. Rev. 105 (2005) 2227–2252. [6] E.I. Soloman, U.M. Sundaram, T.E. Machonkin, Chem. Rev. 96 (1996) 2563–5606. [7] A.G. Blackman, W.B. Tolman, Copper-Dioxygen and Copper Oxo Species Relevant to Copper Oxygenases and Oxidases, Springer, New York, 2000. [8] E.I. Solomon, D.E. Heppner, E.M. Johnston, J.W. Ginsbach, J. Cierera, M. Qayyum, M.T. Kieber-Emmons, C.H. Kjaergaard, R.G. Hadt, L. Tian, Chem. Rev. 114 (2014) 3659–3853. [9] M.J. Maroney, S. Ciurli, Chem. Rev. 114 (2014) 4206–4228. [10] A.R. Deshpande, T.C. Pochapsky, D. Ringe, Chem. Rev. 117 (2017) 10474–10501. [11] W. Lubitz, H. Ogata, O. Rüdiger, E. Reijerse, Chem. Rev. 114 (2014) 4081–4148. [12] R.A. Johnson, F.K. Johnson, Curr. Opin. Neurol. 13 (2000) 709–713. [13] A.R. Deshpande, K. Wagenpfeil, T.C. Pochapsky, G.A. Petsko, D. Ringe, Biochemist 55 (2016) 1398–1407. [14] RCSB Protein Data Bank, http://www.rcsb.org/pdb/explore.do?structureId=4QGN 2015, Accessed date: 30 November 2017. [15] A.R. Deshpande, T.C. Pochapsky, G.A. Petsko, D. Ringe, Protein Eng. Des. Sel. 30 (2017) 197–206. [16] J. Pratt, M. Iddir, S. Bourgault, B. Annabi, Mol. Carcinog. 55 (2016) 148–160. [17] Oram SW, Ai J, Pagani GM, Hitchens MR, Stern JA, Eggener S, Pins M, Xiao W, Cai X, Haleem R, Jiang F, Pochapsky TC, Hedstrom L, Wang Z (2007) 9:643–651. [18] S. Oram, F. Jiang, X. Cai, R. Haleem, Z. Dincer, Z. Wang, Endocrinology 145 (2014) 1933–1942. [19] L. Gunther, P.O. Berberat, M. Haga, S. Brouard, R.N. Smith, M.P. Soares, F.H. Bach, E. Tobisach, Diabetes 97 (2002) 1305–1310. [20] R.S. Thom, D. Fisher, Y.A. Xu, K. Notarfancesco, H. Ischiropoulos, Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 1305–1310. [21] C.J. Allpress, K. Grubel, E. Szanjna-fuller, A.M. Arif, L.M. Berreau, J. Am. Chem. Soc. 135 (2013) 659–668. [22] M. Sparta, C.E. Valdez, A.N. Alexandrova, J. Mol. Biol. 425 (2013) 3007–3018. [23] T. Dai, T.C. Pochapsky, R.H. Abeles, Biochemist 40 (2001) 6379–6387. [24] C.E. Valdez, Q.A. Smith, M.R. Nechay, A.N. Alexandrova, Acc. Chem. Res. 47 (2014) 3110–3117. [25] E. Szajna, A.M. Arif, L.M. Berreau, J. Am. Chem. Soc. 127 (2005) 17186–17187. [26] A. Roth, E.T. Spielberg, W. Plass, Inorg. Chem. 46 (2007) (4362-4264). [27] K. Grubel, G.K. Ingle, A.L. Fuller, A.M. Arif, L.M. Berreau, Dalton Trans. 40 (2011) 10609–10620. [28] C.J. Allpress, L.M. Berreau, Eur. J. Inorg. Chem. 27 (2014) 4642–4649. [29] T. Nagataki, K. Ishii, T. Tachi, S. Itoh, Dalton Trans. 11 (2007) 1120–1128. [30] C.L. Perrin, J.B. Nielson, Annu. Rev. Phys. Chem. 48 (1997) 511–544. [31] (a) L. Yang, S. Zhang, W. Wang, J. Guo, Q.P. Huang, R. Zhao, C. Zhang, G. Muller, Polyhedron 74 (2014) 49–56; (b) H. Adams, D. Bradshaw, D.E. Fenton, Supramol. Chem. 13 (2001) 513–519; (c) P.E. Kruger, V. McKee, Chem. Commun. 15 (1997) 1341–1342; (d) P. Li, M.J. Niu, M. Hong, S. Cheng, J.M. Dou, J. Inorg. Biochem. 137 (2014) 101–108; (e) G. Mugesh, H.B. Singh, R.J. Butcher, Eur. J. Inorg. Chem. 3 (2001) 669–678; (f) B. Shafaatian, A. Soleymanpour, N.K. Oskouei, B. Notash, S.A. Rezvani, Spectrochim. Acta A 128 (2014) 363–369; (g) J.M. Bruenig, J.W. Bats, H.W. Lerner, Acta Cryst 70 (2014) m13; (h) K. Mochizuki, J. Takahashi, Inorg. Chim. Acta 414 (2014) 27–32; (i) D. Volkner, A. Horstmann, K. Griesar, W. Haase, B. Krebs, Inorg. Chem. 35 (1996) 1132–1135. [32] L. Benhamou, M. Lachkar, D. Mandon, R. Welter, Dalton Trans. 48 (2008) 6996–7003. [33] S. Kisslinger, Reaction Behavior of Iron- and Copper-complexes with Tripodal Ligands, Justus-Liebig-Universität Giessen, 2012. [34] E. Szanjna, M.M. Makowska-Grzyska, C.C. Wasden, A.M. Arif, L.M. Berreau, Inorg. Chem. 44 (2005) 7595–7605. [35] (a) A. Atlamsan, J.M. Brégeault, Synthesis 1 (1993) 79–81; (b) J.M. Brégeau ...
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TabbyK
School: Cornell University

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Surname 1
Name
Instructor
Course
Date
Target Molecule
Introduction
The target molecule in this paper is based on a slight modification of the original molecule.
The original molecule is nickel acireductone dioxygenase (Ni-ARD). Nickel acireductone
dioxygenase is the only known dioxygenase existing naturally. The target molecule, which is the
molecule of study in this case, differs from the original molecule in that an ocetate group has
been added instead of water.
Literature Background
Nickel acireductone dioxygenase is the nickel-bound form of ARD, which catalyzes offpathway reactions leading in formate, 5-(thiomethyl) propionate, and carbon monoxide. The Ni
element is crucial to the thriving of various life forms (Chen & Costa, 2009). However, excess
levels of Ni are highly carcinogenic and toxic. As such, living cells have structured mechanisms
to sense the Ni concentration and then maintain homeostatic control of the metal ion accord...

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