(Un)suitability of the use of pH buffers in biological, biochemical and environmental studies and their interaction with metal ions – a review

Ferreira, Carlos; Pinto, Isabel S.S.; Soares, Eduardo V.; Soares, Helena

doi:10.1039/c4ra15453c

Cited by 271 publications

(176 citation statements)

References 185 publications

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“…Many of the common buffers used for biochemistry also coordinate iron, thus significantly affecting the molecular identity of the species available for transport (29). These hurdles have likely contributed to a dearth of in vitro validation of iron transport by mitoferrins and any detailed biophysical and mutational analyses.…”

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confidence: 99%

In vitro reconstitution, functional dissection, and mutational analysis of metal ion transport by mitoferrin-1

Christenson

Gallegos

Banerjee

2018

Journal of Biological Chemistry

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Mitoferrin-1 is a promiscuous transition metal transporterThe reactivity of iron is exploited across all kingdoms of life. The physiological roles that iron takes on are many-iron readily participates in redox reactions where it can donate or accept electrons, depending on its oxidation state. Iron plays essential roles in gas transport and sensing and can also act as a non-redox active metal ion cofactor in enzymes. Additionally, iron-containing cofactors can impart stability to folded proteins (1). Iron naturally occurs in the 2+ and the 3+ oxidation states but owing to the insolubility of Fe(III), the bioavailable form of iron is almost exclusively the 2+ form. The main route of cellular iron uptake is via the transferrin receptor pathway whereby transferrin-bound iron is targeted to endosomes and subsequently released from transferrin during endosomal acidification. Fe(II) is transported out of endosomes by divalent metal ion transporter (DMT1) and becomes available for incorporation into iron-containing proteins and cofactors (2).In eukaryotes, mitochondria are the hotspots for iron utilization-these organelles house heme assembly and the majority of Fe-S cluster biosynthesis apparatus (3,4). Mitochondria contain respiratory complexes which comprise many ironcontaining cofactors. Not surprisingly, http://www.jbc.org/cgi

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confidence: 99%

In vitro reconstitution, functional dissection, and mutational analysis of metal ion transport by mitoferrin-1

Christenson

Gallegos

Banerjee

2018

Journal of Biological Chemistry

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“…The reactivity of commonly used buffering compounds towards a wide range of biomolecules, particularly ones incorporating metal ions, is now widely recognized . Tris (tris (hydroxymethyl)‐aminomethane) in particular is known to form complexes with a variety of transition metals, and we recently observed facile oxidation and ligand exchange within the [Ru II (NH 3 ) 5 Cl] + complex upon its placement in Tris buffer under aerobic conditions .…”

Section: Resultsmentioning

confidence: 99%

Ruthenium coordination preferences in imidazole‐containing systems revealed by electrospray ionization mass spectrometry and molecular modeling: Possible cues for the surprising stability of the Ru (III)/tris (hydroxymethyl)‐aminomethane/imidazole complexes

et al. 2019

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Ruthenium is a platinoid that exhibits a range of unique chemical properties in solution, which are exploited in a variety of applications, including luminescent probes, anticancer therapies, and artificial photosynthesis. This paper focuses on a recently demonstrated ability of this metal in its +3 oxidation state to form highly stable complexes with tris (hydroxymethyl)aminomethane (H2NC(CH2OH)3, Tris‐base or T) and imidazole (Im) ligands, where a single RuIII cation is coordinated by two molecules of each T and Im. High‐resolution electrospray ionization mass spectrometry (ESI MS) is used to characterize RuIII complexes formed by placing a RuII complex [(NH3)5RuIICl]Cl in a Tris buffer under aerobic conditions. The most abundant ionic species in ESI MS represent mononuclear complexes containing an oxidized form of the metal, ie, [XnRuIIIT2 – 2H]+, where X could be an additional T (n = 1) or NH3 (n = 0‐2). Di‐ and tri‐metal complexes also give rise to a series of abundant ions, with the highest mass ion representing a metal complex with an empirical formula Ru3C24O21N6H66 (interpreted as cyclo(T2RuO)3, a cyclic oxo‐bridged structure, where the coordination sphere of each metal is completed by two T ligands). The empirical formulae of the binuclear species are consistent with the structures representing acyclic fragments of cyclo(T2RuO)3 with addition of various combinations of ammonia and dioxygen as ligands. Addition of histidine in large molar excess to this solution results in complete disassembly of poly‐nuclear complexes and gives rise to a variety of ionic species in the ESI mass spectrum with a general formula [RuIIIHiskTm (NH3)n − 2H]+, where k = 0 to 2, m = 0 to 3, and n = 0 to 4. Ammonia adducts are present for all observed combinations of k and m, except k = m = 2, suggesting that [His2RuIIIT2 − 2H]+ represents a complex with a fully completed coordination sphere. The observed cornucopia of RuIII complexes formed in the presence of histidine is in stark contrast to the previously reported selective reactivity of imidazole, which interacts with the metal by preserving the RuT2 core and giving rise to a single abundant ruthenium complex (represented by [Im2RuIIIT2 − 2H]+ in ESI mass spectra). Surprisingly, the behavior of a hexa‐histidine peptide (HHHHHH) is similar to that of a single imidazole, rather than a single histidine amino acid: The RuT2 core is preserved, with the following ionic species observed in ESI mass spectra: [HHHHHH·(RuIIIT2)m − (3m‐1)H]+ (m = 1‐3). The remarkable selectivity of the imidazole interaction with the RuIIIT2 core is rationalized using energetic considerations at the quantum mechanical level of theory.

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“…In 0.1 M Tris, pH 7.5, the binding was confirmed for Zn 2+ , Ni 2+ , Cd 2+ , and Co 2+ ions, no detectable heat was observed for Mn 2+ , Ca 2+ , Mg 2+ , Al 3+ , and Fe 3+ (in agreement with the previously mentioned metal screening results). However, the apparent binding affinity in Tris buffer was decreased ( K a = 10 3 M −1 ) due to the well‐known ability of Tris buffer to compete with the protein for the binding of metal ions, and the thermodynamic parameters could not be determined accurately ( c value < 1).…”

Section: Resultsmentioning

confidence: 99%

Structure and properties of AB21, a novel Agaricus bisporus protein with structural relation to bacterial pore‐forming toxins

et al. 2018

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We report the characterization of the dimeric protein AB21 from Agaricus bisporus, one of the most commonly and widely consumed mushrooms in the world. The protein shares no significant sequence similarity with any protein of known function, and it is the first characterized member of its protein family. The coding sequence of the ab21 gene was determined and the protein was expressed in E. coli in a recombinant form. We demonstrated a high thermal and pH stability of AB21 and proved the weak affinity of the protein to divalent ions of some transition metals (nickel, zinc, cadmium, and cobalt). The reported crystallographic structure exhibits an interesting rod-like helical bundle fold with structural similarity to bacterial toxins of the ClyA superfamily. By immunostaining, we demonstrated an abundance of AB21 in the fruiting bodies of A. bisporus.

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(Un)suitability of the use of pH buffers in biological, biochemical and environmental studies and their interaction with metal ions – a review

Cited by 271 publications

References 185 publications

In vitro reconstitution, functional dissection, and mutational analysis of metal ion transport by mitoferrin-1

In vitro reconstitution, functional dissection, and mutational analysis of metal ion transport by mitoferrin-1

Ruthenium coordination preferences in imidazole‐containing systems revealed by electrospray ionization mass spectrometry and molecular modeling: Possible cues for the surprising stability of the Ru (III)/tris (hydroxymethyl)‐aminomethane/imidazole complexes

Structure and properties of AB21, a novel Agaricus bisporus protein with structural relation to bacterial pore‐forming toxins

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