Interdomain communication revealed in the diabetes drug target mitoNEET

Baxter, E.L.; Jennings, Patricia A.; Onuchic, José N.

doi:10.1073/pnas.1017604108

Cited by 27 publications

(45 citation statements)

References 43 publications

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“…Thus, identifying residues that contribute frustration in folding may be an effective way to predict and identify important sites for protein-protein interactions, as well as new binding regions for potential drug targets. (18). In our current study, we test this hypothesis by experimentally introducing perturbations into this distal loop (Fig.…”

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confidence: 99%

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Allosteric control in a metalloprotein dramatically alters function

Baxter

Zuris²,

Wang³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Metalloproteins (MPs) comprise one-third of all known protein structures. This diverse set of proteins contain a plethora of unique inorganic moieties capable of performing chemistry that would otherwise be impossible using only the amino acids found in nature. Most of the well-studied MPs are generally viewed as being very rigid in structure, and it is widely thought that the properties of the metal centers are primarily determined by the small fraction of amino acids that make up the local environment. Here we examine both theoretically and experimentally whether distal regions can influence the metal center in the diabetes drug target mitoNEET. We demonstrate that a loop (L2) 20 Å away from the metal center exerts allosteric control over the cluster binding domain and regulates multiple properties of the metal center. Mutagenesis of L2 results in significant shifts in the redox potential of the [2Fe-2S] cluster and orders of magnitude effects on the rate of [2Fe-2S] cluster transfer to an apo-acceptor protein. These surprising effects occur in the absence of any structural changes. An examination of the native basin dynamics of the protein using all-atom simulations shows that twisting in L2 controls scissoring in the cluster binding domain and results in perturbations to one of the cluster-coordinating histidines. These allosteric effects are in agreement with previous folding simulations that predicted L2 could communicate with residues surrounding the metal center. Our findings suggest that long-range dynamical changes in the protein backbone can have a significant effect on the functional properties of MPs.allostery | CISD1 | energy landscape theory | iron-sulfur cluster | protein frustration

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confidence: 99%

“…We recently used energy landscape theoretical studies to investigate the factors that govern cluster properties in mitoNEET (18,19). Briefly, energy landscape theory indicates that proteins fold in a funneled fashion with minimal frustration, with the native state and functional fluctuations occurring toward the bottom of this funnel (20,21).…”

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confidence: 99%

Allosteric control in a metalloprotein dramatically alters function

Baxter

Zuris²,

Wang³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…A single-coordinating histidine (H87) along with three cysteine ligands (C72, C74, C83) bind the [2Fe-2S] cluster and the single histidine has been shown to effect cluster redox and stability properties (6)(7)(8)(30)(31)(32)(33). Our previous studies on the biophysical properties of the protein led us to investigate whether mNT could serve in FeS cluster transfer (6,7,(31)(32)(33)(34).…”

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confidence: 99%

“…These observations are consistent with the localization of the FeS cluster biogenesis machinery and key FeS protein metabolic functions in mitochondria (16,23). Moreover, as mitochondria are the primary energy providers of mammalian cells and key players in a large variety of metabolic processes (25), they have been implicated in metabolic diseases such as type II diabetes (26-29).Human mNT is composed of two protomers intertwined to form a unique structure with two domains; the β-cap and the cluster binding domain and is the founding member of the NEET fold (6,13,14,30). A single-coordinating histidine (H87) along with three cysteine ligands (C72, C74, C83) bind the [2Fe-2S] cluster and the single histidine has been shown to effect cluster redox and stability properties (6)(7)(8)(30)(31)(32)(33).…”

mentioning

confidence: 99%

“…Human mNT is composed of two protomers intertwined to form a unique structure with two domains; the β-cap and the cluster binding domain and is the founding member of the NEET fold (6,13,14,30). A single-coordinating histidine (H87) along with three cysteine ligands (C72, C74, C83) bind the [2Fe-2S] cluster and the single histidine has been shown to effect cluster redox and stability properties (6)(7)(8)(30)(31)(32)(33).…”

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Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein

Zuris

Harir

Conlan

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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MitoNEET (mNT) is an outer mitochondrial membrane target of the thiazolidinedione diabetes drugs with a unique fold and a labile [2Fe-2S] cluster. The rare 1-His and 3-Cys coordination of mNT's [2Fe-2S] leads to cluster lability that is strongly dependent on the presence of the single histidine ligand (His87). These properties of mNT are similar to known [2Fe-2S] shuttle proteins. Here we investigated whether mNT is capable of cluster transfer to acceptor protein(s). cluster transfer is observed between oxidized mNT and apo-ferredoxin (a-Fd) using UV-VIS spectroscopy and native-PAGE, as well as with a mitochondrial iron detection assay in cells. The transfer is unidirectional, proceeds to completion, and occurs with a second-order-reaction rate that is comparable to known iron-sulfur transfer proteins. Mutagenesis of His87 with Cys (H87C) inhibits transfer of the [2Fe-2S] clusters to a-Fd. This inhibition is beyond that expected from increased cluster kinetic stability, as the equivalently stable Lys55 to Glu (K55E) mutation did not inhibit transfer. The H87C mutant also failed to transfer its iron to mitochondria in HEK293 cells. The diabetes drug pioglitazone inhibits iron transfer from WT mNT to mitochondria, indicating that pioglitazone affects a specific property, [2Fe-2S] cluster transfer, in the cellular environment. This finding is interesting in light of the role of iron overload in diabetes. Our findings suggest a likely role for mNT in [2Fe-2S] and/or iron transfer to acceptor proteins and support the idea that pioglitazone's antidiabetic mode of action may, in part, be to inhibit transfer of mNT's [2Fe-2S] cluster.CISD1 | diabetes | FeS cluster | oxidative stress M itoNEET (mNT) is a newly discovered target (1) of the insulin-sensitizing thiazolidinedione (TZD) class of type II diabetes drugs (2, 3), which interact with the canonical target PPARγ (4, 5). The interaction of TZD drugs with mNT has been proposed to be of therapeutic importance (1,6). This is the first iron-sulfur protein to be directly targeted by drug binding (1, 6). The protein contains two [2Fe-2S] clusters, which have been shown to be chemically labile (7). Initial characterization of mNT's redox active and pH labile [2Fe-2S] clusters show that both properties are modulated by binding of TZDs (6,8), indicating a direct interaction of the protein with the TZD drugs. A second related member of the human NEET protein family, Miner1, is structurally homologous to mNT (9). Miner1 has recently been linked to autophagy, apoptosis, and aging (10, 11), and mis-splicing is associated with a rare disease, known as Wolfram Syndrome 2 (12). Together, mNT and Miner1 represent a new class of NEET iron-sulfur (FeS) proteins characterized structurally by their unique homodimeric fold and rare 3-Cys-1-His [2Fe-2S] cluster ligand environment (6,9,13,14).Iron-sulfur (FeS) cluster-containing proteins are key players in many essential processes, such as photosynthesis, respiration, and nitrogen fixation (15, 16). They appear in various compositions and ...

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Simulating Biomolecular Folding and Function by Native‐Structure‐Based/Go‐Type Models

Sinner¹,

Lutz²,

John³

et al. 2014

Israel Journal of Chemistry

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The 2013 Nobel Prize in Chemistry highlights how crucial computer simulations have become for many scientific and engineering fields. Nowadays, scientific progress is not only driven by the interplay of new experimental measurements and increasingly sophisticated theoretical frameworks, but also by an incredible toolbox of complex computational models meeting ubiquitously available computing power and data storage facilities. Quantum mechanical (QM) calculations can be condensed into molecular mechanics (MM) force fields and coupled QM/MM calculations can derive atomic and molecular properties of biomolecular or materials science systems with high accuracy. Pure MM simulations driven by Monte Carlo or molecular dynamics algorithms are widely applied in biological chemistry/physics and can investigate large biomolecular systems, such as proteins, DNA, or RNA. One coarse‐grained class of these models, native‐structure‐based or Go models, are based on energy landscape theory and the principle of minimal frustration. Herein, an ensemble of converging pathways guide protein folding on a funnel‐like shape of the entire energy landscape towards the native state. Simulations based on these ideas have been tremendously successful in explaining protein folding and function. Their history and recent application highlights are reviewed.

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Interdomain communication revealed in the diabetes drug target mitoNEET

Cited by 27 publications

References 43 publications

Allosteric control in a metalloprotein dramatically alters function

Allosteric control in a metalloprotein dramatically alters function

Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein

Simulating Biomolecular Folding and Function by Native‐Structure‐Based/Go‐Type Models

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