Papers by Timothy Stemmler
Acta Crystallographica Section A Foundations of Crystallography, 1999
The electron microscope provides an ideal environment for the structural analysis of small volume... more The electron microscope provides an ideal environment for the structural analysis of small volumes of amorphous and polycrystalline materials by enabling the collection of scattering information as a function of energy loss and momentum transfer. The scattered intensity at zero energy loss can be readily processed to a reduced density function, providing information on nearest-neighbour distances and bond angles. A method for collecting and processing the scattered intensity, which allows for the collection of an energy-loss spectrum for a range of momentum transfers, is discussed. A detailed structural determination from a reduced density function alone is difficult and it is shown that a more detailed structural model can be obtained by combining the experimental reduced density function with model structures obtained from molecular dynamics based on first-principles quantum mechanics. This method is applied to tetrahedral amorphous carbon, as an example of a monatomic network, an...
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In this study, we report for the first time that both t-SNAREs and v-SNARE and their complexes in... more In this study, we report for the first time that both t-SNAREs and v-SNARE and their complexes in buffered suspension, exhibit defined peaks at CD signals of 208 and 222 nm wavelengths, consistent with a higher degree of helical secondary structure. Surprisingly, when incorporated in lipid membrane, both SNAREs and their complexes exhibit reduced folding. In presence of NSF-ATP, the SNARE complex disassembles, as reflected from the CD signals demonstrating elimination of α-helices within the structure.
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International Journal of Molecular Sciences
Iron–sulfur clusters are essential to almost every life form and utilized for their unique struct... more Iron–sulfur clusters are essential to almost every life form and utilized for their unique structural and redox-targeted activities within cells during many cellular pathways. Although there are three different Fe–S cluster assembly pathways in prokaryotes (the NIF, SUF and ISC pathways) and two in eukaryotes (CIA and ISC pathways), the iron–sulfur cluster (ISC) pathway serves as the central mechanism for providing 2Fe–2S clusters, directly and indirectly, throughout the entire cell in eukaryotes. Proteins central to the eukaryotic ISC cluster assembly complex include the cysteine desulfurase, a cysteine desulfurase accessory protein, the acyl carrier protein, the scaffold protein and frataxin (in humans, NFS1, ISD11, ACP, ISCU and FXN, respectively). Recent molecular details of this complex (labeled NIAUF from the first letter from each ISC protein outlined earlier), which exists as a dimeric pentamer, have provided real structural insight into how these partner proteins arrange th...
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The FASEB Journal
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Metallomics
Mitochondrial Fe-S cluster biosynthesis is accomplished within yeast utilizing the biophysical ch... more Mitochondrial Fe-S cluster biosynthesis is accomplished within yeast utilizing the biophysical characteristics of the “Isu1” scaffold protein. As a member of a highly homologous protein family, Isu1 has sequence conservation...
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Biomolecular NMR Assignments
Ebola viral infections have resulted in several deadly epidemics in recent years in West and Cent... more Ebola viral infections have resulted in several deadly epidemics in recent years in West and Central Africa. Because only one of the seven proteins encoded by the viral genome possesses enzymatic activity, disruption of protein–protein interactions is a promising route for antiviral drug development. We carried out a screening campaign to identify small, drug-like compounds that bind to the C-terminal region of the multifunctional Ebola nucleoprotein (eNP) with the objective of discovering ones that disrupt its binding to other Ebola proteins or to the single-stranded RNA genome. In the course of this effort we assigned the backbone 1H, 15N, and 13C resonances of residues 600‒739, the region that contains the critical eVP30 binding region 600‒615 targeted by host factors, and used the assigned chemical shifts to predict secondary structural features and peptide dynamics. This work supports and extends the previous X-ray crystal structures and NMR studies of residues 641‒739. We found that the 600‒739 domain consists of separate regions that are largely disordered and ordered.
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Nature communications, Oct 15, 2018
Methane-oxidizing microbes catalyze the oxidation of the greenhouse gas methane using the copper-... more Methane-oxidizing microbes catalyze the oxidation of the greenhouse gas methane using the copper-dependent enzyme particulate methane monooxygenase (pMMO). Isolated pMMO exhibits lower activity than whole cells, however, suggesting that additional components may be required. A pMMO homolog, ammonia monooxygenase (AMO), converts ammonia to hydroxylamine in ammonia-oxidizing bacteria (AOB) which produce another potent greenhouse gas, nitrous oxide. Here we show that PmoD, a protein encoded within many pmo operons that is homologous to the AmoD proteins encoded within AOB amo operons, forms a copper center that exhibits the features of a well-defined Cu site using a previously unobserved ligand set derived from a cupredoxin homodimer. PmoD is critical for copper-dependent growth on methane, and genetic analyses strongly support a role directly related to pMMO and AMO. These findings identify a copper-binding protein that may represent a missing link in the function of enzymes critical ...
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Journal of inorganic biochemistry, 2018
Transition metal homeostasis is necessary to sustain life. First row transition metals act as cof... more Transition metal homeostasis is necessary to sustain life. First row transition metals act as cofactors within the cell, performing vital functions ranging from DNA repair to respiration. However, intracellular metal concentrations exceeding physiological requirements may be toxic. In E. coli, the YqjH flavoprotein is thought to play a role in iron homeostasis. YqjH is transcriptionally regulated by the ferric uptake regulator and a newly discovered regulator encoded by yqjI. The apo-form of YqjI is a transcriptional repressor of both the yqjH and yqjI genes. YqjI repressor function is disrupted upon binding of nickel. The YqjI N-terminus is homologous to nickel-binding proteins, implicating this region as a nickel-binding domain. Based on function, yqjI and yqjH should be renamed Ni-responsive Fe-uptake regulator (nfeR) and Ni-responsive Fe-uptake flavoprotein (nfeF), respectively. X-ray Absorption Spectroscopy was employed to characterize the nickel binding site(s) within YqjI. Pu...
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The Journal of biological chemistry, Jan 8, 2018
Particulate methane monooxygenase (pMMO) is a copper-dependent, integral membrane metalloenzyme t... more Particulate methane monooxygenase (pMMO) is a copper-dependent, integral membrane metalloenzyme that converts methane to methanol in methanotrophic bacteria. Studies of isolated pMMO have been hindered by loss of enzymatic activity upon its removal from the native membrane. To characterize pMMO in a membrane-like environment, we reconstituted pMMOs from () (Bath) and () 20Z into bicelles. Reconstitution into bicelles recovers methane oxidation activity lost upon detergent solubilization and purification without substantial alterations to copper content or copper electronic structure as observed by electron paramagnetic resonance (EPR) spectroscopy.. These findings suggest that loss of pMMO activity upon isolation is due to removal from the membranes rather than caused by loss of the catalytic copper ions. A 2.7 Å resolution crystal structure of pMMO from 20Z revealed a mononuclear copper center in the PmoB subunit and indicated that the transmembrane PmoC subunit may be conformation...
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PloS one, 2018
The Nogo-B receptor (NgBR) is involved in oncogenic Ras signaling through directly binding to far... more The Nogo-B receptor (NgBR) is involved in oncogenic Ras signaling through directly binding to farnesylated Ras. It recruits farnesylated Ras to the non-lipid-raft membrane for interaction with downstream effectors. However, the cytosolic domain of NgBR itself is only partially folded. The lack of several conserved secondary structural elements makes this domain unlikely to form a complete farnesyl binding pocket. We find that inclusion of the extracellular and transmembrane domains that contain additional conserved residues to the cytosolic region results in a well folded protein with a similar size and shape to the E.coli cis-isoprenyl transferase (UPPs). Small Angle X-ray Scattering (SAXS) analysis reveals the radius of gyration (Rg) of our NgBR construct to be 18.2 Å with a maximum particle dimension (Dmax) of 61.0 Å. Ab initio shape modeling returns a globular molecular envelope with an estimated molecular weight of 23.0 kD closely correlated with the calculated molecular weight...
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Metallomics
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Environmental Science & Technology
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Inorganic chemistry, Jan 17, 2017
Ni-containing superoxide dismutase (NiSOD) represents an unusual member of the SOD family due to ... more Ni-containing superoxide dismutase (NiSOD) represents an unusual member of the SOD family due to the presence of oxygen-sensitive Ni-SCys bonds at its active site. Reported in this account is the synthesis and properties of the Ni(II) complex of the N3S2 ligand [N3S2(Me2)](3-) ([N3S2(Me2)](3-) = deprotonated form of 2-((2-mercapto-2-methylpropyl)(pyridin-2-ylmethyl)amino)-N-(2-mercaptoethyl)acetamide), namely Na[Ni(N3S2(Me2))] (2), as a NiSOD model that features sterically robust gem-(CH3)2 groups on the thiolate α-C positioned trans to the carboxamide. The crystal structure of 2, coupled with spectroscopic measurements from (1)H NMR, X-ray absorption, IR, UV-vis, and mass spectrometry (MS), reveal a planar Ni(II) (S = 0) ion coordinated by only the N2S2 basal donors of the N3S2 ligand. While the structure and spectroscopic properties of 2 resemble those of NiSODred and other models, the asymmetric S ligands open up new reaction paths upon chemical oxidation. One unusual oxidation p...
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The Journal of biological chemistry, Apr 21, 2017
Hydrogen sulfide is a critical signaling molecule, but high concentrations cause cellular toxicit... more Hydrogen sulfide is a critical signaling molecule, but high concentrations cause cellular toxicity. A four-enzyme pathway in the mitochondrion detoxifies H2S by converting it to thiosulfate and sulfate. Recent studies have shown that globins like hemoglobin and myoglobin can also oxidize H2S to thiosulfate and hydropolysulfides. Neuroglobin, a globin enriched in the brain, was reported to bind H2S tightly and was postulated to play a role in modulating neuronal sensitivity to H2S in conditions such as stroke. However, the H2S reactivity of the coordinately saturated heme in neuroglobin is expected a priori to be substantially lower than that of the 5-coordinate hemes present in myoglobin and hemoglobin. To resolve this discrepancy, we explored the role of the distal histidine residue in muting the reactivity of human neuroglobin toward H2S. Ferric neuroglobin is slowly reduced by H2S and catalyzes its inefficient oxidative conversion to thiosulfate. Mutation of the distal His(64) re...
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Inorganic chemistry, Jan 6, 2017
The complex Na3[{Ni(II)(nmp)}3S3BTA(alk))] (1) (nmp(2-) = deprotonated form of N-(2-mercaptoethyl... more The complex Na3[{Ni(II)(nmp)}3S3BTA(alk))] (1) (nmp(2-) = deprotonated form of N-(2-mercaptoethyl)picolinamide; H3S3BTA(alk) = N(1),N(3),N(5)-tris(2-mercaptoethyl)benzene-1,3,5-tricarboxamide, where H = dissociable protons), supported by the thiolate-benzenetricarboxamide scaffold (S3BTA(alk)), has been synthesized as a trimetallic model of nickel-containing superoxide dismutase (NiSOD). X-ray absorption spectroscopy (XAS) and (1)H NMR measurements on 1 indicate that the Ni(II) centers are square-planar with N2S2 coordination, and Ni-N and Ni-S distances of 1.95 and 2.16 Å, respectively. Additional evidence from IR indicates the presence of H-bonds in 1 from the approximately -200 cm(-1) shift in νNH from free ligand. The presence of H-bonds allows for speciation that is temperature-, concentration-, and solvent-dependent. In unbuffered water and at low temperature, a dimeric complex (1(A); λ = 410 nm) that aggregates through intermolecular NH···O═C bonds of BTA units is observed. D...
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ACS chemical neuroscience, Apr 20, 2017
Parkinson's disease (PD) is a progressive neurodegenerative disorder and development of disea... more Parkinson's disease (PD) is a progressive neurodegenerative disorder and development of disease-modifying treatment is still an unmet medical need. Considering the implication of free iron (II) in PD, we report here the design and characterization of a novel hybrid iron chelator, (-)-12 (D-607) as a multitarget-directed ligand against PD. Binding and functional assays at dopamine D2/D3 receptors indicate potent agonist activity of (-)-12. The molecule displayed an efficient preferential iron (II) chelation properties along with potent in vivo activity in a reserpinized PD animal model. The compound also rescued PC12 cells from toxicity induced by iron delivered intracellularly in a dose-dependent manner. However, Fe3+ selective dopamine agonist 1 and a well-known antiparkinsonian drug pramipexole produced almost no neuroprotection effect under the same experimental condition. These observations strongly suggest that 12 should be a promising multifunctional lead molecule for a vi...
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The Journal of biological chemistry, Jan 7, 2016
Mammalian cytochrome c (Cytc) plays a key role in cellular life and death decisions, functioning ... more Mammalian cytochrome c (Cytc) plays a key role in cellular life and death decisions, functioning as an electron carrier in the electron transport chain (ETC) and as a trigger of apoptosis when released from the mitochondria. However, its regulation is not well understood. We show that the major fraction of Cytc isolated from kidneys is phosphorylated on Thr28, leading to a partial inhibition of respiration in the reaction with cytochrome c oxidase. To further study the effect of Cytc phosphorylation in vitro, we generated Thr28Glu phosphomimetic Cytc, revealing superior behavior regarding protein stability and its ability to degrade reactive oxygen species compared to wild-type unphosphorylated Cytc. Introduction of Thr28Glu phosphomimetic Cytc into Cytc knockout cells shows that intact cell respiration, mitochondrial membrane potential (ΔΨm), and ROS levels are reduced compared to wild-type. As we show by high resolution crystallography of wild-type and Thr28Glu, Cytc in combinatio...
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Journal of the American Chemical Society, Sep 15, 2016
Metal-nitroxyl (M-HNO/M-NO(-)) coordination units are found in denitrification enzymes of the glo... more Metal-nitroxyl (M-HNO/M-NO(-)) coordination units are found in denitrification enzymes of the global nitrogen cycle, and free HNO exhibits pharmacological properties related to cardiovascular physiology that are distinct from nitric oxide (NO). To elucidate the properties that control the binding and release of coordinated nitroxyl or its anion at these biological metal sites, we synthesized {CoNO}(8) (1, 2) and {CoNO}(9) (3, 4) complexes that contain diimine-dipyrrolide supporting ligands. Experimental (NMR, IR, MS, EPR, XAS, XRD) and computational data (DFT) support an oxidation state assignment for 3 and 4 of high spin Co(II) (SCo = 3/2) coordinated to (3)NO(-) (SNO = 1) for Stot = 1/2. As suggested by DFT, upon protonation, a spin transition occurs to generate a putative low spin Co(II)-(1)HNO (SCo = Stot = 1/2); the Co-NO bond is ∼0.2 Å longer, more labile, and facilitates the release of HNO. This property was confirmed experimentally through the detection and quantification of...
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Journal of the American Chemical Society, Jul 30, 2016
Enzymes in the sulfur network generate the signaling molecule, hydrogen sulfide (H2S), from the a... more Enzymes in the sulfur network generate the signaling molecule, hydrogen sulfide (H2S), from the amino acids cysteine and homocysteine. Since it is toxic at elevated concentrations, cells are equipped to clear H2S. A canonical sulfide oxidation pathway operates in mitochondria, converting H2S to thiosulfate and sulfate. We have recently discovered the ability of ferric hemoglobin to oxidize sulfide to thiosulfate and iron-bound hydropolysulfides. In this study, we report that myoglobin exhibits a similar capacity for sulfide oxidation. We have trapped and characterized iron-bound sulfur intermediates using cryo-mass spectrometry and X-ray absorption spectroscopy. Further support for the postulated intermediates in the chemically challenging conversion of H2S to thiosulfate and iron-bound catenated sulfur products is provided by EPR and resonance Raman spectroscopy in addition to density functional theory computational results. We speculate that the unusual sensitivity of skeletal mus...
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Inorganic Chemistry, Jun 1, 2004
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Papers by Timothy Stemmler