Chemistry & Biochemistry

Permanent URI for this collectionhttps://hdl.handle.net/11274/15372

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Arginyltransferase, its specificity, putative substrates, bidirectional promoter, and splicing-derived isoforms
(Elsevier, 2006) Hu, Rong-Gui; Brower, Christopher S.; Wang, Haiqing; Davydov, Ilia V.; Sheng, Jun; Zhou, Jianmin; Tae Kwon, Yong; Varshavsky, Alexander
Substrates of the N-end rule pathway include proteins with destabilizing N-terminal residues. Three of them, Asp, Glu, and (oxidized) Cys, function through their conjugation to Arg, one of destabilizing N-terminal residues that are recognized directly by the pathway’s ubiquitin ligases. The conjugation of Arg is mediated by arginyltransferase, encoded by ATE1. Through its regulated degradation of specific proteins, the arginylation branch of the N-end rule pathway mediates, in particular, the cardiovascular development, the fidelity of chromosome segregation, and the control of signaling by nitric oxide.We show that mouse ATE1 specifies at least six mRNA isoforms, which are produced through alternative splicing, encode enzymatically active arginyltransferases, and are expressed at varying levels in mouse tissues. We also show that the ATE1 promoter is bidirectional, mediating the expression of bothATE1 and an oppositely oriented, previously uncharacterized gene. In addition, we identified GRP78 (glucose-regulated protein 78) and protein-disulfide isomerase as putative physiological substrates of arginyltransferase. Purified isoforms of arginyltransferase that contain the alternative first exons differentially arginylate these proteins in extract from ATE1 / embryos, suggesting that specific isoforms may have distinct functions. Although the N-end rule pathway is apparently confined to the cytosol and the nucleus, and although GRP78 and protein-disulfide isomerase are located largely in the endoplasmic reticulum, recent evidence suggests that these proteins are also present in the cytosol and other compartments in vivo, where they may become N-end rule substrates.
Mouse DFA is a repressor of TATA-box promoters and interacts with the Abt1 activator of basal transcription
(Elsevier, 2010) Brower, Christopher S.; Veiga, Lucia; Jones, Richard H.; Varshavsky, Alexander
Our study of the mouse Ate1 arginyltransferase, a component of the N-end rule pathway, has shown that Ate1 pre-mRNA is produced from a bidirectional promoter that also expresses, in the opposite direction, a previously uncharacterized gene (Hu, R. G., Brower, C. S., Wang, H., Davydov, I. V., Sheng, J., Zhou, J., Kwon, Y. T., and Varshavsky, A. (2006) J. Biol. Chem. 281, 32559–32573). In this work, we began analyzing this gene, termed Dfa (divergent from Ate1). Mouse Dfa was found to be transcribed from both the bidirectional PAte1/Dfa promoter and other nearby promoters. The resulting transcripts are alternatively spliced, yielding a complex set of Dfa mRNAs that are present largely, although not exclusively, in the testis. A specific Dfa mRNA encodes, via its 3′-terminal exon, a 217-residue protein termed DfaA. Other Dfa mRNAs also contain this exon. DfaA is sequelogous (similar in sequence) to a region of the human/mouse HTEX4 protein, whose physiological function is unknown. We produced an affinity-purified antibody to recombinant mouse DfaA that detected a 35-kDa protein in the mouse testis and in several cell lines. Experiments in which RNA interference was used to down-regulate Dfa indicated that the 35-kDa protein was indeed DfaA. Furthermore, DfaA was present in the interchromatin granule clusters and was also found to bind to the Ggnbp1 gametogenetin-binding protein-1 and to the Abt1 activator of basal transcription that interacts with the TATA-binding protein. Given these results, RNA interference was used to probe the influence of Dfa levels in luciferase reporter assays. We found that DfaA acts as a repressor of TATA-box transcriptional promoters.
Contributions of fungi to carbon flow and nutrient cycling from standing dead Typha angustifolia leaf litter in a temperate freshwater marsh
(Association for the Sciences of Limnology and Oceanography, 2011-02-03) Neely, Robert; Ohsowski, B.; Francoeur, S.; Kuehn, K.
Standing dead plant litter often constitutes a large fraction of the detritus in many freshwater marshes and lake littoral habitats. Despite this evidence, microbial decay processes in standing litter and its contribution to wetland carbon and nutrient cycling have rarely been quantified. We examined the contribution of fungi to carbon flow and nutrient cycling from Typha angustifolia during senescence and standing litter decomposition. Naturally standing Typha leaves were collected in August and then periodically over 1 yr. We quantified losses in leaf carbon (C), fungal biomass, and fungal production rates and constructed a partial budget estimating C flow into fungal decomposers. Additionally, we determined leaf litter N and P concentrations to assess the effect of fungi on detrital nutrient dynamics. Significant losses in leaf C occurred during plant senescence and standing litter decay (∼ 55%). Fungal biomass increased during litter decay, reaching a maximum of 106 ± 7 mg C g−1 detrital C. Cumulative fungal production totaled 123 mg C g−1 initial detrital C, indicating that 22% of the Typha leaf C lost was assimilated into fungal biomass. Fungi also transformed and immobilized nutrients within Typha leaves, with fungal N and P accounting for > 50% of the total detrital N and P during later stages of leaf decay. Significant transformation and decomposition of emergent macrophyte litter occurs during the standing dead phase, and a large portion of the plant C and nutrients are channeled into and through fungal decomposers.
Priming in the microbial landscape: Periphytic algal stimulation of litter-associated microbial decomposers
(Ecological Society of America, 2014-03) Kuehn, Kevin A.; Francoeur, Steven N.; Findlay, Robert H.; Neely, Robert
Microbial communities associated with submerged detritus in aquatic ecosystems often comprise a diverse mixture of autotrophic and heterotrophic microbes, including algae, bacteria, protozoa, and fungi. Recent studies have documented increased rates of plant litter mass loss when periphytic algae are present. We conducted laboratory and field experiments to assess potential metabolic interactions between natural autotrophic and heterotrophic microbial communities inhabiting submerged decaying plant litter of Typha angustifolia and Schoenoplectus acutus. In the field, submerged plant litter was either exposed to natural sunlight or placed under experimental canopies that manipulated light availability and growth of periphytic algae. Litter was collected and returned to the laboratory, where algal photosynthesis was manipulated (light/dark incubation), while rates of bacterial and fungal growth and productivity were simultaneously quantified. Bacteria and fungi were rapidly stimulated by exposure to light, thus establishing the potential for algal priming of microbial heterotrophic decay activities. Experimental incubations of decaying litter with 14C- and 13C-bicarbonate established that inorganic C fixed by algal photosynthesis was rapidly transferred to and assimilated by heterotrophic microbial decomposers. Periphytic algal stimulation of microbial heterotrophs, especially fungal decomposers, is an important and largely unrecognized interaction within the detrital microbial landscape, which may transform our current conceptual understanding of microbial secondary production and organic matter decomposition in aquatic ecosystems.
Genetic mutations in the S-loop of human glutathione synthetase: Links between substrate binding, active site structure and allostery
(Elsevier, 2018) Anderson, Mary; Ingle, Brandall; Shrestha, Bisesh; De Jesus, Margarita; Conrad-Webb, Heather; Cundari, Thomas
The second step in the biosynthesis of the cellular antioxidant glutathione (GSH) is catalyzed by human glutathione synthetase (hGS), a negatively cooperative homodimer. Patients with mutations in hGS have been reported to exhibit a range of symptoms from hemolytic anemia and metabolic acidosis to neurological disorders and premature death. Several patient mutations occur in the S-loop of hGS, a series of residues near the negatively cooperative γ-GC substrate binding site. Experimental point mutations and molecular dynamic simulations show the S-loop not only binds γ-GC through a salt bridge and multiple hydrogen bonds, but the residues also modulate allosteric communication in hGS. By elucidating the role of S-loop residues in active site structure, substrate binding, and allostery, the atomic level sequence of events that leads to the detrimental effects of hGS mutations in patients are more fully understood.
The N termini of tar DNA-binding protein 43 (TDP43) C-terminal fragments influence degradation, aggregation propensity, and morphology
(Taylor and Francis, 2018) Kasu, Yasar Arfat T.; Alemu, Samrawit; Lamari, Angela; Loew, Nicole; Brower, Christopher S.
Fragments of the TAR DNA-binding protein 43 (TDP43) are major components of intracellular aggregates associated with amyotrophic lateral sclerosis and frontotemporal dementia. A variety of C-terminal fragments (CTFs) exist, with distinct N termini; however, little is known regarding their differences in metabolism and aggregation dynamics. Previously, we found that specific CTFs accumulate in the absence of the Arg/N-end rule pathway of the ubiquitin proteasome system (UPS) and that their degradation requires arginyl-tRNA protein transferase 1 (ATE1). Here, we examined two specific CTFs of TDP43 (TDP43219 and TDP43247), which are 85% identical and differ at their N termini by 28 amino acids. We found that TDP43247 is degraded primarily by the Arg/N-end rule pathway, whereas degradation of TDP43219 continues in the absence of ATE1. These fragments also differ in their aggregation propensities and form morphologically distinct aggregates. This work reveals that the N termini of otherwise similar CTFs have profound effects on fragment behavior and may influence clinical outcomes in neurodegeneration associated with aggregation.
Site-specific pegylation crosslinking of L-asparaginase subunits to improve its therapeutic efficiency
(Cold Spring Harbor Laboratory, 2018) Ramirez-Paz, Josell; Saxena, Manoj; Delinois, Louis J.; Joaquín-Ovalle, Freisa; Lin, Shiru; Chen, Zhongfang; Rojas-Nieves, Virginia A.; Griebenow, Kai
L-Asparaginase is an enzyme successfully being used in the treatment of acute lymphoblastic leukemia, acute myeloid leukemia, and non-Hodgkin’s lymphoma. However, some disadvantages still limit its full application potential, e.g., allergic reactions, pancreatitis, and blood clotting impairment. Therefore, much effort has been directed at improving its performance. A popular strategy is to randomly conjugate L-asparaginase with mono-methoxy polyethylene glycol, which became a commercial FDA approved formulation widely used in recent years. To improve this formulation by PEGylation, herein we performed cysteine-directed site-specific conjugation of the four L-asparaginase subunits to prevent dissociation-induced loss of activity. The conjugation sites were selected at surface-exposed positions on the protein to avoid affecting the catalytic activity. Three conjugates were obtained using different linear PEGs of 1000, 2000, and 5000 g/mol, with physical properties ranging from a semi-solid gel to a fully soluble state. The soluble-conjugate exhibited higher catalytic activity than the non-conjugated mutant, and the same activity than the native enzyme. Site-specific crosslinking of the L-asparaginase subunits produced a higher molecular weight conjugate compared to the native tetrameric enzyme. This strategy might improve L-asparaginase efficiency for leukemia treatment by reducing glomerular filtration due to the increase in hydrodynamic size thus extending half-live, while at the same time retaining full catalytic activity.
Linking temperature, cation concentration and water activity for the B to Z conformational transition in DNA
(MDPI, 2018) Sheardy, Richard Dean; Ferreira, Jaime M.
High concentrations of Na+ or [Co(NH3)6]3+ can induce the B to Z conformational transition in alternating (dC-dG) oligo and polynucleotides. The use of short DNA oligomers (dC-dG)4 and (dm5C-dG)4 as models can allow a thermodynamic characterization of the transition. Both form right handed double helical structures (B-DNA) in standard phosphate buffer with 115 mM Na+ at 25 °C. However, at 2.0 M Na+ or 200 μM [Co(NH3)6]3+, (dm5C-dG)4 assumes a left handed double helical structure (Z-DNA) while the unmethylated (dC-dG)4 analogue remains right handed under those conditions. We have previously demonstrated that the enthalpy of the transition at 25 °C for either inducer can be determined using isothermal titration calorimetry (ITC). Here, ITC is used to investigate the linkages between temperature, water activity and DNA conformation. We found that the determined enthalpy for each titration varied linearly with temperature allowing determination of the heat capacity change (ΔCp) between the initial and final states. As expected, the ΔCp values were dependent upon the cation (i.e., Na+ vs. [Co(NH3)6]3+) as well as the sequence of the DNA oligomer (i.e., methylated vs. unmethylated). Osmotic stress experiments were carried out to determine the gain or loss of water by the oligomer induced by the titration. The results are discussed in terms of solvent accessible surface areas, electrostatic interactions and the role of water.
Interaction between ΓC87 and ΓR242 residues participates in energy coupling between catalysis and proton translocation in escherichia coli ATP synthase
(Elsevier, 2019) Li, Yunxiang; Ma, Xinyou; Weber, Joachim
Functioning as a nanomotor, ATP synthase plays a vital role in the cellular energy metabolism. Interactions at the rotor and stator interface are critical to the energy transmission in ATP synthase. From mutational studies, we found that the γC87K mutation impairs energy coupling between proton translocation and nucleotide synthesis/hydrolysis. An additional glutamine mutation at γR242 (γR242Q) can restore efficient energy coupling to the γC87K mutant. Arrhenius plots and molecular dynamics simulations suggest that an extra hydrogen bond could form between the side chains of γC87K and βTPE381 in the γC87K mutant, thus impeding the free rotation of the rotor complex. In the enzyme with γC87K/γR242Q double mutations, the polar moiety of γR242Q side chain can form a hydrogen bond with γC87K, so that the amine group in the side chain of γC87K will not hydrogen-bond with βE381. As a conclusion, the intra-subunit interaction between positions γC87 and γR242 modulates the energy transmission in ATP synthase. This study should provide more information of residue interactions at the rotor and stator interface in order to further elucidate the energetic mechanism of ATP synthase.
Identification of two segments of the γ subunit of ATP synthase responsible for the different affinities of the catalytic nucleotide-binding sites
(American Society for Biochemistry and Molecular Biology, 2019) Mnatsakanyan, Nelli; Li, Yunxiang; Weber, Joachim
ATP synthase uses a rotary mechanism to couple transmembrane proton translocation to ATP synthesis and hydrolysis, which occur at the catalytic sites in the β subunits. In the presence of Mg2+, the three catalytic sites of ATP synthase have vastly different affinities for nucleotides, and the position of the central γ subunit determines which site has high, medium, or low affinity. Affinity differences and their changes as rotation progresses underpin the ATP synthase catalytic mechanism. Here, we used a series of variants with up to 45- and 60-residue-long truncations of the N- and C-terminal helices of the γ subunit, respectively, to identify the segment(s) responsible for the affinity differences of the catalytic sites. We found that each helix carries an affinity-determining segment of ∼10 residues. Our findings suggest that the affinity regulation by these segments is transmitted to the catalytic sites by the DELSEED loop in the C-terminal domain of the β subunits. For the N-terminal truncation variants, presence of the affinity-determining segment and therefore emergence of a high-affinity binding site resulted in WT-like catalytic activity. At the C terminus, additional residues outside of the affinity-determining segment were required for optimal enzymatic activity. Alanine substitutions revealed that the affinity changes of the catalytic sites required no specific interactions between amino acid side chains in the γ and α3β3 subunits but were caused by the presence of the helices themselves. Our findings help unravel the molecular basis for the affinity changes of the catalytic sites during ATP synthase rotation.
Correction: Machine-learning-assisted screening of pure-silica zeolites for effective removal of linear siloxanes and derivatives
(Royal Society of Chemistry, 2020) Lin, Shiru; Wang, Yekun; Zhao, Yinghe; Pericchi, Luis R.; Hernandez-Maldonado, Arturo J.; Chen, Zhongfang
As emerging organic contaminants, siloxanes have severe impacts on the environment and human health. Simple linear siloxanes and derivates, trimethylsilanol (TMS), dimethylsilanediol (DMSD), monomethylsilanetriol (MMST), and dimethylsulfone (DMSO2), are four persistent and common problematic compounds (PCs) from the hydroxylation and sulfuration of polydimethylsiloxanes. Herein, through a two-step computational process, namely Grand Canonical Monte Carlo (GCMC) simulations and machine learning (ML), we systematically screened 50 959 hypothetical pure-silica zeolites and identified 230 preeminent zeolites with excellent adsorption performances with all these four linear siloxanes and derivates. This work vividly demonstrates that the collocation of data-driven science and computational chemistry can greatly accelerate materials discovery and help solve the most challenging separation problems in environmental science.
The nucleotide binding affinities of two critical conformations of escherichia coli ATP synthase
(Elsevier, 2021) Li, Yunxiang; Valdez, Neydy A.; Mnatsakanyan, Nelli; Weber, Joachim
ATP synthase is essential in aerobic energy metabolism, and the rotary catalytic mechanism is one of the core concepts to understand the energetic functions of ATP synthase. Disulfide bonds formed by oxidizing a pair of cysteine mutations halted the rotation of the γ subunit in two critical conformations, the ATP-waiting dwell (αE284C/γQ274C) and the catalytic dwell (αE284C/γL276C). Tryptophan fluorescence was used to measure the nucleotide binding affinities for MgATP, MgADP and MgADP-AlF4 (a transition state analog) to wild-type and mutant F1 under reducing and oxidizing conditions. In the reduced state, αE284C/γL276C F1 showed a wild-type-like nucleotide binding pattern; after oxidation to lock the enzyme in the catalytic dwell state, the nucleotide binding parameters remained unchanged. In contrast, αE284C/γQ274C F1 showed significant differences in the affinities of the oxidized versus the reduced state. Locking the enzyme in the ATP-waiting dwell reduced nucleotide binding affinities of all three catalytic sites. Most importantly, the affinity of the low affinity site was reduced to such an extent that it could no longer be detected in the binding assay (Kd > 5 mM). The results of the present study allow to present a model for the catalytic mechanism of ATP synthase under consideration of the nucleotide affinity changes during a 360° cycle of the rotor.
A wireless resonant LC sensor for glucose detection
(MDPI, 2022) Li, Hong; Xu, Haibo; Lin, Shiru; Jia, Yi
This paper proposes a wireless resonant inductive and capacitive (LC) sensor for glucose sensing. A sensor composed of a capacitor with interdigital electrodes and an inductor for glucose sensing is presented. Resonance frequency and impedance were measured as the sensing parameters. A glucose beverage concentration from 0% to 44% is used, resulting in a resonance frequency change from 1.9217 MHz to 1.8681 MHz, and the impedance of the sensor changes from 170.33 Ω to 110.68 Ω . The relationship of both resonance frequency and impedance to glucose beverage concentration is well presented by a decreasing exponential function. Using an exponential regression, the resonance frequency shows an average regression error of 1.38%. Likewise, the impedance shows an average error of 3.47%. The linear range of the sensor is also analyzed in a glucose concentration range between 0% and 4%. The sensor exhibited a sensitivity of 424.6 kHz and 721.6416 Ω , respectively, with a linear regression r2 of 0.9853 and 0.9553, respectively.
Machine-learning-accelerated screening of single metal atoms anchored on MNPS3 monolayer as promising bifunctional oxygen electrocatalysts
(Royal Society of Chemistry, 2023) Li, Xinyi; Lin, Shiru; Yan, Tingyu; Wang, Zhongxu; Cai, Qinghai; Zhao, Jingxiang
Searching for bifunctional oxygen electrocatalysts with good catalytic performance to promote the oxygen evolution/reduction reactions (OER/ORR) is of great significance to the development of sustainable and renewable clean energy. Herein, we performed density functional theory (DFT) and machine-learning (DFT–ML) hybrid computations to investigate the potential of a series of single transition metal atoms anchored on the experimentally available MnPS3 monolayer (TM/MnPS3) as the bifunctional electrocatalysts for the ORR/OER. The results revealed that the interactions of these metal atoms with MnPS3 are rather strong, thus guaranteeing their high stability for practical applications. Remarkably, the highly efficient ORR/OER can be achieved on Rh/MnPS3 and Ni/MnPS3 with lower overpotentials than those of metal benchmarks, which can be further rationalized by establishing the volcano and contour plots. Furthermore, the ML results showed that the bond length of TM atoms with the adsorbed O species (dTM–O), the number of d electrons (Ne), the d-center (εd), the radius (rTM) and the first ionization energy (Im) of the TM atoms are the primary descriptors featuring the adsorption behavior. Our findings not only suggest novel highly efficient bifunctional oxygen electrocatalysts, but also provide cost-effective opportunities for the design of single-atom catalysts using the DFT–ML hybrid method.
A new insight into the molecular rearrangement of sulfurized polyacrylonitrile cathode in ether electrolyte
(Elsevier, 2023) Wang, Wei; Wangcong, Xu; Xia, Shuhang; Xue, Wenying; Wang, Jin; Wang, Xiaofei; Li, Huilan; Lin, Shiru; Zhao, Yu; Wang, Lina; Wang, Yonggang
Sulfurized polyacrylonitrile (SPAN) is one of the most promising cathode materials with high energy density. However, irreversible shuttling effect is easily triggered by formation of soluble polysulfides (Li2Sn, 2< n ≤8) in ether electrolytes. The major challenge relies in the control of molecular rearrangement of SPAN to avoid spontaneous generation of Li2Sn. This work reveals the morphological and structural roles that responsible for the compatibility of SPAN with ether electrolytes. Besides the length of the covalently bonded –Sx– chains in the pyrolyzed PAN backbone, the protection of SPAN fragments from robust interactions with solvents enables a stable cycling of electrodes. The freestanding SPAN cathode with a continuous fibrous network exhibits a much higher electrochemical stability than its powder counterparts. The single-phase solid-solid reaction of SPAN with Li+ can be realized with Li2S as the sole discharge product. Nevertheless, the reversible reaction is kinetically dominated by the activation of the produced Li2S. The recharge ability and rate capability can be improved by rationally controlling the molecular rearrangement of SPAN. The trace amount of in-situ generated Li2Sn acting as a chemical mediator can promote the reversible decomposition of Li2S, offering a new insight into cathode design of Li–S batteries.

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