Publications by authors named "Chittaranjan Das"

73 Publications

Crystal structure of the Thr316Ala mutant of a yeast JAMM deubiquitinase: implication of active-site loop dynamics in catalysis.

Acta Crystallogr F Struct Biol Commun 2021 Jun 24;77(Pt 6):163-170. Epub 2021 May 24.

Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.

AMSH, an endosome-associated deubiquitinase (DUB) with a high specificity for Lys63-linked polyubiquitin chains, plays an important role in endosomal-lysosomal sorting and down-regulation of cell-surface receptors. AMSH belongs to the JAMM family of DUBs that contain two insertion segments, Ins-1 and Ins-2, in the catalytic domain relative to the JAMM core found in the archaebacterial AfJAMM. Structural analyses of the AMSH homologs human AMSH-LP and fission yeast Sst2 reveal a flap-like structure formed by Ins-2 near the active site that appears to open and close during its catalytic cycle. A conserved phenylalanine residue of the flap interacts with a conserved aspartate residue of the Ins-1 β-turn to form a closed `lid' over the active site in the substrate-bound state. Analyses of these two residues (Phe403 and Asp315) in Sst2 showed that their interaction plays an important role in controlling the flexibility of Ins-2. The Lys63-linked diubiquitin substrate-bound form of Sst2 showed that the conserved phenylalanine also interacts with Thr316 of Ins-1, which is substituted by tyrosine in other AMSH orthologs. Although Thr316 makes no direct interaction with the substrate, its mutation to alanine resulted in a significant loss of activity. In order to understand the contribution of Thr316 to catalysis, the crystal structure of this mutant was determined. In spite of the effect of the mutation on catalytic activity, the structure of the Sst2 Thr316Ala mutant did not reveal significant changes in either the overall structure or the active-site arrangement relative to the wild type. The Phe403-Thr316 van der Waals interaction is impaired by the Thr316Ala mutation, abrogating the adoption of the closed active-site conformation required for catalysis. Since van der Waals interactions with phenylalanine are conserved across substrate-bound forms of AMSH-LP and Sst2, these interactions may be critical for loop immobilization and the positioning of the isopeptide bond of Lys63-linked polyubiquitin-chain substrates.
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http://dx.doi.org/10.1107/S2053230X21005124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8186415PMC
June 2021

Optimization and Anti-Cancer Properties of Fluoromethylketones as Covalent Inhibitors for Ubiquitin C-Terminal Hydrolase L1.

Molecules 2021 Feb 25;26(5). Epub 2021 Feb 25.

Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA.

The deubiquitinating enzyme (DUB) UCHL1 is implicated in various disease states including neurodegenerative disease and cancer. However, there is a lack of quality probe molecules to gain a better understanding on UCHL1 biology. To this end a study was carried out to fully characterize and optimize the irreversible covalent UCHL1 inhibitor VAEFMK. Structure-activity relationship studies identified modifications to improve activity versus the target and a full cellular characterization was carried out for the first time with this scaffold. The studies produced a new inhibitor, , with an IC value of 7.7 µM against UCHL1 and no observable activity versus the closest related DUB UCHL3. The molecule was also capable of selectively inhibiting UCHL1 in cells and did not demonstrate any discernible off-target toxicity. Finally, the molecule was used for initial probe studies to assess the role of UCHL1 role in proliferation of myeloma cells and migration behavior in small cell lung cancer cells making a new tool to be used in the biological evaluation of UCHL1.
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http://dx.doi.org/10.3390/molecules26051227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7956625PMC
February 2021

Acquisition of a Mysterious New Domain Modulates the Function of a Bacterial Effector.

Biochemistry 2021 03 23;60(9):635-636. Epub 2021 Feb 23.

Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States.

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http://dx.doi.org/10.1021/acs.biochem.1c00069DOI Listing
March 2021

Acquisition of a Mysterious New Domain Modulates the Function of a Bacterial Effector.

Biochemistry 2021 03 23;60(9):635-636. Epub 2021 Feb 23.

Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States.

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http://dx.doi.org/10.1021/acs.biochem.1c00069DOI Listing
March 2021

Intermetallic FeGe formation and decay of a core-shell structure during the oxygen evolution reaction.

Chem Commun (Camb) 2021 Mar;57(17):2184-2187

Department of Chemistry, Technische Universität Berlin, Strasse des 17, Juni 135, Sekr. C2, Berlin 10623, Germany.

Herein, we report on intermetallic iron germanide (Fe6Ge5) as a novel oxygen evolution reaction (OER) precatalyst with a Tafel slope of 32 mV dec-1 and an overpotential of 272 mV at 100 mA cm-2 in alkaline media. Furthermore, we uncover the in situ formation of a core-shell like structure that slowly collapses under OER conditions.
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http://dx.doi.org/10.1039/d0cc08035gDOI Listing
March 2021

Synthesis and Characterization of a Multication Doped Mn Spinel, LiNiCuFeMnO, as 5 V Positive Electrode Material.

ACS Omega 2020 Sep 31;5(36):22861-22873. Epub 2020 Aug 31.

Institute for Applied Materials (IAM), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.

The suitability of multication doping to stabilize the disordered 3̅ structure in a spinel is reported here. In this work, LiNiCuFeMnO was synthesized via a sol-gel route at a calcination temperature of 850 °C. LiNiCuFeMnO is evaluated as positive electrode material in a voltage range between 3.5 and 5.3 V (vs Li/Li) with an initial specific discharge capacity of 126 mAh g at a rate of /2. This material shows good cycling stability with a capacity retention of 89% after 200 cycles and an excellent rate capability with the discharge capacity reaching 78 mAh g at a rate of 20. X-ray diffraction (XRD) measurements with a laboratory X-ray source between 3.5 and 5.3 V at a rate of /10 reveal that the (de)lithiation occurs via a solid-solution mechanism where a local variation of lithium content is observed. A simplified estimation based on the XRD analysis suggests that around 17-31 mAh g of discharge capacity in the first cycle is used for a reductive parasitic reaction, hindering a full lithiation of the positive electrode at the end of the first discharge.
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http://dx.doi.org/10.1021/acsomega.0c02174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7495482PMC
September 2020

Development of Ubiquitin Variants with Selectivity for Ubiquitin C-Terminal Hydrolase Deubiquitinases.

Biochemistry 2020 09 8;59(37):3447-3462. Epub 2020 Sep 8.

Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.

Ubiquitin (Ub) is a highly conserved protein that is covalently attached to substrate proteins as a post-translational modification to regulate signaling pathways such as proteasomal degradation and cell cycle/transcriptional regulation in the eukaryotic cellular environment. Ub signaling is regulated by the homeostasis of substrate protein ubiquitination/deubiquitination by E3 ligases and deubiquitinating enzymes (DUBs) in healthy eukaryotic systems. One such DUB, ubiquitin C-terminal hydrolase L1 (UCHL1), is endogenously expressed in the central nervous system under normal physiological conditions, but overexpression and/or mutation has been linked to various cancers and neurodegenerative diseases. The lack of UCHL1 probing strategies suggests development of a selective Ub variant (UbV) for probing UCHL1's role in these disease states would be beneficial. We describe a computational design approach to investigate UbVs that lend selectivity, both binding and inhibition, to UCHL1 over the close structural homologue UCHL3 and members of other DUB families. A number of UbVs, mainly those containing Thr9 mutations, displayed appreciable binding and inhibition selectivity for UCHL1 over UCHL3, compared to wild-type Ub in assays. By appending reactive electrophiles to the C-terminus of the UbVs, we created the first activity-based probe (ABP) with demonstrated reaction selectivity for UCH family DUBs over other families in cell lysates. Further kinetic analysis of covalent inhibition by the UbV-ABP with UCHL1 and UCHL3 offers insight into the future design of UCHL1 selective UbV-ABP. These studies serve as a proof of concept of the viability of the design of ubiquitin variants for UCH family DUBs as a step toward the development of macromolecular UCHL1 inhibitors.
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http://dx.doi.org/10.1021/acs.biochem.9b01076DOI Listing
September 2020

Surface, Interface, and Bulk Electronic and Chemical Properties of Complete Perovskite Solar Cells: Tapered Cross-Section Photoelectron Spectroscopy, a Novel Solution.

ACS Appl Mater Interfaces 2020 Sep 28;12(36):40949-40957. Epub 2020 Aug 28.

Materials Science Department, Darmstadt University of Technology, Otto-Berndt-Str. 3, D-64287 Darmstadt, Germany.

The surface, interface, and bulk properties are a few of the most critical factors that influence the performance of perovskite solar cells. The photoelectron spectroscopy (PES) is used as a technique to analyze these properties. However, the information depth of PES is limited to 10-20 nm, which makes it not suitable to study the complete devices, which have a thickness of ∼1 μm. Here, we introduce a novel and simple technique of PES on a tapered cross section (TCS-PES). It provides both lateral and vertical resolutions compared to the conventional PES so that it is suitable to study a complete perovskite solar cell. It offers many benefits over conventional PES methods such as the chemical composition in the micrometer scale from the surface to the bulk and the electronic properties at the multiple interfaces. The chemical natures of different layers of the perovskite-based solar cells [(FAPbI)(MAPbBr)] can be identified precisely for the first time using the TCS-PES method. We found that the perovskite layer has higher iodine concentration at the Spiro/perovskite interface and higher bromine concentration at the TiO/perovskite interface. UPS measurements on the tapered cross section revealed that the perovskite is n-type, and the solar cell studied here is a p-n-n structure type device. The unique possibilities to analyze the complete solar cell by XPS and UPS allow us to estimate the band bending in a working solar cell. Moreover, this technique can further be used to study the device under operating conditions, and it can be applied in other solid-state devices like solid electrolyte Li-ion batteries, LEDs, or photoelectrodes.
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http://dx.doi.org/10.1021/acsami.0c11484DOI Listing
September 2020

Legionella effector MavC targets the Ube2N~Ub conjugate for noncanonical ubiquitination.

Nat Commun 2020 05 12;11(1):2365. Epub 2020 May 12.

Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.

The bacterial effector MavC modulates the host immune response by blocking Ube2N activity employing an E1-independent ubiquitin ligation, catalyzing formation of a γ-glutamyl-ε-Lys (Gln40-Lys92) isopeptide crosslink using a transglutaminase mechanism. Here we provide biochemical evidence in support of MavC targeting the activated, thioester-linked Ube2N~ubiquitin conjugate, catalyzing an intramolecular transglutamination reaction, covalently crosslinking the Ube2N and Ub subunits effectively inactivating the E2~Ub conjugate. Ubiquitin exhibits weak binding to MavC alone, but shows an increase in affinity when tethered to Ube2N in a disulfide-linked substrate that mimics the charged E2~Ub conjugate. Crystal structures of MavC in complex with the substrate mimic and crosslinked product provide insights into the reaction mechanism and underlying protein dynamics that favor transamidation over deamidation, while revealing a crucial role for the structurally unique insertion domain in substrate recognition. This work provides a structural basis of ubiquitination by transglutamination and identifies this enzyme's true physiological substrate.
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http://dx.doi.org/10.1038/s41467-020-16211-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217864PMC
May 2020

The Two Deubiquitinating Enzymes from Have Distinct Ubiquitin Recognition Properties.

Biochemistry 2020 04 14;59(16):1604-1617. Epub 2020 Apr 14.

Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States.

is the cause of several diseases such as sexually transmitted urogenital disease and ocular trachoma. The pathogen contains a small genome yet, upon infection, expresses two enzymes with deubiquitinating activity, termed ChlaDUB1 and ChlaDUB2, presumed to have redundant deubiquitinase (DUB) function because of the similarity of the primary structure of their catalytic domain. Previous studies have led to structural characterization of the enzymatic properties of ChlaDUB1; however, ChlaDUB2 has yet to be investigated thoroughly. In this study, we investigated the deubiquitinase properties of ChlaDUB2 and compared them to those of ChlaDUB1. This revealed a distinct difference in hydrolytic activity with regard to di- and polyubiquitin chains while showing similar ability to cleave a monoubiquitin-based substrate, ubiquitin aminomethylcoumarin (Ub-AMC). ChlaDUB2 was unable to cleave a diubiquitin substrate efficiently, whereas ChlaDUB1 could rapidly hydrolyze this substrate like a prototypical prokaryotic DUB, SdeA. With polyubiquitinated green fluorescent protein substrate (GFP-Ub), whereas ChlaDUB1 efficiently disassembled the polyubiquitin chains into the monoubiquitin product, the deubiquitination activity of ChlaDUB2, while showing depletion of the substrate, did not produce appreciable levels of the monoubiquitin product. We report the structures of a catalytic construct of ChlaDUB2 and its complex with ubiquitin propargyl amide. These structures revealed differences in residues involved in substrate recognition between the two DUBs. On the basis of the structures, we conclude that the distal ubiquitin binding is equivalent between the two DUBs, consistent with the Ub-AMC activity result. Therefore, the difference in activity with longer ubiquitinated substrates may be due to the differential recognition of these substrates involving additional ubiquitin binding sites.
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http://dx.doi.org/10.1021/acs.biochem.9b01107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7700883PMC
April 2020

Fluorescent Probes for Monitoring Serine Ubiquitination.

Biochemistry 2020 04 27;59(13):1309-1313. Epub 2020 Mar 27.

Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States.

In a radical departure from the classical E1-E2-E3 three-enzyme mediated ubiquitination of eukaryotes, the recently described bacterial enzymes of the SidE family of effectors utilize NAD to ligate ubiquitin onto target substrate proteins. This outcome is achieved via a two-step mechanism involving (1) ADP ribosylation of ubiquitin followed by (2) phosphotransfer to a target serine residue. Here, using fluorescent NAD analogues as well as synthetic substrate mimics, we have developed continuous assays enabling real-time monitoring of both steps of this mechanism. These assays are amenable to biochemical studies and high-throughput screening of inhibitors of these effectors, and the discovery and characterization of putative enzymes similar to members of the SidE family in other organisms. We also show their utility in studying enzymes that can reverse and inhibit this post-translational modification.
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http://dx.doi.org/10.1021/acs.biochem.0c00067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7294441PMC
April 2020

A Low-Temperature Molecular Precursor Approach to Copper-Based Nano-Sized Digenite Mineral for Efficient Electrocatalytic Oxygen Evolution Reaction.

Chem Asian J 2020 Mar 20;15(6):852-859. Epub 2020 Feb 20.

Department of Chemistry Metalorganics and Inorganic Materials, Technische Universität Berlin, Straße des 17 Juni 135, Sekr. C2, 10623, Berlin, Germany.

In the urge of designing noble metal-free and sustainable electrocatalysts for oxygen evolution reaction (OER), herein, a mineral Digenite Cu S has been prepared from a molecular copper(I) precursor, [{(PyHS) Cu (PyHS)} ](OTf) (1), and utilized as an anode material in electrocatalytic OER for the first time. A hot injection of 1 yielded a pure phase and highly crystalline Cu S , which was then electrophoretically deposited (EPD) on a highly conducting nickel foam (NF) substrate. When assessed as an electrode for OER, the Cu S /NF displayed an overpotential of merely 298±3 mV at a current density of 10 mA cm in alkaline media. The overpotential recorded here supersedes the value obtained for the best reported Cu-based as well as the benchmark precious-metal-based RuO and IrO electrocatalysts. In addition, the choronoamperometric OER indicated the superior stability of Cu S /NF, rendering its suitability as the sustainable anode material for practical feasibility. The excellent catalytic activity of Cu S can be attributed to the formation of a crystalline CuO overlayer on the conductive Cu S that behaves as active species to facilitate OER. This study delivers a distinct molecular precursor approach to produce highly active copper-based catalysts that could be used as an efficient and durable OER electro(pre)catalysts relying on non-precious metals.
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http://dx.doi.org/10.1002/asia.202000022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155036PMC
March 2020

Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination.

EMBO J 2020 02 11;39(4):e102806. Epub 2019 Dec 11.

Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.

The Legionella pneumophila effector MavC induces ubiquitination of the E2 ubiquitin-conjugating enzyme UBE2N by transglutamination, thereby abolishing its function in the synthesis of K -type polyubiquitin chains. The inhibition of UBE2N activity creates a conundrum because this E2 enzyme is important in multiple signaling pathways, including some that are important for intracellular L. pneumophila replication. Here, we show that prolonged inhibition of UBE2N activity by MavC restricts intracellular bacterial replication and that the activity of UBE2N is restored by MvcA, an ortholog of MavC (50% identity) with ubiquitin deamidase activity. MvcA functions to deubiquitinate UBE2N-Ub using the same catalytic triad required for its deamidase activity. Structural analysis of the MvcA-UBE2N-Ub complex reveals a crucial role of the insertion domain in MvcA in substrate recognition. Our study establishes a deubiquitination mechanism catalyzed by a deamidase, which, together with MavC, imposes temporal regulation of the activity of UBE2N during L. pneumophila infection.
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http://dx.doi.org/10.15252/embj.2019102806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7024838PMC
February 2020

Ubiquitin C-Terminal Hydrolase L1: Biochemical and Cellular Characterization of a Covalent Cyanopyrrolidine-Based Inhibitor.

Chembiochem 2020 03 7;21(5):712-722. Epub 2019 Nov 7.

Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA.

The deubiquitinase (DUB) ubiquitin C-terminal hydrolase L1 (UCHL1) is expressed primarily in the central nervous system under normal physiological conditions. However, UCHL1 is overexpressed in various aggressive forms of cancer with strong evidence supporting UCHL1 as an oncogene in lung, glioma, and blood cancers. In particular, the level of UCHL1 expression in these cancers correlates with increased invasiveness and metastatic behavior, as well as poor patient prognosis. Although UCHL1 is considered an oncogene with potential as a therapeutic target, there remains a significant lack of useful small-molecule probes to pharmacologically validate in vivo targeting of the enzyme. Herein, we describe the characterization of a new covalent cyanopyrrolidine-based UCHL1 inhibitory scaffold in biochemical and cellular studies to better understand the utility of this inhibitor in elucidating the role of UCHL1 in cancer biology.
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http://dx.doi.org/10.1002/cbic.201900434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7042063PMC
March 2020

Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase.

Nature 2019 08 22;572(7769):387-391. Epub 2019 Jul 22.

Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.

The bacterial pathogen Legionella pneumophila creates an intracellular niche permissive for its replication by extensively modulating host-cell functions using hundreds of effector proteins delivered by its Dot/Icm secretion system. Among these, members of the SidE family (SidEs) regulate several cellular processes through a unique phosphoribosyl ubiquitination mechanism that bypasses the canonical ubiquitination machinery. The activity of SidEs is regulated by another Dot/Icm effector known as SidJ; however, the mechanism of this regulation is not completely understood. Here we demonstrate that SidJ inhibits the activity of SidEs by inducing the covalent attachment of glutamate moieties to SdeA-a member of the SidE family-at E860, one of the catalytic residues that is required for the mono-ADP-ribosyltransferase activity involved in ubiquitin activation. This inhibition by SidJ is spatially restricted in host cells because its activity requires the eukaryote-specific protein calmodulin (CaM). We solved a structure of SidJ-CaM in complex with AMP and found that the ATP used in this reaction is cleaved at the α-phosphate position by SidJ, which-in the absence of glutamate or modifiable SdeA-undergoes self-AMPylation. Our results reveal a mechanism of regulation in bacterial pathogenicity in which a glutamylation reaction that inhibits the activity of virulence factors is activated by host-factor-dependent acyl-adenylation.
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http://dx.doi.org/10.1038/s41586-019-1439-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855250PMC
August 2019

Can Metallic Sodium Electrodes Affect the Electrochemistry of Sodium-Ion Batteries? Reactivity Issues and Perspectives.

ChemSusChem 2019 Jul 11;12(14):3312-3319. Epub 2019 Jun 11.

Institute for Applied Materials (IAM), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.

Sodium-ion batteries (NIBs) are promising energy-storage devices with advantages such as low cost and highly abundant raw materials. To probe the electrochemical properties of NIBs, sodium metal is most frequently applied as the reference and/or counter electrode in state-of-the-art literature. However, the high reactivity of the sodium metal and its impact on the electrochemical performance is usually neglected. In this study, it is shown that spontaneous reactions of sodium metal with organic electrolytes and the importance of critical interpretation of electrochemical experiments is emphasized. When using sodium-metal half-cells, decomposition products contaminate the electrolyte during the electrochemical measurement and can easily lead to wrong conclusions about the stability of the active materials. The cycling stability is highly affected by these electrolyte contaminations, which is proven by comparing sodium-metal-free cell with sodium-metal-containing cells. Interestingly, a more stable cycling performance of the Li Ti O half-cells can be observed when replacing the Na metal counter and reference electrodes with activated carbon electrodes. This difference is attributed to the altered properties of the electrolyte as a result of contamination and to different surface chemistries.
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http://dx.doi.org/10.1002/cssc.201901056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771488PMC
July 2019

Purification and functional characterization of the DUB domain of SdeA.

Methods Enzymol 2019 1;618:343-355. Epub 2019 Feb 1.

Department of Chemistry, Purdue University, West Lafayette, IN, United States. Electronic address:

Intracellular pathogens like Legionella pneumophila hijack the host ubiquitination network in order to create a facultative niche for their survival by means of effector molecules secreted into the host cell. Some of these effectors function as ubiquitin ligases or deubiquitinases, among other types of enzymes. Deubiquitinating enzymes (DUBs) remove ubiquitin or ubiquitin-like modifiers from conjugated substrates to regulate various cellular processes. Members of the SidE effector family from the L. pneumophila pathogen harbor multiple functional domains that possess discrete biochemical activities impinging on host ubiquitin signaling. At the N-terminal end of these ~1500-residue proteins is a ~200-residue conserved DUB domain capable of recognizing both ubiquitin and the NEDD8 Ubl. SdeA, a member of the SidE family, plays an important role in intracellular bacterial replication. Downstream domains in this protein also catalyze substrate ubiquitination via a phosphoribosyl linkage. Several mammalian Rab proteins (Rab1, Rab30, and Rab33) have been shown to be targeted. The novel mechanism is independent of the classical E1 and E2 ubiquitin ligation machinery and does not require ATP. The N-terminal DUB domain, which does not appear to affect this ubiquitination activity, but it catalyzes cleavage of three different types of polyubiquitination chains (K11, K48, and K63) commonly found in host cells. This chapter describes methods, including purification of recombinant SdeA (full-length and DUB domain alone), and enzymatic assays that have been utilized to characterize the deubiquitination activity of SdeA.
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http://dx.doi.org/10.1016/bs.mie.2018.12.024DOI Listing
November 2019

Cytogenetic effects of silver and gold nanoparticles on roots.

J Genet Eng Biotechnol 2018 Dec 3;16(2):519-526. Epub 2018 Aug 3.

Environmental Chemistry Laboratory, Department of Environmental Science, The University of Burdwan, West Bengal, India.

The present study evaluates the cytogenetic effects of both silver and gold nanoparticles on the root cells of . In this study, the root cells of were treated with both gold and silver nanoparticles of different concentrations (1 mg/L, 5 mg/L and 10 mg/L) along with control for 72 h. Experimental results revealed that after 72 h of exposure, a significant decrease in mitotic index (MI) from 68% (control) to 52.4% (1 mg/L), 47.3% (5 mg/L) and 41.4% (10 mg/L) for gold nanoparticles and 57.1% (1 mg/L), 53% (5 mg/l), 55.8% (10 mg/L) for silver nanoparticles. Through minute observation of the photograph, it was recorded that some specific chromosomal abnormalities such as stickiness of chromosome, chromosome breaks, nuclear notch, and clumped chromosome at different exposure conditions. Therefore, present results clearly suggest that root tip assay could be a viable path through which negative impact of both gold and silver nanoparticles can be demonstrated over a wide range of concentrations.
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http://dx.doi.org/10.1016/j.jgeb.2018.07.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6353767PMC
December 2018

Uncovering the Structural Basis of a New Twist in Protein Ubiquitination.

Trends Biochem Sci 2019 05 21;44(5):467-477. Epub 2018 Dec 21.

Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA. Electronic address:

Members of the SidE effector family from Legionella pneumophila represent a new paradigm in the ubiquitin world. These enzymes catalyze ubiquitination of target proteins via a mechanism different from that of conventional E1-E2-E3 biochemistry and play important roles in L. pneumophila virulence. They combine mono-ADP-ribosylation and phosphodiesterase activities to attach ubiquitin onto substrates, in great contrast to the orthodox pathway. A series of recent structural and mechanistic studies have clarified the action of these enzymes. Herein, we summarize the key insights into the structure and function of these proteins, emphasizing their modular nature, and discuss the biochemical implications of these proteins as well as areas of further exploration.
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http://dx.doi.org/10.1016/j.tibs.2018.11.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465118PMC
May 2019

Crystal structure of the ribonuclease-P-protein subunit from Staphylococcus aureus.

Acta Crystallogr F Struct Biol Commun 2018 Oct 19;74(Pt 10):632-637. Epub 2018 Sep 19.

Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA.

Staphylococcus aureus ribonuclease-P-protein subunit (RnpA) is a promising antimicrobial target that is a key protein component for two essential cellular processes, RNA degradation and transfer-RNA (tRNA) maturation. The first crystal structure of RnpA from the pathogenic bacterial species, S. aureus, is reported at 2.0 Å resolution. The structure presented maintains key similarities with previously reported RnpA structures from bacteria and archaea, including the highly conserved RNR-box region and aromatic residues in the precursor-tRNA 5'-leader-binding domain. This structure will be instrumental in the pursuit of structure-based designed inhibitors targeting RnpA-mediated RNA processing as a novel therapeutic approach for treating S. aureus infections.
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http://dx.doi.org/10.1107/S2053230X18011512DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168776PMC
October 2018

Room-Temperature Atomic-Layer-Deposited Al O Improves the Efficiency of Perovskite Solar Cells over Time.

ChemSusChem 2018 Oct 26;11(20):3640-3648. Epub 2018 Sep 26.

Applied Physics and Sensors, Brandenburg University of Technology Cottbus-Senftenberg, Konrad-Wachsmann-Allee 17, 03046, Cottbus, Germany.

Electrical characterisation of perovskite solar cells consisting of room-temperature atomic-layer-deposited aluminium oxide (RT-ALD-Al O ) film on top of a methyl ammonium lead triiodide (CH NH PbI ) absorber showed excellent stability of the power conversion efficiency (PCE) over a long time. Under the same environmental conditions (for 355 d), the average PCE of solar cells without the ALD layer decreased from 13.6 to 9.6 %, whereas that of solar cells containing 9 ALD cycles of depositing RT-ALD-Al O on top of CH NH PbI increased from 9.4 to 10.8 %. Spectromicroscopic investigations of the ALD/perovskite interface revealed that the maximum PCE with the ALD layer is obtained when the so-called perovskite cleaning process induced by ALD precursors is complete. The PCE enhancement over time is probably related to a self-healing process induced by the RT-ALD-Al O film. This work may provide a new direction for further improving the long-term stability and performance of perovskite solar cells.
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http://dx.doi.org/10.1002/cssc.201801434DOI Listing
October 2018

Ubiquitin Chains Modified by the Bacterial Ligase SdeA Are Protected from Deubiquitinase Hydrolysis.

Biochemistry 2017 09 18;56(36):4762-4766. Epub 2017 Aug 18.

Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47906, United States.

The SidE family of Legionella pneumophila effectors is a unique group of ubiquitin-modifying enzymes. Along with catalyzing NAD-dependent ubiquitination of certain host proteins independent of the canonical E1/E2/E3 pathway, they have also been shown to produce phosphoribosylated free ubiquitin. This modified ubiquitin product is incompatible with conventional E1/E2/E3 ubiquitination processes, with the potential to lock down various cellular functions that are dependent on ubiquitin signaling. Here, we show that in addition to free ubiquitin, Lys63-, Lys48-, Lys11-, and Met1-linked diubiquitin chains are also modified by SdeA in a similar fashion. Both the proximal and distal ubiquitin moieties are targeted in the phosphoribosylation reaction. Furthermore, this renders the ubiquitin chains unable to be processed by a variety of deubiquitinating enzymes. These observations broaden the scope of SdeA's modulatory functions during Legionella infection.
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http://dx.doi.org/10.1021/acs.biochem.7b00664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769467PMC
September 2017

New insights into water photooxidation on reductively pretreated hematite photoanodes.

Phys Chem Chem Phys 2017 Aug;19(32):21807-21817

Departament de Química Física i Institut Universitari d'Electroquímica, Universitat d'Alacant, Apartat 99, E-03080, Alicante, Spain.

It has been recently demonstrated that the photoactivity toward oxygen evolution of a number of n-type metal oxides can be substantially improved by a reductive electrochemical pretreatment. Such an enhancement has been primarily linked to the formation of low valent metal species that increase electrode conductivity. In this work, we report new insights into the electrochemical doping using highly ordered (110)-oriented hematite nanorods directly grown on FTO. The reductive pretreatment consists in applying negative potentials for a controlled period of time. Such a pretreatment was optimized in both potentiostatic and potentiodynamic regimes. We show that the optimized pretreatment enhances electrode conductivity due to an increase in charge carrier density. However, it additionally triggers changes in the morphologic, catalytic and electronic properties that facilitate the separation and collection of the photogenerated charge carriers causing an up to 8-fold enhancement in the photocurrent for water oxidation. The reductive pretreatment can be considered as a highly controllable electrochemical n-type doping with the amount of generated Fe/polaron species and the change in film morphology as the main factors determining the final efficiency for water photooxidation of the resulting electrodes.
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http://dx.doi.org/10.1039/c7cp03958aDOI Listing
August 2017

Alkaline electrochemical water oxidation with multi-shelled cobalt manganese oxide hollow spheres.

Chem Commun (Camb) 2017 Aug 5;53(62):8641-8644. Epub 2017 Jul 5.

Department of Chemistry, Metalorganics and Inorganic Materials, Technische Universität Berlin, Strasse des 17 Juni 135, D-10623 Berlin, Germany.

Multi-shelled hollow spheres of cobalt manganese oxides (CMOs) deposited on Ni foam exhibited superior alkaline electrochemical water oxidation activity and surpassed those of bulk CMO and commercial noble metal-based catalysts. A higher amount of cobalt in the spinel structure resulted in the transformation of the tetragonal to the cubic phase with a decrease in the overpotential of oxygen evolution.
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http://dx.doi.org/10.1039/c7cc03566gDOI Listing
August 2017

A unique deubiquitinase that deconjugates phosphoribosyl-linked protein ubiquitination.

Cell Res 2017 Jul 12;27(7):865-881. Epub 2017 May 12.

Center of Infection and Immunity, The First Hospital, Jilin University, Changchun, Jilin 130001, China.

Ubiquitination regulates many aspects of host immunity and thus is a common target for infectious agents. Recent studies have revealed that members of the SidE effector family of the bacterial pathogen Legionella pneumophila attack several small GTPases associated with the endoplasmic reticulum by a novel ubiquitination mechanism that does not require the E1 and E2 enzymes of the host ubiquitination machinery. In this case, ubiquitin is first activated by ADP-ribosylation at Arg by a mono-ADP-ribosyltransferase activity; the intermediate is then cleaved by a phosphodiesterase activity also residing within SdeA, concomitant with the attachment of ubiquitin to serine residues of substrate proteins via a phosphoribosyl linker. Here we demonstrate that the effect of SidEs is antagonized by SidJ, an effector encoded by a gene situated in the locus coding for three members of the SidE family (SdeC, SdeB and SdeA). SidJ reverses ubiquitination of SidEs-modified substrates by cleaving the phosphodiester bond that links phosphoribosylated ubiquitin to protein substrates. SidJ also displays classical deubiquitinase activity but does not require catalytic cysteine residues. Further, these deubiquitinase activities of SidJ are essential for its role in L. pneumophila infection. Finally, the activity of SidJ is required for efficiently reducing the abundance of ubiquitinated Rab33b in infected cells within a few hours after bacterial uptake. Our results establish SidJ as a ubiquitin-deconjugating enzyme that functions to impose temporal regulation on the activity of SidE effectors. SidJ may be important in future studies of signaling cascades mediated by this unique ubiquitination, one that also potentially regulates cellular processes in eukaryotic cells.
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http://dx.doi.org/10.1038/cr.2017.66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5518988PMC
July 2017

Selective Deposition of an Ultrathin Pt Layer on a Au-Nanoisland-Modified Si Photocathode for Hydrogen Generation.

ACS Omega 2017 Apr 10;2(4):1360-1366. Epub 2017 Apr 10.

Angewandte Physik-Sensorik, Brandenburgische Technische Universität Cottbus-Senftenberg, Konrad-Wachsmann-Allee 17, 03046 Cottbus, Germany.

Platinum, being the most efficient and stable catalyst, is used in photoelectrochemical (PEC) devices. However, a minimal amount of Pt with maximum catalytic activity is required to be used to minimize the cost of production. In this work, we use an environmentally friendly, cost-effective, and less Pt-consuming method to prepare PEC devices for the hydrogen evolution reaction (HER). The Pt monolayer catalyst is selectively deposited on a Au-nanoisland-supported boron-doped p-type Si (100) photocathode. The PEC device based on the Si photocathode with an ultralow loading of the Pt catalyst exhibits a comparable performance for the HER to that of devices with a thick Pt layer. In addition, we demonstrate that by using a thin TiO layer deposited by atomic layer deposition photo-oxidation of the Si photocathode can be blocked resulting in a stable PEC performance.
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http://dx.doi.org/10.1021/acsomega.6b00374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6641136PMC
April 2017

Synchrotron X-Ray Diffraction Dynamic Sampling for Protein Crystal Centering.

IS&T Int Symp Electron Imaging 2017 29;2017:6-9. Epub 2017 Jan 29.

Department of Chemistry, Purdue University, West Lafayette, IN, 47907.

A supervised learning approach for dynamic sampling (SLADS) was developed to reduce X-ray exposure prior to data collection in protein structure determination. Implementation of this algorithm allowed reduction of the X-ray dose to the central core of the crystal by up to 20-fold compared to current raster scanning approaches. This dose reduction corresponds directly to a reduction on X-ray damage to the protein crystals prior to data collection for structure determination. Implementation at a beamline at Argonne National Laboratory suggests promise for the use of the SLADS approach to aid in the analysis of X-ray labile crystals. The potential benefits match a growing need for improvements in automated approaches for microcrystal positioning.
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http://dx.doi.org/10.2352/ISSN.2470-1173.2017.17.COIMG-415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5842693PMC
January 2017

Dynamic X-ray diffraction sampling for protein crystal positioning.

J Synchrotron Radiat 2017 01 1;24(Pt 1):188-195. Epub 2017 Jan 1.

Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations.
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http://dx.doi.org/10.1107/S160057751601612XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5182024PMC
January 2017

Room-Temperature Atomic Layer Deposition of Al O : Impact on Efficiency, Stability and Surface Properties in Perovskite Solar Cells.

ChemSusChem 2016 Dec 7;9(24):3401-3406. Epub 2016 Dec 7.

Applied Physics and Sensors, Brandenburg University of Technology Cottbus-Senftenberg, Konrad-Wachsmann-Allee 17, 03046, Cottbus, Germany.

In this work, solar cells with a freshly made CH NH PbI perovskite film showed a power conversion efficiency (PCE) of 15.4 % whereas the one with 50 days aged perovskite film only 6.1 %. However, when the aged perovskite was covered with a layer of Al O deposited by atomic layer deposition (ALD) at room temperature (RT), the PCE value was clearly enhanced. X-ray photoelectron spectroscopy study showed that the ALD precursors are chemically active only at the perovskite surface and passivate it. Moreover, the RT-ALD-Al O -covered perovskite films showed enhanced ambient air stability.
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http://dx.doi.org/10.1002/cssc.201601186DOI Listing
December 2016
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