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Das, Chittaranjan

Publications and source records attributed to Das, Chittaranjan.

11 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain

ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen Legionella pneumophila mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. Here, we show that the Legionella macrodomain effector MavL regulates this pathway by reversing the arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by the modified ubiquitin. We determine the crystal structure of ADP-ribose-bound MavL, providing structural insights into recognition of the ADP-ribosyl group and catalytic mechanism of its removal. Further analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes whose representative members show unique selectivity for mono-ADP-ribosylated arginine residue in synthetic substrates. We find such enzymes are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in Drosophila melanogaster . Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. Collectively, our study reveals a new regulatory layer of SidE-catalyzed ubiquitination and expands the current understanding of macrodomain enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An Integrated Deposition and Passivation Strategy for Controlled Crystallization of 2D/3D Halide Perovskite Films

Abstract This work introduces a simplified deposition procedure for multidimensional (2D/3D) perovskite thin films, integrating a phenethylammonium chloride (PEACl)‐treatment into the antisolvent step when forming the 3D perovskite. This simultaneous deposition and passivation strategy reduces the number of synthesis steps while simultaneously stabilizing the halide perovskite film and improving the photovoltaic performance of resulting solar cell devices to 20.8%. Using a combination of multimodal in situ and additional ex situ characterizations, it is demonstrated that the introduction of PEACl during the perovskite film formation slows down the crystal growth process, which leads to a larger average grain size and narrower grain size distribution, thus reducing carrier recombination at grain boundaries and improving the device's performance and stability. The data suggests that during annealing of the wet film, the PEACl diffuses to the surface of the film, forming hydrophobic (quasi‐)2D structures that protect the bulk of the perovskite film from humidity‐induced degradation.

2D/3D perovskites↗
DOE OSTI2023

Analysis of a macrophage carbamylated proteome reveals a function in post-translational modification crosstalk

Background. Lysine carbamylation is a biomarker of rheumatoid arthritis and kidney diseases. However, its cellular function is understudied due to the lack of tools for systematic analysis of this post-translational modification (PTM). Methods. We adapted a method to analyze carbamylated peptides by co-affinity purification with acetylated peptides based on the cross-reactivity of anti-acetyllysine antibodies. We also performed immobilized-metal affinity chromatography to enrich for phosphopeptides, which allowed us to obtain multi-PTM information from the same samples. Results. By testing the pipeline with RAW 264.7 macrophages treated with bacterial lipopolysaccharide, 7,299, 8,923 and 47,637 acetylated, carbamylated, and phosphorylated peptides were identified, respectively. Our analysis showed that carbamylation occurs on proteins from a variety of functions on sites with similar as well as distinct motifs compared to acetylation. To investigate possible PTM crosstalk, we integrated the carbamylation data with acetylation and phosphorylation data, leading to the identification 1,183 proteins that were modified by all 3 PTMs. Among these proteins, 54 had all 3 PTMs regulated by lipopolysaccharide and were enriched in immune signaling pathways, and in particular, the ubiquitin-proteasome pathway. We found that carbamylation of linear diubiquitin blocks the activity of the anti-inflammatory deubiquitinase OTULIN. Conclusions. Overall, our data show that anti-acetyllysine antibodies can be used for effective enrichment of carbamylated peptides. Moreover, carbamylation may play a role in PTM crosstalk with acetylation and phosphorylation, and that it is involved in regulating ubiquitination in vitro.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genetically Encoded Crosslinking Enables Identification of Multivalent Ubiquitin‐Deubiquitylating Enzyme Interactions

Abstract Ubiquitin (Ub) proteoforms control nearly every aspect of eukaryotic cell biology through their diversity. Inspired by the widely used Ub C‐terminal electrophiles (Ub−E), here we report the identification of multivalent binding of Ub with deubiquitylating enzymes (Dubs) using genetic code expansion (GCE) and crosslinking mass spectrometry. While the Ub−Es only gather structural information with the S1 Dub sites, we demonstrate that GCE of Ub with p‐benzoyl‐L‐phenylalanine enables identification of interaction modes beyond the S1 site with a panel of Dubs of both eukaryotic and prokaryotic origin. Collectively, this represents the next generation of Ub‐based affinity probes with a unique ability to unravel Ub interaction landscapes beyond what is afforded by cysteine‐based chemistries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Coordination Chemistry as a Universal Strategy for a Controlled Perovskite Crystallization

The most efficient and stable perovskite solar cells (PSCs) are made from complex mixture of precursors, which are practically always dissolved in combinations of the volatile (and toxic) N, N-Dimethylformamide (DMF), and the non-volatile (and green) dimethyl sulfoxide (DMSO) solvents. Typically, to then form a thin film, an extreme oversaturation of the perovskite precursor is initiated to trigger nucleation sites, e.g. by vacuum, an airstream or a so-called antisolvent. Unfortunately, most such oversaturation triggers do not expel the lingering (and highly coordinating) DMSO, which is highly coordinating, from the thin films; this detrimentally affects long-term stability. Here, for the first time, we introduce (the green) dimethyl sulfide (DMS) as a novel nucleation trigger for perovskite films combining, uniquely, high coordination and high vapor pressure. More precisely, DMS coordinates more strongly than all currently used solvents, hence replacing them, including DMSO, effectively during film formation. Crucially, DMS also has among the highest vapor pressures reported in literature, thus effectively leaving the thin film shortly after formation. This gives DMS a universal scope: DMS replaces other solvents by coordinating more strongly and removes itself once the film formation is finished. To demonstrate this novel coordination chemistry approach, we process MAPbI 3 PSCs, typically dissolved in hard-to-remove (and green) DMSO achieving 21.6% efficiency, among the highest reported efficiencies for this system. To confirm the universality of our strategy, we tested DMS for FAPbI 3 as another composition, which showed higher efficiency of 23.5% compared to 20.9% for fabricated device with CB. Finally, this work provides a universal strategy to control perovskite crystallization using coordination chemistry heralding the revival of perovskite compositions with pure DMSO, such as MAPbI 3 .

36 MATERIALS SCIENCE↗
DOE OSTI2020

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

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 Ub -Lys92 Ube2N ) 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.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase

The bacterial pathogen Legionella pneumophila creates an intracellular niche permissive for its replication by extensively modulating the function of host cells using hundreds of effector proteins delivered via its Dot/Icm secretion system1. Among these, members of the SidE family (SidEs) regulate multiple cellular processes by a unique phosphoribosyl ubiquitination mechanism that bypasses the requirement of ATP and the E1, E2 enzymes of the canonical ubiquitination machinery2-4. The activity of SidEs is regulated by SidJ, another Dot/Icm effector5, but the mechanism of such regulation is not completely understood6,7. Here we demonstrate that SidJ functions to inhibit the activity of SidEs by inducing covalent attachment of a glutamate moiety to Glu860 of SdeA, which is one of the catalytic residues for the mono-ADP-ribosyltransferase activity involved in ubiquitin activation2. Furthermore, we found that the inhibition of SidEs activity by SidJ is restricted in host cells and such spatial regulation is achieved by the requirement of calmodulin (CaM), a eukaryote-specific protein, for its activity. Our results reveal a novel mechanism of regulation in bacterial virulence that features a posttranslational modification and its dependence upon a co-factor specific for host cells.

Gan, Ninghai↗