Crystal structure and nucleic acid binding activity of the conserved UPF0235 family protein PF1765 from Pyrococcus furiosus.

The UPF0235 UniProt family proteins are conserved across archaea, bacteria, and eukaryotes; however, they remain functionally uncharacterized. Here, we report the high resolution (1.3 Å) crystal structure of UPF0235 protein (PF1765, UniProt: Q8U052) from Pyrococcus furiosus.

An Electroporation Cytometry Protocol for Live-Cell, Fluorescence Microscopy Using U2 OS Cell Culture.

Pulsed electric fields (PEFs) have a wide range of applications in medical research and clinical applications. A key area of research focuses on electroporation (reversible or irreversible). Reversible electroporation has been used for several decades for transferring molecules through cell membranes such as plasmid DNA, typically referred to as gene electrotransfer (GET).

Recombinant production of de novo designed miniprotein using various fusion protein tags.

Numerous designed miniprotein (4-12 kDa) binders have been developed and reported to exhibit high-affinity interactions with disease targets that show great promise as therapeutic and diagnostic candidates. Despite these advances, detailed methodologies for their production have not been thoroughly explored. We chose two de novo miniprotein binders, LCB1 and AHB2, as model proteins to study their production by recombinant technology using various fusion protein tags.

An efficient strategy for producing RNA-free Nucleocapsid protein of SARS-CoV-2 for biochemical and structural investigations.

The SARS-CoV-2 Nucleocapsid (N) protein plays a crucial role in genome packaging, replication, transcription, and pathogenesis, making it a promising target for antiviral drug development. However, its large intrinsically disordered regions and propensity to form RNA condensates pose significant challenges for recombinant expression and purification. In this study, we successfully expressed and purified full-length N protein with a cleavable N-terminal Thioredoxin (Trx) fusion to enhance solubility and stability.

Structure-function studies on drug-reactivating β-glucuronidase from mucin-degrading gut symbiont .

Gut microbial β-glucuronidases (mGUS) not only regulate several hormones and neurotransmitters, they also impact the efficacy and toxicity of xenobiotics. On certain anticancer drugs, e.g.

BioID-Based Proximity Mapping of Transmembrane Proteins in Human Airway Cell Models.

The cystic fibrosis transmembrane conductance regulator (CFTR), a chloride channel residing primarily at the apical membrane of epithelial cells, plays a major role in fluid secretion and the maintenance of epithelial surface hydration. Mutations in the CFTR gene lead to the fatal disease known as cystic fibrosis (CF). Drugs that improve mutant CFTR protein folding and channel function have dramatically improved CF patient outcomes.

Structure and stability of phycocyanin from thermotolerant Oscillatoria.

Phycocyanin (PC), a pigment-protein complex with diverse biotechnological applications, plays a key role in light energy transfer for photosynthesis in cyanobacteria. PC (O-PC) from a thermotolerant cyanobacteria Oscillatoria sp. N09DM exhibits remarkable stability compared to its mesophilic counterparts, making it highly valuable for industrial and medical applications.

An electroporation cytometry system for long-term, live cell cycle analysis.

Electric fields are used in biology to address a broad range of questions and through a variety of techniques, including electroporation, gene electrotransfer (GET), electrostimulation (ES), and electrochemotherapy. Each of these modalities requires specific conditions and has drastically different target outcomes on the cell. ES has demonstrated that non-pore forming electric fields alter cell cycle progression.

Unveiling potential inhibitors targeting the nucleocapsid protein of SARS-CoV-2: Structural insights into their binding sites.

The Nucleocapsid (N) protein of SARS-CoV-2 plays a crucial role in viral replication and pathogenesis, making it an attractive target for developing antiviral therapeutics. In this study, we used differential scanning fluorimetry to establish a high-throughput screening method for identifying high-affinity ligands of N-terminal domain of the N protein (N-NTD). We screened an FDA-approved drug library of 1813 compounds and identified 102 compounds interacting with N-NTD.

Synthesis and Evaluation of Ivacaftor Derivatives with Reduced Lipophilicity.

Mutations in the unique ATP-binding cassette anion channel, the cystic fibrosis conductance regulator (CFTR), lead to the inherited fatal disease known as cystic fibrosis (CF). Ivacaftor enhances channel gating of CFTR by stabilizing its open state and has been approved as monotherapy for CF patients with CFTR gating mutations (e.g.

Proximity Mapping of Ciliary Proteins by BioID.

The primary cilium is a highly conserved microtubule-based organelle present in most vertebrate cell types. Mutations in ciliary protein genes can lead to dysfunctional or absent cilia and are the cause of a large group of heterogeneous diseases known as ciliopathies. ARL13B is a member of the ARF family of regulatory GTPases and is highly enriched on the ciliary membrane.

A Proteomic Survey of the Cystic Fibrosis Transmembrane Conductance Regulator Surfaceome.

The aim of this review article is to collate recent contributions of proteomic studies to cystic fibrosis transmembrane conductance regulator (CFTR) biology. We summarize advances from these studies and create an accessible resource for future CFTR proteomic efforts. We focus our attention on the CFTR interaction network at the cell surface, thus generating a CFTR 'surfaceome'.

Structural characterization of transcription-coupled repair protein UVSSA and its interaction with TFIIH protein.

UV-stimulated scaffold protein A (UVSSA) is a key protein in the Transcription-Coupled Nucleotide Excision Repair (TC-NER) pathway. UVSSA, an intrinsically disordered protein, interacts with multiple members of the pathway, tethering them into the complex. Several studies have reported that UVSSA recruits Transcription Factor IIH (TFIIH) via direct interaction, following which CSB is degraded and the lesion recognition TC-NER complex dissociates from the damage site to facilitate the DNA repair.

Crystal structure of phycocyanin: implications of light-harvesting and antioxidant properties.

Unlabelled: Phycobiliproteins is a family of chromophore-containing proteins having light-harvesting and antioxidant capacity. The phycocyanin (PC) is a brilliant blue coloured phycobiliprotein, found in rod structure of phycobilisome and has been widely studied for their therapeutic and fluorescent properties. In the present study, the hexameric assembly structure of phycocyanin (Syn-PC) from Sp.

Crystal structure analysis of phycoerythrin from marine cyanobacterium .

Phycoerythrin (PE) is green light-absorbing pigment-protein that assists in efficient light harvesting in cyanobacteria and red-algae. PE in cyanobacteria stays less studied so far as compared to that in red algae. In this study, PE from marine cyanobacteria sp.

Proximity Profiling of the CFTR Interaction Landscape in Response to Orkambi.

Deletion of phenylalanine 508 (∆F508) of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) anion channel protein is the leading cause of Cystic Fibrosis (CF). Here, we report the analysis of CFTR and ∆F508-CFTR interactomes using BioID (proximity-dependent biotin identification), a technique that can also detect transient associations. We identified 474 high-confidence CFTR proximity-interactors, 57 of which have been previously validated, with the remainder representing novel interaction space.

Molecular basis for reduced cleavage activity and drug resistance in D30N HIV-1 protease.

Nelfinavir is one of the FDA-approved HIV-1 protease inhibitors and a part of highly active anti-retroviral therapy (HAART) for the treatment of HIV-AIDS. Nelfinavir was the first HIV-1 protease inhibitor to be approved as a paediatric formulation. The application of HAART had resulted in significant improvement in the lives of AIDS patients.

Structure-function analysis reveals Trichoderma virens Tsp1 to be a novel fungal effector protein modulating plant defence.

Trichoderma virens colonizes roots and develops a symbiotic relationship with plants where the fungal partner derives nutrients from plants and offers defence, in return. Tsp1, a small secreted cysteine-rich protein, was earlier found to be upregulated in co-cultivation of T. virens with maize roots.

Rec(F/O/R) proteins of the nitrogen-fixing cyanobacterium Nostoc PCC7120: In silico and expression analysis.

The high radioresistance of Nostoc sp. strain PCC7120 is indicative of a robust DNA repair pathway. In the absence of NHEJ pathway and the canonical RecBCD proteins, the RecF pathway proteins are expected to play an important role in double strand break repair in this organism.

Production, characterization and in-vitro applications of single-domain antibody against thyroglobulin selected from novel T7 phage display library.

Single- domain antibodies (SdAbs) have been deployed in various biomedical applications in the recent past. However, there are no reports of their use in the immunoradiometric assays (IRMA) for thyroglobulin (Tg). Tg is the precursor molecule for the biosynthesis of thyroid hormones: thyroxine and triiodothyronine, which are essential for the regulation of normal metabolism in all vertebrates.

Pharmacological characterization of a structurally new class of antibacterial compound, triphenyl-phosphonium conjugated diarylheptanoid: Antibacterial activity and molecular mechanism.

Many pathogenic species of bacteria are showing increasing drug resistance against clinically used antibiotics. Molecules structurally distant from known antibiotics and possessing membrane targeting bactericidal activities are more likely to display activity against drug-resistant pathogens. Mitocurcumin (MitoC) is one of such compounds, synthesized by triphenyl-phosphonium conjugation with curcumin, and has been shown recently from our laboratory to have broad-spectrum bactericidal activity (Kumari 2019 143, 140-145).

Structural insights into SARS-CoV-2 proteins.

The unprecedented scale of the ongoing COVID-19 pandemic has catalyzed an intense effort of the global scientific community to unravel different aspects of the disease in a short time. One of the crucial aspects of these developments is the determination of more than three hundred experimental structures of SARS-CoV-2 proteins in the last few months. These include structures of viral non-structural, structural, and accessory proteins and their complexes determined by either X-ray diffraction or cryo-electron microscopy.