1,915 results match your criteria loop superfamily

A negative feedback loop involving NF-κB/TIR8 regulates IL-1β-induced epithelial- myofibroblast transdifferentiation in human tubular cells.

J Cell Commun Signal 2021 May 4. Epub 2021 May 4.

Department of Nephrology, The Second Affiliated Hospital, Anhui Medical University (AHMU), No. 678 Fu Rong Road, Hefei, China.

Renal tubular epithelial-myofibroblast transdifferentiation (EMT) plays a central role in the development of renal interstitial fibrosis (RIF). The profibrotic cytokine interleukin (IL)-1 and the IL-1 receptor (IL-1R) also participate in RIF development, and Toll/IL-1R 8 (TIR8), a member of the Toll-like receptor superfamily, has been identified as a negative regulator of IL-1R signaling. However, the functions of TIR8 in IL-1-induced RIF remain unknown. Read More

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The SpeG Spermidine/Spermine -Acetyltransferase Allosteric Loop and β6-β7 Structural Elements Are Critical for Kinetic Activity.

Front Mol Biosci 2021 13;8:645768. Epub 2021 Apr 13.

Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States.

Polyamines regulate many important biological processes including gene expression, intracellular signaling, and biofilm formation. Their intracellular concentrations are tightly regulated by polyamine transport systems and biosynthetic and catabolic pathways. Spermidine/spermine -acetyltransferases (SSATs) are catabolic enzymes that acetylate polyamines and are critical for maintaining intracellular polyamine homeostasis. Read More

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Genome-Wide Identification and Characterization of TALE Superfamily Genes in Soybean ( L.).

Int J Mol Sci 2021 Apr 16;22(8). Epub 2021 Apr 16.

Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.

The three-amino-acid-loop-extension (TALE) superfamily genes broadly existed in plants, which played important roles in plant growth, development and abiotic stress responses. In this study, we identified 68 TALE (GmTALE) superfamily members. Phylogenetic analysis divided the GmTALE superfamily into the BEL1-like (BLH/BELL homeodomain) and the KNOX (KNOTTED-like homeodomain) subfamilies. Read More

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Transition metal cation inhibition of Mycobacterium tuberculosis esterase RV0045C.

Protein Sci 2021 Apr 29. Epub 2021 Apr 29.

Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN.

Mycobacterium tuberculosis virulence is highly metal-dependent with metal availability modulating the shift from the dormant to active states of M. tuberculosis infection. Rv0045c from M. Read More

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Endocytosis of nutrient transporters in fungi: The ART of connecting signaling and trafficking.

Comput Struct Biotechnol J 2021 19;19:1713-1737. Epub 2021 Mar 19.

Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal.

Plasma membrane transporters play pivotal roles in the import of nutrients, including sugars, amino acids, nucleobases, carboxylic acids, and metal ions, that surround fungal cells. The selective removal of these transporters by endocytosis is one of the most important regulatory mechanisms that ensures a rapid adaptation of cells to the changing environment (e.g. Read More

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Empagliflozin Disrupts a Tnfrsf12a-Mediated Feed Forward Loop That Promotes Left Ventricular Hypertrophy.

Cardiovasc Drugs Ther 2021 Apr 22. Epub 2021 Apr 22.

Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, 209 Victoria Street, Toronto, Ontario, M5B 1T8, Canada.

Purpose: Although the cardioprotective benefits of sodium-glucose cotransporter 2 (SGLT2) inhibitors are now widely appreciated, the mechanisms underlying these benefits remain unresolved. Tumor necrosis factor receptor superfamily member 12a (Tnfrsf12a) is a receptor for tumor necrosis factor superfamily member 12 (Tnfsf12). Tnfrsf12a is highly inducible and plays a key role in the development of cardiac hypertrophy and heart failure. Read More

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A noncanonical heme oxygenase specific for the degradation of c-type heme.

J Biol Chem 2021 Apr 13:100666. Epub 2021 Apr 13.

Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA. Electronic address:

Heme oxygenases (HOs) play a critical role in recouping iron from the labile heme pool. The acquisition and liberation of heme iron is especially important for the survival of pathogenic bacteria. All characterized HOs, including those belonging to the HugZ superfamily, preferentially cleave free b-type heme. Read More

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In silico approach to understand the epigenetic mechanism of SARS-CoV-2 and its impact on the environment.

Virusdisease 2021 Apr 5:1-12. Epub 2021 Apr 5.

Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025 India.

The novel coronavirus (2019-nCoV) has led to the apex pandemic in 2020, responsible for the recent sequential spread. The 2019-nCoV has been discerned to be a Beta-BAT-SARS-CoV-2 lineage. The gene ontology (GO) identifies the virus to be localized in the Golgi apparatus with a vital molecular function of and viral progression. Read More

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Stepwise Reversion of Multiply Mutated Recombinant Antitrypsin Reveals a Selective Inhibitor of Coagulation Factor XIa as Active as the M358R Variant.

Front Cardiovasc Med 2021 19;8:647405. Epub 2021 Mar 19.

Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada.

Alpha-1 antitrypsin (AAT, also known as alpha-1 proteinase inhibitor or SERPINA1) is the most abundant member of the serpin superfamily found in human plasma. The naturally occurring variant AAT M358R, altered at the P1 position of the critical reactive center loop (RCL), is re-directed away from inhibition of AAT's chief natural target, neutrophil elastase, and toward accelerated inhibition of thrombin (FIIa), kallikrein (Kal), and other proteases such as factor XIa (FXIa). FXIa is an emerging target for the development of antithrombotic agents, since patients with FXI deficiency are protected from thromboembolic disease and do not exhibit a strong bleeding tendency. Read More

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The RelA hydrolase domain acts as a molecular switch for (p)ppGpp synthesis.

Commun Biol 2021 Mar 31;4(1):434. Epub 2021 Mar 31.

Department of Biology, University of Copenhagen, Copenhagen, Denmark.

Bacteria synthesize guanosine tetra- and penta phosphate (commonly referred to as (p)ppGpp) in response to environmental stresses. (p)ppGpp reprograms cell physiology and is essential for stress survival, virulence and antibiotic tolerance. Proteins of the RSH superfamily (RelA/SpoT Homologues) are ubiquitously distributed and hydrolyze or synthesize (p)ppGpp. Read More

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Ceramide-1-phosphate transfer protein (CPTP) regulation by phosphoinositides.

J Biol Chem 2021 Mar 26:100600. Epub 2021 Mar 26.

Hormel Institute, University of Minnesota, 801 16(th) Ave NE, Austin, MN, 55912. Electronic address:

Ceramide-1-phosphate transfer proteins (CPTPs) are members of the glycolipid transfer protein (GLTP) superfamily that shuttle ceramide-1-phosphate (C1P) between membranes. CPTPs regulate cellular sphingolipid homeostasis in ways that impact programmed cell death and inflammation. CPTP downregulation specifically alters C1P levels in the plasma and trans-Golgi membranes, stimulating pro-inflammatory eicosanoid production and autophagy-dependent inflammasome-mediated cytokine release. Read More

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Evolution and insights into the structure and function of the DedA superfamily containing TMEM41B and VMP1.

J Cell Sci 2021 Apr 28;134(8). Epub 2021 Apr 28.

Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.

TMEM41B and VMP1 are endoplasmic reticulum (ER)-localizing multi-spanning membrane proteins required for ER-related cellular processes such as autophagosome formation, lipid droplet homeostasis and lipoprotein secretion in eukaryotes. Both proteins have a VTT domain, which is similar to the DedA domain found in bacterial DedA family proteins. However, the molecular function and structure of the DedA and VTT domains (collectively referred to as DedA domains) and the evolutionary relationships among the DedA domain-containing proteins are largely unknown. Read More

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Genome-wide identification and characterization of basic helix-loop-helix genes in nine molluscs.

Gene 2021 Jun 23;785:145604. Epub 2021 Mar 23.

Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Zhejiang, China. Electronic address:

The basic helix-loop-helix (bHLH) transcription factors form a large superfamily that plays an important role in numerous physiological processes, including development and response to environmental stresses. In this study, the distribution of bHLH genes in nine molluscs was systematically investigated (including five bivalves, three gastropods and one cephalopod). Finally, 53-85 bHLH genes were identified from each genome and classified into corresponding families by using phylogenetic analysis. Read More

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Structure and gating mechanism of the α7 nicotinic acetylcholine receptor.

Cell 2021 Apr 17;184(8):2121-2134.e13. Epub 2021 Mar 17.

Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

The α7 nicotinic acetylcholine receptor plays critical roles in the central nervous system and in the cholinergic inflammatory pathway. This ligand-gated ion channel assembles as a homopentamer, is exceptionally permeable to Ca, and desensitizes faster than any other Cys-loop receptor. The α7 receptor has served as a prototype for the Cys-loop superfamily yet has proven refractory to structural analysis. Read More

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Role of a cysteine residue in substrate entry and catalysis in MtHIBADH: Analysis by chemical modifications and site-directed mutagenesis.

IUBMB Life 2021 Mar 16. Epub 2021 Mar 16.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Despite sharing conserved substrate-binding residues, members of 3-hydroxyisobutyrate dehydrogenase (HIBADH) superfamily show remarkable differences in substrate preference. Cysteine residues were identified within a radius of 6 Å surrounding both the active site and the substrate entry site of HIBADH enzyme from Mycobacterium tuberculosis (MtHIBADH). Chemical modification with thiol-modifying reagents, pCMB and DTNB, abrogated the dehydrogenase activity of the enzyme. Read More

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Sleep-related hypermotor epilepsy associated mutations uncover important kinetic roles of α4β2- nicotinic acetylcholine receptor intracellular structures.

PLoS One 2021 3;16(3):e0247825. Epub 2021 Mar 3.

Division of Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, United States of America.

Sleep-related hypermotor epilepsy (SHE) is a group of seizure disorders prominently associated with mutations in nicotinic acetylcholine receptors (nAChR). The most prevalent central nervous system nAChR subtype contains α4 and β2 subunits, in two ratios. (α4β2)2β2-nAChR have high agonist sensitivity (HS-isoform), whereas (α4β2)2α4-nAChR agonist responses exhibit a small high-sensitivity, and a predominant low-sensitivity, phase of function (LS-isoform). Read More

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Staphylococcus aureus Tet38 Efflux Pump Structural Modeling and Roles of Essential Residues in Drug Efflux and Host Cell Internalization.

Infect Immun 2021 Apr 16;89(5). Epub 2021 Apr 16.

Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA

The Tet38 membrane protein has distinct functions, including drug efflux and host cell attachment and internalization mediated by interaction with host cell CD36. Using structural modeling and site-directed mutagenesis, we identified key amino acids involved in different functions. Tet38, a member of the major facilitator superfamily, is predicted to have 14 transmembrane segments (TMS), 6 cytoplasmic loops, and 7 external loops. Read More

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BcfH Is a Trimeric Thioredoxin-Like Bifunctional Enzyme with Both Thiol Oxidase and Disulfide Isomerase Activities.

Antioxid Redox Signal 2021 Apr 12. Epub 2021 Apr 12.

Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.

Thioredoxin (TRX)-fold proteins are ubiquitous in nature. This redox scaffold has evolved to enable a variety of functions, including redox regulation, protein folding, and oxidative stress defense. In bacteria, the TRX-like disulfide bond (Dsb) family mediates the oxidative folding of multiple proteins required for fitness and pathogenic potential. Read More

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Structural basis for the design of bisubstrate inhibitors of protein kinase CK2 provided by complex structures with the substrate-competitive inhibitor heparin.

Eur J Med Chem 2021 Mar 26;214:113223. Epub 2021 Jan 26.

Universität zu Köln, Department für Chemie, Institut für Biochemie, Zülpicher Straße 47, D-50674 Köln, Germany. Electronic address:

The Ser/Thr kinase CK2, a member of the superfamily of eukaryotic protein kinases, has an acidophilic substrate profile with the substrate recognition sequence S/T-D/E-X-D/E, and it is inhibited by polyanionic substances like heparin. The latter, a highly sulphated glucosamino glycan composed mainly of repeating 2-O-sulpho-α-l-idopyranuronic acid/N,O6-disulpho-α-d-glucosamine disaccharide units, is the longest known substrate-competitive CK2 inhibitor. The structural basis of CK2's preference for anionic substrates and substrate-competitive inhibitors is only vaguely known which limits the value of the substrate-binding region for the structure-based development of CK2 bisubstrate inhibitors. Read More

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Generation of cd63-deficient zebrafish to analyze the role of cd63 in viral infection.

Fish Shellfish Immunol 2021 Apr 6;111:152-159. Epub 2021 Feb 6.

Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea. Electronic address:

The tetraspanin superfamily proteins are transmembrane proteins identified in a diverse range of eukaryotic organisms. Tetraspanins are involved in a variety of essential biological functions, including cell differentiation, adhesion, migration, signal transduction, intracellular trafficking, and immune responses. For an infection to occur, viruses must interact with various cell surface components, including receptors and signaling molecules. Read More

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Effect of variations in the conserved residues E371 and S359 on the structural dynamics of protein Z dependent protease inhibitor (ZPI): a molecular dynamic simulation study.

J Biomol Struct Dyn 2021 Feb 8:1-10. Epub 2021 Feb 8.

Department of Chemistry, Sri Sivasubramaniya Nadar College of Engineering, Chennai, India.

Protein Z (PZ) dependent protease inhibitor (ZPI) is a natural anticoagulant inhibiting blood coagulation proteases fXa and fXIa. Despite being a member of the serpin superfamily, it possesses unique structural features such as activation by PZ, regulating its inhibitory function. In order to understand the Reactive Centre Loop (RCL) dynamics of ZPI, which is absolutely critical for its activity, we performed Molecular Dynamics (MD) simulation on ZPI and its E371 and S359 variants located at important conserved functional sites. Read More

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February 2021

Apple MdSAT1 encodes a bHLHm1 transcription factor involved in salinity and drought responses.

Planta 2021 Jan 23;253(2):46. Epub 2021 Jan 23.

State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.

Main Conclusion: This study identified a new bHLHm1 transcription factor MdSAT1 which functioned in mediating tolerance to salt and drought resistance. Changes in the expression of stress-related genes play crucial roles in response to environmental stress. Basic helix-loop-helix (bHLH) proteins are the largest superfamily of transcription factors and a large number of bHLH proteins function in plant responses to abiotic stresses. Read More

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January 2021

The short third intracellular loop and cytoplasmic tail of bitter taste receptors provide functionally relevant GRK phosphorylation sites in TAS2R14.

J Biol Chem 2021 Jan 16:100216. Epub 2021 Jan 16.

Departments of Medicine and Molecular Pharmacology and Physiology, University of South Florida Morsani College of Medicine, Tampa, FL, USA. Electronic address:

For most GPCRs, the third intracellular loops (IL3) and C-terminal tails (CT) are sites for GRK-mediated phosphorylation, leading to β-arrestin binding and agonist-specific desensitization. These regions of the G protein-coupled bitter taste receptors (TAS2Rs) are short compared to the superfamily, and their functional role is unclear. TAS2R14 expressed on human airway smooth muscle (HASM) cells relax the cell, suggesting a novel target for bronchodilators. Read More

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January 2021

The complete mitochondrial genome of (Teleostei, Cypriniformes) in Lantsang River and its phylogenetic analysis.

Rui Li Xingjian Yue

Mitochondrial DNA B Resour 2020 Sep 29;5(3):3447-3449. Epub 2020 Sep 29.

School of Life Science, Neijiang Normal University, Neijiang, China.

is a small-sized benthopelagic fish species in the family Nemacheilidae, superfamily Cobitidea. In this study, the entire mitogenome sequence of the has been sequenced by using sanger sequencing method. The circular mitochondrial genome was 16,570 bp in length and contained of 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, an origin of light-strand replication (OL), and one displacement loop locus (D-loop). Read More

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September 2020

The complete mitochondrial genome of large odorous frog, (Amphibia: Ranidae) and phylogenetic analysis.

Mitochondrial DNA B Resour 2020 Aug 9;5(3):3139-3140. Epub 2020 Aug 9.

Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangzhou, China.

The mitochondrial genome of was sequenced and analyzed. The complete mitochondrial genome is 18,106 bp in length, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 21 transfer RNA genes, and a control region (D-loop). All PCGs are initiated by ATN codons, except for GTG for and . Read More

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Mitochondrial genomes of two eucotylids as the first representatives from the superfamily Microphalloidea (Trematoda) and phylogenetic implications.

Parasit Vectors 2021 Jan 14;14(1):48. Epub 2021 Jan 14.

State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, People's Republic of China.

Background: The Eucotylidae Cohn, 1904 (Superfamily: Microphalloidea), is a family of digeneans parasitic in kidneys of birds as adults. The group is characterized by the high level of morphological similarities among genera and unclear systematic value of morphological characters traditionally used for their differentiation. In the present study, we sequenced the complete or nearly complete mitogenomes (mt genome) of two eucotylids representing the genera Tamerlania (T. Read More

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January 2021

Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites.

Biol Direct 2021 Jan 12;16(1). Epub 2021 Jan 12.

Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.

Background: The human proteins TMTC1, TMTC2, TMTC3 and TMTC4 have been experimentally shown to be components of a new O-mannosylation pathway. Their own mannosyl-transferase activity has been suspected but their actual enzymatic potential has not been demonstrated yet. So far, sequence analysis of TMTCs has been compromised by evolutionary sequence divergence within their membrane-embedded N-terminal region, sequence inaccuracies in the protein databases and the difficulty to interpret the large functional variety of known homologous proteins (mostly sugar transferases and some with known 3D structure). Read More

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January 2021

Multi-scale architecture of archaeal chromosomes.

Mol Cell 2021 02 30;81(3):473-487.e6. Epub 2020 Dec 30.

Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA; Biology Department, Indiana University, Bloomington, IN, USA. Electronic address:

Chromosome conformation capture (3C) technologies have identified topologically associating domains (TADs) and larger A/B compartments as two salient structural features of eukaryotic chromosomes. These structures are sculpted by the combined actions of transcription and structural maintenance of chromosomes (SMC) superfamily proteins. Bacterial chromosomes fold into TAD-like chromosomal interaction domains (CIDs) but do not display A/B compartment-type organization. Read More

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February 2021

Biochemical and Biophysical Characterization of the dsDNA Packaging Motor from the Bacteriophage Asccphi28.

Viruses 2020 12 23;13(1). Epub 2020 Dec 23.

Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.

Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the biochemical and biophysical characterization of the packaging ATPase from phage asccφ28. Read More

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December 2020

Repurposing the McoTI-II Rigid Molecular Scaffold in to Inhibitor of 'Papain Superfamily' Cysteine Proteases.

Pharmaceuticals (Basel) 2020 Dec 23;14(1). Epub 2020 Dec 23.

Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar 201314, India.

Clan C1A or 'papain superfamily' cysteine proteases are key players in many important physiological processes and diseases in most living systems. Novel approaches towards the development of their inhibitors can open new avenues in translational medicine. Here, we report a novel design of a re-engineered chimera inhibitor Mco-cysteine protease inhibitor (CPI) to inhibit the activity of C1A cysteine proteases. Read More

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December 2020