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NUDT15 polymorphism influences the metabolism and therapeutic effects of acyclovir and ganciclovir.

Nucleobase and nucleoside analogs (NNA) are widely used as anti-viral and anti-cancer agents, and NNA phosphorylation is essential for the activity of this class of drugs. Recently, diphosphatase NUDT15 was linked to thiopurine metabolism with NUDT15 polymorphism associated with drug toxicity in patients. Profiling NNA drugs, we identify acyclovir (ACV) and ganciclovir (GCV) as two new NNAs metabolized by NUDT15. NUDT15 hydrolyzes ACV and GCV triphosphate metabolites, reducing their effects against cytomegalovirus (CMV) in vitro. Loss of NUDT15 potentiates cytotoxicity of ACV and GCV in host c

Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease.

COVID-19 was declared a pandemic on March 11 by WHO, due to its great threat to global public health. The coronavirus main protease (Mpro, also called 3CLpro) is essential for processing and maturation of the viral polyprotein, therefore recognized as an attractive drug target. Here we show that a clinically approved anti-HCV drug, Boceprevir, and a pre-clinical inhibitor against feline infectious peritonitis (corona) virus (FIPV), GC376, both efficaciously inhibit SARS-CoV-2 in Vero cells by targeting Mpro. Moreover, combined application of GC376 with Remdesivir, a nucleotide analogue that in

Effect of the additional cysteine 503 of vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F (AhpF) and the mechanism of AhpF and subunit C assembling.

The vancomycin-resistant Enterococcus faecalis alkyl hydroperoxide reductase complex (AhpR) with its subunits AhpC (EfAhpC) and AhpF (EfAhpF) is of paramount importance to restore redox homeostasis. Therefore, knowledge about this defense system is essential to understand its antibiotic-resistance and survival in hosts. Recently, we described the crystallographic structures of EfAhpC, the two-fold thioredoxin-like domain of EfAhpF, the novel phenomenon of swapping of the catalytic domains of EfAhpF as well as the unique linker length, connecting the catalytically active N-and C-terminal domain

A Conserved Basic Patch and Central Kink in the Nipah Virus Phosphoprotein Multimerization Domain Are Essential for Polymerase Function.

Nipah virus is a highly lethal zoonotic pathogen found in Southeast Asia that has caused human encephalitis outbreaks with 40%-70% mortality. NiV encodes its own RNA-dependent RNA polymerase within the large protein, L. Efficient polymerase activity requires the phosphoprotein, P, which tethers L to its template, the viral nucleocapsid. P is a multifunctional protein with modular domains. The central P multimerization domain is composed of a long, tetrameric coiled coil. We investigated the importance of structural features found in this domain for polymerase function using a newly constructed

TraN: A novel repressor of an Enterococcus conjugative type IV secretion system.

The dissemination of multi-resistant bacteria represents an enormous burden on modern healthcare. Plasmid-borne conjugative transfer is the most prevalent mechanism, requiring a type IV secretion system that enables bacteria to spread beneficial traits, such as resistance to last-line antibiotics, among different genera. Inc18 plasmids, like the Gram-positive broad host-range plasmid pIP501, are substantially involved in propagation of vancomycin resistance from Enterococci to methicillin-resistant strains of Staphylococcus aureus. Here, we identified the small cytosolic protein TraN as a repr

Azole Resistance Reduces Susceptibility to the Tetrazole Antifungal VT-1161.

Tetrazole antifungals designed to target fungal lanosterol 14α-demethylase (LDM) appear to be effective against a range of fungal pathogens. In addition, a crystal structure of the catalytic domain of Candida albicans LDM in complex with the tetrazole VT-1161 has been obtained. We have addressed concern about artifacts that might arise from crystallizing VT-1161 with truncated recombinant CYP51s and measured the impact on VT-1161 susceptibility of genotypes known to confer azole resistance. A yeast system was used to overexpress recombinant full-length Saccharomyces cerevisiae LDM with a C-ter

Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A-SF3b complex.

Pladienolide, herboxidiene and spliceostatin have been identified as splicing modulators that target SF3B1 in the SF3b subcomplex. Here we report that PHF5A, another component of this subcomplex, is also targeted by these compounds. Mutations in PHF5A-Y36, SF3B1-K1071, SF3B1-R1074 and SF3B1-V1078 confer resistance to these modulators, suggesting a common interaction site. RNA-seq analysis reveals that PHF5A-Y36C has minimal effect on basal splicing but inhibits the global action of splicing modulators. Moreover, PHF5A-Y36C alters splicing modulator-induced intron-retention/exon-skipping profil

The binding of a monoclonal antibody to the apical region of SCARB2 blocks EV71 infection.

Entero virus 71 (EV71) causes hand, foot, and mouth disease (HFMD) and occasionally leads to severe neurological complications and even death. Scavenger receptor class B member 2 (SCARB2) is a functional receptor for EV71, that mediates viral attachment, internalization, and uncoating. However, the exact binding site of EV71 on SCARB2 is unknown. In this study, we generated a monoclonal antibody (mAb) that binds to human but not mouse SCARB2. It is named JL2, and it can effectively inhibit EV71 infection of target cells. Using a set of chimeras of human and mouse SCARB2, we identified that the

Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN.

Covalent DNA-protein crosslinks (DPCs) are toxic DNA lesions that interfere with essential chromatin transactions, such as replication and transcription. Little was known about DPC-specific repair mechanisms until the recent identification of a DPC-processing protease in yeast. The existence of a DPC protease in higher eukaryotes is inferred from data in Xenopus laevis egg extracts, but its identity remains elusive. Here we identify the metalloprotease SPRTN as the DPC protease acting in metazoans. Loss of SPRTN results in failure to repair DPCs and hypersensitivity to DPC-inducing agents. SPR

The EBNA-2 N-Terminal Transactivation Domain Folds into a Dimeric Structure Required for Target Gene Activation.

Epstein-Barr virus (EBV) is a γ-herpesvirus that may cause infectious mononucleosis in young adults. In addition, epidemiological and molecular evidence links EBV to the pathogenesis of lymphoid and epithelial malignancies. EBV has the unique ability to transform resting B cells into permanently proliferating, latently infected lymphoblastoid cell lines. Epstein-Barr virus nuclear antigen 2 (EBNA-2) is a key regulator of viral and cellular gene expression for this transformation process. The N-terminal region of EBNA-2 comprising residues 1-58 appears to mediate multiple molecular functions in

Secondary anchor polymorphism in the HA-1 minor histocompatibility antigen critically affects MHC stability and TCR recognition.

T cell recognition of minor histocompatibility antigens (mHags) underlies allogeneic immune responses that mediate graft-versus-host disease and the graft-versus-leukemia effect following stem cell transplantation. Many mHags derive from single amino acid polymorphisms in MHC-restricted epitopes, but our understanding of the molecular mechanisms governing mHag immunogenicity and recognition is incomplete. Here we examined antigenic presentation and T-cell recognition of HA-1, a prototypic autosomal mHag derived from single nucleotide dimorphism (HA-1(H) versus HA-1(R)) in the HMHA1 gene. The H

Novel 2,3-dihydro-1,4-benzoxazines as potent and orally bioavailable inhibitors of tumor-driven angiogenesis.

Angiogenesis is vital for solid tumor growth, and its prevention is a proven strategy for the treatment of disease states such as cancer. The vascular endothelial growth factor (VEGF) pathway provides several opportunities by which small molecules can act as inhibitors of endothelial proliferation and migration. Critical to these processes is signaling through VEGFR-2 or the kinase insert domain receptor (KDR) upon stimulation by its ligand VEGF. Herein, we report the discovery of 2,3-dihydro-1,4-benzoxazines as inhibitors of intrinsic KDR activity (IC 50 < 0.1 microM) and human umbilical vein

The Gemin6-Gemin7 heterodimer from the survival of motor neurons complex has an Sm protein-like structure.

The survival of motor neurons (SMN) protein, product of the disease gene of the common neurodegenerative disease spinal muscular atrophy, is part of the large multiprotein "SMN complex." The SMN complex functions as an assembly machine for small nuclear ribonucleoproteins (snRNPs)-the major components of the spliceosome. Here, we report the crystal structure of two components of the human SMN complex, Gemin6 and Gemin7. Although Gemin6 and Gemin7 have no significant sequence similarity with Sm proteins, both adopt canonical Sm folds. Moreover, Gemin6 and Gemin7 exist as a heterodimer, and inte

Identification of putative sulfurtransferase genes in the extremophilic Acidithiobacillus ferrooxidans ATCC 23270 genome: structural and functional characterization of the proteins.

Eight nucleotide sequences containing a single rhodanese domain were found in the Acidithiobacillus ferrooxidans ATCC 23270 genome: p11, p14, p14.3, p15, p16, p16.2, p21, and p28. Amino acids sequence comparisons allowed us to identify the potentially catalytic Cys residues and other highly conserved rhodanese family features in all eight proteins. The genomic contexts of some of the rhodanese-like genes and the determination of their expression at the mRNA level by using macroarrays suggested their implication in sulfur oxidation and metabolism, formation of Fe-S clusters or detoxification me

X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation.

The retinoic acid-related orphan receptor beta (RORbeta) exhibits a highly restricted neuronal-specific expression pattern in brain, retina and pineal gland. So far, neither a natural RORbeta target gene nor a functional ligand have been identified, and the physiological role of the receptor is not well understood. We present the crystal structure of the ligand-binding domain (LBD) of RORbeta containing a bound stearate ligand and complexed with a coactivator peptide. In the crystal, the monomeric LBD adopts the canonical agonist-bound form. The fatty acid ligand-coactivator peptide combined a

Superantigens: structure and relevance to human disease.

Superantigens are a class of immunostimulatory molecules produced by bacteria and viruses. Their potent immune effects are due to their unique ability to bind to the major histocompatibility complex (MHC) outside the antigen-binding cleft and to stimulate T cells in a T-cell receptor (TCR) Vbeta-specific manner. Structural studies have revealed the binding sites involved in the MHC/superantigen/TCR complex. The bacterial superantigens are responsible for a number of syndromes, including food poisoning and toxic shock syndrome, but their effects may be not only acute but also chronic and comple

Reimagination in art and science: Seeing the familiar in a new light and creating new things that didn't exist before.

Many groundbreaking works in art and science owe their origins to the creative spark ignited by reimagination-the process whereby artists and scientists reinterpret and reframe past and existing knowledge, envisioning it in a new context that reveals new possibilities. Artistic and scientific innovation originating from reimagination brings to mind William Faulkner's famous line, "The past is never dead. It's not even past." [W. Faulkner, Requiem for a Nun (1)].

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… Examples of reimagined discoveries in biomedical science Reimagined discovery | How existing concepts are reimagined to form new insights and possibilities AlphaFold | Time-consuming and laborious X-ray crystallography and cryo-EM replaced by rapid, highly accurate artificial-intelligence (technology …

Структурно-ориентированное понимание специфичности 2ДГ-III реберосчег.

Рибосчемы сохраняют некодированные домена РНК, в основном расположенные на 5'-конец бактериальных MRNA, которые служат регулятором генного экспрессии. Недавно третий класс 2Дексигуанозин реберосколка.2'-dG-III) был идентифицирован из семейства рибоколдов, проявляющих сопоставимую связь с 2ДиДжи, Гунанин и гуанозин. Чтобы прояснить уникальный механизм распознавания лиганда, мы раскрыли его кристаллы в комплексе с различными производными пурины, включая 2ДиДжи, Гунанин и гуанозин. Трехсторонняя структура показывает типичную архитектуру, похожую на вилку, с three вырезки, соединяющиеся в центре t

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… To elucidate the overall folding of the 2′-dG-III riboswitch, we employed X-ray crystallography to determine its tertiary structure. … Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr. 1994; 50:760–3. 10.1107/S0907444994003112. 24. Emsley P, Lohkamp B, Scott WG et al. Features and development of Coot. …

Революция онкологии: роль искусственного интеллекта (AI) в качестве антителного дизайна и средств оптимизации.

Антитела играют решающую роль в защите человеческого тела от болезней, включая такие опасные для жизни заболевания, как рак. Они оказывают посреднические услуги в связи с иммунной реакцией на иностранные антигены и, в некоторых случаях, на самоантигены. С течением времени антителные технологии эволюционировали от моноклонных антител (mAbs) до химерика антигенных рецепторов Т (клеток CAR-T), оказывая значительное влияние на биотехнологию, диагностику и лечение. Хотя эти достижения способствовали активизации терапевтического вмешательства, интеграция искусственного интеллекта (АИ) революционизир

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… Experimental methods, including X-ray crystallography, NMR spectroscopy, peptide ELISAs, and mass spectrometry, provide direct evidence of antibody binding [ 111 ]. … Structure-guided approaches analyze and optimizes antibody-antigen interactions using hydrogen bonding, electrostatics, and shape complementarity, while experimental methods like phage display, mutagenesis, and X-ray crystallography validate these predictions [ 282 , 283 ]. …

Impact of World Trade Center-Related Health Research: An Application of the NIEHS Translational Framework.

The World Trade Center Health Program (WTCHP) has a research mission to identify physical and mental health conditions that may be related to the 9/11 terrorist attacks as well as effective diagnostic procedures and treatments for WTC-related health conditions. The ability of the WTCHP to serve its members and realize positive impacts on all of its stakeholders depends on effective translation of research findings. As part of an ongoing assessment of the translational impact of World Trade Center (WTC)-related research, we applied the National Institute of Environmental Health Sciences (NIEHS)

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… MARINE FRESHWATER BIOLOGY OR PLANT SCIENCES OR INSTRUMENTS INSTRUMENTATION OR PHYSICS OR REMOTE SENSING OR FORESTRY OR HISTORY PHILOSOPHY OF SCIENCE OR ENERGY FUELS OR THERMODYNAMICS OR ENTOMOLOGY OR WATER RESOURCES OR ASTRONOMY ASTROPHYSICS OR AUTOMATION CONTROL SYSTEMS OR ZOOLOGY OR OCEANOGRAPHY OR CRYSTALLOGRAPHY … MARINE FRESHWATER BIOLOGY OR PLANT SCIENCES OR INSTRUMENTS INSTRUMENTATION OR PHYSICS OR REMOTE SENSING OR FORESTRY OR HISTORY PHILOSOPHY OF SCIENCE OR ENERGY FUELS OR THERMODYNAMICS OR ENTOMOLOGY OR WATER RESOURCES OR ASTRONOMY ASTROPHYSICS OR AUTOMATION CONTROL SYSTEMS OR ZOOLOGY OR OCEANOGRAPHY OR CRYSTALLOGRAPHY …