Tag: phenix

[ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

Hi Structural biologist colleagues! Our article that helps you make the case that the experiment is still very much needed is now out: www.nature.com/articles/s41592-023-02087-4 “AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination.” Nature Methods (2023) Also, here is a video on the Phenix Tutorials…

Continue Reading [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons

Padeken, J., Methot, S. P. & Gasser, S. M. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat. Rev. Mol. Cell Biol. 23, 623–640 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Tchasovnikarova, I. A. et al. Epigenetic silencing by the HUSH complex mediates position-effect variegation…

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Mechanisms of neurotransmitter transport and drug inhibition in human VMAT2

Kandel, E. R., Koester, J. D., Mack, S. H. & Siegelbaum, S. A. Principles of Neural Science 6th edn (McGraw Hill Professional, 2021). Ng, J., Papandreou, A., Heales, S. J. & Kurian, M. A. Monoamine neurotransmitter disorders—clinical advances and future perspectives. Nat. Rev. Neurol. 11, 567–584 (2015). Article  CAS  PubMed …

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Structure of human TRPM8 channel

Reagents and chemicals pFastBac Dual His6 MBP N10 TEV LIC cloning vector (5 C) was purchased from Addgene (Addgene plasmid no. 30123; www.addgene.org/30123). All restriction enzymes, the pFastBac1 vector, and DH10Bac cells were purchased from Thermo Fisher Scientific. Sf9 cells were purchased from ATCC. Q5® High-Fidelity DNA Polymerase, the Monarch® DNA…

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Simulation of undiagnosed patients with novel genetic conditions

Simulated patient initialization We simulate patients for each of the 2134 diseases in Orphanet20 (orphadata.org, accessed October 29, 2019) that do not correspond to a group of clinically heterogeneous disorders (i.e., Orphanet’s “Category” classification31), have at least one associated phenotype, and have at least one causal gene. For Orphanet diseases…

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Computational optimization of antibody humanness and stability by systematic energy-based ranking

Raybould, M. I. J. et al. Thera-SAbDab: the therapeutic structural antibody database. Nucleic Acids Res. 48, D383–D388 (2020). Article  CAS  PubMed  Google Scholar  Schroff, R. W., Foon, K. A., Beatty, S. M., Oldham, R. K. & Morgan, A. C. Jr Human anti-murine immunoglobulin responses in patients receiving monoclonal antibody therapy….

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Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry

Constructs and expression of human SERINC proteins SERINC3 The gene that encodes human SERINC3 (Genscript-OHu02717D) was inserted upstream of a thrombin protease cleavable linker (LVPRGS) and Strep II epitope (WSHPQFEK) in a modified pFastBac vector by In-Fusion cloning (Clontech). Mutagenesis using the QuikChange Site-Directed Mutagenesis kit (Agilent) was performed to…

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Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein

Hirotsu, Y. et al. SARS-CoV-2 Omicron sublineage BA.2 replaces BA.1.1: genomic surveillance in Japan from September 2021 to March 2022. J. Infect. 85, 174–211 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Lyngse, F. P. et al. Household transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in…

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Membrane recruitment of the polarity protein Scribble by the cell adhesion receptor TMIGD1

Buckley, C. E. & St Johnston, D. Apical-basal polarity and the control of epithelial form and function. Nat. Rev. Mol. Cell Biol. 23, 559–577 (2022). Article  CAS  PubMed  Google Scholar  Buchheit, C. L., Weigel, K. J. & Schafer, Z. T. Cancer cell survival during detachment from the ECM: multiple barriers…

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Regulation of the macrolide resistance ABC-F translation factor MsrD

Crowe-McAuliffe, C. et al. Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. PNAS 115, 8978–8983 (2018). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Crowe-McAuliffe, C. et al. Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nat. Commun….

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Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage

Wyatt, G. R. & Cohen, S. S. A new pyrimidine base from bacteriophage nucleic acids. Nature 170, 1072–1073 (1952). Article  CAS  PubMed  Google Scholar  Kallen, R. G., Simon, M. & Marmur, J. The new occurrence of a new pyrimidine base replacing thymine in a bacteriophage DNA:5-hydroxymethyl uracil. J. Mol. Biol….

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Class B1 GPCR activation by an intracellular agonist

Expression and purification of human PTH1R The plasmid encoding human PTH1R (GenBank identifier: U17418.1; residues 27–491) was constructed and purified as previously reported17. The construct was expressed in HEK293 GnTI (N-acetylglucosaminyltransferase I-negative) cells (American Type Culture Collection, CRL-3022) using the BacMam system (Thermo Fisher Scientific), and the cells were grown…

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Nuclear export of pre-60S particles through the nuclear pore complex

Hampoelz, B., Andres-Pons, A., Kastritis, P. & Beck, M. Structure and assembly of the nuclear pore complex. Annu. Rev. Biophys. 48, 515–536 (2019). Article  CAS  PubMed  Google Scholar  Lin, D. H. & Hoelz, A. The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725–783 (2019). Article …

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Structural basis of amine odorant perception by a mammal olfactory receptor

Liberles, S. D. & Buck, L. B. A second class of chemosensory receptors in the olfactory epithelium. Nature 442, 645–650 (2006). Article  ADS  CAS  PubMed  Google Scholar  Buck, L. & Axel, R. A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65, 175–187 (1991)….

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Histone modifications regulate pioneer transcription factor cooperativity

Protein expression, mutagenesis and purification Xenopus laevis histones for nucleosome assembly were overexpressed in the Escherichia coli BL21(DE3) pLysS strain and purified from inclusion body as previously described48. The cells were grown in LB medium at 37 °C and induced with 1 mM IPTG when OD600 reached 0.6. After 3 h of expression,…

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Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation

Borzi, A. Le communicazioni intracellulari delle nostochinee. Malpighia – Rassegna mensuale di botanica 1 (1886–1887). Simon, R. D. Cyanophycin granules from the blue-green alga anabaena cylindrica: A reserve material consisting of copolymers of aspartic acid and arginine. Proc. Natl. Acad. Sci. U. S. A. 68, 265–267 (1971). Article  ADS  CAS …

Continue Reading Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation

Structural atlas of a human gut crassvirus

Shkoporov, A. N. & Hill, C. Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe 25, 195–209 (2019). Article  CAS  PubMed  Google Scholar  Dutilh, B. E. et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498…

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Complete integration of carbene-transfer chemistry into biosynthesis

Arnold, F. H. Directed evolution: bringing new chemistry to life. Angew. Chem. Int. Ed. Engl. 57, 4143–4148 (2018). Article  CAS  PubMed  Google Scholar  Wallace, S. & Balskus, E. P. Interfacing microbial styrene production with a biocompatible cyclopropanation reaction. Angew. Chem. Int. Ed. Engl. 54, 7106–7109 (2015). Article  CAS  PubMed  PubMed…

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Meloxicam inhibits STING phosphorylation and alleviates intracellular DNA-mediated autoimmune responses

Mice Trex1+/– mice (C57BL/6) were gifts from D. Barnes and T. Lindahl (Cancer Research UK). All animal experiments were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals and with the approval of the Institutional Animal Care and Use Committee (IACUC-DWZX-2020-511)….

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Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine

Centers for Disease Control and Prevention. Past Seasons Vaccine Effectiveness Estimates, www.cdc.gov/flu/vaccines-work/past-seasons-estimates.html (2022). Accessed 10 March 2022. Centers for Disease Control and Prevention. Pandemic influenza—past pandemics, www.cdc.gov/flu/pandemic-resources/basics/past-pandemics.html (2022). Accessed 10 March 2022. Erbelding, E. J. et al. A universal influenza vaccine: the strategic plan for the National Institute of Allergy…

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Human CEACAM1 is targeted by a Streptococcus pyogenes adhesin implicated in puerperal sepsis pathogenesis

Ethics Human blood was obtained from healthy donors, approved by the Regional Ethics Committee and Imperial College Healthcare NHS Trust Tissue Bank (Regional Ethics Committee approval no. 17/WA/0161, Imperial College Healthcare Tissue Bank Human Tissue Authority license no. 12275, and Imperial College Research Ethics Committee no. 19IC5166). All samples were…

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Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein

Olina, A. V., Kulbachinskiy, A. V., Aravin, A. A. & Esyunina, D. M. Argonaute Proteins and Mechanisms of RNA Interference in Eukaryotes and Prokaryotes. Biochem. 83, 483–497. doi.org/10.1134/S0006297918050024 (2018). Article  CAS  Google Scholar  Wu, J., Yang, J., Cho, W. C. & Zheng, Y. Argonaute proteins: Structural features, functions and emerging…

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Sensory specializations drive octopus and squid behaviour

van Giesen, L., Kilian, P. B., Allard, C. A. H. & Bellono, N. W. Molecular basis of chemotactile sensation in octopus. Cell 183, 594–604.e14 (2020). Article  PubMed  PubMed Central  Google Scholar  Noviello, C. M. et al. Structure and gating mechanism of the α7 nicotinic acetylcholine receptor. Cell 184, 2121–2134 (2021)….

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PhD Position Multiscale Modelling of Interfaces Sorbonne University – LAMMPS

Dear lammps community, We are looking for a PhD candidate to develop a multi-scale computational methodology to model interfaces. If you are interested, please send us your CV and one or two contact references at rocio.semino@sorbonne-universite.fr and alessandra.serva@sorbonne-universite.fr More details on the project and how to apply at: phenix.cnrs.fr/en/job/fully-funded-phd-development-and-implementation-of-hybrid-atomistic-coarse-grained-modelling-applied-to-the-interfaces-2/ All…

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Cryo-EM structure of the transposon-associated TnpB enzyme

Sample preparation The genes encoding ISDra2 TnpB (TnpB from D. radiodurans ISDra2; residues 1 to 408) and the 247-nt ωRNA were synthesized by Eurofin Genomics and cloned into the modified pETDuet vector (Novagen). The N-terminally MBP-tagged TnpB and ωRNA were co-expressed in Escherichia coli Rosetta2 (DE3). The E. coli cells were cultured…

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Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants

Research reported in this study complies with all relevant ethical regulations, and our animal study protocol has been approved by the Animal Experimental Board of Finland (license number ESAVI/28687/2020. Phage panning Sherpabody phage display library (size ~1011 cfu) was obtained from Next Biomed Therapies Oy. To develop sherpabodies specific for SARS-CoV-2…

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Structural basis for bacterial energy extraction from atmospheric hydrogen

Statistics and reproducibility Huc purification and PAGE analysis Huc was purified from M. smegmatis cells on eight separate occasions throughout the course of the study. The yield of purified Huc (mg per litre of culture) varied by a factor of five between purifications. The relative abundance of the Huc oligomer…

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Engineering protein glycosylation in CHO cells to be highly similar to murine host cells

1 Introduction Recombinant therapeutic proteins, also known as biologics, have been successfully used to treat a wide range of diseases, including cancers, inflammatory disorders, and cardiovascular diseases (Walsh, 2018). Biosimilars with comparable efficacy and safety profiles have emerged as alternative options to innovator therapies. A biosimilar is a biologic that…

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Research Associate in Stem Cell Neurobiology job with KINGS COLLEGE LONDON

  Job description We are looking for a skilled research associate with a molecular biological background to join a vibrant group investigating amyotrophic lateral sclerosis-frontotemporal dementia (ALS-FTD). You will be using CRISPR to gene edit human stem cells to introduce unpublished disease-linked mutations. This work will entail the use of…

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Cryo-EM structure and protease activity of the type III-E CRISPR-Cas effector

Hampton, H. G., Watson, B. N. J. & Fineran, P. C. The arms race between bacteria and their phage foes. Nature 577, 327–336 (2020). Article  CAS  Google Scholar  Makarova, K. S. et al. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467–477 (2011). Article  CAS  Google Scholar …

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Structural basis for intrinsic transcription termination

Ray-Soni, A., Bellecourt, M. J. & Landick, R. Mechanisms of bacterial transcription termination: all good things must end. Annu. Rev. Biochem. 85, 319–347 (2016). Article  CAS  Google Scholar  Proudfoot, N. J. Transcriptional termination in mammals: stopping the RNA polymerase II juggernaut. Science 352, aad9926 (2016). Arimbasseri, A. G. & Maraia,…

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Evasion of cGAS and TRIM5 defines pandemic HIV

Cells and reagents HEK293T and U87 cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Labtech) and 100 U ml−1 penicillin plus 100 μg ml−1 streptomycin (Pen/Strep; Gibco). THP-1-IFIT1 cells that had been modified to express Gaussia luciferase under the control of the IFIT1 promoter were described previously62. THP-1…

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2022-2027 Global and Regional Multi-Channel Reagent Reservoirs Industry Status and Prospects Professional Market Research Report Standard Version

The global Multi-Channel Reagent Reservoirs market is expected to reach US$ XX Million by 2027, with a CAGR of XX% from 2022 to 2027, based on Research newly published report. The prime objective of this report is to provide the insights on the post COVID-19 impact which will help market…

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HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription

Orkin, S. H. Globin gene regulation and switching: circa 1990. Cell 63, 665–672 (1990). Sankaran, V. G. & Orkin, S. H. The switch from fetal to adult hemoglobin. Cold Spring Harb. Perspect. Med. 3, a011643 (2013). PubMed  PubMed Central  Article  CAS  Google Scholar  Huang, P. et al. Comparative analysis of…

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Activation of STING by targeting a pocket in the transmembrane domain

Zhang, X., Bai, XC & Chen, ZJ Structures and mechanisms of the cGAS-STING innate immunity pathway. Immunity 5343–53 (2020). CAS PubMed Google Scholar Article Ishikawa, H. & Barber, GN STING is an endoplasmic reticulum adapter that facilitates innate immune signaling. Nature 455674–678 (2008). ADS CAS PubMed PubMed Central Article Google…

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Epistasis shapes the fitness landscape of an allosteric specificity switch

Computational design Protein modeling and design was performed with Rosetta version 3.5 (2015.19.57819)35,37. Python and shell scripts for generating input from Rosetta and analyzing from Rosetta are available at: github.com/raman-lab/biosensor_design The high-resolution TtgR structure co-crystalized with tetracycline was selected as the starting point for computational design (PDB: 2UXH)28. The structure…

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