@article{HutinLingTarbouriechetal.2022, author = {Hutin, Stephanie and Ling, Wai Li and Tarbouriech, Nicolas and Schoehn, Guy and Grimm, Clemens and Fischer, Utz and Burmeister, Wim P.}, title = {The vaccinia virus DNA helicase structure from combined single-particle cryo-electron microscopy and AlphaFold2 prediction}, series = {Viruses}, volume = {14}, journal = {Viruses}, number = {10}, issn = {1999-4915}, doi = {10.3390/v14102206}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-290523}, year = {2022}, abstract = {Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323-785) with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 {\AA} structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus, still allowing the fit of the predicted structure. The N-terminal domain is partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements.}, language = {en} } @article{KoernerMeyerMarincolaetal.2023, author = {K{\"o}rner, Maria and Meyer, Susanne R. and Marincola, Gabriella and Kern, Maximilian J. and Grimm, Clemens and Schuelein-Voelk, Christina and Fischer, Utz and Hofmann, Kay and Buchberger, Alexander}, title = {The FAM104 proteins VCF1/2 promote the nuclear localization of p97/VCP}, series = {eLife}, volume = {12}, journal = {eLife}, doi = {10.7554/eLife.92409}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-350222}, year = {2023}, abstract = {The ATPase p97 (also known as VCP, Cdc48) has crucial functions in a variety of important cellular processes such as protein quality control, organellar homeostasis, and DNA damage repair, and its de-regulation is linked to neuromuscular diseases and cancer. p97 is tightly controlled by numerous regulatory cofactors, but the full range and function of the p97-cofactor network is unknown. Here, we identify the hitherto uncharacterized FAM104 proteins as a conserved family of p97 interactors. The two human family members VCP nuclear cofactor family member 1 and 2 (VCF1/2) bind p97 directly via a novel, alpha-helical motif and associate with p97-UFD1-NPL4 and p97-UBXN2B complexes in cells. VCF1/2 localize to the nucleus and promote the nuclear import of p97. Loss of VCF1/2 results in reduced nuclear p97 levels, slow growth, and hypersensitivity to chemical inhibition of p97 in the absence and presence of DNA damage, suggesting that FAM104 proteins are critical regulators of nuclear p97 functions.}, language = {en} } @article{HofrichterMojaradDolletal.2018, author = {Hofrichter, Michaela A. H. and Mojarad, Majid and Doll, Julia and Grimm, Clemens and Eslahi, Atiye and Hosseini, Neda Sadat and Rajati, Mohsen and M{\"u}ller, Tobias and Dittrich, Marcus and Maroofian, Reza and Haaf, Thomas and Vona, Barbara}, title = {The conserved p.Arg108 residue in S1PR2 (DFNB68) is fundamental for proper hearing: evidence from a consanguineous Iranian family}, series = {BMC Medical Genetics}, volume = {19}, journal = {BMC Medical Genetics}, number = {81}, doi = {10.1186/s12881-018-0598-5}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-175755}, year = {2018}, abstract = {Background: Genetic heterogeneity and consanguineous marriages make recessive inherited hearing loss in Iran the second most common genetic disorder. Only two reported pathogenic variants (c.323G>C, p.Arg108Pro and c.419A>G, p.Tyr140Cys) in the S1PR2 gene have previously been linked to autosomal recessive hearing loss (DFNB68) in two Pakistani families. We describe a segregating novel homozygous c.323G>A, p.Arg108Gln pathogenic variant in S1PR2 that was identified in four affected individuals from a consanguineous five generation Iranian family. Methods: Whole exome sequencing and bioinformatics analysis of 116 hearing loss-associated genes was performed in an affected individual from a five generation Iranian family. Segregation analysis and 3D protein modeling of the p.Arg108 exchange was performed. Results: The two Pakistani families previously identified with S1PR2 pathogenic variants presented profound hearing loss that is also observed in the affected Iranian individuals described in the current study. Interestingly, we confirmed mixed hearing loss in one affected individual. 3D protein modeling suggests that the p.Arg108 position plays a key role in ligand receptor interaction, which is disturbed by the p.Arg108Gln change. Conclusion: In summary, we report the third overall mutation in S1PR2 and the first report outside the Pakistani population. Furthermore, we describe a novel variant that causes an amino acid exchange (p.Arg108Gln) in the same amino acid residue as one of the previously reported Pakistani families (p.Arg108Pro). This finding emphasizes the importance of the p.Arg108 amino acid in normal hearing and confirms and consolidates the role of S1PR2 in autosomal recessive hearing loss.}, language = {en} } @article{VendelovadeLimaLorenzattoetal.2016, author = {Vendelova, Emilia and de Lima, Jeferson Camargo and Lorenzatto, Karina Rodrigues and Monteiro, Karina Mariante and Mueller, Thomas and Veepaschit, Jyotishman and Grimm, Clemens and Brehm, Klaus and Hrčkov{\´a}, Gabriela and Lutz, Manfred B. and Ferreira, Henrique B. and Nono, Justin Komguep}, title = {Proteomic Analysis of Excretory-Secretory Products of Mesocestoides corti Metacestodes Reveals Potential Suppressors of Dendritic Cell Functions}, series = {PLoS Neglected Tropical Diseases}, volume = {10}, journal = {PLoS Neglected Tropical Diseases}, number = {10}, doi = {10.1371/journal.pntd.0005061}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166742}, pages = {e0005061}, year = {2016}, abstract = {Accumulating evidences have assigned a central role to parasite-derived proteins in immunomodulation. Here, we report on the proteomic identification and characterization of immunomodulatory excretory-secretory (ES) products from the metacestode larva (tetrathyridium) of the tapeworm Mesocestoides corti (syn. M. vogae). We demonstrate that ES products but not larval homogenates inhibit the stimuli-driven release of the pro-inflammatory, Th1-inducing cytokine IL-12p70 by murine bone marrow-derived dendritic cells (BMDCs). Within the ES fraction, we biochemically narrowed down the immunosuppressive activity to glycoproteins since active components were lipid-free, but sensitive to heat- and carbohydrate-treatment. Finally, using bioassay-guided chromatographic analyses assisted by comparative proteomics of active and inactive fractions of the ES products, we defined a comprehensive list of candidate proteins released by M. corti tetrathyridia as potential suppressors of DC functions. Our study provides a comprehensive library of somatic and ES products and highlight some candidate parasite factors that might drive the subversion of DC functions to facilitate the persistence of M. corti tetrathyridia in their hosts.}, language = {en} } @article{VeepaschitViswanathanBordonneetal.2021, author = {Veepaschit, Jyotishman and Viswanathan, Aravindan and Bordonne, Remy and Grimm, Clemens and Fischer, Utz}, title = {Identification and structural analysis of the Schizosaccharomyces pombe SMN complex}, series = {Nucleic Acids Research}, volume = {49}, journal = {Nucleic Acids Research}, number = {13}, doi = {10.1093/nar/gkab158}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259880}, pages = {7207-7223}, year = {2021}, abstract = {The macromolecular SMN complex facilitates the formation of Sm-class ribonucleoproteins involved in mRNA processing (UsnRNPs). While biochemical studies have revealed key activities of the SMN complex, its structural investigation is lagging behind. Here we report on the identification and structural determination of the SMN complex from the lower eukaryote Schizosaccharomyces pombe, consisting of SMN, Gemin2, 6, 7, 8 and Sm proteins. The core of the SMN complex is formed by several copies of SMN tethered through its C-terminal alpha-helices arranged with alternating polarity. This creates a central platform onto which Gemin8 binds and recruits Gemins 6 and 7. The N-terminal parts of the SMN molecules extrude via flexible linkers from the core and enable binding of Gemin2 and Sm proteins. Our data identify the SMN complex as a multivalent hub where Sm proteins are collected in its periphery to allow their joining with UsnRNA.}, language = {en} } @article{GrimmPelzSchneideretal.2020, author = {Grimm, Clemens and Pelz, Jann-Patrick and Schneider, Cornelius and Sch{\"a}ffler, Katrin and Fischer, Utz}, title = {Crystal Structure of a Variant PAM2 Motif of LARP4B Bound to the MLLE Domain of PABPC1}, series = {Biomolecules}, volume = {10}, journal = {Biomolecules}, number = {6}, issn = {2218-273X}, doi = {10.3390/biom10060872}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-207800}, year = {2020}, abstract = {Eukaryotic cells determine the protein output of their genetic program by regulating mRNA transcription, localization, translation and turnover rates. This regulation is accomplished by an ensemble of RNA-binding proteins (RBPs) that bind to any given mRNA, thus forming mRNPs. Poly(A) binding proteins (PABPs) are prominent members of virtually all mRNPs that possess poly(A) tails. They serve as multifunctional scaffolds, allowing the recruitment of diverse factors containing a poly(A)-interacting motif (PAM) into mRNPs. We present the crystal structure of the variant PAM motif (termed PAM2w) in the N-terminal part of the positive translation factor LARP4B, which binds to the MLLE domain of the poly(A) binding protein C1 cytoplasmic 1 (PABPC1). The structural analysis, along with mutational studies in vitro and in vivo, uncovered a new mode of interaction between PAM2 motifs and MLLE domains.}, language = {en} } @article{WernerPoppFichtneretal.2022, author = {Werner, Anne and Popp, Maria and Fichtner, Falk and Holzmann-Littig, Christopher and Kranke, Peter and Steckelberg, Anke and L{\"u}hnen, Julia and Redlich, Lisa Marie and Dickel, Steffen and Grimm, Clemens and Moerer, Onnen and Nothacker, Monika and Seeber, Christian}, title = {COVID-19 intensive care — Evaluation of public information sources and current standards of care in German intensive care units: a cross sectional online survey on intensive care staff in Germany}, series = {Healthcare}, volume = {10}, journal = {Healthcare}, number = {7}, issn = {2227-9032}, doi = {10.3390/healthcare10071315}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-281865}, year = {2022}, abstract = {Backround: In February 2021, the first formal evidence and consensus-based (S3) guidelines for the inpatient treatment of patients with COVID-19 were published in Germany and have been updated twice during 2021. The aim of the present study is to re-evaluate the dissemination pathways and strategies for ICU staff (first evaluation in December 2020 when previous versions of consensus-based guidelines (S2k) were published) and question selected aspects of guideline adherence of standard care for patients with COVID-19 in the ICU. Methods: We conducted an anonymous online survey among German intensive care staff from 11 October 2021 to 11 November 2021. We distributed the survey via e-mail in intensive care facilities and requested redirection to additional intensive care staff (snowball sampling). Results: There was a difference between the professional groups in the number, selection and qualitative assessment of information sources about COVID-19. Standard operating procedures were most frequently used by all occupational groups and received a high quality rating. Physicians preferred sources for active information search (e.g., medical journals), while nurses predominantly used passive consumable sources (e.g., every-day media). Despite differences in usage behaviour, the sources were rated similarly in terms of the quality of the information on COVID-19. The trusted organizations have not changed over time. The use of guidelines was frequently stated and highly recommended. The majority of the participants reported guideline-compliant treatment. Nevertheless, there were certain variations in the use of medication as well as the criteria chosen for discontinuing non-invasive ventilation (NIV) compared to guideline recommendations. Conclusions: An adequate external source of information for nursing staff is lacking, the usual sources of physicians are only appropriate for the minority of nursing staff. The self-reported use of guidelines is high.}, language = {en} }