Publications

Selected papers from CMBI labs

Kugler V, Lieb A, Guerin N, Donald BR, Stefan E, Kaserer T. (2023) Disruptor: Computational identification of oncogenic mutants disrupting protein-protein and protein-DNA interactions. Commun. Biol. 6, 720.
Ortner NJ, Sah A, Paradiso E, Shin J, Stojanovic S, Hammer N, Haritonova M, Hofer NT, Marcantoni A, Guarina L, Tuluc P, Theiner T, Pitterl F, Ebner K, Oberacher H, Carbone E, Stefanova N, Ferraguti F, Singewald N, Roeper J, Striessnig J. (2023) The human channel gating-modifying A749G CACNA1D (Cav1.3) variant induces a neurodevelopmental syndrome-like phenotype in mice. JCI Insight 8, e162100.
Plangger I, Pinkert T, Wurst K, Magauer T. (2023) A Divergent Polyene Cyclization for the Total Synthesis of Greenwayodendrines, Greenwaylactams, Polysin and Polyveoline. Angew. Chem. Int. Ed. 62, e202307719.
Cazet JF, Siebert S, Little HM, Bertemes P, Primack AS, Ladurner P, Achrainer M, Fredriksen MT, Moreland RT, Singh S, Zhang S, Wolfsberg TG, Schnitzler CE, Baxevanis AD, Simakov O, Hobmayer B, Juliano CE. (2023) A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state. Genome Res. 33, 283-298.
Grabska J, Beć KB, Ueno N, Huck CW. (2023) Analyzing the Quality Parameters of Apples by Spectroscopy from Vis/NIR to NIR Region: A Comprehensive Review. Foods. 12, 1946.
García-Risco M, Calatayud S, Pedrini-Martha V, Albalat R, Palacios Ò, Capdevila M, Dallinger R. (2023) A de novo evolved domain improves the cadmium detoxification capacity of limpet metallothioneins. Sci. Rep. 13, 8895.
Heel SV, Bartosik K, Juen F, Kreutz C, Micura R, Breuker K. (2023) Native Top-Down Mass Spectrometry Uncovers Two Distinct Binding Motifs of a Functional Neomycin-Sensing Riboswitch Aptamer. J. Am. Chem. Soc. 145, 15284-15294.
Orfanoudaki M, Alilou M, Hartmann A, Mayr J, Karsten U, Nguyen-Ngoc H, Ganzera M. (2023) Isolation and Structure Elucidation of Novel Mycosporine-like Amino Acids from the Two Intertidal Red Macroalgae Bostrychia scorpioides and Catenella caespitosa. Mar. Drugs. 21, 543.
Polikanov YS, Etheve-Quelquejeu M, Micura R. (2023) Synthesis of Peptidyl-tRNA Mimics for Structural Biology Applications. Acc. Chem. Res. 56, 2713-2725.
Seitter H, Obkircher J, Grabher P, Hartl J, Zanetti L, Lux UT, Fotakis G, Fernández-Quintero ML, Kaserer T, Koschak A. (2023) A novel calcium channel Cavβ2 splice variant with unique properties predominates in the retina. J. Biol. Chem. 299, 102972.
Muratspahić E., Deibler K., Han J., Tomašević N.,Jadhav K.B., Olivé-Marti A.-L., Hochrainer N.,Hellinger R.,Koehbach J., Fay J.F., Rahman M.H., Hegazy L., Craven T., Varga B.R., Bhardwaj G., Appourchaux K., Majumdar S.,Muttenthaler M., Hosseinzadeh P., Craik D.J., Spetea M., Che T., Baker D., Gruber C.W. (2023) De novo design and structural validation of peptide–drug conjugate ligands of the kappa-opioid receptor. Nat. Commun. 14:8064 .
Aigner GP, Peer V, Fiechtner B, Piechnik CA, Höckner M. (2023) Wound healing and Cadmium detoxification in the earthworm Lumbricus terrestris - a potential case for coelomocytes? Front. Immunol. 14, 1272191.
Koeberle SC, Kipp AP, Stuppner H, Koeberle A. (2023) Ferroptosis-modulating small molecules for targeting drug-resistant cancer: Challenges and opportunities in manipulating redox signaling. Med. Res. Rev. 43, 614-682.
Rainer T, Egger AS, Zeindl R, Tollinger M, Kwiatkowski M, Müller T. (2022) 3D-Printed High-Pressure-Resistant Immobilized Enzyme Microreactor (μIMER) for Protein Analysis. Anal. Chem. 94, 8580-8587.
Mack HID, Kremer J, Albertini E, Mack EKM, Jansen-Dürr P. (2022) Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans. BMC Genomics 23, 25.
Gruber K, Csitkovits V, Łyskowski A, Kratky C, Kräutler B. (2022) Structure-Based Demystification of Radical Catalysis by a Coenzyme B12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues. Angew. Chem. Int. Ed. 61, e202208295.
Thürmer M, Gollowitzer A, Pein H, Neukirch K, Gelmez E, Waltl L, Wielsch N, Winkler R, Löser K, Grander J, Hotze M, Harder S, Döding A, Meßner M, Troisi F, Ardelt M, Schlüter H, Pachmayr J, Gutiérrez-Gutiérrez Ó, Rudolph KL, Thedieck K, Schulze-Späte U, González-Estévez C, Kosan C, Svatoš A, Kwiatkowski M, Koeberle A. (2022) PI(18:1/18:1) is a SCD1-derived lipokine that limits stress signaling. Nat. Commun. 13, 2982.
Siller A, Hofer NT, Tomagra G, Burkert N, Hess S, Benkert J, Gaifullina A, Spaich D, Duda J, Poetschke C, Vilusic K, Fritz EM, Schneider T, Kloppenburg P, Liss B, Carabelli V, Carbone E, Ortner NJ, Striessnig J. (2022) β2-subunit alternative splicing stabilizes Cav2.3 Ca2+ channel activity during continuous midbrain dopamine neuron-like activity. Elife 11, e67464.
Rinkevich B, Ballarin L, Martinez P, Somorjai I, Ben-Hamo ., Borisenko I, Berezikov E, Ereskovsky AV, Gazave E, Khnykin D, Manni L, Petukhova O, Rosner A, Röttinger E, Spagnuolo A, Sugni M, Tiozzo S, Hobmayer B. (2022). A pan-metazoan concept for adult stem cells: the wobbling Penrose landscape. Biological Reviews 97, 299.
Brooun M, Salvenmoser W, Dana C, Sudol M, Steele R, Hobmayer B, McNeill H. (2022). The Hippo pathway regulates axis formation and morphogenesis in Hydra. PNAS 119, e2203257119.
Bereiter R, Renard E, Breuker K, Kreutz C, Ennifar E, Micura R. (2022) 1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis. J. Am. Chem. Soc. 144, 10344.
Paciorek J, Höfler D, Sokol KR, Wurst K, Magauer T. (2022) Total Synthesis of the Dihydrooxepine-Spiroisoxazoline Natural Product Psammaplysin A. J. Am. Chem. Soc. 144, 19704.
Fernández-Quintero ML, Vangone A, Loeffler JR, Seidler CA, Georges G, Liedl KR. (2022) Paratope states in solution improve structure prediction and docking. Structure, 30, 430.
Tisch M, Carmen De Mingo Alemany M, Suarez-Cubero M, Fauth C, Defrancesco M, Zschocke J, Günther K, Edenhofer F. (2022) Generation of the human induced pluripotent stem cell line (IBKMOLi002-A) from PBMCs of a patient carrying the heterozygous L271H mutation of the voltage-gated calcium channel subunit Cav1.3-encoding CACNA1D gene. Stem Cell Res. 61, 102784.
Puls K, Olivé-Marti AL, Pach S, Pinter B, Erli F, Wolber G, Spetea M. (2022). In Vitro, In Vivo and In Silico Characterization of a Novel Kappa-Opioid Receptor Antagonist. Pharmaceuticals 15, 680.
Ozaki Y, Beć KB, Morisawa Y, Yamamoto S, Tanabe I, Huck CW, Hofer TS (2021). Advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Chem. Soc. Rev. 50, 10917.
Führer S, Kamenik AS, Zeindl R, Nothegger B, Hofer F, Reider N, Liedl KR, Tollinger M (2021). Inverse relation between structural flexibility and IgE reactivity of Cor a 1 hazelnut allergens. Scientific Reports 11, 4173.
Prentzell MT, Rehbein U, Cadena Sandoval M, De Meulemeester AS, Baumeister R, Brohée L, Berdel B, Bockwoldt M, Carroll B, Chowdhury SR, von Deimling A, Demetriades C, Figlia G; Genomics England Research Consortium, de Araujo MEG, Heberle AM, Heiland I, Holzwarth B, Huber LA, Jaworski J, Kedra M, Kern K, Kopach A, Korolchuk VI, van 't Land-Kuper I, Macias M, Nellist M, Palm W, Pusch S, Ramos Pittol JM, Reil M, Reintjes A, Reuter F, Sampson JR, Scheldeman C, Siekierska A, Stefan E, Teleman AA, Thomas LE, Torres-Quesada O, Trump S, West HD, de Witte P, Woltering S, Yordanov TE, Zmorzynska J, Opitz CA, Thedieck K (2021). G3BPs tether the TSC complex to lysosomes and suppress mTORC1 signaling. Cell 184, 655-674.
Striessnig J. (2021). Voltage-Gated Ca2+-Channel α1-Subunit de novo Missense Mutations: Gain or Loss of Function - Implications for Potential Therapies. Front Synaptic Neurosci. 13, 634760.
Haut FL, Habiger C, Wein LA, Wurst K, Podewitz M, Magauer T. (2021). Rapid Assembly of Tetrasubstituted Furans via Pummerer-Type Rearrangement. J. Am. Chem. Soc. 143, 1216-1223.
Krasheninina OA, Thaler J, Erlacher MD, Micura R. (2021). Amine-to-Azide Conversion on Native RNA via Metal-Free Diazotransfer Opens New Avenues for RNA Manipulations. Angew. Chem. Int. Ed. 60, 6970-6974.
Fernández-Quintero ML, El Ghaleb Y, Tuluc P, Campiglio M, Liedl KR, Flucher BE. (2021). Structural determinants of voltage-gating properties in calcium channels. Elife 10, e64087.
Mertens J, Herdy JR, Traxler L, Schafer ST, Schlachetzki JCM, Böhnke L, Reid DA, Lee H, Zangwill D, Fernandes DP, Agarwal RK, Lucciola R, Zhou-Yang L, Karbacher L, Edenhofer F, Stern S, Horvath S, Paquola ACM, Glass CK, Yuan SH, Ku M, Szücs A, Goldstein LSB, Galasko D, Gage FH. (2021). Age-dependent instability of mature neuronal fate in induced neurons from Alzheimer's patients. Cell Stem Cell 28, 1-16, S1934-5909(21)00161-2.
Zanetti L, Kilicarslan I, Netzer M, Babai N, Seitter H, Koschak A. (2021) Function of cone and cone-related pathways in CaV1.4 IT mice. Sci Rep. 11, 2732.
Gerna D, Arc E, Holzknecht M, Roach T, Jansen-Dürr P, Weiss AKH, Kranner I. (2021). AtFAHD1a: A New Player Influencing Seed Longevity and Dormancy in Arabidopsis? Int. J. Mol. Sci. 22, 2997.
Calatayud S, Garcia-Risco M, Pedrini-Martha V, Eernisse DJ, Dallinger R, Palacios Ò, Capdevila M, Albalat R (2021). Modularity in Protein Evolution: Modular Organization and De Novo Domain Evolution in Mollusk Metallothioneins. Mol. Biol. Evol. 38, 424-436.
Arthur-Baidoo E, Ameixa J, Ziegler P, Ferreira da Silva F, Ončák M, Denifl S. (2020). Reactions in Tirapazamine Induced by the Attachment of Low-Energy Electrons: Dissociation Versus Roaming of OH. Angew. Chem. Int. Ed. 59, 17177-17181.
Mayrhofer JE, Enzler F, Feichtner A, Röck R, Fleischmann J, Raffeiner A, Tschaikner P, Ogris E, Huber RG, Hartl M, Schneider R, Troppmair J, Torres-Quesada O, Stefan E (2020). Mutation-oriented profiling of autoinhibitory kinase conformations predicts RAF inhibitor efficacies. PNAS 117, 31105-31113.
Mitter M, Gasser C, Takacs Z, Langer CCH, Tang W, Jessberger G, Beales CT, Neuner E, Ameres SL, Peters JM, Goloborodko A, Micura R, Gerlich DW. (2020). Conformation of sister chromatids in the replicated human genome. Nature 586, 139-144.
Schneeberger E-M, Halper M, Palasser M, Heel SV, Vušurović J, Plangger R, Juen M, Kreutz C, Breuker K (2020). Native mass spectrometry reveals the initial binding events of HIV-1 rev to RRE stem II RNA. Nat. Commun. 11, 5750.
Steinborn C, Wildermuth RE, Barber DM, Magauer T (2020). Total Synthesis of (+)-Cornexistin. Angew. Chem. Int. Ed. 59, 17282-17285.
Nußbaumer F, Plangger R, Roeck M, Kreutz C (2020). Aromatic ¹⁹F-¹³C TROSY - [¹⁹F,¹³C] pyrimidine labeling for NMR spectroscopy of RNA. Angew. Chem. Int. Ed. 59, 17062-17069.
Calderisi G, Glasner H, Breuker K (2020). Radical transfer dissociation for de novo characterization of modified ribonucleic acids by mass spectrometry. Angew. Chem. Int. Ed. 59, 4309-4313.
Gonzalez S, Dumitrascuta M, Eiselt E, Louis S, Kunze L, Blasiol A, Vivancos M, Previti S, Dewolf E, Martin C, Tourwé D, Cavelier F, Gendron L, Sarret P, Spetea M, Ballet S. (2020). Optimized Opioid-Neurotensin Multitarget Peptides: From Design to Structure-Activity Relationship Studies. J. Med. Chem. 63, 12929-12941.
Kieninger C, Wurst K, Podewitz M, Stanley M, Deery E, Lawrence AD, Liedl KR, Warren MJ, Kräutler B. (2020). Replacement of the Cobalt Center of Vitamin B12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal-Free B12 Ligands Hydrogenobalamin and Hydrogenobyric Acid. Angew. Chem. Int. Ed. 59, 20129-20136.
Fuchs E, Falschlunger C, Micura R, Breuker K (2019). The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry. Nucleic Acids Res. 47, 7223-7234.
Sun A, Gasser C, Li F, Chen H, Mair S, Krasheninina O, Micura R, Ren A (2019). SAM-VI riboswitch structure and signature for ligand discrimination. Nat. Commun. 10, 5728.
Haut FL, Habiger C, Speck K, Wurst K, Mayer P, Korber JN, Müller T, Magauer T (2019). Synthetic Entry to Polyfunctionalized Molecules through the [3+2]-Cycloaddition of Thiocarbonyl Ylides. J. Am. Chem. Soc. 141, 13352-13357.
Plangger R, Juen AR, Hoernes TP, Nußbaumer F, Kremser J, Strebitzer S, Klingler D, Erharter K, Tollinger M, Erlacher MD, Kreutz C (2019). Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing. Nucleic Acids Res. 2019 47, 11430-11440.
Dikova V, Vorhauser J, Geng A, Pelster B, Sandbichler AM (2019). Metabolic interaction of hydrogen peroxide and hypoxia in zebrafish fibroblasts. Free Rad. Biol. Med. 152, 469-481.
Mandl M, Wagner SA, Hatzmann FM, Mitterberger-Vogt MC, Zwierzina ME, Mattesich M, Zwerschke W (2019). Sprouty1 is a weight-loss target gene in human adipose stem/progenitor cells that is mandatory for the initiation of adipogenesis. Cell Death Dis. 10, 411.
Spetea M, Rief SB, Ben Haddou T, Fink M, Kristeva E, Mittendorfer H, Haas S, Hummer N, Follia V, Guerrieri E, Asim MF, Sturm S, Schmidhammer H (2019). Synthesis, Biological and Structural Explorations of New Zwitterionic Derivatives of 14-O-Methyloxymorphone, as Potent Mu/Delta Opioid Agonists and Peripherally Selective Antinociceptives. J. Med. Chem. 62, 641–653.
Porpora M, Sauchella S, Rinaldi L, Delle Donne R, Sepe M, Torres-Quesada O, Intartaglia D, Garbi C, Insabato L, Santoriello M, Bachmann V, Synofzik M, Lindner H, Conte I, Stefan E, Feliciello A (2018). Counterregulation of cAMP-directed kinase activities controls ciliogenesis. Nat. Commun. 9, e1224.
Haushalter K, Casteel DE, Raffeiner A, Stefan E , Patel HH, Taylor SS (2018). Phosphorylation of Protein Kinase A (PKA) regulatory subunit RIa by Protein Kinase G (PKG) primes PKA for catalytic activity in cells. J. Biol. Chem. 293, 4411-4421.
Martin C, Dumitrascuta M, Mannes M, Lantero A, Bucher D, Walker K, Van Wanseele Y, Oyen E, Hernot S, Van Eeckhaut A, Madder A, Hoogenboom R, Spetea M, Ballet S (2018). Biodegradable Amphipathic Peptide Hydrogels as Extended-Release System for Opioid Peptides. J. Med. Chem. 61, 9784-9789.
Schweiger S, Matthes F, Posey K, Kickstein E, Weber S, Hettich MM, Pfurtscheller S, Ehninger D, Schneider R, Krauß S (2017). Resveratrol induces dephosphorylation of Tau by interfering with the MID1-PP2A complex. Scientific Reports 7, 13753.
Baumann C, Beil A, Jurt S, Niederwanger M, Palacios O, Capdevila M, Atrian S, Dallinger R, Zerbe O (2017). Structural Adaptation of a Protein to Increased Metal Stress: NMR Structure of a Marine Snail Metallothionein with an Additional Domain. Angew. Chem. Int. Ed. 56, 4617–4622.
Liu JJ, Sharma K, Zangrandi L, Chen C, Humphrey SJ, Chiu YT, Spetea M, Liu-Chen LY, Schwarzer C, Mann M (2018). In vivo brain GPCR signaling elucidated by phosphoproteomics. Science 360, pii: eaao4927.
Kremser J, Strebitzer E, Plangger R, Juen MA, Nußbaumer F, Glasner H, Breuker K, Kreutz C (2017). Chemical synthesis and NMR spectroscopy of long stable isotope labelled RNA. Chem. Comm. 53, 12938-12941.
Zheng L, Mairhofer E, Teplova M, Zhang Y, Ma J, Patel D J, Micura R, Ren A (2017). Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme. Nat. Commun. 8, 1180.
Erli F, Guerrieri E, Ben Haddou T, Lantero A, Mairegger M, Schmidhammer H, Spetea M (2017). Highly Potent and Selective New Diphenethylamines Interacting with the κ-Opioid Receptor: Synthesis, Pharmacology, and Structure-Activity Relationships. J Med Chem. 60, 7579-7590.
Riml C, Amort T, Rieder D, Gasser C, Lusser A, Micura R (2017). Osmium-Mediated Transformation of 4-Thiouridine to Cytidine as Key To Study RNA Dynamics by Sequencing. Angew Chem Int Ed Engl. 56, 13479-13483.
Aufschnaiter R, Wedlich-Söldner R, Zhang X, Hobmayer B (2017). Apical and basal epitheliomuscular F-actin dynamics during Hydra bud evagination. Biology Open 6, 1137-1148.
Spetea M, Eans S O, Ganno M L, Lantero Aquilino, Mairegger M, Toll L, Schmidhammer H. McLaughlin J P (2017). Selective κ opioid receptor partial agonist HS666 produces potent antinociception without inducing aversion after i.c.v. administration in mice. Br. J. Pharmacol. 174, 2444-2456.
Stefan E, Bister K (2017). MYC and RAF: Key effectors in cellular signaling and major drivers in human cancer. Curr. Top. Microbiol. Immunol. 407, 117-151.
Raffeiner P, Schraffl A, Schwarz T, Röck R, Ledolter K, Hartl M, Konrat R, Stefan E, Bister K (2017). Calcium-dependent binding of Myc to calmodulin. Oncotarget 8, 3327-3343.
Lagard C, Chevillard L, Guillemyn K, Risède P, Laplanche J.-L., Spetea M, Ballet S, Mégarbane B (2017). Bifunctional peptide-based opioid agonist/nociceptin antagonist ligand for dual treatment of nociceptive and neuropathic pain. Pain 158, 505-515.
Moschen T, Grutsch S, Juen, MA, Wunderlich CH, Kreutz C, Tollinger M (2016). Measurement of ligand-target residence times by 1H relaxation dispersion NMR spectroscopy. J. Med. Chem. 59, 10788-10793.
Zhou H, Kimsey IJ , Nikolova EN, Sathyamoorthy B, Grazioli G, McSally J, Bai T, Wunderlich CH, Kreutz C, Andricioaei I, Al-Hashimi HM (2016). m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nat. Struct. Mol. Biol. 23, 803–810.
Bachmann VA, Mayrhofer JE, Ilouz R, Tschaikner PM, Raffeiner P, Röck R, Courcelles M, Apelt F, Lu T, Baillie GS, Thibault P, Aanstad P, Stelzl U, Taylor SS, Stefan E (2016). Gpr161 anchoring of PKA consolidates GPCR and cAMP signaling. Proc Natl Acad Sci USA 113, 7786-7791.
Ren A, Vusurovic N, Gebetsberger J, Gao P, Juen M, Kreutz C, Micura R, Patel DJ (2016). Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage. Nat. Chem. Biol. 12, 702-708.
Schennach M, Schneeberger EM, Breuker K (2016). Unfolding and folding of the three-helix bundle protein KIX in the absence of solvent. J. Am. Soc. Mass Spectrom. 27, 1079-1088
Grutsch S, Brüschweiler S, Tollinger M (2016). NMR methods to study dynamic allostery. PLoS Comput Biol. 12 e1004620.
Frener M, Micura R (2016). Conformational rearrangements of individual nucleotides during RNA-ligand binding are rate-differentiated. J. Am. Chem. Soc. 138, 3627-3630.
Kaserer T, Lantero A, Schmidhammer H, Spetea M, Schuster D (2016). μ Opioid receptor: Novel antagonists and structural modeling. Sci. Rep. 6, 21548.
Comprehensive lists of publications are available on the individual web sites of the CMBI labs.