CEMCE publications 2021

• Teppor, M., Žusinaite, E. and Merits, A. (2021). Phosphorylation sites in the hypervariable domain in chikungunya virus nsP3 are crucial for viral replication. Journal of Virology, 95(9):e02276-20. doi: 10.1128/JVI.02276-20.
• Teppor, M., Žusinaite, E., Karo-Astover, L., Omler, A., Rausalu, K., Lulla, V., Lulla, A. and Merits, A. (2021). Semliki forest virus chimeras with functional replicase modules from related alphaviruses survive by adaptive mutations in functionally important hotspots. Journal of Virology, doi: 10.1128/JVI.00973-21
• Lello, L.S., Bartholomeeusen, K., Wang, S., Coppens, S., Fragkoudis, R., Alphey, L., Arien, K.K., Merits, A. and Utt, A. (2021). nsP4 is a major determinant of alphavirus replicase activity and template selectivity. Journal of Virology, doi: 10.1128/JVI.00355-21.
• Szemiel, A.M., Merits, A., Orton, R.J., MacLean, O.A., Pinto, R.M., Wickenhagen, A., Lieber, G., Turnbull, M.L., Wang, S., Furnon, W., Suarez, N., Mair. D., Filipe, A.S., Willett, B.J., Wilson, J.S., Patel, A.H., Thomson, E.C., Palmarini, M., Kohl, A., and Stewart, M.E. In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. PLoS Pathogens, https://doi.org/10.1371/journal.ppat.1009929
• Kõllo M, Kasari M, Kasari V, Pehk T, Järving I, Lopp M, Jõers A, Kanger T. Beilstein Designed whole-cell-catalysis-assisted synthesis of 9,11-secosterols.J Org Chem. 2021 Mar 1;17:581-588. doi: 10.3762/bjoc.17.52. eCollection 2021.PMID: 33747232 
• Kerkez I, Tulkens PM, Tenson T, Van Bambeke F, Putrinš M. Uropathogenic Escherichia coli Shows Antibiotic Tolerance and Growth Heterogeneity in an In Vitro Model of Intracellular Infection. Antimicrob Agents Chemother. 2021 Nov 17;65(12):e0146821. doi: 10.1128/AAC.01468-21. Epub 2021 Sep 27.PMID: 34570646
• Kurata T, Brodiazhenko T, Alves Oliveira SR, Roghanian M, Sakaguchi Y, Turnbull KJ, Bulvas O, Takada H, Tamman H, Ainelo A, Pohl R, Rejman D, Tenson T, Suzuki T, Garcia-Pino A, Atkinson GC, Hauryliuk V. RelA-SpoT Homolog toxins pyrophosphorylate the CCA end of tRNA to inhibit protein synthesis.Mol Cell. 2021 Aug 5;81(15):3160-3170.e9. doi: 10.1016/j.molcel.2021.06.005. Epub 2021 Jun 25.PMID: 34174184 
• Pochopien AA, Beckert B, Kasvandik S, Berninghausen O, Beckmann R, Tenson T, Wilson DN.Structure of Gcn1 bound to stalled and colliding 80S ribosomes.Proc Natl Acad Sci U S A. 2021 Apr 6;118(14):e2022756118. doi: 10.1073/pnas.2022756118.PMID: 33790014 
• Kõiv V, Tenson T. Gluten-degrading bacteria: availability and applications.Appl Microbiol Biotechnol. 2021 Apr;105(8):3045-3059. doi: 10.1007/s00253-021-11263-5. Epub 2021 Apr 10.PMID: 33837830 
• Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V. Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP. Mol Cell. 2021 Jan 7;81(1):115-126.e7. doi: 10.1016/j.molcel.2020.11.002. Epub 2020 Nov 30.PMID: 33259810
• Takada H, Crowe-McAuliffe C, Polte C, Sidorova ZY, Murina V, Atkinson GC, Konevega AL, Ignatova Z, Wilson DN, Hauryliuk V. RqcH and RqcP catalyze processive poly-alanine synthesis in a reconstituted ribosome-associated quality control system.Nucleic Acids Res. 2021 Aug 20;49(14):8355-8369. doi: 10.1093/nar/gkab589.PMID: 34255840 
• Roghanian M, Van Nerom K, Takada H, Caballero-Montes J, Tamman H, Kudrin P, Talavera A, Dzhygyr I, Ekström S, Atkinson GC, Garcia-Pino A, Hauryliuk V. (p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains.Mol Cell. 2021 Aug 19;81(16):3310-3322.e6. doi: .1016/j.molcel.2021.07.026.PMID: 34416138 
• Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O’Neill AJ, Hauryliuk V, Wilson DN. Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nat Commun. 2021 Jun 11;12(1):3577. doi: 10.1038/s41467-021-23753-1.
• Jalakas P, Nuhkat M, Vahisalu T, Merilo E, Brosche M, Kollist H. (2021a). Combined Action of Guard Cell Plasma Membrane Rapid- and Slow-Type Anion Channels in Stomatal Regulation. Plant Physiology, doi.org/10.1093/plphys/kiab202. 
• Jalakas P, Takahashi Y, Waadt R, Schroeder, JIS, Merilo E. (2021b) Molecular mechanism of stomatal closure in response to rising vapor pressure deficit. Viewpoint article, New Phytologist 232: 468-475. https://doi.org/10.1111/nph.17592.
• Hsu P-K, Takahashi Y, Merilo E, Costa A, Zhang L, Kernig, K, Lee KH, Schroeder JI (2021) Raf-like kinases and receptor-like pseudokinase GHR1 are required for stomatal vapor pressure difference response.  PNAS doi: 10.1073/pnas.2107280118.
• Nuhkat M, Brosche M, Stoelzle-Feix S, Dietrich P, Hedrich R, Roelfsema MRG, Kollist H (2021) Rapid depolarization and cytosolic calcium increase go hand-in-hand in mesophyll cells’ ozone response. New Phytologist, 232: 1692-1702. https://doi.org/10.1111/nph.17711
• Waadt R,  Kudla J, Kollist H (2021) Multiparameter in vivo imaging in plants using genetically encoded fluorescent indicator multiplexing. Plant Physiology, 187: 537–549. https://doi.org/10.1093/plphys/kiab399
• Zamora O, Schulze S, Azoulay-Shemer T, Parik H, Unt J, Brosche M, Schroeder JI, Yarmolinsky D, Kollist, H (2021) Jasmonic acid and salicylic acid play minor roles in stomatal regulation by CO2, abscisic acid, darkness, vapor pressure deficit and ozone. The Plant Journal, https://doi.org/10.1111/tpj.15430.
• Morales LO, Shapiguzov A, Safronov O, Leppälä J, Vaahtera L, Yarmolinsky D, Kollist H, Brosché M (2021) Ozone responses in Arabidopsis: beyond stomatal conductance. Plant Physiology, 186: 180–192. doi: 10.1093/plphys/kiab097
• Aasumets, K., Basikhina, Y., Pohjoismäki, J. L., Goffart, S., Gerhold, J. (2021). TFAM knockdown-triggered mtDNA-nucleoid aggregation and a decrease in mtDNA copy number induce the reorganization of nucleoid populations and mitochondria-associated ER-membrane contacts. Biochemistry and Biophysics Reports 28: 1–8. 

• Ivanova, L.; Rausalu, K.; Ošeka, M.; Kananovich, D. G.; Žusinaite, E.; Tammiku-Taul, J.; Lopp, M.; Merits, A.; Karelson, M. (2021). Novel Analogues of the Chikungunya Virus Protease Inhibitor: Molecular Design, Synthesis, and Biological Evaluation. ACS Omega, 6 (16), 10884−10896. DOI: 10.1021/acsomega.1c00625.
• Kaasik, M.; Martõnova, J.; Erkman, K.; Metsala, A.; Järving, I.; Kanger, T. (2021). Enantioselective Michael addition to vinyl phosphonates via hydrogen bond-enhanced halogen bond catalysis. Chemical Science, 21, 7561−7568. DOI: 10.1039/D1SC01029H. 
• Kaldas, K.; Niidu, A.; Preegel, G.; Uustalu, J. M.; Muldma, K.; Lopp, M. (2021). Aspects of kerogen oxidative dissolution in subcritical water using oxygen from air. Oil Shale, 38 (3), 199−214. DOI: 10.3176/oil.2021.3.02. 
• Kananovich, D.; Elek, G. Z.; Lopp, M.; Borovkov, V. (2021). Aerobic Oxidations in Asymmetric Synthesis: Catalytic Strategies and Recent Developments. Frontiers in Chemistry, 9. DOI: 10.3389/fchem.2021.614944.
• Kimm, M.; Järving, I.; Ošeka, M.; Kanger, T. (2021). Asymmetric Organocatalytic [2,3]‐Wittig Rearrangement of Cyclohexanone Derivatives. European Journal of Organic Chemistry. DOI: 10.1002/ejoc.202100435.
• Kooli, A.; Shalima, T.; Lopušanskaja, E.; Paju, A.; Lopp, M. (2021). Selective C-alkylation of substituted naphthols under non-aqueous conditions. Tetrahedron, 95, 132278. DOI: 10.1016/j.tet.2021.132278.
• Lopušanskaja, E.; Kooli, A.; Paju, A.; Järving, I.; Lopp, M. (2021). Towards ortho-selective electrophilic substitution/addition to phenolates in anhydrous solvents. Tetrahedron, 131935. DOI: 10.1016/j.tet.2021.131935.
• Murre, A.; Erkman, K.; Järving, I.; Kanger, T. (2021). Asymmetric Chemoenzymatic One-Pot Synthesis of α-Hydroxy Half-Esters. ACS Omega, 6 (31), 20686−20698. DOI: 10.1021/acsomega.1c02973.
• Trubitsõn, D.; Martõnova, J.; Kudrjašova, M.; Erkman; K.; Järving, I.; Kanger T. (2021). Enantioselective Organocatalytic Michael Addition to Unsaturated Indolyl Ketones. Organic Letters, 23 (5), 1820−1824. DOI: 10.1021/acs.orglett.1c00222.
• Böhm, M.; Killinger, K.; Dudziak, A.; Pant, P.; Jänen, K.; Hohoff, S.; Mechtler, K.; Örd, M.; Loog, M.; Garcia, E.S.; Westermann, S. (2021). Cdc4 phospho-degrons allow differential regulation of ame1^cenp-u protein stability across the cell cycle. eLife, 10. DOI: 10.7554/eLife.67390.
• Faustova, I.; Bulatovic, L.; Matiyevskaya, F.; Valk, E.; Örd, M.; Loog, M. (2021). A new linear cyclin docking motif that mediates exclusively S-phase CDK-specific signaling. The EMBO Journal, 40 (2). DOI: 10.15252/embj.2020105839.
• Faustova, I.; Möll, K.; Valk, E.; Loog, M.; Örd, Ml (2021). Docking to a basic helix promotes specific phosphorylation by G1-Cdk1. International Journal of Molecular Sciences, 22 (17), 9514. DOI: 10.3390/ijms22179514.
• Asfaha, J.B., Örd, M., Carlson, C.R., Faustova, I.,  Loog, M., Morgan, D.O. (2021). Multisite phosphorylation by Cdk1 initiates delayed negative feedback to control mitotic transcription. Current Biology, Nov 16:S0960-9822(21)01522-0. doi: 10.1016/j.cub.2021.11.001
• Brumele, B.; Mutso, M.; Telanne, L.; Õunap, K.; Spunde, K.; Abroi, A.; Kurg, R. (2021). Human TRMT112-Methyltransfersae Network consists of seven partners interacting with a common co-factor. International Journal of Molecular Sciences, 22, 13593. DOI: 10.3390/ijms222413593.
• Reinsalu, O.; Samel, A.; Niemeister, E.; Kurg, R. (2021). MAGEA4 Coated Extracellular Vesicles Are Stable and Can Be Assembled In Vitro. International Journal of Molecular Sciences, 22 (10), 5208. DOI: 10.3390/ijms22105208.
• Ivanova, L.; Rausalu, Kai; Žusinaite, E.; Tammiku-Taul, J.; Merits, A.; Karelson, M.. 1,3-Thiazolbenzamide Derivatives as Chikungunya Virus nsP2 Protease Inhibitors. ACS Omega, 2021, 6 (8), 5786−5794. DOI: 10.1021/acsomega.0c06191. <https://www.etis.ee/Portal/Publications/Display/e7200319-fe8a-43bf-908e-447db2ca178f>
• Ivanova, L.; Rausalu, K.; Ošeka, M.; Kananovich, D. G.; Žusinaite, E.; Tammiku-Taul, J.; Lopp, M.; Merits, A.; Karelson, M. Novel Analogues of the Chikungunya Virus Protease Inhibitor: Molecular Design, Synthesis, and Biological Evaluation. ACS Omega 2021, 6 (16), 10884−10896. DOI: 10.1021/acsomega.1c00625. <https://www.etis.ee/Portal/Publications/Display/87b31ba0-c5e6-487e-b563-f72fd62aca4b>
• Selberg, S.; Žusinaite, E.; Herodes, K.; Seli, N.; Kankuri, E.; Merits, A.; Karelson, M. HIV Replication Is Increased by RNA Methylation METTL3/METTL14/WTAP Complex Activators. ACS Omega 2021, 6, 24, 15957–15963. DOI: 10.1021/acsomega.1c01626 <https://www.etis.ee/Portal/Publications/Display/5a8a6315-df89-4bb0-bd22-6a73edfc6b2e>
• Piir, G.; Sild, S.; Maran, U. Binary and multi-class classification for androgen receptor agonists, antagonists and binders. Chemosphere, 2021, 262, 128313. DOI: https://doi.org/10.1016/j.chemosphere.2020.128313 
• .Rice, M.; Wong, B.; Oja, M.; Samuels, K.; Williams, A. K.; Fong, F.; Sapse, A.-M.; Maran, U.; Korobkova, E. A. A role of flavonoids in cytochrome c-cardiolipin interactions. Bioorg. Med. Chem. 2021, 116043. DOI: https://doi.org/10.1016/j.bmc.2021.116043 
• García-Sosa, A.T.; Maran, U. Combined Naïve Bayesian, Chemical Fingerprints and Molecular Docking Classifiers to Model and Predict Androgen Receptor Binding Data for Environmentally- and Health-Sensitive Substances. Int. J. Mol. Sci. 2021, 22, 6695. DOI: https://doi.org/10.3390/ijms22136695 
• Toots, K. M.; Sild, S.; Leis, J.; Acree Jr., W. E.: Maran, U. The quantitative structure-property relationships for the gas-ionic liquid partition coefficient of a large variety of organic compounds in three ionic liquids, Journal of Molecular Liquids, 2021, 343, 117573. DOI: https://doi.org/10.1016/j.molliq.2021.117573 
• Malmberg, S.; Arulepp, M.; Laanemets, K.; Käärik, M.; Laheäär, A.; Tarasova, E.; Vassiljeva, V.; Krasnou, I.; Krumme, A. (2021). The Performance of Fibrous CDC Electrodes in Aqueous and Non-Aqueous Electrolytes. C – Journal of Carbon Research, 2021, 7 (2), 46. DOI: https://doi.org/10.1016/10.3390/c7020046 
• Kumar, Y.; Kibena‐Põldsepp, E.; Kozlova, J.; Kikas, A.; Käärik, M.; Aruväli, J.; Kisand, V.; Leis, J.; Tamm, A.; Tammeveski, K. Bimetal phthalocyanine‐modified carbon nanotube‐based bifunctional catalysts for zinc‐air batteries. ChemElectroChem, 2021, 8 (14), 2662−2670. DOI: https://doi.org/10.1016/10.1002/celc.202100498 
• Sokka, A.; Mooste, M.; Käärik, M.; Gudkova, V.; Kozlova, J.; Kikas, A.; Kisand, V.; Treshchalov, A.; Tamm, A.; Paiste, P.; Aruväli, J.; Leis, J.; Krumme, A.; Holdcroft, S.; Cavaliere, S.; Jaouen, F.; Tammeveski, K. Iron and cobalt containing electrospun carbon nanofibre-based cathode catalysts for anion exchange membrane fuel cell. International Journal of Hydrogen Energy, 2021, 46 (61), 31275−31287. DOI: https://doi.org/10.1016/10.1016/j.ijhydene.2021.07.025 
• Estrada, F. G. A.; Miccoli, S.; Aniceto, N.; Garcia-Sosa, A. T.; Guedes, R. C. Exploring EZH2-Proteasome Dual-Targeting Drug Discovery through a Computational Strategy to Fight Multiple Myeloma. Molecules, 2021, 26 (18), 5574. DOI: 10.3390/molecules26185574 
• Liblekas L, Piirsoo A, Laanemets A, Tombak EM, Laaneväli A, Ustav E, Ustav M, Piirsoo M. Analysis of the Replication Mechanisms of the Human Papillomavirus Genomes. Front Microbiol. 2021 Oct 18;12:738125. doi: 10.3389/fmicb.2021.738125. eCollection 2021.
• Lototskaja E, Sahharov O, Piirsoo M, Kala M, Ustav M, Piirsoo A. Cyclic AMP-Dependent Protein Kinase Exhibits Antagonistic Effects on the Replication Efficiency of Different Human Papillomavirus Types. J Virol. 2021 Jun 10;95(13):e0025121. doi: 10.1128/JVI.00251-21. Epub 2021 Jun 10.
• Kiisholts K, Kurrikoff K, Arukuusk P, Porosk L, Peters M, Salumets A, Langel Ü.Cell-Penetrating Peptide and siRNA-Mediated Therapeutic Effects on Endometriosis and Cancer In Vitro Models. Pharmaceutics. 2021 Oct 5;13(10):1618. doi: 10.3390/pharmaceutics13101618.PMID: 34683911
• Kurrikoff K, Vunk B, Langel Ü. Status update in the use of cell-penetrating peptides for the delivery of macromolecular therapeutics. Expert Opin. Biol. Ther. 2021 Mar;21(3):361-370. doi: 10.1080/14712598.2021.1823368. PMID: 32938243
• Kurrikoff K, Oskolkov N, Eriste E, Langel Ü. Design and Synthesis of a Peptide-Based Glioma-Targeted Drug Delivery Vector gHope2. Methods Mol Biol. 2021;2355:117-129. doi: 10.1007/978-1-0716-1617-8_11.PMID: 34386955
• Porosk,L., Põhako, K., Arukuusk, P. and Langel, Ü. Cell-Penetrating Peptides Predicted From CASC3, AKIP1, and AHRR Proteins.  Front. Pharmacol., 24 August 2021 | https://doi.org/10.3389/fphar.2021.716226
• de Mello, L.R., PoroskL., Lourenço, T.C., Garcia, B.B.M., Costa, C.A.R, Han, S.W., de Souza, J.S., Langel, Ü. and da Silva, E.R. Amyloid-like Self-Assembly of a Hydrophobic Cell-Penetrating Peptide and Its Use as a Carrier for Nucleic Acids.  ACS Appl. Bio Mater. 2021, 4, 8, 6404–6416 Publication Date:August 4, 2021 https://doi.org/10.1021/acsabm.1c00601