My Bibliography

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Brzezinski D, Kowiel M, Cooper DR, Cymborowski M, Grabowski M, Wlodawer A, Dauter Z, Shabalin IG, Gilski M, Rupp B, Jaskolski M, Minor W. Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models. Protein Sci. 2021 Jan;30(1):115-124. doi: 10.1002/pro.3959. Epub 2020 Oct 8. PubMed PMID: 32981130; PubMed Central PMCID: PMC7537053.

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Wlodawer A, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Minor W, Rupp B, Jaskolski M. Ligand-centered assessment of SARS-CoV-2 drug target models in the Protein Data Bank. FEBS J. 2020 Sep;287(17):3703-3718. doi: 10.1111/febs.15366. Epub 2020 Jun 24. PubMed PMID: 32418327; PubMed Central PMCID: PMC7276724.

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Dauter Z, Jaskolski M. Multiplicity-weighted Euler's formula for symmetrically arranged space-filling polyhedra. Acta Crystallogr A Found Adv. 2020 Sep 1;76(Pt 5):580-583. doi: 10.1107/S2053273320007093. Epub 2020 Jul 9. PubMed PMID: 32869755; PubMed Central PMCID: PMC7459769.

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Brzezinski D, Dauter Z, Minor W, Jaskolski M. On the evolution of the quality of macromolecular models in the PDB. FEBS J. 2020 Jul;287(13):2685-2698. doi: 10.1111/febs.15314. Epub 2020 Apr 20. PubMed PMID: 32311227; PubMed Central PMCID: PMC7340579.

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Smietanska J, Sliwiak J, Gilski M, Dauter Z, Strzalka R, Wolny J, Jaskolski M. A new modulated crystal structure of the ANS complex of the St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell. Acta Crystallogr D Struct Biol. 2020 Jul 1;76(Pt 7):653-667. doi: 10.1107/S2059798320006841. Epub 2020 Jun 17. PubMed PMID: 32627738; PubMed Central PMCID: PMC7336385.

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Sekula B, Ruszkowski M, Dauter Z. S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. Int J Biol Macromol. 2020 May 15;151:554-565. doi: 10.1016/j.ijbiomac.2020.02.100. Epub 2020 Feb 11. PubMed PMID: 32057875.

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Ruszkowska A, Ruszkowski M, Hulewicz JP, Dauter Z, Brown JA. Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples. Nucleic Acids Res. 2020 Apr 6;48(6):3304-3314. doi: 10.1093/nar/gkz1222. PubMed PMID: 31930330; PubMed Central PMCID: PMC7102945.

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Ruszkowski M, Sekula B, Ruszkowska A, Contestabile R, Nogues I, Angelaccio S, Szczepaniak A, Dauter Z. Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models. Sci Rep. 2019 Dec 23;9(1):19614. doi: 10.1038/s41598-019-56043-4. PubMed PMID: 31873125; PubMed Central PMCID: PMC6928210.

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Dauter Z. Sulfur-SAD phasing from microcrystals utilizing low-energy X-rays. IUCrJ. 2019 Jul 1;6(Pt 4):503-504. doi: 10.1107/S2052252519008698. eCollection 2019 Jul 1. PubMed PMID: 31316793; PubMed Central PMCID: PMC6608617.

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Sekula B, Dauter Z. Spermidine Synthase (SPDS) Undergoes Concerted Structural Rearrangements Upon Ligand Binding - A Case Study of the Two SPDS Isoforms From Arabidopsis thaliana. Front Plant Sci. 2019;10:555. doi: 10.3389/fpls.2019.00555. eCollection 2019. PubMed PMID: 31134111; PubMed Central PMCID: PMC6514230.

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Muslinkina L, Roldán-Salgado A, Gaytán P, Juárez-González VR, Rudiño E, Pletneva N, Pletnev V, Dauter Z, Pletnev S. Structural Factors Enabling Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming Residue. J Mol Biol. 2019 Mar 29;431(7):1397-1408. doi: 10.1016/j.jmb.2019.02.013. Epub 2019 Feb 22. PubMed PMID: 30797856; PubMed Central PMCID: PMC6544178.

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Sekula B, Dauter Z. Structural Study of Agmatine Iminohydrolase From Medicago truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants. Front Plant Sci. 2019;10:320. doi: 10.3389/fpls.2019.00320. eCollection 2019. PubMed PMID: 30984210; PubMed Central PMCID: PMC6447857.

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Ruszkowski M, Dauter Z. Comment on Wang's paper on the covalent Cys-X-Lys bridges. Protein Sci. 2019 Mar;28(3):470-471. doi: 10.1002/pro.3576. PubMed PMID: 30666728; PubMed Central PMCID: PMC6371628.

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Li M, Srp J, Gustchina A, Dauter Z, Mares M, Wlodawer A. Crystal structures of the complex of a kallikrein inhibitor from Bauhinia bauhinioides with trypsin and modeling of kallikrein complexes. Acta Crystallogr D Struct Biol. 2019 Jan 1;75(Pt 1):56-69. doi: 10.1107/S2059798318016492. Epub 2019 Jan 7. PubMed PMID: 30644845; PubMed Central PMCID: PMC6333282.

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Dauter Z, Wlodawer A. Crystallographically correct but confusing presentation of structural models deposited in the Protein Data Bank. Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):939-945. doi: 10.1107/S2059798318009828. Epub 2018 Sep 5. PubMed PMID: 30198902; PubMed Central PMCID: PMC6130463.

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Wlodawer A, Dauter Z. Do structures matter any more?. FEBS J. 2018 Sep;285(18):3322-3323. doi: 10.1111/febs.14630. PubMed PMID: 30221844.

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Sekula B, Ruszkowski M, Dauter Z. Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) From Arabidopsis thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis. Front Plant Sci. 2018;9:876. doi: 10.3389/fpls.2018.00876. eCollection 2018. PubMed PMID: 30034403; PubMed Central PMCID: PMC6043687.

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Ruszkowski M, Sekula B, Ruszkowska A, Dauter Z. Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization. Front Plant Sci. 2018;9:584. doi: 10.3389/fpls.2018.00584. eCollection 2018. PubMed PMID: 29868052; PubMed Central PMCID: PMC5958214.

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Dauter Z, Wlodawer A. Unexpected Specificity of a Trypsin-like Enzyme. Structure. 2018 Apr 3;26(4):530-531. doi: 10.1016/j.str.2018.03.007. PubMed PMID: 29617650.

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Ruszkowska A, Ruszkowski M, Dauter Z, Brown JA. Structural insights into the RNA methyltransferase domain of METTL16. Sci Rep. 2018 Mar 28;8(1):5311. doi: 10.1038/s41598-018-23608-8. PubMed PMID: 29593291; PubMed Central PMCID: PMC5871880.

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Luo Z, Dauter Z. The crystal structure of Z-DNA with untypically coordinated Ca²⁺ ions. J Biol Inorg Chem. 2018 Mar;23(2):253-259. doi: 10.1007/s00775-017-1526-4. Epub 2017 Dec 21. PubMed PMID: 29270817.

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Dauter Z, Jaskolski M. On the helical arrangements of protein molecules. Protein Sci. 2018 Mar;27(3):643-652. doi: 10.1002/pro.3356. Epub 2017 Dec 20. PubMed PMID: 29194829; PubMed Central PMCID: PMC5818761.

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Sekula B, Dauter Z. Crystal structure of thermospermine synthase from Medicago truncatula and substrate discriminatory features of plant aminopropyltransferases. Biochem J. 2018 Feb 23;475(4):787-802. doi: 10.1042/BCJ20170900. PubMed PMID: 29367265.

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Wlodawer A, Dauter Z, Porebski PJ, Minor W, Stanfield R, Jaskolski M, Pozharski E, Weichenberger CX, Rupp B. Detect, correct, retract: How to manage incorrect structural models. FEBS J. 2018 Feb;285(3):444-466. doi: 10.1111/febs.14320. Epub 2017 Nov 27. Review. PubMed PMID: 29113027; PubMed Central PMCID: PMC5799025.

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Brzezinski K, Czyrko J, Sliwiak J, Nalewajko-Sieliwoniuk E, Jaskolski M, Nocek B, Dauter Z. S-adenosyl-L-homocysteine hydrolase from a hyperthermophile (Thermotoga maritima) is expressed in Escherichia coli in inactive form - Biochemical and structural studies. Int J Biol Macromol. 2017 Nov;104(Pt A):584-596. doi: 10.1016/j.ijbiomac.2017.06.065. Epub 2017 Jun 16. PubMed PMID: 28629859.

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Luo Z, Dauter Z, Gilski M. Four highly pseudosymmetric and/or twinned structures of d(CGCGCG)₂ extend the repertoire of crystal structures of Z-DNA. Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):940-951. doi: 10.1107/S2059798317014954. Epub 2017 Oct 30. PubMed PMID: 29095165; PubMed Central PMCID: PMC5683016.

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Wlodawer A, Li M, Dauter Z. High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective. Structure. 2017 Oct 3;25(10):1589-1597.e1. doi: 10.1016/j.str.2017.07.012. Epub 2017 Aug 31. PubMed PMID: 28867613; PubMed Central PMCID: PMC5657611.

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Ruszkowski M, Dauter Z. Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD⁺ Binding and the Cofactor Positioned to Accept a Hydride. Sci Rep. 2017 Sep 5;7(1):10476. doi: 10.1038/s41598-017-10859-0. PubMed PMID: 28874718; PubMed Central PMCID: PMC5585171.

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Pyra A, Brzozowska E, Pawlik K, Gamian A, Dauter M, Dauter Z. Tail tubular protein A: a dual-function tail protein of Klebsiella pneumoniae bacteriophage KP32. Sci Rep. 2017 May 22;7(1):2223. doi: 10.1038/s41598-017-02451-3. PubMed PMID: 28533535; PubMed Central PMCID: PMC5440376.

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Wlodawer A, Dauter Z. `Atomic resolution': a badly abused term in structural biology. Acta Crystallogr D Struct Biol. 2017 Apr 1;73(Pt 4):379-380. doi: 10.1107/S205979831700225X. Epub 2017 Mar 31. PubMed PMID: 28375149; PubMed Central PMCID: PMC5379937.

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Luo Z, Dauter Z. Embarras de richesses - It is not good to be too anomalous: Accurate structure of selenourea, a chiral crystal of planar molecules. PLoS One. 2017;12(2):e0171740. doi: 10.1371/journal.pone.0171740. eCollection 2017. PubMed PMID: 28207770; PubMed Central PMCID: PMC5313157.

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Dauter M, Dauter Z. Many Ways to Derivatize Macromolecules and Their Crystals for Phasing. Methods Mol Biol. 2017;1607:349-356. doi: 10.1007/978-1-4939-7000-1_14. Review. PubMed PMID: 28573580; PubMed Central PMCID: PMC5557042.

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Dauter Z. Collection of X-Ray Diffraction Data from Macromolecular Crystals. Methods Mol Biol. 2017;1607:165-184. doi: 10.1007/978-1-4939-7000-1_7. Review. PubMed PMID: 28573573; PubMed Central PMCID: PMC5557013.

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Luo Z, Dauter Z. Detection of twinning in macromolecular crystallography. ZEITSCHRIFT FUR KRISTALLOGRAPHIE-CRYSTALLINE MATERIALS. 2016 October; 231(10, Special Issue):561-571. doi: 10.1515/zkri-2016-1946.

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Malinska M, Dauter M, Dauter Z. Geometry of guanidinium groups in arginines. Protein Sci. 2016 Sep;25(9):1753-6. doi: 10.1002/pro.2970. Epub 2016 Jul 4. PubMed PMID: 27326702; PubMed Central PMCID: PMC5338231.

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Ruszkowski M, Dauter Z. On methylene-bridged cysteine and lysine residues in proteins. Protein Sci. 2016 Sep;25(9):1734-6. doi: 10.1002/pro.2958. Epub 2016 Jun 17. PubMed PMID: 27261771; PubMed Central PMCID: PMC5338236.

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Pletneva NV, Pletnev S, Pakhomov AA, Chertkova RV, Martynov VI, Muslinkina L, Dauter Z, Pletnev VZ. Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms. Acta Crystallogr D Struct Biol. 2016 Aug;72(Pt 8):922-32. doi: 10.1107/S205979831601038X. Epub 2016 Jul 13. PubMed PMID: 27487823; PubMed Central PMCID: PMC4973210.

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Xu B, Luo Z, Wilson AJ, Chen K, Gao W, Yuan G, Chopra HD, Chen X, Willets KA, Dauter Z, Ren S. Multifunctional Charge-Transfer Single Crystals through Supramolecular Assembly. Adv Mater. 2016 Jul;28(26):5322-9. doi: 10.1002/adma.201600383. Epub 2016 May 4. PubMed PMID: 27146726; PubMed Central PMCID: PMC7798091.

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Malinska M, Dauter Z. Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data. Acta Crystallogr D Struct Biol. 2016 Jun;72(Pt 6):770-9. doi: 10.1107/S2059798316006355. Epub 2016 May 25. PubMed PMID: 27303797; PubMed Central PMCID: PMC4908868.

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Sliwiak J, Dauter Z, Jaskolski M. Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin. Front Plant Sci. 2016;7:668. doi: 10.3389/fpls.2016.00668. eCollection 2016. PubMed PMID: 27242869; PubMed Central PMCID: PMC4870859.

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Ruszkowski M, Dauter Z. Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants. J Biol Chem. 2016 May 6;291(19):9960-73. doi: 10.1074/jbc.M115.708727. Epub 2016 Mar 18. PubMed PMID: 26994138; PubMed Central PMCID: PMC4859000.

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Dauter Z. Objective evaluation of radiation damage in a nucleoprotein complex. Acta Crystallogr D Struct Biol. 2016 May;72(Pt 5):601-2. doi: 10.1107/S2059798316006550. Epub 2016 Apr 28. PubMed PMID: 27139623; PubMed Central PMCID: PMC4931811.

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Xu BB, Luo ZP, Gao WX, Wilson AJ, He C, Chen X, Yuan GL, Dai HL, Rao Y, Willets K, Dauter Z, Ren SQ. Solution-Processed Molecular Opto-Ferroic Crystals. CHEMISTRY OF MATERIALS. 2016 April; 28(7):2441-2448. doi: 10.1021/acs.chemmater.6b00836.

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Xu BB, Luo ZP, Gao WX, Wilson AJ, He C, Chen X, Yuan GL, Dai HL, Rao Y, Willets K, Dauter Z, Ren SQ. Solution-Processed Molecular Opto-Ferroic Crystals. CHEMISTRY OF MATERIALS. 2016 April; 28(7):2441-2448. doi: 10.1021/acs.chemmater.6b00836.

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Sekula B, Ruszkowski M, Malinska M, Dauter Z. Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants. Front Plant Sci. 2016;7:350. doi: 10.3389/fpls.2016.00350. eCollection 2016. PubMed PMID: 27066023; PubMed Central PMCID: PMC4812014.

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Kiliszek A, Banaszak K, Dauter Z, Rypniewski W. The first crystal structures of RNA-PNA duplexes and a PNA-PNA duplex containing mismatches--toward anti-sense therapy against TREDs. Nucleic Acids Res. 2016 Feb 29;44(4):1937-43. doi: 10.1093/nar/gkv1513. Epub 2015 Dec 29. PubMed PMID: 26717983; PubMed Central PMCID: PMC4770230.

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Minor W, Dauter Z, Helliwell JR, Jaskolski M, Wlodawer A. Safeguarding Structural Data Repositories against Bad Apples. Structure. 2016 Feb 2;24(2):216-20. doi: 10.1016/j.str.2015.12.010. Review. PubMed PMID: 26840827; PubMed Central PMCID: PMC4743038.

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Minor W, Dauter Z, Jaskolski M. The young person's guide to the PDB. Postepy Biochem. 2016;62(3):242-249. Review. PubMed PMID: 28132477; PubMed Central PMCID: PMC5610703.

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Dauter Z, Wlodawer A. Progress in protein crystallography. Protein Pept Lett. 2016;23(3):201-10. doi: 10.2174/0929866523666160106153524. PubMed PMID: 26732246; PubMed Central PMCID: PMC6287266.

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Dauter Z, Jaskólski M. Crystal pathologies in macromolecular crystallography. Postepy Biochem. 2016;62(3):401-407. Review. PubMed PMID: 28132496.