Education:
  • Graduate Certificate in Leadership, University of Virginia (2016-2019)
  • Ph.D. in Chemistry - A.N. Bach Institute of Biochemistry, Russian Academy of Sciences (2006-2010)
  • M.Sc. - Moscow State University (2001-2006)
Research Interest:
  • Macromolecular structure elucidation and refinement. Exploration of novel methods for crystallographic structure solution and solving "mission impossible" structures.
  • Studies of serum albumin as the transporter of drugs, metals, and hormones in the mammalian blood plasma
  • High-throughput structure determination and functional studies of proteins, including potential drug-targets, from pathogens causing emerging and re-emerging infectious diseases using a combination of X-ray crystallography and other biophysical methods.
  • Developing integrative techniques for highly efficient protein crystallization with a goal of maximizing the number of successful crystallizations, yet minimizing the resources used.
  • Quality assessment of crystallographic protein structures. Ligand and metal identification and judicious modeling.
  • Metal binding to protein and RNA. Developing a protocol for characterizing metal binding sites in proteins with X-ray crystallography. Developing a protocol for Mg-binding sites validation and classification in RNA crystal structures.
CV:
  • Published 33 peer-reviewed publications and 3 book chapters
  • Deposited more than 130 protein structures to the PDB
  • Presentated at 24 conferences and workshops, including 7 invited talks
  • Taught a 5-day course “Structure determination with HKL3000” at RapiData – a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution, Stanford University (2017, 2018, and 2019)
  • Lectured on data processing with HKL3000, structure refinement and validation at Workshop on data collection and structure solving in macromolecular X-ray diffraction. Krakow, Poland (2019)
  • Co-developed an integrative protocol for highly efficient protein crystallization. Achieved 45% success rate for a set of 95 proteins (structure determined for 46 proteins)
  • Co-developed an integrative protocol for characterizing metal-binding sites in proteins with X-ray crystallography
  • Recipient of the Best Postdoc Poster Award at 43rd Mid-Atlantic Macromolecular Crystallography Meeting (2013)
  • Four awards during graduate/undergraduate studies
  • Contributed to the development of MgRNA server https://csgid.org/csgid/metalnas/
  • Contributed to the development of CheckMyMetal server https://csgid.org/csgid/metal_sites/
  • Contributed to the development of 2HADH knowledgebase http://2hadh.bioreproducibility.org/
  • Contributed content to https://covid-19.bioreproducibility.org//

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Publications with the Minor Lab

  1. Grabowski M, Macnar JM, Cymborowski M, Cooper DR, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Dauter Z, Rupp B, Wlodawer A, Jaskolski M, Minor W (2021)
    Rapid response to emerging biomedical challenges and threats
    IUCrJ [DOI:10.1107/S2052252521003018]
  2. Grabowski M, Cooper DR, Brzezinski D, Macnar JM, Shabalin IG, Cymborowski M, Otwinowski Z, Minor W (2021)
    Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective.
    Nucl Instrum Methods Phys Res B 489: 30-40. [DOI:10.1016/j.nimb.2020.12.016] [Pub Med ID: 33603257] [Pub Med Central ID: PMC7886262]
  3. Cooper DR, Grabowski M, Zimmerman MD, Porebski PJ, Shabalin IG, Woinska M, Domagalski MJ, Zheng H, Sroka P, Cymborowski M, Czub MP, Niedzialkowska E, Venkataramany BS, Osinski T, Fratczak Z, Bajor J, Gonera J, MacLean E, Wojciechowska K, Konina K, Wajerowicz W, Chruszcz M, Minor W (2020)
    State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and in Vitro Biochemical Experiments.
    Methods Mol Biol 2199: 209-236. [DOI:10.1007/978-1-0716-0892-0_13] [Pub Med ID: 33125653] [Pub Med Central ID: PMC8019398]
  4. Brzezinski D, Kowiel M, Cooper DR, Cymborowski M, Grabowski M, Wlodawer A, Dauter Z, Shabalin IG, Gilski M, Rupp B, Jaskolski M, Minor W (2020)
    Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models.
    Protein Sci 30: 115-124. [DOI:10.1002/pro.3959] [Pub Med ID: 32981130] [Pub Med Central ID: PMC7537053] Times cited: 4
  5. Shabalin IG, Czub MP, Majorek KA, Brzezinski D, Grabowski M, Cooper DR, Panasiuk M, Chruszcz M, Minor W (2020)
    Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy.
    IUCrJ [DOI:10.1107/S2052252520012944] [Pub Med ID: 33063792] [Pub Med Central ID: PMC7553145] Times cited: 4
  6. Wlodawer A, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Minor W, Rupp B, Jaskolski M (2020)
    Ligand-centered assessment of SARS-CoV-2 drug target models in the Protein Data Bank.
    FEBS J 287: 3703-3718. [DOI:10.1111/febs.15366] [Pub Med ID: 32418327] [Pub Med Central ID: PMC7276724] Times cited: 10
  7. Czub MP, Handing KB, Venkataramany BS, Cooper DR, Shabalin IG, Minor W (2020)
    Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma.
    J Med Chem 63: 6847-6862. [DOI:10.1021/acs.jmedchem.0c00225] [Pub Med ID: 32469516] [Pub Med Central ID: PMC7902233] Times cited: 5
  8. Minasov G, Lam MR, Rosas-Lemus M, Rosas Lemus M, Sławek J, Woinska M, Shabalin IG, Shuvalova L, Palsson BØ, Godzik A, Minor W, Satchell KJF (2020)
    Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis.
    Protein Sci 29: 1618-1628. [DOI:10.1002/pro.3876] [Pub Med ID: 32306515] [Pub Med Central ID: PMC7314395]
  9. Majorek KA, Zimmerman MD, Grabowski M, Shabalin I, Zheng H, Minor W (2020)
    Assessment of Crystallographic Structure Quality and Protein–Ligand Complex Structure Validation
    in Structural Biology in Drug Discovery: Methods, Techniques, and Practices : 253-275. [DOI:10.1002/9781118681121.ch11]
  10. Shabalin IG, Gritsunov A, Hou J, Sławek J, Miks CD, Cooper DR, Minor W, Christendat D (2019)
    Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.
    FEBS J 287: 2235-2255. [DOI:10.1111/febs.15150] [Pub Med ID: 31750992] [Pub Med Central ID: PMC7239764] Times cited: 1
  11. Grabowski M, Cymborowski M, Porebski PJ, Osinski T, Shabalin IG, Cooper DR, Minor W (2019)
    The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years.
    Struct Dyn 6: 064301. [DOI:10.1063/1.5128672] [Pub Med ID: 31768399] [Pub Med Central ID: PMC6874509] Times cited: 6
  12. Lipowska J, Miks CD, Kwon K, Shuvalova L, Zheng H, Lewiński K, Cooper DR, Shabalin IG, Minor W (2019)
    Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae.
    Int J Biol Macromol 136: 1176-1187. [DOI:10.1016/j.ijbiomac.2019.05.149] [Pub Med ID: 31207330] [Pub Med Central ID: PMC6686667] Times cited: 3
  13. Czub MP, Venkataramany BS, Majorek KA, Handing KB, Porebski PJ, Beeram SR, Suh K, Woolfork AG, Hage DS, Shabalin IG, Minor W (2019)
    Testosterone meets albumin - the molecular mechanism of sex hormone transport by serum albumins.
    Chem Sci 10: 1607-1618. [DOI:10.1039/c8sc04397c] [Pub Med ID: 30842823] [Pub Med Central ID: PMC6371759] Times cited: 13
  14. Kowiel M, Brzezinski D, Porebski PJ, Shabalin IG, Jaskolski M, Minor W (2019)
    Automatic recognition of ligands in electron density by machine learning.
    Bioinformatics 35: 452-461. [DOI:10.1093/bioinformatics/bty626] [Pub Med ID: 30016407] [Pub Med Central ID: PMC6361236] Times cited: 8
  15. Grabowski M, Shabalin I, Porebski PJ, Domagalski MJ, Zheng H, Cooper D, Venkataramany BS, Bourne PE, Minor W (2019)
    Data Sharing in Structural Biology: Advances and Challenges
    in Data Sharing: Recent Progress and Remaining Challenges - Computer Science, Technology and Applications, Nova Science Publishers, New York : 29-68.
  16. Matelska D, Shabalin IG, Jabłońska J, Domagalski MJ, Kutner J, Ginalski K, Minor W (2019)
    Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.
    BMC Evol Biol 18: 199. [DOI:10.1186/s12862-018-1309-8] [Pub Med ID: 30577795] [Pub Med Central ID: PMC6303947] Times cited: 6
  17. Mussakhmetov A, Shumilin IA, Nugmanova R, Shabalin IG, Baizhumanov T, Toibazar D, Khassenov B, Minor W, Utepbergenov D (2018)
    A transient post-translational modification of active site cysteine alters binding properties of the parkinsonism protein DJ-1.
    Biochem. Biophys. Res. Commun. 504: 328-333. [DOI:10.1016/j.bbrc.2018.08.190] [Pub Med ID: 30190129] Times cited: 7
  18. Raczynska JE, Shabalin IG, Minor W, Wlodawer A, Jaskolski M (2018)
    A close look onto structural models and primary ligands of metallo-β-lactamases.
    Drug Resist Updat 40: 1-12. [DOI:10.1016/j.drup.2018.08.001] [Pub Med ID: 30466711] [Pub Med Central ID: PMC6260963] Times cited: 28
  19. Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W (2018)
    Characterizing metal-binding sites in proteins with X-ray crystallography.
    Nat Protoc 13: 1062-1090. [DOI:10.1038/nprot.2018.018] [Pub Med ID: 29674755] [Pub Med Central ID: PMC6235626] Times cited: 25
    F1000 Recommended Publication
  20. Kutner J, Shabalin IG, Matelska D, Handing KB, Gasiorowska O, Sroka P, Gorna MW, Ginalski K, Wozniak K, Minor W (2018)
    Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
    Biochemistry 57: 963-977. [DOI:10.1021/acs.biochem.7b01137] [Pub Med ID: 29309127] [Pub Med Central ID: PMC6469932] Times cited: 9
  21. Shabalin IG, Porebski PJ, Minor W (2018)
    Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment.
    Crystallogr Rev 24: 236-262. [DOI:10.1080/0889311X.2018.1521805] [Pub Med ID: 30416256] [Pub Med Central ID: PMC6219471] Times cited: 16
  22. Zheng H, Cooper DR, Porebski PJ, Shabalin IG, Handing KB, Minor W (2017)
    CheckMyMetal: a macromolecular metal-binding validation tool.
    Acta Crystallogr D Struct Biol 73: 223-233. [DOI:10.1107/S2059798317001061] [Pub Med ID: 28291757] [Pub Med Central ID: PMC5349434] Times cited: 109
  23. Handing KB, Shabalin IG, Kassaar O, Khazaipoul S, Blindauer CA, Stewart AJ, Chruszcz M, Minor W (2016)
    Circulatory zinc transport is controlled by distinct interdomain sites on mammalian albumins.
    Chem Sci 7: 6635-6648. [DOI:10.1039/c6sc02267g] [Pub Med ID: 28567254] [Pub Med Central ID: PMC5450522] Times cited: 29
  24. Handing KB, Shabalin IG, Szlachta K, Majorek KA, Minor W (2016)
    Crystal structure of equine serum albumin in complex with cetirizine reveals a novel drug binding site.
    Mol. Immunol. 71: 143-151. [DOI:10.1016/j.molimm.2016.02.003] [Pub Med ID: 26896718] [Pub Med Central ID: PMC4800003] Times cited: 15
  25. Niedzialkowska E, Gasiorowska O, Handing KB, Majorek KA, Porebski PJ, Shabalin IG, Zasadzinska E, Cymborowski M, Minor W (2016)
    Protein purification and crystallization artifacts: The tale usually not told.
    Protein Sci 25: 720-33. [DOI:10.1002/pro.2861] [Pub Med ID: 26660914] [Pub Med Central ID: PMC4815408] Times cited: 24
  26. Shabalin I, Dauter Z, Jaskolski M, Minor W, Wlodawer A (2015)
    Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.
    Acta Crystallogr D Biol Crystallogr. 71: 1965-79. [DOI:10.1107/S139900471500629X] [Pub Med ID: 26327386] [Pub Med Central ID: PMC4556316] Times cited: 39
  27. Zhou D, Hansen D, Shabalin IG, Gustchina A, Vieira DF, de Brito MV, Araújo AP, Oliva ML, Wlodawer A (2015)
    Structure of BbKI, a disulfide-free plasma kallikrein inhibitor.
    Acta Crystallogr F Struct Biol Commun 71: 1055-62. [DOI:10.1107/S2053230X15011127] [Pub Med ID: 26249699] [Pub Med Central ID: PMC4528941] Times cited: 3
  28. Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W (2015)
    Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection.
    Nucleic Acids Res. 43: 3789-801. [DOI:10.1093/nar/gkv225] [Pub Med ID: 25800744] [Pub Med Central ID: PMC4402538] Times cited: 48
  29. Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W (2015)
    X-ray crystallography over the past decade for novel drug discovery - where are we heading next?
    Expert Opin Drug Discov 10: 975-89. [DOI:10.1517/17460441.2015.1061991] [Pub Med ID: 26177814] [Pub Med Central ID: PMC4655606] Times cited: 32
  30. Shabalin IG, Porebski PJ, Cooper DR, Grabowski M, Onopriyenko O, Grimshaw S, Savchenko A, Chruszcz M, Minor W (2012)
    Structure of anabolic ornithine carbamoyltransferase from Campylobacter jejuni at 2.7 Å resolution.
    Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68: 1018-24. [DOI:10.1107/S1744309112031259] [Pub Med ID: 22949186] [Pub Med Central ID: PMC3433189] Times cited: 4