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Andrzej Joachimiak

Argonne Distinguished Fellow

Andrzej’s current research focuses on proteins and protein-nucleic acid interactions and includes enzymes, transcription factors and molecular chaperones.


Andrzej Joachimiak is the Director of Structural Biology Center and Midwest Center for Structural Genomics. He is an expert in synchrotron-based X-ray crystallography and structural biology. At Argonne, he has made significant contributions to the high-throughput crystallography using synchrotron radiation and the development of state-of-the-art facilities for macromolecular crystallography. The development and integration of the novel synchrotron beamlines, exploitation of the anomalous signal-based phasing methods in the third-generation environment and integration of hardware and software at the Structural Biology Center beamlines at the Advanced Photon Source contributed very strongly to the enhanced efficiency of such facilities worldwide.

Andrzej’s research has also contributed to methods development in protein expression and purification, crystallization and data collection using synchrotron radiation. The methods for phasing novel structures using X-ray crystallography have effectively reduced time and cost of structure determination. The contribution to high-throughput molecular biology and crystallography has also made a major impact on structural biology in the U.S. and globally as well. This encouraged the initiation of structural genomics and structural proteomics projects and also led to the determination of thousands of novel protein structures.

He has also made highly important contributions to the field of structural genomics. The Argonne-based Midwest Center for Structural Genomics (MCSG) is a highly successful program and major component of NIH funded Protein Structure Initiative (PSI). A number of technologies have been developed in the MCSG, including gene cloning and protein expression, new vectors for protein expression in bacteria, automated protein purification techniques, automated protein crystallization, robot-assisted crystal mounting and automated structure determination.

In addition to his duties at Argonne, Andrzej is also a Professor at the University of Chicago, Adjunct Professor at Northwestern University, Senior Fellow at the  Computation Institute  and the Institute for Genomics and Systems Biology.


  • Ph.D., Chemistry, University of A. Mickiewicz of Poznan
  • D. Sc., Molecular Biology, Institute of Biochemistry and Biophysics, Warsaw

Awards, Honors and Memberships

  • Fellow of the American Association for the Advancement of Science
  • Member of the American Crystallographic Association
  • Member of Protein Society
  • University of Chicago Award for Distinguished Performance
  • Member European Academy of Sciences
  • Member International Structural Genomics Organization Advisory Board
  • Member Protein Data Bank Advisory Committee
  • Arthur H. Compton Award, Advanced Photon Source
  • Member Polish Academy of Arts and Sciences

Selected Publications 

  • Tan K, Tesar C, Wilton R, Keigher L, Babnigg G, Joachimiak A. Novel {alpha}-glucosidase from human gut microbiome: substrate specificities and their switch.  (2010) The FASEB Journal, 24:3939-49.
  • Kim YC, Zhou M, Moy S, Morales J, Cunningham MA, Joachimiak A. Structure and analysis of the nitrile reductase QueF from V. cholera.  (2010) J. Mol. Biol. 404:127-137.
  • Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. (2011) Mol Microbiol. 79:484-502.
  • Kim Y, Joachimiak G, Ye Z, Binkowski TA, Zhang R, Gornicki P, Callahan SM, Hess WR, Haselkorn R, Joachimiak A. Structure of transcription factor HetR required for heterocyst differentiation in cyanobacteria. (2011) Proc Natl Acad Sci U S A. 108:10109-14.
  • Kern J, Wilton R, Zhang R, Binkowski TA, Joachimiak A, Schneewind O. Structure of the SLH domains from Bacillus anthracis surface array protein. (2011) J Biol Chem. 286:26042-9.
  • Kim Y, Tesar C, Mire J, Jedrzejczak R, Binkowski A, Babnigg G,  Sacchettini J, Joachimiak A. Structure of Apo- and Monometalated Forms of NDM-1 – a Highly Potent Carbapenem-Hydrolyzing Metallo-β-Lactamase. (2011) Plos One, 6:e24621.
  • Nusca TD, Kim Y, Maltseva N, Lee JY, Eschenfeldt W, Stols L, Schofield MM, Scaglione JB, Dixon SD, Oves-Costales D, Challis GL, Hanna PC, Pfleger BF, Joachimiak A, Sherman DH. Functional and Structural Analysis of the Siderophore Synthetase AsbB through Reconstitution of the Petrobactin Biosynthetic Pathway from Bacillus anthracis. (2012) J Biol Chem. 287(19):16058-72.
  • Osipiuk J, Mulligan R, Bargassa M, Hamilton JE, Cunningham MA, Joachimiak A. Characterization of Member of DUF1888 Protein Family, Self-cleaving and Self-assembling Endopeptidase. (2012) J Biol Chem. 287(23):19452-61
  • Nocek B, Tikhonov A, Babnigg G, Gu M, Zhou M, Makarova KS, Vondenhoff G, Aerschot AV, Kwon K, Anderson WF, Severinov K, Joachimiak A. Structural and Functional Characterization of Microcin C Resistance Peptidase MccF from Bacillus anthracis.  (2012) J Mol Biol. 420(4-5):366-83 
  • Yang DC, Tan K, Joachimiak A, Bernhardt TG.  A conformational switch controls cell wall-remodelling enzymes required for bacterial cell division. (2012) Mol Microbiol. 85(4):768-81.
  • Michalska K, Chang C, Mack JC, Zerbs S, Joachimiak A, Collart FR. Characterization of Transport Proteins for Aromatic Compounds Derived from Lignin: Benzoate Derivative Binding Proteins. (2012) J Mol Biol. 423(4):555-75
  • Binkowski TA, Marino SR, Joachimiak A. Predicting HLA Class I Non-Permissive Amino Acid Residues Substitutions. (2012) PLoS One. 7(8):e41710
  • Kim Y, Cunningham MA, Mire J, Tesar C, Sacchettini J, Joachimiak A. NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism. (2013) FASEB J. 27(5):1917-27
  • Michalska K, Tan K, Li H, Hatzos-Skintges C, Bearden J, Babnigg G, Joachimiak A. GH1 family 6-P-β-glucosidases from human microbiome lactic acid bacteria. (2013) Acta Crystallographica Section D, 69(Pt 3):451-63
  • Kim Y, Ye Z, Joachimiak G, Videau P, Young J, Hurd K, Callahan SM, Gornicki P, Zhao J, Haselkorn R, Joachimiak A. (2013) Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets, Proc. Nat. Acad. Sci. USA, 110(19):E1716-23
  • Finfrock YZ, Stern EA, Alkire RW, Kas JJ, Evans-Lutterodt K, Stein A, Duke N, Lazarski K, Joachimiak A. Mitigation of X-ray damage in macromolecular crystallography by submicrometre line focusing. (2013) Acta Crystallogr D Biol Crystallogr. 69(Pt 8):1463-9
  • Lemak S, Beloglazova N, Nocek B, Skarina T, Flick R, Brown G, Popovic A, Joachimiak A, Savchenko A, Yakunin AF. The Ring” of the CRISPR: toroidal structure and nuclease activity of the Cas4 protein of CRISPR interference, (2013) J. Am. Chem. Soc. 135(46):17476-87
  • Tan K, Chhor G, Binkowski TA, Jedrzejczak RP, Makowska-Grzyska M, Joachimiak A. Sensor domain of histidine kinase KinB of Pseudomonas — a helix-swapped dimer, (2014) J. Biol. Chem. 89(18): 12232-44
  • Michalska K, Chhor G, Clancy S, Jedrzejczak R, Babnigg G, Winans SC, Joachimiak A. RsaM: a transcriptional regulator of Burkholderia spp, with novel fold. (2014) FEBS Letters 281(18):4293-306
  • Lemak S, Nocek B, Beloglazova N, Skarina T, Flick R, Brown G, Joachimiak A, Savchenko A, Yakunin AF. The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity. (2014) Nucleic Acids Res. 42(17):11144-55
  • Sun Z, Khan J, Makowska-Grzyska M, Zhang M, Cho JH, Suebsuwong , Vo ,  Gollapalli DR, Kim Y, Joachimiak A, Hedstrom L, Cuny GD. Synthesis, in vitro evaluation and co-crystal structure of 4-oxo-[1]benzopyrano[4,3-c]pyrazole Cryptosporidium par-vum inosine 5’-monophosphate dehydrogenase (CpIMPDH) inhibitors. (2014) J Medicinal Chemistry. 57(24):10544-50
  • Makowska-Grzyska M, Kim Y, Maltseva N, Osipiuk J, Gu M, Zhang M, Mandapati K, Gollapalli DR, Gorla SK, Hedstrom L, Joachimiak A. A Novel Cofactor Binding Mode in Bacterial IMP Dehydrogenases Explains Inhibitor Selectivity. (2014) J. Biol. Chem. 290(9):5893-911
  • Hammerstrom TG, Horton LB, Swick MC, Joachimiak A, Osipiuk J, Koehler TM. Crystal structure of Bacillus anthracis virulence regulator AtxA and effects of phosphorylated histidines on multimerization and activity. (2015) Mol Microbiol.  95(3):426-41
  • Paul S, Aggarwal C, Thakur JK, Bandeppa GS, Khan MA, Pearson LM, Babnigg G, Giometti CS, Joachimiak A. Induction of Osmoadaptive Mechanisms and Modulation of Cellular Physiology Help Bacillus licheniformis Strain SSA 61 Adapt to Salt Stress. (2015) Curr Microbiol. 70(4):610-7
  • Filippova EV, Kuhn ML, Osipiuk J, Kiryukhina O, Joachimiak A, Ballicora MA, Anderson WF. A Novel Polyamine Allosteric Site of SpeG from Vibrio cholerae Is Revealed by Its Dodecameric Structure. (2015) J Mol Biol 427(6ptB):1316-34
  • Yu HY, Ziegelhoffer T, Osipiuk J, Ciesielski SJ, Baranowski M, Zhou M, Joachimiak A, Craig EA. Roles of Intramolecular and Intermolecular Interactions in Functional Regulation of the Hsp70 J-protein Co-Chaperone Sis1. (2015) J Mol Biol. 427(7):1632-43
  • Fan Y, Tan K, Chhor G, Butler EK, Jedrzejczak RP, Missiakas D, Joachimiak A. EsxB, a secreted protein from Bacillus anthracis forms two distinct helical bundles. (2015) Protein Sci. 24(9):1389-400
  • Michalska K, Steen AD, Chhor G, Endres M, Webber AT, Bird J, Lloyd KG, Joachimiak A. New aminopeptidase from microbial dark matter” archaeon. (2015) FASEB J. 29(30):18678-98
  • Glaza P, Osipiuk J, Wenta T, Zurawa-Janicka D, Jarzab M, Lesner A, Banecki B, Skorko-Glonek J, Joachimiak A, Lipinska B. Structural and Functional Analysis of Human HtrA3 Protease and Its Subdomains. (2015) PLoS One 10(6):e0131142
  • Filippova EV, Weigand S, Osipiuk J, Kiryukhina O, Joachimiak A, Anderson WF. Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG. (2015) J Mol BIol.  427(22):3538-53
  • Lohman JR, Ma M, Osipiuk J, Nocek B, Kim Y, Chang C, Cuff M, Mack J, Bigelow L, Li H, Endres M, Babnigg G, Joachimiak A, Phillips GN Jr, Shen B. Structural and evolutionary relationships of AT-less” type I polyketide synthase ketosynthases. (2015) Proc Natl Acad Sci USA. 112(41):12693-8
  • Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A. A novel transcriptional regulator of L-arabinose utilization in human gut bacteria. (2015) Nucleic Acids Res. 43(21):10546-59
  • Makowska-Grzyska M, Kim Y, Gorla SK, Wei Y, Mandapati K, Zhang M, Maltseva N, Modi G, Boshoff HI, Gu M, Aldrich C, Cuny GD, Hedstrom L, Joachimiak A. Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds. (2015) PLoS One. 10(10):e0138976
  • Tan K, Zhou Q, Cheng B, Zhang Z, Joachimiak A, Tse-Dinh YC. Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I. (2015) Nucleic Acids Res. 43(22):11031-46
  • Michalska K, Tan K, Chang C, Li H, Hatzos-Skintges C, Molitsky M, Alkire R, Joachimiak A. In situ X-ray data collection and structure phasing of protein crystals at Structural Biology Center 19-ID. (2015) J Synchrotron Radiat. 22(Pt 6):1386-95
  • Tan K, Cao N, Cheng B, Joachimiak A, Tse-Dinh YC. Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold. (2016) J Mol Biol. 428(1):182-93
  • Manjasetty BA, Halavaty AS, Luan CH, Osipiuk J, Mulligan R, Kwon K, Anderson WF, Joachimiak A. Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity. (2016) J Struct Biol. 194(1):18-28
  • Sung N, Lee J, Kim JH, Chang C, Joachimiak A, Lee S, Tsai FT. Mitochondrial Hsp90 is a ligand-activated molecular chaperone coupling ATP binding to dimer closure through a coiled-coil intermediate. (2016) Proc Natl Acad Sci USA. 113(11):2952-7
  • Verduzco-Castro EA, Michalska K, Endres M, Juárez-Vazquez AL, Noda-García L, Chang C, Henry CS, Babnigg G, Joachimiak A, Barona-Gómez F. Co-occurrence of Analogous Enzymes Determines Evolution of a Novel (βα)8-Isomerase Sub-family After Non-conserved Mutations in Flexible Loop. (2016) Biochem J. 473(9):1141-52
  • Kim Y, Joachimiak G, Bigelow L, Babnigg G, Joachimiak A. How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator. (2016) J Biol Chem. 291(25):13243-56.
  • Hajighasemi M, Nocek BP, Tchigvintsev A, Brown G, Flick R, Xu X, Cui H, Hai T, Joachimiak A, Golyshin PN, Savchenko A, Edwards EA, Yakunin AF. Biochemical and Structural Insights into Enzymatic Depolymerization of Polylactic Acid and Other Polyesters by Microbial Carboxylesterases. (2016) Biomacromolecules. 17(6):2027-39
  • Huang L, Khusnutdinova A, Nocek B, Brown G, Xu X, Cui H, Petit P, Flick R, Zallot R, Balmant K, Ziemak MJ, Shanklin J, de Crécy-Lagard V, Fiehn O, Gregory JF 3rd, Joachimiak A, Savchenko A, Yakunin AF, Hanson AD. A family of metal-dependent phosphatases implicated in metabolite damage-control. (2016) Nat Chem Biol. 12(8):621-7
  • Huang T, Chang CY, Lohman JR, Rudolf JD, Kim Y, Chang C, Yang D, Ma M, Yan X, Crnovcic I, Bigelow L, Clancy S, Bingman CA, Yennamalli RM, Babnigg G, Joachimiak A, Phillips GN, Shen B. Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027. (2016) J Antibiot (Tokyo). 69(10):731-740
  • Rudolf JD, Dong LB, Cao H, Hatzos-Skintges C, Osipiuk J, Endres M, Chang CY, Ma M, Babnigg G, Joachimiak A, Phillips GN Jr, Shen B. Structure of the ent-Copalyl Diphosphate Synthase PtmT2 from Streptomyces platensis CB00739, a Bacterial Type II Diterpene Synthase. (2016) J Am Chem Soc. 138(34): 10905-15
  • Jha RK, Kern TL, Kim Y, Tesar C, Jedrzejczak R, Joachimiak A, and Strauss CEM. A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor. (2016) Nucleic Acids Res. 44(17): 8490-500
  • Popovic A, Hai T, Tchigvintsev A, Hajighasemi M, Nocek B, Khusnutdinova AN, Brown G, Glinos J, Flick R, Skarina T, Chernikova TN, Yim V, Brüls T, Paslier DL, Yakimov MM, Joachimiak A, Ferrer M, Golyshina OV, Savchenko A, Golyshin PN, Yakunin AF. Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families. (2017) Sci Rep. 7:44103.
  • Batot G, Michalska K, Ekberg G, Irimpan EM, Joachimiak G, Jedrzejczak R, Babnigg G, Hayes CS, Joachimiak A, Goulding CW. The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily. (2017) Nucleic Acid Res. 45(9): 5013-5025.
  • Tan K, Deatherage Kaiser BL, Wu R, Cuff M, Fan Y, Bigelow L, Jedrzejczak RP, Adkins JN, Cort JR, Babnigg G, Joachimiak A. Insights into PG-binding, conformational change, and dimerization of the OmpA C-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi. (2017) Protein Sci. 26(9):1738-1748.
  • Forlani G, Nocek B, Chakravarthy S, Joachimiak A. Functional Characterization of Four Putative δ(1)-Pyrroline-5-Carboxylate Reductases from Bacillus subtilis. (2017) Front Microbiol. 8:1442.
  • Wellington S, Nag PP, Michalska K, Johnston SE, Jedrzejczak RP, Kaushik VK, Clatworthy AE, Siddiqi N, McCarren P, Bajrami B, Maltseva NI, Combs S, Fisher SL, Joachimiak A, Schreiber SL, Hung DT. A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase. (2017) Nat Chem Biol. Sep;13(9):943-950.
  • Michalska K, Gucinski GC, Garza-Sánchez F, Johnson PM, Stols LM, Eschenfeldt WH, Babnigg G, Low DA, Goulding CW, Joachimiak A, Hayes CS. Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs, (2017) Nucleic Acids Research, 45(17):10306-10320.
  • van den Bosch TJM, Tan K, Joachimiak A, Welte CU. Functional profiling and crystal structures of isothiocyanate hydrolases found in gut-associated and plant pathogenic bacteria. (2018) Appl Environ Microbiol. pii: AEM.00478-18.
  • Tan K, Tesar C, Wilton R, Jedrzejczak RP, Joachimiak A. Interaction of antidiabetic α-glucosidase inhibitors and gut bacteria α-glucosidase. Protein Sci. 2018 27(8):1498-1508.
  • Michalska K, Quan Nhan D, Willett JLE, Stols LM, Eschenfeldt WH, Jones AM, Nguyen JY, Koskiniemi S, Low DA, Goulding CW, Joachimiak A, Hayes CS. Functional  plasticity of antibacterial EndoU toxins. Mol Microbiol. 2018 109(4):509-527.
  • Cao N, Tan K, Annamalai T, Joachimiak A, Tse-Dinh YC. Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site. (2018) Nucleic Acids Res. Jun 14.
  • Chang C, Amer BR, Osipiuk J, McConnell SA, Huang IH, Hsieh V, Fu J, Nguyen HH, Muroski J, Flores E, Ogorzalek Loo RR, Loo JA, Putkey JA, Joachimiak A, Das A, Clubb RT, Ton-That H. In vitro reconstitution of sortase-catalyzed pilus polymerization reveals structural elements involved in pilin cross-linking. (2018) Proc Natl Acad Sci USA. 12;115(24):E5477-E5486.
  • Chang CY, Yan X, Crnovcic I, Annaval T, Chang C, Nocek B, Rudolf JD, Yang D, Hindra, Babnigg G, Joachimiak A, Phillips GN Jr, Shen B. Resistance to Enediyne Antitumor Antibiotics by Sequestration. Cell Chem Biol. 2018 25(9):1075-1085.e4.
  • Kim Y, Chhor G, Tsai CS, Winans JB, Jedrzejczak R, Joachimiak A, Winans SC. Crystal structure of the ligand-binding domain of a LysR-type transcriptional regulator: transcriptional activation via a rotary switch. Mol Microbiol. 2018 110(4):550-561.
  • Dementiev A, Joachimiak A, Nguyen H, Gorelik A, Illes K, Shabani S, Gelsomino M, Ahn EE, Nagar B, Doan N. Molecular mechanism of inhibition of acid ceramidase by carmofur.  (2019) J Med Chem. Jan 24;62(2):987-992
  • Michalska K, Zhang K, March ZM, Hatzos-Skintges C, Pintilie G, Bigelow L, Castellano LM, Miles LJ, Jackrel ME, Chuang E, Jedrzejczak R, Shorter J, Chiu W, Joachimiak A. Structure of Calcarisporiella thermophila Hsp104 disaggregase that antagonizes diverse proteotoxic misfolding events. (2019) Structure Mar 5;27(3):449-463
  • Yu R, Kim Y, Maltseva N, Braunstein P, Joachimiak A, Hedstrom L. Oxanosine monophosphate is a covalent inhibitor of inosine 5′-monophosphate dehydrogenase. (2019) Chem Res Toxicol. Mar 18;32(3):456-466
  • Michalska k, Gale J, Joachimiak G, Chang C, Hatzos-Skintges C, Nocek B, Johnston SE, Bigelow L, Bajrami B, Jedrzejczak RP, Wellington S, Hung DT, Nag P, Fisher SL, Endres M, Joachimiak A. Conservation of the structure and function of bacterial tryptophan synthases. (2019). IUCrJ. May 29;6(Pt 4):649-664