Skip to main content

Youngchang Kim

Protein Crystallographer

Prof. Youngchang Kim is a structural biologist/crystallographer with an extensive background in protein purification and characterization.


I am a structural biologist/crystallographer with an extensive background in protein purification and characterization. I have been a part of NIH structural genomics programs Midwest Center for Structural Genomics (MCSG, PSI:biology, NIGMS) and Center for Structural Genomics of Infectious Diseases (CSGID, NIAID) working to build high-throughput pipeline for protein structure determination. I helped to develop automated methods for protein purification at the beginning of MCSG program and participated in characterizing crystals for suitability for structure determination, collecting data and determining crystal structures, and have contributed about 500 structures to the PDB. In addition, supervised the group carrying out purification and crystallization and led the crystallography group determining structures for structural genomics program. Main targets of the structural genomics have been proteins of new folds, unknown function, and health-related: proteins from human/animal pathogens, drug targets, and others involved in virulence. Also as a member of the Structural Biology Center (SBC), one of the best Synchrotron X-ray beam lines for macromolecule crystallography, hosting public users, reviewing proposals for beamtime application for Advanced Photon Sources, testing instrumentation, software, and protocols at the sector 19 beamlines. Starting more recently, became a part of Chicago Center for Functional Annotation (CCFA, NIAID) as a director of technological core at Argonne National Lab site carrying out biochemical/biophysical characterization to complement efforts by U. Chicago researchers studying biological functions of unknown genes from Brucella and Yesinia. 


Graduated from Seoul National University (Seoul, Korea) College of Education (Science, Chemistry) went to the graduate school majoring in chemstry learning X-ray crystallography at the same university, College of Natural Sciences. Had my Ph.D at University of Pittsburgh in Crystallography, spent an additional year as a postdoc before move to Yale for another postdocral stay. Got a faculty position as an assistant professorof of department of Biochemistry at Vanderbilt University for seven year. The final year was spent for sabbatical at SBC/BIO at Argonne National Lab. Became a full staff BIO/SBC since.

Research interests

Structural genomics in general: technology involved in purification and crystallization of proteins and protein complexes, Synchrotron based X-ray crystallography including data collection and structure determination as well as hardware and software involved (robotics).

Interesting biological subjects includes broadly, molecular recognition, protein selects partners - either small molecules, other proteins, or nucleic acids, through specific physical interactions carrying out particular roles in time inside various cellular process. As a structual biologist, intersted in studying the structural basis of molecular recognition.

Particularly, protein-protein/nucleic interactions mostly in regulation of gene expression, such as HetR, HcaR, CepR, OccR; proteins involved in iron acquisition, AsbABCDEF are the proteins involved in petrobactin synthesis , petrobactin is one of main siderophores used in Bacillus anthracis (Anthrax) which can avoid human innate immunity. And NDM-1, hydrolyzing all clinically available lactam-based antibiotics including the last-resort antibiotics carbapenum. Interested in mechanistic activity of promiscuous binding of antibiotics and its efficient hydrolysis for searching of inhibitors and drugs against superbugs utilizing this kind of enzymes.


  1. Kim Y, Ye Z, Joachimiak G, Videau P, Young, J, Hurd K, Callahan SM, Gornicki P, Zhao J, Haselkorn R, Joachimiak A, (2013), Structure of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets”, Proc Natl Acad Sci U S A., 110(19):E1716-1723.
  2. Chandra V, Huang P, Potluri N, Wu D, Kim Y, Rastinejad F., (2013) Multidomain integration in the structure of the HNF-4α nuclear receptor complex., Nature. 2013, 495(744):394-398.
  3. Kim Y, Cunningham MA, Mire J, Tesar C, Sacchettini J, Joachimiak A, (2013), NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism., FASEB J. 2013, 275(5):1971-1927
  4. Pfleger BF, Kim Y, Nusca TD, Maltseva N, Lee JY, Rath CM, Scaglione JB, Janes BK, Anderson EC, Bergman NH, Hanna PC, Joachimiak A, Sherman DH., Structural and Functional Analysis of AsbF: Origin of the Stealth 3,4-Dihydroxybenzoic Acid Subunit for Petrobactin Biosynthesis”, Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17133-8
  5. J. F. Flanagan, L.-Z. Mi, M. Chruszcz, M.  Cymborowski, K. L. Clines, Y. Kim, W. Minor„ F. Rastinejad &  S. Khorasanizadeh, (2005),” Double Chromodomains Cooperate to Recognize the  Methylated Histone H3 Tail”, Nature, 438:1181-5