Education

Molecular Biophysics (Biochemistry and Physical Chemistry)

Ph.D.
Washington University

Physics

B.S.
Calvin College

Expertise

Biophysics, Solid-State NMR, LCMS, Biochemistry

Research

Specialty

My laboratory focuses on structure and chemical composition analysis of complex biological systems using combined solid-state NMR and MS. Solid-state NMR provides atomic resolution structure and composition, and LC-MS for identification of chemical compo

Funding

Description of active research and research interests 

My primary research interest is a structural, functional, and compositional analysis of bacterial cell walls and the mode of action of novel antimicrobial agents that target them. The cell wall is a supramacromolecule with heterogeneous structures that is not compatible with most biophysical and biochemical techniques but readily accessible by solid-state nuclear magnetic resonance (SSNMR).  The use of SSNMR has led to determining the mode of actions of second-generation glycopeptide antibiotics and structural characterization of the peptidoglycan tertiary structures in Gram-positive pathogens including S. aureus, E. faecalis, and E. faecium.  As a natural extension of this work, my lab has been focusing on the application and development of liquid chromatography-mass spectrometry to characterize the peptidoglycan compositions in bacteria. My lab is also actively involved in the development of multiple-resonance magic-angle spinning transmission-line probes for SSNMR.

Group Website: https://sites.google.com/view/kim-research-group/home  

ORCID: https://orcid.org/0000-0002-2007-6606

Publications
(A complete list is available from Google Scholar)

1. Rimal B., Senzani S., Ealand C., Lamichhane G., Kana B., and Kim SJ. (2022) Peptidoglycan compositional analysis of Mycobacterium smegmatis using high-resolution LC-MS. Scientific Reports 12, 11061. https://doi.org/10.1038/s41598-022-15324-1. 
2. Olademehin O., Shuford K., and Kim SJ. (2022) Molecular dynamics simulation of the secondary-binding site in disaccharide-modified glycopeptide antibiotics. Scientific Reports 12, 7087. https://doi.org/10.1038/s41598-022-10735-6.
3. Olademehin O., Kim SJ., and Shuford K. (2021) Molecular dynamics simulation of atomic interactions in the vancomycin binding site. ACS OMEGA 6, 775-785; https://doi.org/10.1021/acsomega.0c05353.
4. Olademehin O., Liu C., Rimal B., Adegboyega N., Chen F., Sim C., and Kim SJ. (2020) Dsi-RNA injection targeting genes regulated by Foxo transcription factor reduce glycogen and lipid storage in diapause Culex pipiens. Scientific Reports 10, 17201; doi.org/10.1038/s41598-020-74292-6.
5. King B., Li L., Liu C., Kim SJ., and Sim C. (2020) Suppression of glycogen synthase expression reduces glycogen and lipid storage during mosquito overwintering diapause, Journal of Insect Physiology, Vol. 120 https://doi.org/10.1016/j.jinsphys.2019.103971.
6. Pidgeon S., Apostolos, A., Nelson J., Shaku M., Rimal B., Islam N., Crick D., Kim SJ., Pavelka M., Kana B., and Pires M. (2019) L,D-transpeptidase specific probe reveals spatial activity of peptidoglycan crosslinking, ACS Chem. Bio., https://doi.org/10.1021/acschembio.9b00427.  Highlighted in Faculty of 1000 (https://f1000.com/prime/736558771).
7. Chang J., Wallace A.*, Foster E.*, and Kim SJ. (2018) Peptidoglycan compositional analysis of Enterococcus faecalis biofilm by stable isotope labeling by amino acids in bacterial culture, Biochemistry, Jan 25, 2018, DOI: 10.1021/acs.biochem.7b01207.
8. Wang F., Zhou H., Olademehin, O., Kim SJ., and Tao P. (2018) Insights into key interactions between vancomycin and bacteria cell wall structure, ACS Omega, 3(1): 37-45.
9. Srivastava D., Seo J., Rimal B., Kim SJ., Zhen S., and Darwin A. (2018) A proteolytic complex targets multiple cell wall hydrolases in Pseudomonas aeruginosa. mBio, DOI: 10.1128/mBio.00972-18
10. Ealand C., Rimal B., Chang J., Mashigo L., Chengalroyen M., Mapela L., Beukes G., Machowski E., Kim SJ., and Kana B. (2018) Resuscitation promoting factors are required for biofilm formation in Mycobacterium smegmatis. Applied and Environmental Microbiology, DOI: 10.1128/AEM.00687-18.
11. Kim SJ., Chang J., Rimal B., Hao Y., and Schaefer J. (2017) Surface proteins and the formation of biofilm by Staphylococcus aureus, Biochemica et Biophysica Acta (Biomembrane), Vol. 1860 (3): 749-756.
12. Yang H., Singh M., Kim SJ., and Schaefer J. (2017) Characterization of the tertiary structure of the peptidoglycan of Enterococcus faecalis. Biochimica et Biophysica Acta Biomembrane, 1859 (11): 2171-2180. PMID: 28784459 PMCID: PMC5610627
13. Chang J., Foster E.*, Thadani A.*, Ramirez A., and Kim SJ.  (2017) Inhibition of Staphylococcus aureus cell wall biosynthesis by desleucyl-oritavancin: a quantitative peptidoglycan composition analysis by mass spectrometry. Journal of Bacteriology, 199 (15): e00278-17. PMCID: PMC5512225
14. Chang J., Coffman L.*, and Kim SJ.  (2017) Inhibition of D-Ala incorporation into wall teichoic acid biosynthesis in Staphylococcus aureus by desleucyl-oritavancin. Chemical Communications, 53, 5649 – 5652.  PMCID: PMC5512289
15. Senzani S., Li D., Ealand C., Chang J., Rimal B., Liu C., Kim SJ., Dhar N., and Kana B.  (2017) An Amidase_3 domain-containing N–acetylmuramyl-L-alanine amidase is required for mycobacterial cell division. Scientific Reports 7, 1140; doi:10.1038/s41598-017-01184-7.
16. Chang J., Foster E.*, Wallace A.*, and Kim SJ.  (2017) Peptidoglycan O-acetylation increases in response to vancomycin treatment in vancomycin-resistant Enterococcus faecalis. Scientific Reports 7, 46500; doi:10.1038/srep46500.
17. Singh M., Chang J., Coffman L.*, and Kim SJ.  (2017) A hidden mode of action for glycopeptide antibiotics: Inhibition of wall teichoic acid biosynthesis. The Journal of Physical Chemistry B, 121 (16): 3925–3932.
18. Kim SJ., Singh M., Sharif S., and Schaefer J.  (2017) Desleucyl-oritavancin with a damaged D-Ala-D-Ala binding site inhibits the transpeptidation step of cell-wall biosynthesis in whole cells of Staphylococcus aureus. Biochemistry, Vol. 56 (10): 1529–1535.
19. O’Connor R., Singh M., Chang J., Kim SJ., VanNieuwenhze M., and Schaefer J.  (2017) Dual mode of action for plusbacin A3 in Staphylococcus aureus. The Journal of Physical Chemistry B, 121 (7): 1499-1505.
20. Chang J., Foster E.*, Yang H., and Kim SJ. (2017) Quantification of D-Ala-D-Lac terminated peptidoglycan structure in vancomycin-resistant Enterococcus faecalis using a combined solid-state NMR and mass spectrometry analysis. Biochemistry, Vol. 56 (4): 612-622.
21. Chang J., Singh M., Kim S., Hockaday W., Sim C., and Kim SJ. (2016) Solid-state NMR reveals differential carbohydrate utilization in diapausing Culex pipiens. Scientific Reports, 6: 37350 doi: 10.1038/srep37350.
22. Chang J., Zhou H., Preobrazhenskaya M., Tao P., and Kim SJ. (2016) The carboxyl-terminus of eremomycin facilitates binding to the non-D-Ala-D-Ala segment of the peptidoglycan pentapeptide stem. Biochemistry, Vol. 55 (24): 3383-3391.
23. Singh M., Chang J., Coffman L.* and Kim SJ. (2016) Solid-state NMR characterization of amphomycin effects on peptidoglycan and wall teichoic acid biosyntheses in Staphylococcus aureus. Scientific Reports, 6: 31757, doi:10.1038/srep31757
24. Karunathilake A, Chang J., Thompson C, Nguyen C, Nguyen D, Rajan A, Sridharan, Vyakaranam M, Adegboyega N, Kim SJ, and Smaldone R. (2016) Hexaphenylbenzene and hexabenzocoronene-based porous polymers for the adsorption of volatile organic compound. RSC Advances, Vol. 6: 65763-65769. (shared corresponding author)
25. Kim SK, Demuth M, Schlesinger, SR, Kim SJ, Urbanczyk J, Shaw RW, Choi SK, Lee D, and Shin H. (2016) Inhibition of Bacillus anthracis Metallo-β-lactamase by Compounds with Hydroxamic Acid Functionality. Journal of Enzyme Inhibition and Medicinal Chemistry, Vol. 31 (4):132-137
26. Kim SJ., Chang J., and Singh M. (2015) Peptidoglycan architecture of Gram-positive bacteria by solid-state NMR.  Biochimica et Biophysica Acta (BBA)-Biomembranes, Vol. 1848 (1): 350-362.  (Kim JS is the corresponding author.)
27. Singh M., Kim SJ., Sharif S., Preobrazhenskaya M., and Schaefer J. (2015) REDOR constraints on the peptidoglycan lattice architecture of Staphylococcus aureus. Biochimica et Biophysica Acta (BBA)-Biomembranes, Vol. 1848 (1): 363-368.   
28. Kim SJ., Singh M., Sharif S., and Schaefer J. (2014) Cross-link formation and peptidoglycan lattice assembly in the FemA mutant of Staphylococcus aureus. Biochemistry, Vol. 53 (9): 1420-1427.
29. Kim SJ., Singh M., Preobrazhenskaya M., and Schaefer J. (2013) Staphylococcus aureus peptidoglycan stem packing by rotational-echo double resonance NMR spectroscopy. Biochemistry, 52 (21): 3651-3659 (Highlighted in Biochemistry).
30. Kim SJ., Tanaka K. S. E., Dietrich E., Rafai Far, A., and Schaefer J. (2013) Locations of the hydrophobic side chains of lipoglycopeptides bound to the peptidoglycan of Staphylococcus aureus. Biochemistry, 52 (20): 3405-3414.
31. Kim SJ., Singh M., Wohlrab A., Yu T., Patti G., O’Connor R. D., VanNieuwenhze M., and Schaefer J. (2013) Isotridecanyl side chain of plusbacin-A3 is essential for the transglycosylase inhibition of peptidoglycan biosynthesis. Biochemistry, 52 (11): 1973-1979.
32. Sharif S., Kim SJ., Labischinski H., and Schaefer J. (2013) Uniformity of glycyl bridge lengths in the mature cell walls of Fem mutants of methicillin-resistant Staphylococcus aureus, Journal of Bacteriology, 195 (7) 1421-1427.
33. Kim SJ., Singh M., and Schaefer J. (2009) Oritavancin binds to isolated protoplast membranes but not intact protoplasts of Staphylococcus aureus, Journal of Molecular Biology 391: 414-425. 
    Highlighted in Faculty of 1000 (www.f1000biology.com/article/id/1163212/evaluation).
34. Patti G., Kim SJ., Yu T. T., Dietrich E., Tanaka K. S. E., Parr T. R., Far A.R., and Schaefer J. (2009) Vancomycin and oritavancin have different mode of action in Enterococcus faecium, Journal of Molecular Biology 392: 1178-1191.
35. Sharif S., Singh M., Kim SJ., and Schaefer J. (2009) Staphylococcus aureus peptidoglycan tertiary structure from carbon-13 spin diffusion, J. Am. Chem. Soc. 131 (20): 7023-7030.
36. Sharif S., Kim SJ., Labischinski H., and Schaefer J. (2009) Characterization of peptidoglycan in Fem-deletion mutants of methicillin-resistant Staphylococcus aureus by solid-state NMR, Biochemistry, 48: 3100-3108.
37. Kim SJ., and Schaefer J. (2008) Hydrophobic side-chain length determines activity and conformational heterogeneity of a vancomycin derivative bound to the cell wall of Staphylococcus aureus, Biochemistry 47: 10155-10161.
38. Kim SJ., Matsuoka S., Patti G., and Schaefer J. (2008) Vancomycin derivative with damaged D-Ala-D-Ala binding cleft binds to cross-linked peptidoglycan in the cell wall of Staphylococcus aureus, Biochemistry 47: 3822-3831.
39. Patti G., Kim SJ, and Schaefer J. (2008) Characterization of the peptidoglycan of vancomycin-susceptible Enterococcus faecium, Biochemistry 47: 8378-8385.
40. Kim SJ., Cegelski L., Stueber D., Singh M., Dietrich E., Tanaka T., Parr T. R., Far A., and Schaefer J. (2008) Oritavancin exhibits dual mode of action to inhibit cell-wall biosynthesis in Staphylococcus aureus, Journal of Molecular Biology 377: 281-293.
41. Kim SJ., Cegelski L., Preobrazhenskaya M. N., and Schaefer J. (2006) Structures of Staphylococcus aureus cell-wall complexes with vancomycin, eremomycin, and chloroeremomycin derivatives by 13C{19F} and 15N{19F} rotational-echo double resonance, Biochemistry 45: 5235-5250.
42. Toke O., Maloy L., Kim SJ., Blazyk J., and Schaefer J. (2004) Secondary structure and lipid contact of a peptide antibiotic in phospholipid bilayers by REDOR, Biophysical Journal 87: 662-674.
43. Kim SJ., Cegelski L., Studelska D. R., O'Connor B., Mehta A., and Schaefer J. (2002) Rotational-echo double resonance characterization of vancomycin binding sites in Staphylococcus aureus, Biochemistry 41: 6967-6977.
44. Cegelski L., Kim SJ., Hing A. W., Studelsa D. R., O'Connor B., Mehta A., and Schaefer J. (2002) Rotational-echo double resonance characterization of the effects of vancomycin on cell wall synthesis in Staphylococcus aureus, Biochemistry 41: 13053-13058.
45. Kim SJ, Cegelski L., Studelska D. R., O'Connor B., Mehta A., and Schaefer J. “REDOR characterization of vancomycin binding sites in S. aureus”.  Abstract published in Journal of Biophysics 82: 469 (2002).
46. Cegelski L., Kim SJ, Hing AW, Studelska D. R., O'Connor B., Mehta A., and Schaefer J. “REDOR characterization of the effects of vancomycin on cell-wall synthesis in S. aureus”.  Abstract published in Journal of Biophysics 82: 468 (2002).
47. Grant G., Kim SJ., Xu X. L., and Hu Z. (1999) The contribution of adjacent subunits to the active sites of D-3-phosphoglycerate dehydrogenase, Journal of Biological Chemistry 274: 5357-5361.
48. Kim SJ., Lee S. A., Carter B. J., and Rupprecht A. (1996) Stabilization of the B conformation in unoriented films of calf thymus DNA by NaCl: A Raman and IR study, Biopolymers 41: 233-238.
49. Mayeres C. H., Lee S. A., Pinnick D. A., Carter B. J., and Kim SJ. (1995) A study of Na-DNA films containing NaCl via scanning electron and tunneling microscopies, Biopolymers 36: 669-673.

Key words

Solid-state nuclear magnetic resonance, molecular biophysics, macromolecular structure and function, carbon-flux analysis, microbial pathogenesis, mass spectrometry, biophysical education