K. Yang, S. Kim

"Integrating two contrasting biosynthetic pathways for peptide natural products"

Chem (2025) 11, 6, 102626 (Preview)

[DOI: 10.1016/j.chempr.2025.102626]

H. W. Kim*, S. Kang*, S. Kim*, H. Lee, Y. Hur, W. J. Song, D.-C. Oh, S. Kim

"Discovery of a Two-Step Enzyme Cascade Converting Aspartate to Aminomalonate in Peptide Natural Product Biosynthesis"

J. Am. Chem. Soc. (2025) 147(24), 20909-20918

[DOI: 10.1021/jacs.5c05071]

J. Park*, Y.-H. Shin*, S. Hwang*, J. Kim, D. H. Moon, I. Kang, Y.-J. Ko, B. Chung, H. Nam, S. Kim, K. Moon,  K.-B. Oh, J,-C. Cho, S. K. Lee, D.-C. Oh

"Discovery of Terminal Oxazole-Bearing Natural Products by a Targeted Metabologenomic Approach"

Angew. Chem. Int. Ed. (2024) 63, e202402465.

[DOI:  10.1002/anie.202402465]

H. Lee, S. H. Park, J. Kim, J. Lee, M. S. Koh, J. H. Lee, S. Kim

"Evolutionary Spread of Distinct O-methyltransferases Guides the Discovery of Unique Isoaspartate-Containing Peptides, Pamtides"

Adv. Sci. (Weinh) (2024) 11, 2305946

[DOI: 10.1002/advs.202305946]

H. Nam*, J. S. An*, J. Lee, Y. Yun, H. Lee, H. Park, Y. Jung, K.-B Oh, D.-C. Oh, S. Kim

"Exploring the Diverse Landscape of Biaryl-Containing Peptides Generated by Cytochrome P450 Macrocyclases"

J. Am. Chem. Soc. (2023) 145(40), 22047–22057

[DOI: 10.1021/jacs.3c07140]

J. S. An*, H. Lee*, H. Kim, S. Woo, H. Nam, J. Lee, J. Y. Lee, S.-J. Nam, S. K. Lee, K.-B. Oh, S. Kim, D.-C. Oh

"Discovery and Biosynthesis of Cihunamides, Macrocyclic Antibacterial RiPPs with a Unique C-N Linkage Formed by CYP450 Catalysis"

Angew. Chem. Int. Ed. (2023) e202300998.

[DOI: 10.1002/anie.202300998]

D. Seo, B. Koh, G.-e. Eom, H. W. Kim, S. Kim

"A dual gene-specific mutator system installs all transition mutations at similar frequencies in vivo"

Nucleic Acids Res. (2023) gkad266.

[DOI: 10.1093/nar/gkad266]

R. S. Molina*, G. Rix*, A. A. Mengiste, B. Alvarez, D. Seo, H. Chen, J. E. Hurtado, Q. Zhang, J. D. Garcia-Garcia, Z. J. Heins, P. J. Almhjell, F. H. Arnold, A. S. Khalil, A. D. Hanson, J. E. Dueber, D. V. Schaffer, F. Chen, S. Kim, L. A. Fernandez, M. D. Shoulders, C. C. Liu

"In vivo hypermutation and continuous evolution"

Nat. Rev. Methods Primers 2, 36 (2022)

[DOI: 10.1038/s43586-022-00119-5]

H. Cho*, H. Lee*, K. T. Hong, H. Chung, I. Song, J.-S. Lee, S. Kim

"Bioinformatic expansion of borosins uncovers trans-acting peptide backbone N-methyltransferases in bacteria"

Biochemistry (2022) 61(3), 183-194. 

[DOI: 10.1021/acs.biochem.1c00764] 

G.-e. Eom, H. Lee, S. Kim

"Development of a genome-targeting mutator for the adaptive evolution of microbial cells"

Nucleic Acids Res. (2022) gkab1244

[DOI: 10.1093/nar/gkab1244]

I. Song, Y. Kim, J. Yu, S. Y. Go, H. G. Lee, W. J. Song, S. Kim

"Molecular mechanism underlying substrate recognition of the peptide macrocyclase PsnB"

Nat. Chem. Biol. (2021) 17(11), 1123-1231

[DOI: 10.1038/s41589-021-00855-x]

H. Park, S. Kim

"Gene-specific mutagenesis enables rapid continuous evolution of enzymes in vivo"

Nucleic Acids Res. (2021) gkaa1231

[DOI: 10.1093/nar/gkaa1231] 

M. M.-López , T. A. Scott, S. Ramesh, I. R. Rahman, A. J. van Heel, J. H. Viel, V. Bandarian, E. Dittmann, O. Genilloud, Y. Goto, M. J. G. Burgos, C. Hill, S. Kim, J. Koehnke, J. A. Latham, A. J. Link, B. Martínez, S. K. Nair, Y. Nicolet, S. Rebuffat, H.-G. Sahl, D. Sareen, E. W Schmidt, L. Schmitt, K. Severinov, R. D. Süssmuth, A. W. Truman, H. Wang, J.-K. Weng, G. P. van Wezel, Q. Zhang, J. Zhong, J. Piel, D. A. Mitchell, O. P. Kuipers, W. A. van der Donk

"New developments in RiPP discovery, enzymology and engineering"

Nat. Prod. Rep. (2021) 38, 130-239

[DOI: 10.1039/d0np00027b]

H. Cho, Y. Choi, K. Min, J.B. Son, H. Park, H.H. Lee, S. Kim

"Over-activation of a Nonessential Bacterial Protease DegP as an Antibiotic Strategy"

Commun. Biol. (2020) 3, 547

[DOI: 10.1038/s42003-020-01266-9] 

H. Lee, M. Choi, J.-U. Park, H. Roh, S. Kim

"Genome Mining Reveals High Topological Diversity of ω-Ester Containing Peptides and Divergent Evolution of ATP-Grasp Macrocyclases"

J. Am. Chem. Soc. (2020) 142(6), 3013-3023

[DOI: 10.1021/jacs.9b12076]

C. Lee, H. Lee, J.-U. Park, S. Kim

"Introduction of Bifunctionality into the Multidomain Architecture of the ω-Ester-Containing Peptide Plesiocin"

Biochemistry (2020) 59(3), 285-289

[DOI: 10.1021/acs.biochem.9b00803]

H. Roh, Y. Han, H. Lee, S. Kim

"A topologically distinct modified peptide with multiple bicyclic core motifs expands the diversity of microviridin‐like peptides."

ChemBioChem (2019) 20(8), 1051-1059

[DOI: 10.1002/cbic.201800678]

G.-e. Eom, S. Kim

"Identification of Nucleophilic Probes for Protease-Mediated Transpeptidation."

Molecules (2018) 23(9), 2109

[DOI: 10.3390/molecules23092109] 

S. Kim*, I. Song*, G. Eom, S. Kim

"A small periplasmic protein with a hydrophobic C-terminal residue enhances DegP proteolysis as a suicide activator."

J. Bacteriol. (2018) 200(3), e00519-17

[DOI: 10.1128/JB.00519-17] 

H. Park*, Y. Kim*, C. Choi, S. Kim

"Tripodal lipoprotein variants with C-terminal hydrophobic residues allosterically modulate activity of the DegP protease."

J. Mol. Biol. (2017) 429(20), 3090-3101 

[DOI: 10.1016/j.jmb.2017.09.011]

H. Lee, Y. Park, S. Kim

"Enzymatic Cross-Linking of Side Chains Generates a Modified Peptide with Four Hairpin-like Bicyclic Repeats."

Biochemistry (2017) 56(37), 4927-4930

[DOI: 10.1021/acs.biochem.7b00808] 

S. Kim, R.T. Sauer

“Distinct regulatory mechanisms balance DegP proteolysis to maintain cellular fitness during heat stress.”

Genes Dev. (2014) 28, 902-911

[DOI: 10.1101/gad.238394.114]

S. Kim, R.T. Sauer

“Cage assembly of DegP protease is not required for substrate-dependent regulation of proteolytic activity or high-temperature cell survival.”

Proc. Natl. Acad. Sci. USA (2012) 109(19), 7263-7268

[DOI: 10.1073/pnas.1204791109]

S. Kim, R.A. Grant, R.T. Sauer

“Covalent linkage of distinct substrate degrons controls assembly and disassembly of DegP proteolytic cages.”

Cell (2011) 145(1), 67-78

[DOI: 10.1016/j.cell.2011.02.024]

C.L. Hagan*, S. Kim*, D. Kahne

“Reconstitution of outer membrane protein assembly from purified components.”

Science (2010) 328(5980), 890-892

[DOI: 10.1126/science.1188919] 

S. Kim, J.C. Malinverni, P. Sliz, T.J. Silhavy, S.C. Harrison, D. Kahne

“Structure and function of an essential component of the outer membrane protein assembly machine.”

Science (2007) 317(5840), 961-964

[DOI: 10.1126/science.1143993]