Publications

Found 22 results
Filters: Author is Shi, Ke and First Letter Of Title is S  [Clear All Filters]
2012
Shi, K., Kurahashi, K., Gao, R., Tsutakawa, S. E., Tainer, J. A., Pommier, Y., and Aihara, H. (2012) Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2. Nat Struct Mol Biol. 19, 1372-7
2013
Chen, L., Shi, K., Yin, Z., and Aihara, H. (2013) Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution. Nucleic Acids Res. 41, 648-56
2016
Chen, X., Randles, L., Shi, K., Tarasov, S. G., Aihara, H., and Walters, K. J. (2016) Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome. Structure. 24, 1257-70
2017
Shi, K., Carpenter, M. A., Banerjee, S., Shaban, N. M., Kurahashi, K., Salamango, D. J., McCann, J. L., Starrett, G. J., Duffy, J. V., Demir, Ö., Amaro, R. E., Harki, D. A., Harris, R. S., and Aihara, H. (2017) Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat Struct Mol Biol. 24, 131-139
2018
Xing, Q., Shi, K., Portaliou, A., Rossi, P., Economou, A., and Kalodimos, C. G. (2018) Structures of chaperone-substrate complexes docked onto the export gate in a type III secretion system. Nat Commun. 9, 1773
Bohl, T. E., Ieong, P., Lee, J. K., Lee, T., Kankanala, J., Shi, K., Demir, Ö., Kurahashi, K., Amaro, R. E., Wang, Z., and Aihara, H. (2018) The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release. J Biol Chem. 10.1074/jbc.RA118.002503
2020
Pomerantz, W. Charles Kr, Cui, H., Divakaran, A., Pandey, A. K., Johnson, J. A., Zahid, H., Hoell, Z. J., Ellingson, M. O., Shi, K., Aihara, H., and Harki, D. A. (2020) Selective N-terminal BRD4 bromodomain inhibitors by targeting non-conserved residues and structured water displacement. Angew Chem Int Ed Engl. 10.1002/anie.202008625
Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., and Li, F. (2020) Structural basis of receptor recognition by SARS-CoV-2. Nature. 10.1038/s41586-020-2179-y
Shi, K., Oakland, J. T., Kurniawan, F., Moeller, N. H., Banerjee, S., and Aihara, H. (2020) Structural basis of superinfection exclusion by bacteriophage T4 Spackle. Commun Biol. 3, 691
Li, N., Shi, K., Rao, T., Banerjee, S., and Aihara, H. (2020) Structural insights into the promiscuous DNA binding and broad substrate selectivity of fowlpox virus resolvase. Sci Rep. 10, 393
Jones, J. Christophe, Banerjee, R., Shi, K., Aihara, H., and Lipscomb, J. D. (2020) Structural Studies of OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel. Biochemistry. 10.1021/acs.biochem.0c00459
2021
Jones, J. C., Banerjee, R., Shi, K., Semonis, M. M., Aihara, H., Pomerantz, W. C. K., and Lipscomb, J. D. (2021) Soluble Methane Monooxygenase Component Interactions Monitored by F NMR. Biochemistry. 60, 1995-2010
Shi, K., Moeller, N. H., Banerjee, S., McCann, J. L., Carpenter, M. A., Yin, L., Moorthy, R., Orellana, K., Harki, D. A., Harris, R. S., and Aihara, H. (2021) Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q. Proc Natl Acad Sci U S A. 10.1073/pnas.2021120118
Tang, H., Demir, Ö., Kurniawan, F., Brown, W. L., Shi, K., Moeller, N. H., Carpenter, M. A., Belica, C., Orellana, K., Du, G., LeBeau, A. M., Amaro, R. E., Harris, R. S., and Aihara, H. (2021) Structural Characterization of a Minimal Antibody against Human APOBEC3B. Viruses. 10.3390/v13040663
Moeller, N. H., Shi, K., Demir, Ö., Banerjee, S., Yin, L., Belica, C., Durfee, C., Amaro, R. E., and Aihara, H. (2021) Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. bioRxiv. 10.1101/2021.04.02.438274
2022
Moeller, N. H., Shi, K., Demir, Ö., Belica, C., Banerjee, S., Yin, L., Durfee, C., Amaro, R. E., and Aihara, H. (2022) Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Proc Natl Acad Sci U S A. 10.1073/pnas.2106379119
Cui, H., Divakaran, A., Hoell, Z. J., Ellingson, M. O., Scholtz, C. R., Zahid, H., Johnson, J. A., Griffith, E. C., Gee, C. T., Lee, A. L., Khanal, S., Shi, K., Aihara, H., Shah, V. H., Lee, R. E., Harki, D. A., and Pomerantz, W. C. K. (2022) A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. J Med Chem. 10.1021/acs.jmedchem.1c01779
2023
Yin, L., Shi, K., and Aihara, H. (2023) Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA. Nat Struct Mol Biol. 10.1038/s41594-023-01034-3
Zhang, W., Shi, K., Geng, Q., Herbst, M., Wang, M., Huang, L., Bu, F., Liu, B., Aihara, H., and Li, F. (2023) Structural evolution of SARS-CoV-2 omicron in human receptor recognition. J Virol. 97, e0082223
2024
Zhang, W., Shi, K., Hsueh, F. - C., Mendoza, A., Ye, G., Huang, L., Perlman, S., Aihara, H., and Li, F. (2024) Structural basis for mouse receptor recognition by bat SARS2-like coronaviruses. Proc Natl Acad Sci U S A. 121, e2322600121
Shi, K., Bagchi, S., Bickel, J., Esfahani, S. H., Yin, L., Cheng, T., Karamyan, V. T., and Aihara, H. (2024) Structural basis of divergent substrate recognition and inhibition of human neurolysin. Sci Rep. 14, 18420
2025
Esler, M. A., Shi, K., Rollie, J. A., Delgado, R., Vishwakarma, J., Dabrowska, A., Prahlad, J., Moghadasi, S. Arad, Harris, R. S., and Aihara, H. (2025) Structural basis for varying drug resistance of SARS-CoV-2 M E166 variants. mBio. 16, e0262424