Macromolecular X-Ray Crystallography Core Publications


Publications Supported by the Core


(Key Publications)

Hu L, Salmen W, Chen R, Zhou Y, Neill F, Crowe JE Jr, Atmar RL, Estes MK, Prasad BVV. Atomic structure of the predominant GII.4 human norovirus capsid reveals novel stability and plasticity. Nat Commun. 2022 10;13(1):1241. PMID: 35273142; PMCID: PMC8913647. 

Hu L, Salmen W, Sankaran B, Crawford SE, Estes MK, Prasad BVV (2022) Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography. Commun. Biol. 2022 5:419, PMID: 35513489; PMCID: PMC9072675

Mercado, J.M., Lee, S., Chang, C., Sung, N., Soong, L., Catic, A. and Tsai, F.T.F. Atomic Structure of the Leishmania spp. Hsp100 N-domain. Proteins 2022; 90:1242-1246. PMID: 35122310, PMCID: PMC9018533.

Chamakuri, S., Lu, S., Ucisik, M.N., Bohren, K.M., Chen, Y.C., Du, H.C., Faver, J.C., Jimmidi, R., Li, F., Li, J.Y., Nyshadham, P., Palmer, S.S., Pollet, J., Qin, X., Ronca, S.E., Sankaran, B., Sharma, K.L., Tan, Z., Versteeg, L., Yu, Z., Matzuk, M.M.*, Palzkill, T.*, Young, D.W.* DNA-encoded chemistry technology yields expedient access to SARS-CoV-2 Mpro inhibitors. Proc. Natl. Acad. Sci. USA  2021 7;118(36) PMID: 34426525, PMCID: PMC8433497

Furey, I.M., Mehta, S.C., Sankaran, B., Hu, L., Prasad, B.V.V., and Palzkill, T. Local interactions with the Glu166 base and the conformation of an active site loop play key roles in carbapenem hydrolysis by KPC-2 -lactamase. J. Biol. Chem. 2021 296:100799. PMID: 34022225, PMCID: PMC8189571.

Stojanoski, V., Hu, L., Sankaran, B., Wang, F., Tao, P., Prasad, B.V.V., and Palzkill, T. Mechanistic basis of OXA-48-like β-lactamases' hydrolysis of carbapenems. ACS Infect. Dis. 2021 7:445-460. PMID: 33492952, PMCID: PMC8571991. 

Mehta, S.C., Furey, I.M., Pemberton, O.A., Boragine, D.M., Chen, Y., and Palzkill, T. KPC-2 β-lactamase enables carbapenem antibiotic resistance through fast deacylation of the covalent intermediate. J. Biol. Chem. 2021 296:100155. PMID: 33273017, PMCID: PMC7895804.

Taylor, D.M., Anglin, J., Hu, L., Wang, L., Sankaran, B., Wang, J., Matzuk, M.M., Prasad, B.V.V., Palzkill, T. Unique diacidic fragments inhibit the OXA-48 carbapenemase and enhance the killing of Escherichia coli producing OXA-48. ACS Infect. Dis. 2021 7:3345-3354. PMID: 34817169.

Maneix, L., Sweeney, M.A., Lee, S., Iakova, P., Moree, S.E., Sahin, E., Lulla, P., Yellapragada, S.V., Tsai, F.T.F. and Catic, A. The Mitochondrial Protease LonP1 Promotes Proteasome Inhibitor Resistance in Multiple Myeloma. Cancers 2021; 13:843. PMID: 33671345, PMCID: PMC7922145.

Yap, Z.Y., Efthymiou, S., Seiffert, S., Parra, K.V., Lee, S., Nasca, A., Maroofian, R., Schrauwen, I., Pendziwiat, M., Bhoj, E., Striano, P., Mankad, K., Vona, B., Cuddapah, S., Wagner, A., Alvi, J.R., Davoudi-Dehaghani, E., Fallah, M.-S., Gannavarapu, S., Lamperti, C., Legati, A., Murtaza, B.N., Rehman, M.U., Saeidi, K., Salpietro, V., Spiczak, S., Zeinali, S., Zeviani, M., SYNaPS Study Group, University of Washington Center for Mendelian Genomics, Helbig, I., Barakat, T.S., Ghezzi, D., Leal, S.M., Weber, Y., Houlden, H., Yoon, W.H. Bi-allelic Variants in OGDHL Cause a Neurodevelopmental Spectrum Disease Featuring Epilepsy, Hearing Loss, Visual Impairment, and Ataxia. Am. J. Hum. Genet. 2021; 108: 1-17. PMID: 34800363, PMCID: PMC8715183.

Lee, M.J., Bhattarai, D., Jang, H., Baek, A., Yeo, I.J., Lee, S., Miller, Z., Lee, S., Hong, J.T., Kim, D.-E., Lee, W., Kim, K.B. Macrocyclic Immunoproteasome Inhibitors as a Potential Therapy for Alzheimer’s Disease. J. Med. Chem. 2021; 64:10934-50. PMID: 34309393.

Yap, Z.Y., Park, Y. Wortmann, S.B., Gunning, A.C., Ezer, S., Lee, S., Duraine, L., Wilichowski, E., Wilson, K., Mayr, J.A., Wagner, M., Li, H., Kini, U., Black, E.D., Monaghan, K.G., Lupski, J.R., Ellard, S., Westphal, D.S., Harel, T., Yoon, W.H. Functional Interpretation of ATAD3A Variants in Neuro-mitochondrial Phenotypes. Genome Med. 2021; 13:55. PMID: 34845882, PMCID: PMC8042885.

Yap, Z.Y., Strucinska, K., Matsuzaki, S., Lee, S., Si, Y., Humphries, K., Tarnopolsky, M.A., and Yoon, W.H. A Biallelic Pathogenic Mutation in the OGDH Gene Results in a Neurological Disorder with Features of a Mitochondrial Disease. J. Inherit. Metab. Dis. 2021; 44:388-400. PMID: 32383294, PMCID: PMC7647956.

Rizzolo, K., Yu, A.Y.H., Ologbenla, A., Kim, S.-R, Zhu, H., Ishimori, K., Thibault, G., Leung, E., Zhang, Y., Teng, M., Haniszewski, M., Miah, N., Phanse, S., Minic, Z., Lee, S., Caballero, J.D., Babu, M., Tsai, F.T.F., Saio, T. and Houry, W.A. Functional Cooperativity Between the Trigger Factor Chaperone and the ClpXP Proteolytic Complex. Nature Commun. 2021; 12:281. PMID: 33436616, PMCID: PMC7804408.

Sharma, R., Choi, K.-J., Quan, M. D.,Sharma, S., Sankaran, B., Park, H., LaGrone, A., Kim, J. J., Mackenzie, K. R., Ferreon, A. C., Kim, C., and Ferreon, J. C. Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization. Nature commun. 2021; 12, 5579, doi:10.1038/s41467-021-25761-7. PMID: 34552088, PMCID: PMC8458463.

Soeung V, Lu S, Hu L, Judge A, Sankaran B, Prasad BVV, Palzkill T. A drug-resistant β-lactamase variant changes the conformation of its active-site proton shuttle to alter substrate specificity and inhibitor potency. J. Biol. Chem. (2020) 295:18239-55. PMID: 33109613.

Pan Y, Ren Z, Gao S, Shen J, Wang L, Xu Z, Yu Y, Bachina P, Zhang H, Fan X, Laganowsky A, Yan N, Zhou M. Structural basis of ion transport and inhibition in ferroportin. Nat. Commun. (2020) 11:5686. PMID: 33173040; PMCID: PMC7655804.

Shen J, Wu G, Tsai AL, Zhou M. Structure and mechanism of a unique diiron center in mammalian stearoyl-CoA desaturase. J. Mol. Biol. (2020) 432:5152-61. PMID:32470559; PMCID: PMC7483794.

Wang L, Qian H, Nian Y, Han Y, Ren Z, Zhang H, Hu L, Prasad BVV, Laganowsky A, Yan N, Zhou M. Structure and mechanism of human diacylglycerol O-acyltransferase 1. Nature (2020) 581:329-32. PMID: 32433610; PMCID: PMC7255049.

Zhang H, Pan Y, Hu L, Hudson MA, Hofstetter KS, Xu Z, Rong M, Wang Z, Prasad BVV, Lockless SW, Chiu W, Zhou M. TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in membrane potential. Nat. Commun. (2020) 11:547. PMID: 31992706; PMCID: PMC6987127.

Taylor DM, Anglin J, Park S, Ucisik MN, Faver JC, Simmons N, Jin Z, Palaniappan M, Nyshadham P, Li F, Campbell J, Hu L, Sankaran B, Prasad BVV, Huang H, Matzuk MM, Palzkill T. Identifying oxacillinase-48 carbapenemase inhibitors using DNA-encoded chemical libraries. ACS Infect. Dis. (2020) 6:1214-27. PMID: 32182432; PMCID: PMC7673237.

Brown CA, Hu L, Sun Z, Patel MP, Singh S, Porter JR, Sankaran B, Prasad BVV, Bowman GR, Palzkill T. Antagonism between substitutions in -lactamase explains a path not taken in the evolution of bacterial drug resistance. J. Biol. Chem. (2020) 295:7376-90. PMID: 32299911; PMCID: PMC7247304.

Wu F, Hua Y, Kaochar S, Nie S, Lin Y-L, Yao Y, Wu J, Wu X, Fu X, Schiff R, Davis CM, Robertson M, Ehli EA, Coarfa C, Mitsiades N, Song Y.* Discovery, structure-activity relationship and biological activity of histone-competitive inhibitors of histone acetyltransferases P300/CBP. J. Med. Chem. (2020) 63:4716-31. PMID: 32314924; PMCID: PMC7340344.

Bhattarai D, Lee MJ, Baek A, Yeo IJ, Miller Z, Baek YM, Lee S, Kim DE, Hong JT, Kim KB. LMP2 inhibitors as a potential treatment for Alzheimer’s disease. J. Med. Chem. (2020) 63:3763-83. PMID: 32189500.

Yu Z, Ku AF, Anglin JL, Sharma R, Ucisik MN, Faver JC, Li F, Nyshadham P, Simmons N, Sharma KL, Nagarajan S, Riehle K, Kaur G, Sankaran B, Srorl-Desmond M, Palmer SS, Young DW, Kim C, Matzuk MM. Discovery and characterization of bromodomain 2-specific inhibitors of BRDT. Proc. Natl. Acad. Sci. USA 2020 118(9) e2021102118 PMID: 33637650, PMCID: PMC7936271

Tsai, J.T., Sung, ​N., Lee, J., Chang, C., Lee, S. and Tsai, F.T.F. Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein. J. Mol. Biol. 2019, 431:3179-90."

Lee J, Sung N, Yeo L, Chang C, Lee S, Tsai FT, Structural determinants for protein unfolding and translocation by the Hsp104 protein disaggregase, Bioscience Reports, 2017, 37(6):BSR20171399.

Lee J, Sung N, Mercado JM, Hryc CF, Chang C, Lee S, Tsai FT, Overlapping and Specific Functions of the Hsp104 N Domain Define Its Role in Protein Disaggregation, Scientific Reports 2017, 7(1):11184.

Sung N, Lee J, Kim JH, Chang C, Tsai FT, Lee S, 2.4 Å resolution crystal structure of human TRAP1NM, the Hsp90 paralog in the mitochondrial matrix, Acta Crystallographica Section D 2016, 72(8):904-911.

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, Proceedings of the National Academy of Sciences of the United Stated of America 2016 113(11):2952-2957.