2021 Publications

  1. Amezcua, M., Cruz, R.S., Ku, A., Moran, W., Ortega, M.E., Salzameda, N.T., 2021. Discovery of Dipeptides as Potent Botulinum Neurotoxin A Light-Chain Inhibitors. ACS Med. Chem. Lett. 12, 295–301. doi:10.1021/acsmedchemlett.0c00674
  2. Ben-Sasson, A.J., Watson, J.L., Sheffler, W., Johnson, M.C., Bittleston, A., Somasundaram, L., Decarreau, J., Jiao, F., Chen, J., Mela, I., Drabek, A.A., Jarrett, S.M., Blacklow, S.C., Kaminski, C.F., Hura, G.L., De Yoreo, J.J., Kollman, J.M., Ruohola-Baker, H., Derivery, E., Baker, D., n.d. Design of biologically active binary protein 2D materials. Nature 589, 468–473. doi:10.1038/s41586-020-03120-8
  3. Chang, L., Campbell, J., Raji, I.O., Guduru, S.K.R., Kandel, P., Nguyen, M., Liu, S., Tran, K., Venugopal, N.K., Taylor, B.C., Holt, M.V., Young, N.L., Samuel, E.L.G., Jain, P., Santini, C., Sankaran, B., MacKenzie, K.R., Young, D.W., 2021. Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery. Sci. Rep. 11, 1121. doi:10.1038/s41598-020-80588-4
  4. Copeland, R.A., Davis, K.M., Shoda, T.K.C., Blaesi, E.J., Boal, A.K., Krebs, C., Bollinger, J.M., 2021. An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme. J. Am. Chem. Soc. 143, 2293–2303. doi:10.1021/jacs.0c10923
  5. Didychuk, A.L., Gates, S.N., Gardner, M.R., Strong, L.M., Martin, A., Glaunsinger, B.A., 2021. A pentameric protein ring with novel architecture is required for herpesviral packaging. elife 10. doi:10.7554/eLife.62261
  6. Flower, T.G., Buffalo, C.Z., Hooy, R.M., Allaire, M., Ren, X., Hurley, J.H., 2021. Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein. Proc Natl Acad Sci USA 118. doi:10.1073/pnas.2021785118
  7. Gee, C.L., Holton, J.M., McPherson, A., 2021. Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase). J. Biosci. Bioeng. doi:10.1016/j.jbiosc.2021.02.008
  8. Gunn, K.H., Gutgsell, A.R., Xu, Y., Johnson, C.V., Liu, J., Neher, S.B., 2021. Comparison of angiopoietin-like protein 3 and 4 reveals structural and mechanistic similarities. J. Biol. Chem. 100312. doi:10.1016/j.jbc.2021.100312
  9. Hammel, M., Rashid, I., Sverzhinsky, A., Pourfarjam, Y., Tsai, M.-S., Ellenberger, T., Pascal, J.M., Kim, I.-K., Tainer, J.A., Tomkinson, A.E., 2021. An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex. Nucleic Acids Res. doi:10.1093/nar/gkaa1188
  10. Harper, C.C., Brauer, D.D., Francis, M.B., Williams, E.R., 2021. Direct observation of ion emission from charged aqueous nanodrops: effects on gaseous macromolecular charging. Chem. Sci. 12, 5185–5195. doi:10.1039/D0SC05707J
  11. Hodge, C.D., Rosenberg, D.J., Grob, P., Wilamowski, M., Joachimiak, A., Hura, G.L., Hammel, M, 2021. Rigid monoclonal antibodies improve detection of SARS-CoV-2 nucleocapsid protein. MAbs 13, 1905978. doi:10.1080/19420862.2021.1905978
  12. Hongdusit, A., Fox, J.M., 2021. Optogenetic analysis of allosteric control in protein tyrosine phosphatases. Biochemistry. doi:10.1021/acs.biochem.0c00841
  13. Hsia, Y., Mout, R., Sheffler, W., Edman, N.I., Vulovic, I., Park, Y.-J., Redler, R.L., Bick, M.J., Bera, A.K., Courbet, A., Kang, A., Brunette, T.J., Nattermann, U., Tsai, E., Saleem, A., Chow, C.M., Ekiert, D., Bhabha, G., Veesler, D., Baker, D., 2021. Design of multi-scale protein complexes by hierarchical building block fusion. Nat. Commun. 12, 2294. doi:10.1038/s41467-021-22276-z
  14. Huang, J., Fraser, M.E., 2021. Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase. Acta Crystallogr. D Struct. Biol. 77, 357–368. doi:10.1107/S2059798321000334
  15. Kang, W., Rettberg, L.A., Stiebritz, M.T., Jasniewski, A.J., Tanifuji, K., Lee, C.C., Ribbe, M.W., Hu, Y., 2021. X-Ray Crystallographic Analysis of NifB with a Full Complement of Clusters: Structural Insights into the Radical SAM-Dependent Carbide Insertion During Nitrogenase Cofactor Assembly. Angew Chem Int Ed 60, 2364–2370. doi:10.1002/anie.202011367
  16. Kim C, Sharma R. Cyclic nucleotide selectivity of protein kinase G isozymes. Protein Sci. 2021 Feb;30(2):316-327. doi: 10.1002/pro.4008. Epub 2020 Dec 10. PMID: 33271627
  17. Knox, H.L., Chen, P.Y.-T., Blaszczyk, A.J., Mukherjee, A., Grove, T.L., Schwalm, E.L., Wang, B., Drennan, C.L., Booker, S.J., n.d. Structural basis for non-radical catalysis by TsrM, a radical SAM methylase. Nat. Chem. Biol. 17, 485–491. doi:10.1038/s41589-020-00717-y
  1. Lapenta, F., Aupič, J., Vezzoli, M., Strmšek, Ž., Da Vela, S., Svergun, D.I., Carazo, J.M., Melero, R., Jerala, R., 2021. Self-assembly and regulation of protein cages from pre-organised coiled-coil modules. Nat. Commun. 12, 939. doi:10.1038/s41467-021-21184-6
  2. McConnell, S.A., McAllister, R.A., Amer, B.R., Mahoney, B.J., Sue, C.K., Chang, C., Ton-That, H., Clubb, R.T., 2021. Sortase-assembled pili in Corynebacterium diphtheriae are built using a latch mechanism. Proc Natl Acad Sci USA 118. doi:10.1073/pnas.2019649118
  3. Nam, S.-E., Cheung, Y.W.S., Nguyen, T.N., Gong, M., Chan, S., Lazarou, M., Yip, C.K., 2021. Insights on autophagosome-lysosome tethering from structural and biochemical characterization of human autophagy factor EPG5. Commun. Biol. 4, 291. doi:10.1038/s42003-021-01830-x
  4. Nixon, C.F., Lim, S.A., Sailer, Z.R., Zheludev, I.N., Gee, C.L., Kelch, B.A., Harms, M.J., Marqusee, S., 2021. Exploring the Evolutionary History of Kinetic Stability in the α-Lytic Protease Family. Biochemistry 60, 170–181. doi:10.1021/acs.biochem.0c00720
  5. Samuels, E.R., Sevrioukova, I.F., 2021. Rational Design of CYP3A4 Inhibitors: A One-Atom Linker Elongation in Ritonavir-Like Compounds Leads to a Marked Improvement in the Binding Strength. Int. J. Mol. Sci. 22. doi:10.3390/ijms22020852
  6. Schuller, M., Correy, G.J., Gahbauer, S., Fearon, D., Wu, T., Díaz, R.E., Young, I.D., Carvalho Martins, L., Smith, D.H., Schulze-Gahmen, U., Owens, T.W., Deshpande, I., Merz, G.E., Thwin, A.C., Biel, J.T., Peters, J.K., Moritz, M., Herrera, N., Kratochvil, H.T., QCRG Structural Biology Consortium, Aimon, A., Bennett, J.M., Brandao Neto, J., Cohen, A.E., Dias, A., Douangamath, A., Dunnett, L., Fedorov, O., Ferla, M.P., Fuchs, M.R., Gorrie-Stone, T.J., Holton, J.M., Johnson, M.G., Krojer, T., Meigs, G., Powell, A.J., Rack, J.G.M., Rangel, V.L., Russi, S., Skyner, R.E., Smith, C.A., Soares, A.S., Wierman, J.L., Zhu, K., O’Brien, P., Jura, N., Ashworth, A., Irwin, J.J., Thompson, M.C., Gestwicki, J.E., von Delft, F., Shoichet, B.K., Fraser, J.S., Ahel, I., n.d. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci. Adv. 7. doi:10.1126/sciadv.abf8711
  7. Scott, A.J., Niitsu, A., Kratochvil, H.T., Lang, E.J.M., Sengel, J.T., Dawson, W.M., Mahendran, K.R., Mravic, M., Thomson, A.R., Brady, R.L., Liu, L., Mulholland, A.J., Bayley, H., DeGrado, W.F., Wallace, M.I., Woolfson, D.N., 2021. Constructing ion channels from water-soluble α-helical barrels. Nat. Chem. doi:10.1038/s41557-021-00688-0
  8. Sevillano, N., Bohn, M.F., Zimanyi, M., Chen, Y., Petzold, C., Gupta, S., Ralston, C.Y., Craik, C.S., n.d. Structure of an affinity-matured inhibitory recombinant fab against urokinase plasminogen activator reveals basis of potency and specificity. Biochim. Biophys. Acta Proteins Proteom. 1869, 140562. doi:10.1016/j.bbapap.2020.140562
  9. Stojanoski, V., L. Hu, B. Sankaran, and F. Wang. 2021. “Mechanistic Basis of OXA-48-like β-Lactamases’ Hydrolysis of Carbapenems.” ACS Infect Dis. 2021 Feb 12;7(2):445-460.doi: 10.1021/acsinfecdis.0c00798. Epub 2021 Jan 25.  PMID: 33492952
  10. Surka, C., Jin, L., Mbong, N., Lu, C.-C., Jang, I.S., Rychak, E., Mendy, D., Clayton, T., Tindall, E., Hsu, C., Fontanillo, C., Tran, E., Contreras, A., Ng, S.W.K., Matyskiela, M., Wang, K., Chamberlain, P., Cathers, B., Carmichael, J., Hansen, J., Wang, J.C.Y., Minden, M.D., Fan, J., Pierce, D.W., Pourdehnad, M., Rolfe, M., Lopez-Girona, A., Dick, J.E., Lu, G., 2021. CC-90009, a novel cereblon E3 ligase modulator, targets acute myeloid leukemia blasts and leukemia stem cells. Blood 137, 661–677. doi:10.1182/blood.2020008676
  11. Thomson, E.C., Rosen, L.E., Shepherd, J.G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J.A., Davis, C., Piccoli, L., Pascall, D.J., Dillen, J., Lytras, S., Czudnochowski, N., Shah, R., Meury, M., Jesudason, N., De Marco, A., Li, K., Bassi, J., O’Toole, A., Pinto, D., Colquhoun, R.M., Culap, K., Jackson, B., Zatta, F., Rambaut, A., Jaconi, S., Sreenu, V.B., Nix, J., Zhang, I., Jarrett, R.F., Glass, W.G., Beltramello, M., Nomikou, K., Pizzuto, M., Tong, L., Cameroni, E., Croll, T.I., Johnson, N., Di Iulio, J., Wickenhagen, A., Ceschi, A., Harbison, A.M., Mair, D., Ferrari, P., Smollett, K., Sallusto, F., Carmichael, S., Garzoni, C., Nichols, J., Galli, M., Hughes, J., Riva, A., Ho, A., Schiuma, M., Semple, M.G., Openshaw, P.J.M., Fadda, E., Baillie, J.K., Chodera, J.D., ISARIC4C Investigators, COVID-19 Genomics UK (COG-UK) Consortium, Rihn, S.J., Lycett, S.J., Virgin, H.W., Telenti, A., Corti, D., Robertson, D.L., Snell, G., 2021. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell 184, 1171-1187.e20. doi:10.1016/j.cell.2021.01.037
  12. Toyama, Y., Harkness, R.W., Lee, T.Y.T., Maynes, J.T., Kay, L.E., 2021. Oligomeric assembly regulating mitochondrial HtrA2 function as examined by methyl-TROSY NMR. Proc Natl Acad Sci USA 118. doi:10.1073/pnas.2025022118
  13. VanBlargan LA, Errico JM, Kafai NM, Burgomaster KE, Jethva PN, Broeckel RM, Meade-White K, Nelson CA, Himansu S, Wang D, Handley SA, Gross ML, Best SM, Pierson TC, Fremont DH, Diamond MS. Broadly neutralizing monoclonal antibodies protect against multiple tick-borne flaviviruses J Exp Med. 2021 May 3;218(5):e20210174. doi: 10.1084/jem.20210174. PMID: 33831142
  14. Viswanathan, T., Chen, J., Wu, M., An, L., Kandavelu, P., Sankaran, B., Radhakrishnan, M., Li, M., Rosen, B.P., 2021. Functional and structural characterization of AntR, an Sb(III) responsive transcriptional repressor. Mol. Microbiol. doi:10.1111/mmi.14721
  15. Walker, R.G., Kattamuri, C., Goebel, E.J., Zhang, F., Hammel, M., Tainer, J.A., Linhardt, R.J., Thompson, T.B., 2021. Heparin-mediated dimerization of follistatin. Exp Biol Med (Maywood) 246, 467–482. doi:10.1177/1535370220966296
  16. Wang, X., Pereira, J.H., Tsutakawa, S., Fang, X., Adams, P.D., Mukhopadhyay, A., Lee, T.S., n.d. Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450. Metab. Eng. 64, 41–51. doi:10.1016/j.ymben.2021.01.004
  17. Yu, D., Kaur, G., Blumenthal, R.M., Zhang, X., Cheng, X., 2021. Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima. J. Biol. Chem. 100270. doi:10.1016/j.jbc.2021.100270
  18. Yu, Z., Ku, A.F., Anglin, J.L., Sharma, R., Ucisik, M.N., Faver, J.C., Li, F., Nyshadham, P., Simmons, N., Sharma, K.L., Nagarajan, S., Riehle, K., Kaur, G., Sankaran, B., Storl-Desmond, M., Palmer, S.S., Young, D.W., Kim, C., Matzuk, M.M., 2021. Discovery and characterization of bromodomain 2-specific inhibitors of BRDT. Proc Natl Acad Sci USA 118. doi:10.1073/pnas.2021102118
  19. Slavik KM, Morehouse BR, Ragucci AE, Zhou W, Ai X, Chen Y, Li L, Wei Z, Bähre H, König M, Seifert R, Lee ASY, Cai H, Imler JL, Kranzusch PJ. cGAS-like receptors sense RNA and control 3’2′-cGAMP signalling in Drosophila. Nature. 2021 Sep;597(7874):109-113. doi: 10.1038/s41586-021-03743-5. Epub 2021 Jul 14. PMID: 34261127
  20. Starr TN, Czudnochowski N, Liu Z, Zatta F, Park YJ, Addetia A, Pinto D, Beltramello M, Hernandez P, Greaney AJ, Marzi R, Glass WG, Zhang I, Dingens AS, Bowen JE, Tortorici MA, Walls AC, Wojcechowskyj JA, De Marco A, Rosen LE, Zhou J, Montiel-Ruiz M, Kaiser H, Dillen JR, Tucker H, Bassi J, Silacci-Fregni C, Housley MP, di Iulio J, Lombardo G, Agostini M, Sprugasci N, Culap K, Jaconi S, Meury M, Dellota E Jr, Abdelnabi R, Foo SC, Cameroni E, Stumpf S, Croll TI, Nix JC, Havenar-Daughton C, Piccoli L, Benigni F, Neyts J, Telenti A, Lempp FA, Pizzuto MS, Chodera JD, Hebner CM, Virgin HW, Whelan SPJ, Veesler D, Corti D, Bloom JD, Snell G. SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape Nature. 2021 Sep;597(7874):97-102. doi: 10.1038/s41586-021-03807-6. Epub 2021 Jul 14. PMID: 34261126
  21. Palayam M, Ganapathy J, Guercio AM, Tal L, Deck SL, Shabek N. Structural insights into photoactivation of plant Cryptochrome-2.Commun Biol. 2021 Jan 4;4(1):28. doi: 10.1038/s42003-020-01531-x. PMID: 33398020
  22. Su Z, Cantlon J, Douthit L, Wiedorn M, Boutet S, Kern J, Yoon CH, DePonte D. J Serial crystallography using automated drop dispensing.  Synchrotron Radiat. 2021 Sep 1;28(Pt 5):1386-1392. doi: 10.1107/S1600577521006160. Epub 2021 Jul 22. PMID: 34475287
  23. Schumacher MA, Gallagher KA, Holmes NA, Chandra G, Henderson M, Kysela DT, Brennan RG, Buttner MJ. Evolution of a σ-(c-di-GMP)-anti-σ switch.  Proc Natl Acad Sci U S A. 2021 Jul 27;118(30):e2105447118. doi: 10.1073/pnas.2105447118. PMID: 34290147

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