Publications
Hill, E.; Hill, A.; Voisin, E.; Byrd, A.; Schoeffler, A.J. Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity. (2025) Proteins: Structure, Function, Bioinformatics, 93:702-715 https://onlinelibrary.wiley.com/doi/10.1002/prot.26760
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Paraan, M.; Nasef, M.; Chou-Zheng, L.; Khweis, S.A.; Schoeffler, A.J.; Hatoum-Aslan, A.; Stagg, S.M.; Dunkle, J.A. The structure of a Type III-A CRISPR-Cas effector complex revelas conserved and idiosyncratic contacts to target RNA and crRNA among Type III-A systems. (2023) PLoS ONE 18(6):e0287461. Full Text; Open Access
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Schoeffler, A.J.; Helgason, E.; Popovych, N.; Dueber, E.C. Diagnosing and mitigating method-based avidity artifacts that confound polyubiquitin-binding assays, (2021) Biophysical Reports 1: 1-12. Full Text; Open Access
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Sharkey, R.E.; Herbert, J.B.; McGaha, D.A.; Nguyen, V.; Schoeffler, A.J.; Dunkle, J.A. Three critical regions of the erythromycin resistance methyltransferase, ErmE, are required for function supporting a model for the interaction of Erm family enzymes with substrate rRNA. (2021) RNA 28: 210-226. Full Text
*corresponding author; undergraduate co-author*
Wertz, I.E.; Newton, K.; Seshasayee, D.; Saritha, K.; Lam, C.; Zhang, J.; Popovych, N.; Helgason, E.; Schoeffler, A.J.; Jeet, S.; Ramamoorthi, N.; Kategaya, L.; Newman, R.J.; Horikawa, K.; Dugger, D.; Sandoval, W.; Mukund, S.; Zindal, A.; Martin, F.; Quan, C.; Tom, J.; Fairbrother, W.J.; Townsend, M.; Warming, S.; DeVoss, J.; Liu, J.; Dueber, E.C.; Capalzi, P.; Lee, W.P.; Goodnow, C.C.; Balazs, M.; Yu, K.; Koluman, G.; Dixit, V.M. Phosphorylation and Linear Ubiquitin Direct A20 Inhibition of Inflammation. (2015) Nature 528: 370-375. Full Text
Yin, J.; Schoeffler, A.J.; Wickliffe, K.; Newton, K.; Starovasnik, M.; Dueber, E.C.; Harris, S.F. Structural Insights into WD-Repeat 48 Activation of Ubiquitin-Specific Protease 46. (2015) Structure 23: 2043-2054. Full Text; Open Access
Phillips, A.H.; Schoeffler, A.J.; Matsui, T.; Weiss, T.M.; Blankenship, J.W.; Zobel, K.; Giannetti, A.M.; Dueber, E.C. Internal motions prime cIAP1 for rapid activation. (2014) Nature Structural and Molecular Biology 21: 1068-1074. Full Text
*co-first authorship*
Vos, S.M.; Lyubimov, A.Y.; Hershey, D.M.; Schoeffler, A.J.; Sengupta, S.; Nagaraja, V.; Berger, J.M. Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein. (2014) Genes & Development 28: 1485-1497. Full Text; Open Access
Fouts, A.E.; Comps-Agrar, L.; Stengel, K.F.; Ellermen, D.; Schoeffler, A.J.; Warming, S.; Eaton, D.L.; Feierbach, B. Mechanism for neutralizing activity by the anti-CMV gH/gL monoclonal antibody MSL-109. (2014) Proceedings of the National Academy of Sciences 111 8209-8214.
Basu, A.; Schoeffler, A.J.; Berger, J.M.; Bryant, Z. ATP binding controls distinct transitions of Escherichia coli DNA gyrase in complex with DNA. (2012) Nature Structural and Molecular Biology 19: 538-546.
Dueber, E.C.; Schoeffler, A.J.; Lingel, A.; Elliott, J.M.; Fedorova, A.V.; Giannetti, A.M.; Zobel, K.; Maurer, B.; Varfolomeev, E.; Wu, P.; Wallweber, H.J.; Hymowitz, S.G.; Deshayes, K.; Vucic, D.; Fairbrother, W.J. Antagonists induce a conformational change in cIAP1 that promotes autoubiquitination. (2011) Science 334: 376-380.
Leonelli, L.; Pelton, J.; Schoeffler, A.J.; Dahlbeck, D.; Berger, J.; Wemmer, D.E.; Stakawicz, B. Structural and functional characterization of the Hyaloperonospora arabidopsidis effector protein ATR13. (2011) PLoS Pathogens 7: e1002428-e1002428.
Li, Y.; Stewart, N.K.; Berger, A.J.; Vos, S.; Schoeffler, A.J.; Berger, J.M.; Chait, B.T.; Oakley, M.G. Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction. (2010) Proceedings of the National Academy of Sciences 107: 18832-18837.
Schoeffler, A.J.; May, A.P.; Berger, J.M. A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. (2010) Nucleic Acids Research 38: 7830-7844.
Li, Y.; Schoeffler, A.J.*; Berger, J.M.; Oakley, M.G. The crystal structure of the hinge domain of the Escherichia coli structural maintenance of chromosomes protein MukB. (2010) Journal of Molecular Biology 395: 11-19.
*co-first authorship*
Tretter, E.M.; Schoeffler, A.J.; Weisfield, S.R.; Berger, J.M. Crystal structure of the DNA gyrase GyrA N-terminal domain from Mycobacterium tuberculosis. (2009) Proteins 78: 492-495.
Stuchinskaya, T.; Michenall, L.A.; Schoeffler, A.J.; Corbett, K.D.; Berger, J.M.; Bates, A.D.; Maxwell, A. How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases. (2009) Journal of Molecular Biology 385: 1397-1408.
Schoeffler, A.J.; Berger, J.M. DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. (2008) Quarterly Reviews of Biophysics 41: 41-101.
Barth, P.; Schoeffler, A.J.; Alber, T. Targeting metastable coiled-coil domains by computational design. (2008) Journal of the American Chemical Society 130: 12038-44.
Schoeffler, A.J.; Berger, J.M. Recent advances in understanding structure-function relationships in type II topoisomerases. (2005) Biochemical Society Transactions 33: 1465-1470.
Corbett, K.D.; Schoeffler, A.J.; Thomsen, N.D.; Berger, J.M. (2005) The structural basis for substrate specificity in DNA topoisomerase IV. Journal of Molecular Biology 351: 545-561.
Schoeffler, A.J.; Joubert, A.M.; Peng, F.G.; Khan, F.H.; Liu, C.C.; LiCata, V.J. Extreme free energy stabilization of Taq DNA polymerase. (2004) Proteins: Structure, Function and Bioinformatics 54: 616-621.
Schoeffler, A.J.; Ruiz, C.R.; Joubert, A.M.; Yang, X.; LiCata, V.J. Salt modulates the stability and lipid binding affinity of the adipocyte lipid binding protein. (2003) Journal of Biological Chemistry 278: 33268-33275.