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Publications from 2000 to 2009


Attia, A.S., Sedillo, J.L., Hoopman, T.C., Liu, W., Liu, L., Brautigam, C.A., & Hansen, E.J. "Identification of a bacteriocin and its cognate immunity factor expressed by Moraxella catarrhalis." BMC Microbiol., 9, 207.

Huerta, C., Borek, D., Machius, M., Grishin, N.V., & Zhang, H. "Structure and mechanism of a eukaryotic FMN adenylyltransferase.J. Mol. Biol., 389, 388-400.

Brautigam, C.A., Wynn, R.M., Chuang, J.L., & Chuang, D.T. "Subunit and catalytic component stoichiometries of an in vitro reconstituted human pyruvate dehydrogenase complex.J. Biol. Chem., 284, 13086-13098.

Davis, L., Abdi, K., Machius, M., Brautigam, C., Tomchick, D.R., Bennett, V., Michaely, P. "Localization and structure of the ankyrin-binding site on beta2-spectrin." J. Biol. Chem., 284, 6982-6987.

Scheuermann, T.H., Tomchick, D.R., Machius, M., Guo, Y., Bruick, R.K., Gardner, K.H. "Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor." Proc. Natl. Acad. Sci. USA, 106, 450-455.


Kato, M., Wynn, R.M., Chuang, J.L., Tso, S.C., Machius, M., Li, J., & Chuang, D.T. "Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops." Structure, 16, 1849-1859.

Padrick, S.B., Cheng, H.C., Ismail, A.M., Panchal, S.C., Doolittle L.K., Kim, S., Skehan, B.M., Umetani, J., Brautigam, C.A., Leong, J.M., Rosen, M.K. "Hierarchical regulation of WASP/WAVE proteins." Mol. Cell, 32, 426-438.

Kang, J., Yang, M., Li, B., Qi, W., Zhang, C., Shokat, K.M., Tomchick, D.R., Machius, M., & Yu, H. "Structure and substrate recruitment of the human spindle checkpoint kinase Bub1." Mol. Cell, 32, 394-405.

Rezacova, P., Kozisek, M., Moy, S.F., Sieglova, I., Joachimiak, A., Machius, M., & Otwinowski, Z. "Crystal structures of the effoector -binding domain of repressor CggR from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates.Mol. Microbiol., 69, 895-910.

Attia, A.S., Sedillo, J.L., Wang, W., Liu, W., Brautigam, C.A., Winkler, W., & Hansen, E.J. "Moraxella catarrhalis expresses an unusual Hfq protein." Infect. Immun., 76, 2520-2530. [PDF]

Lee, J., Tomchick, D.R., Brautigam, C.A., Machius, M., Kort, R., Hellingwerf, H.J., & Gardner, K.H. "Changes at the KinA PAS-A dimerization interface influence histidine kinase function." Biochemistry, 47, 4051-4064.

Yang, M., Li, B. Liu, C.J., Tomchick, D.R., Machius, M., Rizo, J., Yu, H., Luo, X. "Insights into mad2 regulation in the spindle checkpoint revealed by the crystal structure of the symmetric mad2 dimer.PLoS Biol., 6, e50.

Haines, D.C., Chen, B., Tomchick, D.R., Bondlela, M., Hegde, A., Machius, M., & Peterson, J.A. "Crystal structure of inhibitor-bound P450BM-3 reveals open conformation of substrate access channel." Biochemistry, 47, 3662-3670.

Huang, N., Sorci, L., Zhang, X., Brautigam, C., Li, X., Raffaelli, N., Magni, G., Grishin, N.V., Osterman, A., & Zhang, H. "Bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase: structure and function in bacterial NAD metabolism." Structure, 16, 196-209.

Hoopman, T.C., Wang, W., Brautigam, C.A., Reilly, T.J., and Hansen, E.J. "Moraxella catarrhalis synthesizes an autotransporter that is an acid phosphatase." J. Bacteriol., 190, 1459-1472.


Hegde, A., Haines, D.C., Bondlela, M., Chen, B., Schaffer, N., Tomchick, D.R., Machius, M., Nguyen, H., Chowdhary, P.K., Stewart, L, Lopez, C., and Peterson, J.A. "Interactions of substrates at the surface of P450s can greatly enhance substrate potency." Biochemistry, 46, 14010-14017. 

Yang, M., Li, B., Tomchick, D.R., Machius, M., Rizo, J., Yu, H., and Luo, X.  "p31(comet) blocks Mad2 activation through structural mimicry.Cell, 131, 744-755.

Guan, R., Dai, H., Tomchick, D.R., Dulubova, I., Machius, M., Sudhof, T.C., and Rizo, J. "Crystal structure of the RIM1alpha domain at 1.7 A.Biochemistry, 46, 8988-8998.

Yang, M., Culhane, J.C., Szewczuk, L.M., Jalili, P., Ball, H.L., Machius, M., Cole, P.A., and Yu, H. "Structural basis for the inhibition of the LSD1 histone demethylase by the antidepressant trans-2-phenylcyclopropylamine.Biochemistry, 46, 8058-8065.

Machius, M., Brautigam, C.A., Tomchick, D.R., Ward, P., Otwinowski, Z., Blevins, J.S., Deka, R.K., & Norgard, M.V. "Structural and biochemical basis for polyamine binding to the Tp0655 lipoprotein of Treponema pallidum: putative role for Tp0655 (TpPotD) as a polyamine receptor." J. Mol. Biol., 373, 681-694.

Yang, M., Culhane, J.C., Szewczuk, L.M., Gocke, C.B., Brautigam, C.A., Tomchick, D.R., Machius, M., Cole, P.A., & Yu, H. "Structural basis of histone demethylation by LSD1 revealed by suicide inactivation.Nat. Struct. Molec. Biol., 14, 535-539. [PDF]

Li, J., Machius, M., Chuang, J.L., Wynn, R.M., and Chuang, D.T. "The two active sites in human branched-chain alpha-keto acid dehydrogenase operate independently without an obligatory alternating-site mechanism." J. Biol. Chem., 282, 11904-11913.

Chosed, R., Tomchick, D.R., Brautigam, C.A., Mukherjee, S., Negi, V.S., Machius, M., and Orth, K. "Structural analysis of Xanthomonas XopD provides insights into substrate specificity of ULPs." J. Biol. Chem., 282, 6773-6782.

Deka, R.K., Brautigam, C.A., Tomson, F.L., Machius, M., Tomchick, D.R., and Norgard, M.V. "Crystal structure of the Tp34 (TP0971) lipoprotein of Treponema pallidum: biological implications of its metal-bound state and affinity for human lactoferrin." J. Biol. Chem., 282, 5944-5958.


Yang, M., Gocke, C.B., Luo, X., Borek, D., Tomchick, D.R., Machius, M., Otwinowski, Z., and Yu, H. "Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase.Mol. Cell, 23, 377-387.

Gilles-Gonzalez, M.-A., Caceres, A.I., Sousa, E.H.S., Tomchick, D.R., Brautigam, C., Gonzalez, C., and Machius, M. "v." J. Mol. Biol., 360, 80-89.

Lu, J., Machius, M., Dulubova, I., Dai, H., Sudhof, T.C., Tomchick, D.R., and Rizo, J. "Structural basis for a Munc13-1 homodimer to Munc13-1/RIM heterodimer switch." PLoS Biol., 4, e192.

Machius, M., Wynn, R.M., Chuang, J.L., Li, J., Kluger, R., Yu, D., Tomchick, D.R., Brautigam, C.A., and Chuang, D.T. "A versatile conformational switch regulates reactivity in human branched-chain a-ketoacid dehydrogenase." Structure, 14, 287-298.

Brautigam, C.A., Wynn, R.M., Chuang, J.L., Machius, M., Tomchick, D.R., and Chuang, D.T. "Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex." Structure, 14, 611-621.

Deka, R.K., Brautigam, C.A., Yang, X.F., Blevins, J.S., Machius, M., Tomchick, D.R., and Norgard, M.V. "The PnrA (Tp0319; TmpC) lipoprotein represents a new family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC)-like operon in Treponema pallidum.J. Biol. Chem., 281, 8072-8081.


Dai, H., Tomchick, D.R., Garcia, J., Sudhof, T.C., Machius, M., and Rizo, J. "Crystal structure of the RIM2 C2A-domain at 1.4 A resolution." Biochemistry, 44, 13533-13542.

Brautigam, C.A., Chuang, J.L., Tomchick, D.R., Machius, M., and Chuang, D.T. "Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations." J. Mol. Biol., 350, 543-552.

Otomo, T., Otomo, C., Tomchick, D.R., Machius, M., and Rosen, M.K. "Structural basis of Rho GTP-ase-mediated activation of the formin mDia1." Mol. Cell, 18, 273-281.

Otomo, T., Tomchick, D.R., Otomo, C., Panchal, S.C., Machius, M., and Rosen, M.K. "Structural basis of actin filament nucleation and processive capping by a formin homology 2 domain." Nature, 433, 488-494.

Thibodeau, P.H., Brautigam, C.A., Machius, M., and Thomas, P.J. "Side chain and backbone contributions of Phe508 to CFTR folding.Nat. Struct. Molec. Biol., 12, 10-16.


Deka, R.K., Neil, L., Hagman, K.E., Machius, M., Tomchick, D.R., Brautigam, C.A., and Norgard, M.V. "Structural evidence that the 32-Kilodalton lipoprotein (Tp32) of Treponema pallidum is a L-Methionine-binding protein." J. Biol. Chem., 279, 55644-55650.

Wynn, R.M., Kato, M., Machius, M., Chuang, J.L., Li, J., Tomchick, D.R., & Chuang, D.T. "Molecular mechanism for regulation of the human mitochondrial branched-chain a-ketoacid dehydrogenase complex by phosphorylation." Structure, 12, 2185-2196.

Li, J., Wynn, R.M., Machius, M., Chuang, J.L., Karthikeyan, S., Tomchick, D.R. and Chuang, D.T. "Cross-talk between Thiamin Diphosphate Binding and Phosphorylation Loop Conformation in Human Branched-chain a-Keto Acid Decarboxylase/Dehydrogenase.J. Biol. Chem., 279, 32968-32978.

Dai, H., Shin, O.-H., Machius, M., Tomchick, D.R., & Rizo, J. "Structural Basis for the Evolutionary Inactivation of Ca2+ Binding to Synaptotagmin 4." Nat. Struct. Molec. Biol., 11, 844-849.


Wynn, R.W., Machius, M., Chuang, J., Li, J., Tomchick, D.R., and Chuang, D.T. "Roles of His291-a and His146-b' in the Reductive Acylation Reaction Catalyzed by Human Branched-chain a-Ketoacid Dehydrogenase.J. Biol. Chem., 278, 43402-43410.

Hu, X., Machius, M., and Yang, W. "Monovalent Cation Dependence and Preference of GHKL ATPases and Kinases.FEBS Lett., 544, 268-273.


Michaely, P., Tomchick, D.R., Machius, M., and Anderson, R.G.W. "Crystal Structure of a 12 ANK Repeat Stack from Human AnkyrinR." EMBO J., 21, 6387-6396.

Deka, R.K., Machius, M., Norgard, M.V., and Tomchick, D.R. "Crystal Structure of the 47-kDa Lipoprotein of Treponema pallidum Reveals a Novel Penicillin-binding Protein." J. Biol. Chem., 277, 41857-41862.

Chen, X., Tomchick, D.R., Kovrigin, E., Arac, D., Machius, M., Sudhof, T.C., and Rizo, J. "Three-dimensional Structure of the Complexin/SNARE Complex." Neuron, 33, 397-409.

Zhou, T., Kurnasov, O., Tomchick, D.R., Binns, D.D., Grishin, N.V., Marquez, V.E., Osterman, A.L., and Zhang, H. "Structure of Human Nicotinamide/Nicotinic Acid Mononucleotide Adenylyltransferase: Basis for the Dual Substrate Specificity and Activation of the Oncolytic Agent Tiazofurin.J. Biol. Chem., 277, 13148-13154.


Haines, D.C., Tomchick, D.R., Machius, M., and Peterson, J.A. "Pivotal Role of Water in the Mechanism of P450-BM3.Biochemistry, 40, 13456-13465.

Machius, M., Chuang, J.L., Wynn, R.W., Tomchick, D.R., and Chuang, D.T. "Structure of Rat BCKD Kinase: Nucleotide-induced Domain Communication in a Mitochondrial Protein Kinase." Proc. Natl. Acad. Sci. USA, 98, 11218-11213.