NCDIR Publications

2009

• F. Selimi, I.M. Cristea, E. Heller, B.T. Chait, N. Heintz, "Proteomic Studies of a Single CNS Synapse Type: The Parallel Fiber/Purkinje Cell Synapse", PLoS Biology 2009 Apr 14
• Y. Zhong, Q.J. Wang, X. Li, Y. Yan, J.M. Backer, B.T. Chait, N. Heintz, Z. Yue, "Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1-phosphatidylinositol-3-kinase complex", Nat Cell Biol. Mar 8, 2009
• Z. Yue, G.R. Holstein, B. T. Chait, Q.J. Wang, "Using genetic mouse models to study the biology and pathology of autophagy in the central nervous system", Methods Enzymol. 453 (2009) 159-80.
• F. Forster, K. Lasker, F. Beck, S. Nickell, A. Sali, W. Baumeister. An Atomic Model AAA-ATPase/20S core particle sub-complex of the 26S proteasome. Biochem Biophys Res Commun 388, 228-233, 2009.
• T. Lezon, A. Sali, I. Bahar. Global motions of the nuclear pore complex:Insights from Elastic Network Models. PLoS Computational Biology 5, e1000496, 2009.
• J.A. DeGrasse, K.N. DuBois, D. Devos, T.N. Siegel, A. Sali, M.C. Field, M.P. Rout, B.T. Chait. The Establishment of Nuclear Pore Complex Architecture Occurred Early in Evolution. Mol Cell Proteomics 8, 2119-2130, 2009.
• K. Lasker, M. Topf, A. Sali, H.J. Wolfson. Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly. J Mol Biol 388, 180-194, 2009.
• S. Nickell, F. Beck, S.H.W. Scheres, A. Korinek, F. Forster, K. Lasker, O. Mihalache, N. Sun, I. Nagy, A. Sali, J. Plitzko, J.-M. Carazo, M. Mann, W. Baumeister. Insights into the Molecular Architecture of the 26S Proteasome. Proc Natl Acad Sci USA 29, 11943-11947, 2009.
• Wan, Y., Saleem, R. A., Ratushny, A. V., Roda, O., Smith, J. J., Lin, C. H., Chiang, J. H. and Aitchison, J. D. (2009) Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes, Mol Cell Biol, 29: 2346-2358
• Gradolatto, A., Smart, S. K., Byrum, S., Blair, L. P., Rogers, R. S., Kolar, E. A., Lavender, H., Larson, S. K., Aitchison, J. D., Taverna, S. D. and Tackett, A. J. (2009) A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity, Mol Cell Biol, 29: 4604-4611
• Fernandez-Martinez J, Rout MP. Nuclear pore complex biogenesis. Curr Opin Cell Biol. 2009 Aug;21(4):603-12. Epub 2009 Jun 11.
• Lew DJ, Rout MP. Cell structure and dynamics. Curr Opin Cell Biol. 2009 Feb;21(1):1-3
• Jovanovic-Talisman T, Tetenbaum-Novatt J, McKenney AS, Zilman A, Peters R, Rout MP, Chait BT. Artificial nanopores that mimic the transport selectivity of the nuclear pore complex. Nature. 2009 Feb 19;457(7232):1023-7. Epub 2008 Dec 21.

2008

• Alber, F., Chait, B.T., Rout, M.P., Sali, A.
  "Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints," Protein-protein Interactions and Networks. A. Panchenko, T. Przytycka (eds.), Cambridge University Press, Cambridge, UK, 2008.
• Alber, F., Förster, F., Korkin, D., Topf, M., Sali, A.
  "Integrating Diverse Data for Structure Determination of Macromolecular Assemblies." Annual Review of Biochemistry 77, 11.1–11.35, 2008.
• Chandramouli, P., Topf, M., Ménétret, J.F., Eswar, N., Gutell, R.R., Sali, A., Akey, C.W.
  "Structure of the Mammalian 80S Ribosome at 8.7Å Resolution." Structure 16, 535-548, 2008.
• Cong, Y., Topf, M., Sali, A., Matsudaira, P., Dougherty, M.T., Chiu, W., Schmid, M.F.
  "Crystallographic Conformers of Actin in a Biologically Active Bundle of Filaments." J. Mol. Biol. 375, 331-6, 2008.
• Förster, F., Webb, B., Krukenberg, K.A., Tsuruta, H., Agard, D.A., Sali, A.
  "Integration of small angle X-ray scattering and protein structure modeling." J. Mol. Biol 382, 1089-106, 2008.
• Gradolatto, A., Rogers, R., Lavender, H., Taverna, S.D., Allis, C.D., Aitchison, J.D., Tackett, A.J.
  "Saccaromyces cerevisiae Yta7 regulates histone gene expression." Genetics 179(1): 291-304, 2008.
• Hood, L., Rowen, L., Galas, D.J., and Aitchison, J.D.
  "Systems biology at the Institute for Systems Biology. Briefings in functional genomics & proteomics." 2008.
• K.A. Krukenberg, Förster, F., L.M. Rice, Sali, A., Agard, D.A.
  "A novel conformation of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90." Structure 16, 755-765, 2008.
• Lee, D.J., Busby, S.J.W., Westblade, L.F., Chait, B.T.
  "Affinity isolation and I-DIRT mass spectrometric analysis of the Escherichia coli O157:H7 Sakai RNA polymerase complex." J Bacteriol 190, 1284-1289, 2008.
• Marelli, M., Nesvizhskii, A.I., and Aitchison, J.D.
  "Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes." Methods in Molecular Biology, Clifton, NJ 432: 357-371, 2008.
• Moorman, N.J., Cristea, I.M., Terhune, S.S., Rout, M.P., Chait, B.T., Shenk, T.
  "Human cytomegalovirus protein UL38 inhibits host cell stress responses by antagonizing the tuberous sclerosis protein complex." Cell Host Microbe. 3(4), 253-62, 2008.
• Postow, L., Ghenoiu, C., Woo, E.M., Krutchinsky, A.N., Chait, B.T., Funabiki, H.
  "Ku80 removal from DNA through double strand break-induced ubiquitylation." J Cell Biol. 182, 467-479, 2008.
• Ratushny, A.V., Ramsey, S.A., Roda, O., Wan, Y., Smith, J.J., and Aitchison, J.D.
  "Control of Transcriptional Variability by Overlapping Feed-Forward Regulatory Motifs." Biophysical journal, 2008.
• Rout, M.P.
  "The peroxisome: a production in four acts." J Cell Biol. 181(2), 185-7, 2008.
• Saleem, R.A., Knoblach, B., Mast, F.D., Smith, J.J., Boyle, J., Dobson, C.M., Long-O'Donnell, R., Rachubinski, R.A., Aitchison, J.D.
  "Genome-wide analysis of signalling networks regulating fatty acid induced gene expression and organelle biogenesis." J. Cell Biol. 2: 281-292, 2008.
• Savalia, D., Westblade, L.F., Goel, M., Florens, L., Kemp, P., Akulenko, N., Pavlova, O., Padovan, J.C., Chait, B.T., Washburn, M.P., Ackermann, H.W., Mushegian, A., Gabisonia, T., Molineux, I., Severinov, K.
  "Genomic and Proteomic Analysis of phiEco32, a Novel Escherichia coli Phage." J. Mol. Biol., 2008.
• Topf, M., Lasker, K., Webb, B., Wolfson, H., Chiu, W., Sali, A.
  "Protein Structure Fitting and Refinement Guided by cryoEM Density." Structure 16, 295-307, 2008.
• Westblade, L.F., Minakhin, L., Kuznedelov, K., Tackett, A.J., Chang, E.J., Mooney, R.A., Vvedenskaya, I., Wang, Q., Studier, F.W., Rout, M.P., Landick, R., Chait, B.T., Severinov, K., Darst, S.A.
  "Rapid isolation and identification of T4 bacteriophage-encoded modifications of Escherichia coli RNA polymerase using immunoisolation and MALDI MS." J. Proteome Res. 7(3), 1244-50, 2008.
• Woo, E.M., Fenyö, D., Kwok, B.H., Funabiki, H., Chait, B.T.
  "Efficient Identification of Phosphorylation by Mass Spectrometric Phosphopeptide Fingerprinting." Anal. Chem. 2008.
• Yue, Z., Wang, Q.J., Komatsu, M.
  "Neuronal autophagy: Going the distance to the axon." Autophagy 4, 94-96, 2008.



2007

• Aitchison, J. D., and Wozniak, R. W.
  Cell biology: "Pore puzzle." Nature 450, 621-622, 2007
• Alber, F., S. Dokudovskaya, Veenhoff, L.M., Zhang, W., Kipper, J., Devos, D., Suprapto, A., Karni-Schmidt, O., Williams, R., Chait, B.T., Rout, M.P., Sali, A.,
  "Determining the architectures of macromolecular assemblies", Nature 450, 683-694, 2007.
• Albe, F., Dokudovskaya, S., Veenhoff, L.M., Zhang, W., Kipper, J., Devos, D., Suprapto,A., Karni-Schmidt, O., Williams, R., Chait, B.T., Sali, A., Rout, M.P.,
  "The molecular architecture of the nuclear pore complex." Nature 450, 695-701, 2007.
• R. Aragues, Sali, A., Marti-Renom, M.A., Oliva, B..
  "Characterization of protein network hubs by inferring interacting motifs from binary protein interactions." PLoS Comp. Biol. 3, 1761-1771, 2007.
• Glavy, J.S., Krutchinsky, A.N., Cristea, I.M., Berke, I.C., Boehmer, T., Blobel, G., Chait, B.T., "Cell-cycle-dependent phosphorylation of the nuclear pore Nup107-160 subcomplex." Proc Natl Acad Sci, 104, 3811-3816, 2007.
• A.E. Kelly, Sampath, S.C., Maniar, T.A., Woo, E.M., Chait, B.T., Funabiki, H.
  "Chromosomal enrichment and activation of the aurora B pathway are coupled to spatially regulate spindle assembly." Dev. Cell. 12, 31-43, 2007.
• Komatsu, M., Wang, Q.J., Holstein, G.R., Friedrich Jr., V.L., Iwata, J., Kominami, E., Chait, B.T., Tanaka, K., Yue, Z.
  "Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration." Proc Natl Acad Sci, 104, 14489-14494, 2007.
• Makhnevych, T., Ptak, C., Lusk, C. P., *Aitchison, J. D., and *Wozniak, R. W.
  "The role of karyopherins in the regulated sumoylation of septins.", J. Cell Biol. 177, 39-49, 2007.
• M. Oeffinger, A. Fatica, Rout, M.P., D. Tollervey.
  "Yeast Rrp14p is required for ribosomal subunit synthesis and for correct positioning of the mitotic spindle during mitosis." Nucleic Acids Res. 35(4), 1354-66, 2007.
• Oeffinger, M., Wei, K.E., Rogers, R., DeGrasse, J.A., Chait, B.T., Aitchison, J.D. & Rout, M.P. "Comprehensive analysis of diverse ribonucleoprotein complexes." Nature Methods, 4, 951-956, 2007.
• Robinson, C.V., Sali, A., Baumeister, W.
  "Molecular sociology of the cell." Nature 450, 973-982, 2007.
• Smith, J.J., Ramsey, S.A., Marelli, M., Marzolf, B., Hwang, D., Saleem, R.A., Rachubinski, R.A., and Aitchison, J.D.
  "Transcriptional responses to fatty acid are coordinated by combinatorial control." Mol. Syst. Biol. 3, 115, 2007.
• Taverna, S.D., Ueberheide, S.D., Liu, Y., Tackett, A.J., Diaz, R.L., Shabanowitz, J., Chait, B.T., Hunt, D.F., Allis, C.D.
  "Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini." Proc Natl Acad Sci, 104, 2086-2091, 2007.
• Zhang, J., Harnpicharnchai, P., Jakovljevic, J., Tang, L., Guo, Y., Oeffinger, M., Rout, M.P., Hiley, S.L., Hughes, T., Woolford Jr., J.L
  "Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes." Genes Dev. 21(20), 2580-92, 2007.



2006

• Chait, B.T.
  "Mass spectrometry: bottom-up or top-down?." Science, 314 (2006) 65-66.
• I.M. Cristea, J.W. Carroll, Rout, M.P., C.M. Rice, Chait, B.T., M.R. Macdonald
  "Tracking and elucidating alphavirus-host protein interactions." J. Biol. Chem., 281, 30269-30278, 2006.
• F.P. Davis, H. Braberg, M.Y. Shen, U. Pieper, Sali, A., M.S. Madhusudhan.
  "Protein complex compositions predicted by structural similarity." Nucleic Acids Research 34, 2943-2952, 2006.
• Devos D, Dokudovskaya S, Williams R, Alber F, Eswar N, Chait BT, Rout MP, Sali A
  "Simple fold composition and modular architecture of the nuclear pore complex." Proc Natl Acad Sci U S A, 2006.
• Dokudovskaya S, Williams R, Devos D, Sali A, Chait BT, Rout MP
  "Protease Accessibility Technical Advance Laddering: A Proteomic Tool for Probing Protein Structure." Structure, 2006.
• Guermah M, Palhan VB, Tackett AJ, Chait BT, Roeder RG
  "Synergistic functions of SII and p300 in effecting productive activator-dependent transcription of chromatin templates." Cell, 2006.
• McBride KM, Gazumyan A, Woo EM, Barreto VM, Robbiani DF, Chait BT, Nussenzweig MC
  "Regulation of hypermutation by AID phosphorylation." Proc. Natl. Acad. Sci. U S A, 2006.
• Saleem, R. A., Smith, J. J., and Aitchison, J. D.
  "Proteomics of the peroxisome." Biochim. Biophys. Acta. 1763, 1541-1551, 2006.
• M-Y. Shen, Sali, A..
  "Statistical Potential for Assessment and Prediction of Protein Structures." Protein Science 15, 2507-2524, 2006.
• Smith, J. J., Sydorskyy, Y., Marelli, M., Hwang, D., Bolouri, H., Rachubinski, R. A., and Aitchison, J. D.
  "Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism." Mol. Syst. Biol. 2, 2006 0009
• Taverna, S. D., Ilin, S., Rogers, R. S., Tanny, J. C., Lavender, H., Li, H., Baker, L., Boyle, J., Blair, L. P., Chait, B. T., Patel, D. J., Aitchison, J. D., Tackett, A. J., and Allis, C. D.
  "Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs." Mol. Cell 24, 785-796, 2006.
• Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A
  "Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting." J. Mol. Biol., 2006.
• Q.J. Wang, Y. Ding, S. Kohtz, N. Mizushima, I.M. Cristea, Rout, M.P., Chait, B.T., Y. Zhong, N. Heintz, Z. Yue
  "Induction of autophagy in axonal dystrophy and degeneration." J. Neurosci., 26, 8057-68, 2006.
• Wysocka J, Swigut T, Xiao H, Milne TA, Kwon SY, Landry J, Kauer M, Tackett AJ, Chait BT, Badenhorst P, Wu C, Allis CD
  "A PHD finger of the largest NURF subunit couples histone H3 K4 trimethylation with chromatin remodeling." Nature, 2006.



2005

• Alber F, Kim MF, Sali A
  "Structural Characterization of Assemblies from Overall Shape and Subcomplex Compositions." Structure, 2005.
• Cristea IM, Williams R, Chait BT, Rout MP
  "Fluorescent Proteins as Proteomic Probes." Mol Cell Proteomics, 2005.
• Davis FP, Sali A
  "PIBASE: a comprehensive database of structurally defined protein interfaces." Bioinformatics, 2005.
• Dilworth DJ, Tackett AJ, Rogers RS, Yi EC, Christmas RH, Smith JJ, Siegel AF, Chait BT, Wozniak RW, Aitchison JD
  "The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control." J Cell Biol, 2005.
• Dou YL, Milne TA, Tackett AJ, Smith ER, Fukuda A, Wysocka J, Allis CD, Chait BT, Hess JL, Roeder RG
  "Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF." Cell, 2005.
• Jin M, Bateup H, Padovan JC, Greengard P, Nairn AC, Chait BT
  "Quantitative analysis of protein phosphorylation in mouse brain by hypothesis–driven multi–stage mass spectrometry." Anal. Chem., 2005.
• Korkin D, Davis FP, Sali A
  "Localization of protein-binding sites within families of proteins." Protein Sci., 2005.
• Niepel M, Strambio-de-Castillia C, Fasolo J, Chait BT, Rout MP
  "The nuclear pore complex–associated protein, Mlp2p, binds to the yeast spindle pole body and promotes its efficient assembly." J. Cell Biol., 2005.
• Palhan VB, Chen S, Peng GH, Tjernberg A, Gamper AM, Fan Y, Chait BT, La Spada AR, Roeder RG
  "Polyglutamine–expanded ataxin–7 inhibits STAG histone acetylltransferase activity to produce retinal degeneration." Proc. Natl. Acad. Sci. U S A, 2005.
• Sali A
  "Macromolecular Assemblies Highlighted." Structure, 2005.
• Tackett AJ, DeGrasse JA, Sekedat MD, Oeffinger M, Rout MP, Chait BT
  "I–DIRT, A General Method for Distinguishing between Specific and Nonspecific Protein Interactions." J Proteome Res, 2005.
• Topf M, Baker ML, John B, Chiu W, Sali A
  "Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy." J. Struct. Biol., 2005.
• Topf M, Sali A
  "Combining electron microscopy and comparative protein structure modeling." Curr. Opin. Struct. Biol., 2005.



Complete Lists of Publications

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Mike Rout’s complete publication list is located here.

Brian Chait’s complete publication list is located here.

Andrej Sali’s complete publication list is located here.

John Aitchison's complete publication list