2008 Publications

  1. Alber F, Förster F, Korkin D, Topf M, Sali A. “Integrating Diverse Data for Structure Determination of Macromolecular Assemblies.” Annual Review in Biochemistry 77: 443-477. 2008a. PMID: 18318657
  1. Alber F, Chait BT, Rout MP, Sali A. “Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints. In: Protein-protein interactions and networks: identification, characterization and prediction.” Ed: Panchenko, A. and Przytycka, T. Cambridge University Press, Cambridge, p. 99-114, Springer-Verlag, London, UK, 2008b.
  1. Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, Frydman J. “Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.” Nat Struct Mol Biol 15, 746-753, 2008. PMC2546500
  1. Chandramouli P, Topf M, Menetret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW. “Structure of the mammalian 80S ribosome at 8.7 A resolution.” Structure 16, 535-548, 2008. PMC2775484
  1. Cong Y, Topf M, Sali A, Matsudaira P, Dougherty M, Chiu W, Schmid MF. “Crystallographic conformers of actin in a biologically active bundle of filaments.” J. Mol. Biol. 375, 331-336, 2008. PMC2680129
  1. Degrasse JA, Chait BT, Field MC, Rout MP. “High-yield isolation and subcellular proteomic characterization of nuclear and subnuclear structures from trypanosomes.” Methods Mol Biol. 2008;463:77-92. PMID: 18951162
  1. Eramian D, Eswar N, Shen MY, Sali A. “How well can the accuracy of comparative protein structure models be predicted?” Protein Sci. 2008 Nov;17(11):1881-93. doi: 10.1110/ps.036061.108. Epub 2008 Oct 1. PMC2578807
  1. Förster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, Sali A. “Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies.” J. Mol. Biol. 382, 1089-1106, 2008. PMC2745287
  1. Gradolatto A, Rogers RS, Lavender H, Taverna SD, Allis CD, Aitchison JD, Tackett AJ. “Saccharomyces cerevisiae Yta7 regulates histone gene expression.” Genetics 2008 May;179(1):291-304. PMC2390607
  1. Hood L, Rowen L, Galas DJ, Aitchison JD. “Systems biology at the Institute for Systems Biology.” Brief Funct Genomic Proteomic. 2008 Jul;7(4):239-48. Epub 2008 Jun 25. PMID: 18579616
  1. Krukenberg KA, Förster F, Rice LM, Sali A, Agard DA. “Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.” Structure 16, 755-765, 2008. PMC2600884
  1. Lee DJ, Busby SJ, Westblade LF, Chait BT. “Affinity isolation and I-DIRT mass spectrometric analysis of the Escherichia coli O157:H7 Sakai RNA polymerase complex.” J Bacteriol. 2008 Feb;190(4):1284-9. Epub 2007 Dec 14. PMC2238195
  1. Marelli M, Nesvizhskii AI, Aitchison JD. “Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions: an example in peroxisomes.” Methods Mol Biol. 2008;432:357-71. PMID: 18370030
  1. Moorman NJ, Cristea IM, Terhune SS, Rout MP, Chait BT, Shenk T. “Human cytomegalovirus protein UL38 inhibits host cell stress responses by antagonizing the tuberous sclerosis protein complex.” Cell Host Microbe. 2008 Apr 17;3(4):253-62. PMC2759192
  1. Postow L, Ghenoiu C, Woo EM, Krutchinsky AN, Chait BT, Funabiki H. “Ku80 removal from DNA through double strand break-induced ubiquitylation.” J Cell Biol. 2008 Aug 11;182(3):467-79. Epub 2008 Aug 4. PMC2500133
  1. Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD.Control of transcriptional variability by overlapping feed-forward regulatory motifs.” Biophys J. 2008 Oct;95(8):3715-23. Epub 2008 Jul 11. PMC2553142
  1. Rout MP. “The peroxisome: a production in four acts.” J Cell Biol. 2008 Apr 21;181(2):185-7. PMC2315666
  1. Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O'Donnell R, Rachubinski RA, Aitchison JD. “Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis.” J Cell Biol. 2008 Apr 21;181(2):281-92. PMC2315675
  1. Savalia D, Westblade LF, Goel M, Florens L, Kemp P, Akulenko N, Pavlova O, Padovan JC, Chait BT, Washburn MP, Ackermann HW, Mushegian A, Gabisonia T, Molineux I, Severinov K. “Genomic and proteomic analysis of phiEco32, a novel Escherichia coli bacteriophage.” J Mol Biol. 2008 Mar 28;377(3):774-89. Epub 2008 Jan 11. PMC2587145
  1. Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, Chiu W. “Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel.” Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9610-5. Epub 2008 Jul 10. PMC2474495
  1. Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. “Protein structure fitting and refinement guided by cryo-EM density.” Structure 16, 295-307, 2008. PMC2409374
  1. Westblade LF, Minakhin L, Kuznedelov K, Tackett AJ, Chang EJ, Mooney RA, Vvedenskaya I, Wang QJ, Fenyö D, Rout MP, Landick R, Chait BT, Severinov K, Darst SA. “Rapid isolation and identification of bacteriophage T4-encoded modifications of Escherichia coli RNA polymerase: a generic method to study bacteriophage/host interactions.” J Proteome Res. 2008 Mar;7(3):1244-50. Epub 2008 Feb 14. PMC2612130
  1. Woo EM, Fenyo D, Kwok BH, Funabiki H, Chait BT. “Efficient identification of phosphorylation by mass spectrometric phosphopeptide fingerprinting.” Anal Chem. 2008 Apr 1;80(7):2419-25. Epub 2008 Mar 6. PMID: 18321079
  1. Yue Z, Wang QJ, Komatsu M. “Neuronal autophagy: going the distance to the axon.” 2008 January 1; 4(1): 94–96. PMC2675167