2014 Publications

  1. Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait BT, Rout MP, Dokudovskaya S. “Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.” Mol Cell Proteomics. 2014 Nov;13(11):2855-70. doi: 10.1074/mcp.M114.039388. Epub 2014 Jul 29. PMC4223477
  2. Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A. “Determining protein complex structures based on a Bayesian model of in vivo FRET data.” Mol Cell Proteomics. 2014 Nov;13(11):2812-23. doi: 10.1074/mcp.M114.040824. Epub 2014 Aug 19. PMC4223474
  3. Bretes H, Rouviere JO, Leger T, Oeffinger M, Devaux F, Doye V and Palancade B. “Sumoylation of the THO complex regulates the biogenesis of a subset of mRNPs.” Nucleic Acids Res. 2014 Apr;42(8):5043-58. doi: 10.1093/nar/gku124. Epub 2014 Feb 5. PMC4005672
  4. Carpp LN, Rogers RS, Moritz RL, Aitchison JD. “Quantitative proteomic analysis of host-virus interactions reveals a role for GBF1 in dengue infection.” Mol Cell Proteomics. 2014 Nov;13(11):2836-54. doi: 10.1074/mcp.M114.038984. Epub 2014 May 22. PMC4223476
  5. Cevher MA, Shi Y, Li D, Chait BT, Malik S, Roeder RG. Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nat Struct Mol Biol. 2014 Dec;21(12):1028-34. doi: 10.1038/nsmb.2914. Epub 2014 Nov 10. PMC4259101
  6. Danziger SA, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH, Reiss DJ, Baliga NS, Aitchison JD. “Molecular mechanisms of system responses to novel stimuli are predictable from public data.” Nucleic Acids Res. 2014 Feb;42(3):1442-60. doi: 10.1093/nar/gkt938. Epub 2013 Oct 31. PMC3919619
  7. Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CH, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. “Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex.” Cell. 2014 Aug 28;158(5):1123-35. doi: 10.1016/j.cell.2014.07.044. PMC4151992
  8. Field MC, Koreny L, Rout MP. “Enriching the pore: splendid complexity from humble origins.” Traffic. 2014 Feb;15(2):141-56. doi: 10.1111/tra.12141. Epub 2014 Jan 8. PMC3906644
  9. Finney OC, Danziger SA, Molina DM, Vignali M, Takagi A, Ji M, Stanisic DI, Siba PM, Liang X, Aitchison JD, Mueller I, Gardner MJ, Wang R. “Predicting antidisease immunity using proteome arrays and sera from children naturally exposed to malaria.” Mol Cell Proteomics. 2014 Oct;13(10):2646-60. doi: 10.1074/mcp.M113.036632. Epub 2014 Jul 14. PMC4188993
  10. Fridy PC, Li Y, Keegan S, Thompson MK, Nudelman I, Scheid JF, Oeffinger M, Nussenzweig MC, Fenyö D, Chait BT, and Rout MP. “A robust pipeline for rapid production of versatile nanobody repertoires.” Nature Methods. 2014 Dec;11(12):1253-60. doi: 10.1038/nmeth.3170. Epub 2014 Nov 2. PMC4272012
  11. Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Chiang JH, Kelly S, Chait BT, Aitchison JD, Rout MP, Field MC. “Nuclear pore complex evolution: A trypanosome Mlp analog functions in chromosomal segregation but lacks transcriptional barrier activity.” Mol Biol Cell. 2014 Mar 5. [Epub ahead of print] PMC40045926
  12. Holden JM, Koreny L, Kelly S, Chait BT, Rout MP, Field MC, Obado SO. “Touching from a distance: Evolution of interplay between the nuclear pore complex, nuclear basket, and the mitotic spindle.” Nucleus. 2014 Jul 31;5(4). [Epub ahead of print] Review. PMC4152344
  13. Jovanovic-Talisman T, Chait BT, Rout MP. “NPC Mimics: Probing the Mechanism of Nucleocytoplasmic Transport.” Methods Cell Biol. 2014;122:379-93. doi: 10.1016/B978-0-12-417160-2.00017-5. PMC4272007
  14. Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss T, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Almo SC, Rout M, Sali A. “Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.” Mol Cell Proteomics. 2014 Nov;13(11):2911-26. doi: 10.1074/mcp.M114.040915. Epub 2014 Aug 19. PMC4223481
  15. Li Y, Cross FR, Chait BT. “Method for identifying phosphorylated substrates of specific cyclin/cyclin-dependent kinase complexes.” Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11323-8. doi: 10.1073/pnas.1409666111. Epub 2014 Jul 21. PMC4128132
  16. Mast FD, Ratushny AV, Aitchison JD. “Systems cell biology.” J Cell Biol. 2014 Sep 15;206(6):695-706. Review. PMC4164942
  17. Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. “Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ.” Structure. 2014 Sep 2;22(9):1239-51. doi: 10.1016/j.str.2014.04.019. Epub 2014 Jul 31. PMC4322757
  18. Ptak C, Aitchison JD, Wozniak RW. “The multifunctional nuclear pore complex: a platform for controlling gene expression.” Curr Opin Cell Biol. 2014 Mar 20;28C:46-53. doi: 10.1016/j.ceb.2014.02.001. [Epub ahead of print] Review. PMC4061258
  19. Rout MP, Karpen GH. “Editorial overview: Cell nucleus: the nucleus: a dynamic organelle. “Curr Opin Cell Biol. 2014 Jun;28:iv-vii. doi: 10.1016/j.ceb.2014.05.005. Epub 2014 Jun 4. No abstract available. PMID: 24908378
  20. Schneidman-Duhovny D, Pellarin R, Sali A. “Uncertainty in integrative structural modeling.” Curr Opin Struct Biol. 2014 Aug 27;28C:96-104. doi: 10.1016/j.sbi.2014.08.001. [Epub ahead of print] Review. PMC4252396
  21. Schoggins JW, MacDuff DA, Imanaka N, Gainey MD, Shrestha B, Eitson JL, Mar KB, Richardson RB, Ratushny AV, Litvak V, Dabelic R, Manicassamy B, Aitchison JD, Aderem A, Elliott RM, García-Sastre A, Racaniello V, Snijder EJ, Yokoyama WM, Diamond MS, Virgin HW, Rice CM. “Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity.” Nature. 2014 Jan 30;505(7485):691-5. doi: 10.1038/nature12862. Epub 2013 Nov 27. PMC4077721
  22. Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman D, Sali A, Rout MP, Chait BT. “Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.” Mol Cell Proteomics. 2014 Nov;13(11):2927-43. doi: 10.1074/mcp.M114.041673. Epub 2014 Aug 26. PMC4223482
  23. Simon DN, Rout MP. “Cancer and the nuclear pore complex.” Adv Exp Med Biol. 2014;773:285-307. doi: 10.1007/978-1-4899-8032-8_13. PMID: 24563353
  24. Subbotin RI, Chait BT. “A Pipeline for Determining Protein-Protein Interactions and Proximities in the Cellular Milieu.” 2014 Nov;13(11):2824-35. doi: 10.1074/mcp.M114.041095. Epub 2014 Aug 29. PMC4223475
  25. Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A. “Modeling of proteins and their assemblies with the Integrative Modeling Platform.” Methods Mol Biol. 2014;1091:277-95. doi: 10.1007/978-1-62703-691-7_20. Humana Press, London, UK, 2014. PMID: 24203340
  26. Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, Baliga NS. “An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation.” Mol Microbiol. 2014 Apr;92(2):369-82. doi: 10.1111/mmi.12564. Epub 2014 Mar 19. PMC4060883
  27. Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F. “Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling.” J Mol Biol. 2014 Aug 19. pii: S0022-2836(14)00425-2. doi: 10.1016/j.jmb.2014.07.033. [Epub ahead of print] PMC4253074
  28. Zhong Y, Morris DH, Jin L, Patel MS, Karunakaran SK, Fu YJ, Matuszak EA, Weiss HL, Chait BT, Wang QJ. “Nrbf2 Suppresses Autophagy by Modulating Atg14L-containing Beclin 1-Vps34 Protein Complex Architecture and Reducing Intracellular Phosphatidylinositol-3 Phosphate Levels.” J Biol Chem. 2014 Sep 19;289(38):26021-37. doi: 10.1074/jbc.M114.561134. Epub 2014 Aug 1. PMC4176228