PUBLICATIONS 2018-07-23T16:56:50+00:00

SEMC Publications

2018

  1. Alphonse S, Ghose R. wwwwMethyl NMR Spectroscopy: Measurement of Dynamics in Viral RNA-directed RNA Polymerases. Methods. 2018; https://www.ncbi.nlm.nih.gov/pubmed/29857193
  2. Benoit M, Asenjo AB, Sosa H. Cryo-EM reveals the structural basis of microtubule depolymerization by kinesin-13s. Nat Commun. 2018;9(1):1662. PMCID: PMC5916938; http://www.ncbi.nlm.nih.gov/pubmed/29695795
  3. Bepler T, Morin A, Noble AJ, Brasch J, Shapiro L, Berger B. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Res Comput Mol Biol. 2018;10812:245-7. PMCID: PMC5917602; https://www.ncbi.nlm.nih.gov/pubmed/29707703
  4. Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA. Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. eLife. 2018;7. PMCID: PMC5837556; https://www.ncbi.nlm.nih.gov/pubmed/29480804
  5. Cao S, Zhou K, Zhang Z, Luger K, Straight AF. Constitutive centromere-associated network contacts confer differential stability on CENP-A nucleosomes in vitro and in the cell. Molecular biology of the cell. 2018;29(6):751-62; https://www.ncbi.nlm.nih.gov/pubmed/29343552
  6. Cheng A, Eng ET, Alink L, Rice WJ, Jordan KD, Kim LY, Potter CS, Carraggher B. High Resolution Single Particle Cryo-Electron Microscopy using Beam-Image Shift. bioRxiv. 2018; https://www.biorxiv.org/content/early/2018/04/26/306241;
  7. Dandey VP, Wei H, Zhang Z, Tan YZ, Acharya P, Eng ET, Rice WJ, Kahn PA, Potter CS, Carragher B. Spotiton: New features and applications. Journal of structural biology. 2018;202(2):161-9; https://www.biorxiv.org/content/early/2017/12/08/230151; https://www.ncbi.nlm.nih.gov/pubmed/29366716
  8. Dingens AS, Acharya P, Haddox HK, Rawi R, Xu K, Chuang GY, Wei H, Zhang B, Mascola JR, Carragher B, Potter CS, Overbaugh J, Kwong PD, Bloom JD. Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV. PLoS Pathog. 2018;14(7):e1007159; https://www.biorxiv.org/content/early/2018/04/24/307587; https://www.ncbi.nlm.nih.gov/pubmed/29975771
  9. Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA. Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators. Cell. 2018; https://www.ncbi.nlm.nih.gov/pubmed/29887376
  10. Kim LY, Rice WJ, Eng ET, Kopylov M, Cheng A, Raczkowski AM, Jordan KD, Bobe D, Potter CS, Carragher B. Benchmarking cryo-EM Single Particle Analysis Workflow. Front Mol Biosci. 2018;5:50. PMCID: PMC6009202; https://www.biorxiv.org/content/early/2018/05/03/311324; https://www.ncbi.nlm.nih.gov/pubmed/29951483
  11. Liao PC, Boldogh IR, Siegmund SE, Freyberg Z, Pon LA. Isolation of mitochondria from Saccharomyces cerevisiae using magnetic bead affinity purification. PloS one. 2018;13(4):e0196632. PMCID: PMC5919621; https://www.ncbi.nlm.nih.gov/pubmed/29698455
  12. Lin W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M, Srivastava A, Mandal S, Jiang Y, Liu Y, Yin R, Zhang Z, Eng ET, Thomas D, Donadio S, Zhang H, Zhang C, Kapanidis AN, Ebright RH. Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Molecular cell. 2018;70(1):60-71 e15; https://www.ncbi.nlm.nih.gov/pubmed/29606590
  13. Lopez-Redondo ML, Coudray N, Zhang Z, Alexopoulos J, Stokes DL. Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(12):3042-7. PMCID: PMC5866550; https://www.ncbi.nlm.nih.gov/pubmed/29507252
  14. Ma X, Lu M, Gorman J, Terry DS, Hong X, Zhou Z, Zhao H, Altman RB, Arthos J, Blanchard SC, Kwong PD, Munro JB, Mothes W. HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations. eLife. 2018;7. PMCID: PMC5896952; https://www.ncbi.nlm.nih.gov/pubmed/29561264
  15. Malvezzi M, Andra KK, Pandey K, Lee BC, Falzone ME, Brown A, Iqbal R, Menon AK, Accardi A. Out-of-the-groove transport of lipids by TMEM16 and GPCR scramblases. Proceedings of the National Academy of Sciences of the United States of America. 2018; https://www.ncbi.nlm.nih.gov/pubmed/29925604
  16. McGoldrick LL, Singh AK, Saotome K, Yelshanskaya MV, Twomey EC, Grassucci RA, Sobolevsky AI. Opening of the human epithelial calcium channel TRPV6. Nature. 2018;553(7687):233-7. PMCID: PMC5854407; https://www.ncbi.nlm.nih.gov/pubmed/29258289
  17. Niekamp S, Coudray N, Zhang N, Vale RD, Bhabha G. Stalk-mediated communication in the dynein motor domain. bioRxiv. 2018; https://www.biorxiv.org/content/biorxiv/early/2018/04/27/309179.full.pdf
  18. Noble AJ, Dandey VP, Wei H, Brasch J, Chase J, Acharya P, Tan YZ, Zhang Z, Kim LY, Scapin G, Rapp M, Eng ET, Rice WJ, Cheng A, Negro CJ, Shapiro L, Kwong PD, Jeruzalmi D, des Georges A, Potter CS, Carragher B. Routine single particle CryoEM sample and grid characterization by tomography. eLife. 2018;7; https://www.biorxiv.org/content/early/2017/12/11/230276; https://www.ncbi.nlm.nih.gov/pubmed/29809143
  19. Noble AJ, Wei H, Dandey VP, Zhang Z, Potter CS, Carragher B. Reducing effects of particle adsorption to the air-water interface in cryoEM. bioRxiv. 2018; https://www.biorxiv.org/content/early/2018/07/19/288340;
  20. Oliveira LM, Ye Z, Katz A, Alimova A, Wei H, Herman GT, Gottlieb P. Component tree analysis of cystovirus phi6 nucleocapsid Cryo-EM single particle reconstructions. PloS one. 2018;13(1):e0188858. PMCID: PMC5754084; https://www.ncbi.nlm.nih.gov/pubmed/29300742
  21. Paknejad N, Hite RK. Structural basis for the regulation of inositol trisphosphate receptors by Ca(2+) and IP3. Nat Struct Mol Biol. 2018; https://www.ncbi.nlm.nih.gov/pubmed/30013099
  22. Piasecka A, Czapinska H, Vielberg MT, Szczepanowski RH, Kiefersauer R, Reed S, Groll M, Bochtler M. The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers. J Mol Biol. 2018;430(5):611-27; https://www.ncbi.nlm.nih.gov/pubmed/29258816
  23. Pisareva VP, Pisarev AV, Fernandez IS. Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES. eLife. 2018;7. PMCID: PMC5984033; https://www.ncbi.nlm.nih.gov/pubmed/29856316
  24. Rice WJ, Cheng A, Noble AJ, Eng ET, Kim LY, Carragher B, Potter CS. Routine determination of ice thickness for cryo-EM grids. Journal of structural biology. 2018; https://www.biorxiv.org/content/early/2018/04/16/302018; https://www.ncbi.nlm.nih.gov/pubmed/29981485
  25. Scapin G, Dandey VP, Zhang Z, Prosise W, Hruza A, Kelly T, Mayhood T, Strickland C, Potter CS, Carragher B. Structure of the insulin receptor-insulin complex by single-particle cryo-EM analysis. Nature. 2018;556(7699):122-5. PMCID: PMC5886813; https://www.ncbi.nlm.nih.gov/pubmed/29512653
  26. Schmidpeter PAM, Gao X, Uphadyay V, Rheinberger J, Nimigean CM. Ligand binding and activation properties of the purified bacterial cyclic nucleotide-gated channel SthK. J Gen Physiol. 2018;150(6):821-34. PMCID: PMC5987880; https://www.ncbi.nlm.nih.gov/pubmed/29752414
  27. Sun C, Benlekbir S, Venkatakrishnan P, Wang Y, Hong S, Hosler J, Tajkhorshid E, Rubinstein JL, Gennis RB. Structure of the alternative complex III in a supercomplex with cytochrome oxidase. Nature. 2018; https://doi.org/10.1038/s41586-018-0061-y
  28. Sun Y, Zhang Y, Hamilton K, Manley JL, Shi Y, Walz T, Tong L. Molecular basis for the recognition of the human AAUAAA polyadenylation signal. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(7):E1419-E28. PMCID: PMC5816196; https://www.ncbi.nlm.nih.gov/pubmed/29208711
  29. Tan YZ, Aiyer S, Mietzsch M, Hull JA, McKenna R, Grieger J, Samulski RJ, Baker TS, Agbandje-McKenna M, Lyumkis D. Sub-2 Å Ewald Curvature Corrected Single-Particle Cryo-EM. bioRxiv. 2018; https://www.biorxiv.org/content/early/2018/07/13/365940
  30. Wei H, Dandey VP, Zhang Z, Raczkowski A, Rice WJ, Carragher B, Potter CS. Optimizing “self-wicking” nanowire grids. Journal of structural biology. 2018;202(2):170-4. PMCID: PMC5864531; https://www.ncbi.nlm.nih.gov/pubmed/29317278
  31. Weick EM, Puno MR, Januszyk K, Zinder JC, DiMattia MA, Lima CD. Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex. Cell. 2018;173(7):1663-77 e21; https://www.ncbi.nlm.nih.gov/pubmed/29906447
  32. Xu K, Acharya P, Kong R, Cheng C, Chuang GY, Liu K, Louder MK, O’Dell S, Rawi R, Sastry M, Shen CH, Zhang B, Zhou T, Asokan M, Bailer RT, Chambers M, Chen X, Choi CW, Dandey VP, Doria-Rose NA, Druz A, Eng ET, Farney SK, Foulds KE, Geng H, Georgiev IS, Gorman J, Hill KR, Jafari AJ, Kwon YD, Lai YT, Lemmin T, McKee K, Ohr TY, Ou L, Peng D, Rowshan AP, Sheng Z, Todd JP, Tsybovsky Y, Viox EG, Wang Y, Wei H, Yang Y, Zhou AF, Chen R, Yang L, Scorpio DG, McDermott AB, Shapiro L, Carragher B, Potter CS, Mascola JR, Kwong PD. Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1. Nat Med. 2018;24(6):857-67; https://www.ncbi.nlm.nih.gov/pubmed/29867235
  33. Zhang Z, Liang WG, Bailey LJ, Tan YZ, Wei H, Wang A, Farcasanu M, Woods VA, McCord LA, Lee D, Shang W, Deprez-Poulain R, Deprez B, Liu DR, Koide A, Koide S, Kossiakoff AA, Li S, Carragher B, Potter CS, Tang WJ. Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme. eLife. 2018;7; https://www.ncbi.nlm.nih.gov/pubmed/29596046

2017

  1. Alewijnse B, Ashton AW, Chambers MG, Chen S, Cheng A, Ebrahim M, Eng ET, Hagen WJH, Koster AJ, Lopez CS, Lukoyanova N, Ortega J, Renault L, Reyntjens S, Rice WJ, Scapin G, Schrijver R, Siebert A, Stagg SM, Grum-Tokars V, Wright ER, Wu S, Yu Z, Zhou ZH, Carragher B, Potter CS. Best practices for managing large CryoEM facilities. Journal of structural biology. 2017;199(3):225-36. PMCID: PMC5605453. http://www.ncbi.nlm.nih.gov/pubmed/28827185
  2. Baldwin PR, Tan YZ, Eng ET, Rice WJ, Noble AJ, Negro CJ, Cianfrocco MA, Potter CS, Carragher B. Big data in cryoEM: automated collection, processing and accessibility of EM data. Curr Opin Microbiol. 2017;43:1-8. http://www.ncbi.nlm.nih.gov/pubmed/29100109
  3. Benoit MPMH, Asenjo AB, Sosa H. Cryo-EM Reveals the Structural Basis of Microtubule Depolymerization by Kinesin-13s. bioRxiv. 2017.
  4. Campos MP, Hendricks MP, Beecher AN, Walravens W, Swain RA, Cleveland GT, Hens Z, Sfeir MY, Owen JS. A Library of Selenourea Precursors to PbSe Nanocrystals with Size Distributions near the Homogeneous Limit. J Am Chem Soc. 2017;139(6):2296-305. http://www.ncbi.nlm.nih.gov/pubmed/28103035
  5. Chen PE, Anderson NC, Norman ZM, Owen JS. Tight Binding of Carboxylate, Phosphonate, and Carbamate Anions to Stoichiometric CdSe Nanocrystals. J Am Chem Soc. 2017;139(8):3227-36. http://www.ncbi.nlm.nih.gov/pubmed/28125780
  6. Coleman RA, Qiao Z, Singh SK, Peng CS, Cianfrocco M, Zhang Z, Piasecka A, Aldeborgh H, Basishvili G, Liu WL. p53 Dynamically Directs TFIID Assembly on Target Gene Promoters. Mol Cell Biol. 2017;37(13). PMCID: 5472829. http://www.ncbi.nlm.nih.gov/pubmed/28416636
  7. Garcia-Marin V, Kelly JG, Hawken MJ. Major Feedforward Thalamic Input Into Layer 4C of Primary Visual Cortex in Primate. Cereb Cortex. 2017:1-16. http://www.ncbi.nlm.nih.gov/pubmed/29190326
  8. Guo H, Bueler SA, Rubinstein JL. Atomic model for the dimeric FO region of mitochondrial ATP synthase. Science. 2017. http://www.ncbi.nlm.nih.gov/pubmed/29074581
  9. Guo TW, Bartesaghi A, Yang H, Falconieri V, Rao P, Merk A, Eng ET, Raczkowski AM, Fox T, Earl LA, Patel DJ, Subramaniam S. Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex. Cell. 2017;171(2):414-26 e12. http://www.ncbi.nlm.nih.gov/pubmed/28985564
  10. Hamachi LS, Jen-La Plante I, Coryell AC, De Roo J, Owen JS. Kinetic Control over CdS Nanocrystal Nucleation Using a Library of Thiocarbonates, Thiocarbamates, and Thioureas. Chemistry of Materials. 2017;29(20):8711-9. http://dx.doi.org/10.1021/acs.chemmater.7b02861
  11. Han H, Monroe N, Sundquist WI, Shen PS, Hill CP. The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets. eLife. 2017;6. PMCID: PMC5716660. http://www.ncbi.nlm.nih.gov/pubmed/29165244
  12. Hirabayashi Y, Kwon SK, Paek H, Pernice WM, Paul MA, Lee J, Erfani P, Raczkowski A, Petrey DS, Pon LA, Polleux F. ER-mitochondria tethering by PDZD8 regulates Ca2+ dynamics in mammalian neurons. Science. 2017;358(6363):623-30. http://www.ncbi.nlm.nih.gov/pubmed/29097544
  13. James ZM, Borst AJ, Haitin Y, Frenz B, DiMaio F, Zagotta WN, Veesler D. CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel. Proceedings of the National Academy of Sciences of the United States of America. 2017;114(17):4430-5. http://www.ncbi.nlm.nih.gov/pubmed/28396445
  14. Lin W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M, Srivastava A, Mandal S, Jiang Y, Liu Y, Yin R, Zhang Z, Eng E, Thomas D, Donadio S, Zhang H, Zhang C, Kapanidis A, Ebright RH. Structural basis of transcription inhibition by fidaxomicin (lipiarmycin A3). bioRxiv. 2017. https://www.biorxiv.org/content/biorxiv/early/2017/12/20/237123.full.pdf
  15. Liu Q, Acharya P, Dolan MA, Zhang P, Guzzo C, Lu J, Kwon A, Gururani D, Miao H, Bylund T, Chuang GY, Druz A, Zhou T, Rice WJ, Wigge C, Carragher B, Potter CS, Kwong PD, Lusso P. Quaternary contact in the initial interaction of CD4 with the HIV-1 envelope trimer. Nat Struct Mol Biol. 2017;24(4):370-8. http://www.ncbi.nlm.nih.gov/pubmed/28218750
  16. Malyutin AG, Musalgaonkar S, Patchett S, Frank J, Johnson AW. Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis. EMBO J. 2017;36(7):854-68. PMCID: 5376978. http://www.ncbi.nlm.nih.gov/pubmed/28179369
  17. Noble AJ, Dandey VP, Wei H, Brasch J, Chase J, Acharya P, Tan YZ, Zhang Z, Kim LY, Scapin G, Rapp M, Eng ET, Rice WJ, Cheng A, Negro CJ, Shapiro L, Kwong PD, Jeruzalmi D, des Georges A, Potter CS, Carragher B. Routine Single Particle CryoEM Sample and Grid Characterization by Tomography. bioRxiv. 2017. https://www.biorxiv.org/content/biorxiv/early/2017/12/11/230276.full.pdf
  18. Pentakota S, Zhou K, Smith C, Maffini S, Petrovic A, Morgan GP, Weir JR, Vetter IR, Musacchio A, Luger K. Decoding the centromeric nucleosome through CENP-N. eLife. 2017;6:e33442. https://doi.org/10.7554/eLife.33442
  19. Piasecka A, Czapinska H, Vielberg MT, Szczepanowski R, Kiefersauer R, Reed S, Groll M, Bochtler M. The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers. J Mol Biol. 2017. http://www.ncbi.nlm.nih.gov/pubmed/29258816
  20. Ren Y, Schmiege P, Blobel G. Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1. eLife. 2017;6. PMCID: PMC5218534. http://www.ncbi.nlm.nih.gov/pubmed/28059701
  21. Scapin G, Prosise WW, Wismer MK, Strickland C. A novel storage system for cryoEM samples. Journal of structural biology. 2017. http://www.ncbi.nlm.nih.gov/pubmed/28433496
  22. Silva M, Morsci N, Nguyen KCQ, Rizvi A, Rongo C, Hall DH, Barr MM. Cell-Specific alpha-Tubulin Isotype Regulates Ciliary Microtubule Ultrastructure, Intraflagellar Transport, and Extracellular Vesicle Biology. Curr Biol. 2017;27(7):968-80. PMCID: 5688951. http://www.ncbi.nlm.nih.gov/pubmed/28318980
  23. Tan YZ, Baldwin PR, Davis JH, Williamson JR, Potter CS, Carragher B, Lyumkis D. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat Methods. 2017;14(8):793-6. PMCID: PMC5533649. http://www.ncbi.nlm.nih.gov/pubmed/28671674
  24. Twomey EC, Yelshanskaya MV, Grassucci RA, Frank J, Sobolevsky AI. Channel opening and gating mechanism in AMPA-subtype glutamate receptors. Nature. 2017;549(7670):60-5. http://www.ncbi.nlm.nih.gov/pubmed/28737760
  25. Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Structure. 2017;25(3):434-45. PMCID: PMC5342941. http://www.ncbi.nlm.nih.gov/pubmed/28162953
  26. Wang L, Eng ET, Law K, Gordon RE, Rice WJ, Chen BK. Visualization of HIV T Cell Virological Synapses and Virus-Containing Compartments by Three-Dimensional Correlative Light and Electron Microscopy. J Virol. 2017;91(2). PMCID: PMC5215336. http://www.ncbi.nlm.nih.gov/pubmed/27847357
  27. Yang H, Jiang X, Li B, Yang HJ, Miller M, Yang A, Dhar A, Pavletich NP. Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40. Nature. 2017. http://www.ncbi.nlm.nih.gov/pubmed/29236692
  28. Yuan Z, Riera A, Bai L, Sun J, Nandi S, Spanos C, Chen ZA, Barbon M, Rappsilber J, Stillman B, Speck C, Li H. Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1. Nat Struct Mol Biol. 2017;24(3):316-24. http://www.ncbi.nlm.nih.gov/pubmed/28191893

2016

  1. Cheng A, Tan YZ, Dandey VP, Potter CS, Carragher B. Strategies for Automated CryoEM Data Collection Using Direct Detectors. Methods Enzymol. 2016;579:87-102. http://www.ncbi.nlm.nih.gov/pubmed/27572724
  2. Davis JH, Tan YZ, Carragher B, Potter CS, Lyumkis D, Williamson JR. Modular Assembly of the Bacterial Large Ribosomal Subunit. Cell. 2016;167(6):1610-22 e15. PMCID: PMC5145266. http://www.ncbi.nlm.nih.gov/pubmed/27912064
  3. Domanski M, Upla P, Rice WJ, Molloy KR, Ketaren NE, Stokes DL, Jensen TH, Rout MP, LaCava J. Purification and analysis of endogenous human RNA exosome complexes. RNA. 2016;22(9):1467-75. PMCID: 4986900. http://www.ncbi.nlm.nih.gov/pubmed/27402899
  4. Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell. 2016;167(5):1215-28 e25. PMCID: 5130164. http://www.ncbi.nlm.nih.gov/pubmed/27839866
  5. Haka AS, Barbosa-Lorenzi VC, Lee HJ, Falcone DJ, Hudis CA, Dannenberg AJ, Maxfield FR. Exocytosis of macrophage lysosomes leads to digestion of apoptotic adipocytes and foam cell formation. J Lipid Res. 2016;57(6):980-92. PMCID: 4878183. http://www.ncbi.nlm.nih.gov/pubmed/27044658
  6. Leo-Macias A, Agullo-Pascual E, Sanchez-Alonso JL, Keegan S, Lin X, Arcos T, Feng Xia L, Korchev YE, Gorelik J, Fenyo D, Rothenberg E, Delmar M. Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc. Nat Commun. 2016;7:10342. PMCID: PMC4735805. http://www.ncbi.nlm.nih.gov/pubmed/26787348
  7. Peng X, Yuan XZ, Somasundaran P, Patra P. Assessment of micro-polarity anisotropy as a function of surfactant packing in sodium dodecyl sulphonate-hexane reverse micelles. Soft Matter. 2016;12(1):22-5. http://www.ncbi.nlm.nih.gov/pubmed/26446876
  8. Razinkov I, Dandey V, Wei H, Zhang Z, Melnekoff D, Rice WJ, Wigge C, Potter CS, Carragher B. A new method for vitrifying samples for cryoEM. Journal of structural biology. 2016;195(2):190-8. PMCID: 5464370. http://www.ncbi.nlm.nih.gov/pubmed/27288865
  9. Singh RK, Barbosa-Lorenzi VC, Lund FW, Grosheva I, Maxfield FR, Haka AS. Degradation of aggregated LDL occurs in complex extracellular sub-compartments of the lysosomal synapse. J Cell Sci. 2016;129(5):1072-82. PMCID: PMC4813320. http://www.ncbi.nlm.nih.gov/pubmed/26801085
  10. Singh SK, Qiao Z, Song L, Jani V, Rice W, Eng E, Coleman RA, Liu WL. Structural visualization of the p53/RNA polymerase II assembly. Genes & development. 2016;30(22):2527-37. PMCID: 5159667. http://www.ncbi.nlm.nih.gov/pubmed/27920087
  11. Singhvi A, Liu B, Friedman CJ, Fong J, Lu Y, Huang XY, Shaham S. A Glial K/Cl Transporter Controls Neuronal Receptive Ending Shape by Chloride Inhibition of an rGC. Cell. 2016;165(4):936-48. PMCID: PMC4860081. http://www.ncbi.nlm.nih.gov/pubmed/27062922
  12. Tan YZ, Cheng A, Potter CS, Carragher B. Automated data collection in single particle electron microscopy. Microscopy (Oxf). 2016;65(1):43-56. PMCID: PMC4749047. http://www.ncbi.nlm.nih.gov/pubmed/26671944

2015

  1. Chuang JZ, Hsu YC, Sung CH. Ultrastructural visualization of trans-ciliary rhodopsin cargoes in mammalian rods. Cilia. 2015;4:4. PMCID: PMC4320831. http://www.ncbi.nlm.nih.gov/pubmed/25664179
  2. Hall DH, Rice WJ. Electron Tomography Methods for C. elegans. Methods Mol Biol. 2015;1327:141-58. http://www.ncbi.nlm.nih.gov/pubmed/26423973
  3. Hsu YC, Chuang JZ, Sung CH. Light regulates the ciliary protein transport and outer segment disc renewal of mammalian photoreceptors. Dev Cell. 2015;32(6):731-42. PMCID: PMC4374123. http://www.ncbi.nlm.nih.gov/pubmed/25805137
  4. Hurd TR, Sanchez CG, Teixeira FK, Petzold C, Dancel-Manning K, Wang JY, Lehmann R, Liang FX. Ultrastructural Analysis of Drosophila Ovaries by Electron Microscopy. Methods Mol Biol. 2015;1328:151-62. PMCID: 4727969. http://www.ncbi.nlm.nih.gov/pubmed/26324436
  5. Kang Y, Zhou XE, Gao X, He Y, Liu W, Ishchenko A, Barty A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Ke J, Tan MH, Zhang C, Moeller A, West GM, Pascal BD, Van Eps N, Caro LN, Vishnivetskiy SA, Lee RJ, Suino-Powell KM, Gu X, Pal K, Ma J, Zhi X, Boutet S, Williams GJ, Messerschmidt M, Gati C, Zatsepin NA, Wang D, James D, Basu S, Roy-Chowdhury S, Conrad CE, Coe J, Liu H, Lisova S, Kupitz C, Grotjohann I, Fromme R, Jiang Y, Tan M, Yang H, Li J, Wang M, Zheng Z, Li D, Howe N, Zhao Y, Standfuss J, Diederichs K, Dong Y, Potter CS, Carragher B, Caffrey M, Jiang H, Chapman HN, Spence JC, Fromme P, Weierstall U, Ernst OP, Katritch V, Gurevich VV, Griffin PR, Hubbell WL, Stevens RC, Cherezov V, Melcher K, Xu HE. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature. 2015;523(7562):561-7. PMCID: PMC4521999. http://www.ncbi.nlm.nih.gov/pubmed/26200343
  6. Lasala R, Coudray N, Abdine A, Zhang Z, Lopez-Redondo M, Kirshenbaum R, Alexopoulos J, Zolnai Z, Stokes DL, Ubarretxena-Belandia I. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Journal of structural biology. 2015;189(2):123-34. PMCID: PMC4419781. http://www.ncbi.nlm.nih.gov/pubmed/25478971
  7. Leo-Macias A, Liang FX, Delmar M. Ultrastructure of the intercellular space in adult murine ventricle revealed by quantitative tomographic electron microscopy. Cardiovasc Res. 2015;107(4):442-52. PMCID: PMC4540145. http://www.ncbi.nlm.nih.gov/pubmed/26113266
  8. Neel BA, Zong H, Backer JM, Pessin JE. Identification of Atypical Peri-Nuclear Multivesicular Bodies in Oxidative and Glycolytic Skeletal Muscle of Aged and Pompe’s Disease Mouse Models. Front Physiol. 2015;6:393. PMCID: 4685069. http://www.ncbi.nlm.nih.gov/pubmed/26733885
  9. Totland C, Martinez-Santiago J, Ananthapadmanabhan KP, Somasundaran P. Composition and structural transitions of polyelectrolyte-surfactant complexes in the presence of fatty acid studied by NMR and cryo-SEM. Langmuir. 2015;31(5):1623-31. http://www.ncbi.nlm.nih.gov/pubmed/25590530

2014

  1. Block KA, Trusiak A, Katz A, Gottlieb P, Alimova A, Wei H, Morales J, Rice WJ, Steiner JC. Disassembly of the cystovirus varphi6 envelope by montmorillonite clay. Microbiologyopen. 2014;3(1):42-51. PMCID: PMC3937728. http://www.ncbi.nlm.nih.gov/pubmed/24357622
  2. Choudhuri K, Llodra J, Roth EW, Tsai J, Gordo S, Wucherpfennig KW, Kam LC, Stokes DL, Dustin ML. Polarized release of T-cell-receptor-enriched microvesicles at the immunological synapse. Nature. 2014;507(7490):118-23. PMCID: PMC3949170. http://www.ncbi.nlm.nih.gov/pubmed/24487619
  3. Fu X, Himes BA, Ke D, Rice WJ, Ning J, Zhang P. Controlled bacterial lysis for electron tomography of native cell membranes. Structure. 2014;22(12):1875-82. PMCID: PMC4255137. http://www.ncbi.nlm.nih.gov/pubmed/25456413
  4. Katz G, Benkarroum Y, Wei H, Rice WJ, Bucher D, Alimova A, Katz A, Klukowska J, Herman GT, Gottlieb P. Morphology of influenza B/Lee/40 determined by cryo-electron microscopy. PloS one. 2014;9(2):e88288. PMCID: PMC3916419. http://www.ncbi.nlm.nih.gov/pubmed/24516628
  5. Kaushal PS, Sharma MR, Booth TM, Haque EM, Tung CS, Sanbonmatsu KY, Spremulli LL, Agrawal RK. Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(20):7284-9. PMCID: PMC4034187. http://www.ncbi.nlm.nih.gov/pubmed/24799711
  6. Nguyen PA, Liou W, Hall DH, Leroux MR. Ciliopathy proteins establish a bipartite signaling compartment in a C. elegans thermosensory neuron. J Cell Sci. 2014;127(Pt 24):5317-30. PMCID: PMC4265742. http://www.ncbi.nlm.nih.gov/pubmed/25335890
  7. Orlando BJ, McDougle DR, Lucido MJ, Eng ET, Graham LA, Schneider C, Stokes DL, Das A, Malkowski MG. Cyclooxygenase-2 catalysis and inhibition in lipid bilayer nanodiscs. Arch Biochem Biophys. 2014;546:33-40. PMCID: PMC3967765. http://www.ncbi.nlm.nih.gov/pubmed/24503478
  8. Wang J, Silva M, Haas LA, Morsci NS, Nguyen KC, Hall DH, Barr MM. C. elegans ciliated sensory neurons release extracellular vesicles that function in animal communication. Curr Biol. 2014;24(5):519-25. PMCID: PMC4659354. http://www.ncbi.nlm.nih.gov/pubmed/24530063
  9. Yakubovskaya E, Guja KE, Eng ET, Choi WS, Mejia E, Beglov D, Lukin M, Kozakov D, Garcia-Diaz M. Organization of the human mitochondrial transcription initiation complex. Nucleic Acids Res. 2014;42(6):4100-12. PMCID: PMC3973321. http://www.ncbi.nlm.nih.gov/pubmed/24413562

2013

  1. Allen GS, Stokes DL. Modeling, docking, and fitting of atomic structures to 3D maps from cryo-electron microscopy. Methods Mol Biol. 2013;955:229-41. PMCID: PMC3645293. http://www.ncbi.nlm.nih.gov/pubmed/23132064
  2. Asenjo AB, Chatterjee C, Tan D, DePaoli V, Rice WJ, Diaz-Avalos R, Silvestry M, Sosa H. Structural model for tubulin recognition and deformation by kinesin-13 microtubule depolymerases. Cell Rep. 2013;3(3):759-68. http://www.ncbi.nlm.nih.gov/pubmed/23434508
  3. Catanese MT, Uryu K, Kopp M, Edwards TJ, Andrus L, Rice WJ, Silvestry M, Kuhn RJ, Rice CM. Ultrastructural analysis of hepatitis C virus particles. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(23):9505-10. PMCID: PMC3677472. http://www.ncbi.nlm.nih.gov/pubmed/23690609
  4. Choi WS, Rice WJ, Stokes DL, Coller BS. Three-dimensional reconstruction of intact human integrin alphaIIbbeta3: new implications for activation-dependent ligand binding. Blood. 2013;122(26):4165-71. PMCID: PMC3868924. http://www.ncbi.nlm.nih.gov/pubmed/24136164
  5. Coudray N, Valvo S, Hu M, Lasala R, Kim C, Vink M, Zhou M, Provasi D, Filizola M, Tao J, Fang J, Penczek PA, Ubarretxena-Belandia I, Stokes DL. Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(6):2140-5. PMCID: PMC3568326. http://www.ncbi.nlm.nih.gov/pubmed/23341604
  6. Khan LA, Zhang H, Abraham N, Sun L, Fleming JT, Buechner M, Hall DH, Gobel V. Intracellular lumen extension requires ERM-1-dependent apical membrane expansion and AQP-8-mediated flux. Nat Cell Biol. 2013;15(2):143-56. PMCID: PMC4091717. http://www.ncbi.nlm.nih.gov/pubmed/23334498
  7. Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont ME, Fox BG, Fromme P, Hendrickson WA, Malkowski MG, Rees DC, Stokes DL, Stowell MH, Wiener MC, Rost B, Stroud RM, Stevens RC, Sali A. Coordinating the impact of structural genomics on the human alpha-helical transmembrane proteome. Nat Struct Mol Biol. 2013;20(2):135-8. PMCID: PMC3645303. http://www.ncbi.nlm.nih.gov/pubmed/23381628
  8. Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley SK, Sali A, Rout MP, Almo SC. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure. 2013;21(4):560-71. PMCID: PMC3755625. http://www.ncbi.nlm.nih.gov/pubmed/23499021
  9. Stokes DL, Ubarretxena-Belandia I, Gonen T, Engel A. High-throughput methods for electron crystallography. Methods Mol Biol. 2013;955:273-96. PMCID: PMC3644976. http://www.ncbi.nlm.nih.gov/pubmed/23132066
  10. Yang S, Huang FK, Huang J, Chen S, Jakoncic J, Leo-Macias A, Diaz-Avalos R, Chen L, Zhang JJ, Huang XY. Molecular mechanism of fascin function in filopodial formation. J Biol Chem. 2013;288(1):274-84. PMCID: PMC3537022. http://www.ncbi.nlm.nih.gov/pubmed/23184945

2012

  1. Cerrone M, Noorman M, Lin X, Chkourko H, Liang FX, van der Nagel R, Hund T, Birchmeier W, Mohler P, van Veen TA, van Rijen HV, Delmar M. Sodium current deficit and arrhythmogenesis in a murine model of plakophilin-2 haploinsufficiency. Cardiovasc Res. 2012;95(4):460-8. PMCID: PMC3422082. http://www.ncbi.nlm.nih.gov/pubmed/22764151
  2. Delmar M, Liang FX. Connexin43 and the regulation of intercalated disc function. Heart Rhythm. 2012;9(5):835-8. PMCID: PMC3289726. http://www.ncbi.nlm.nih.gov/pubmed/22056332
  3. Durand-Heredia J, Rivkin E, Fan G, Morales J, Janakiraman A. Identification of ZapD as a cell division factor that promotes the assembly of FtsZ in Escherichia coli. J Bacteriol. 2012;194(12):3189-98. PMCID: PMC3370873. http://www.ncbi.nlm.nih.gov/pubmed/22505682
  4. Fernandez-Martinez J, Phillips J, Sekedat MD, Diaz-Avalos R, Velazquez-Muriel J, Franke JD, Williams R, Stokes DL, Chait BT, Sali A, Rout MP. Structure-function mapping of a heptameric module in the nuclear pore complex. J Cell Biol. 2012;196(4):419-34. PMCID: PMC3283990. http://www.ncbi.nlm.nih.gov/pubmed/22331846
  5. Hom N, Mehta KR, Chou T, Foraker AB, Brodsky FM, Kirshenbaum K, Montclare JK. Anisotropic nanocrystal arrays organized on protein lattices formed by recombinant clathrin fragments. J Mater Chem. 2012;22(44):23335-9. PMCID: PMC3702375. http://www.ncbi.nlm.nih.gov/pubmed/23836951
  6. Katz G, Wei H, Alimova A, Katz A, Morgan DG, Gottlieb P. Protein P7 of the cystovirus phi6 is located at the three-fold axis of the unexpanded procapsid. PloS one. 2012;7(10):e47489. PMCID: PMC3471842. http://www.ncbi.nlm.nih.gov/pubmed/23077625
  7. Phoon CK, Acehan D, Schlame M, Stokes DL, Edelman-Novemsky I, Yu D, Xu Y, Viswanathan N, Ren M. Tafazzin knockdown in mice leads to a developmental cardiomyopathy with early diastolic dysfunction preceding myocardial noncompaction. J Am Heart Assoc. 2012;1(2). PMCID: PMC3487377. http://www.ncbi.nlm.nih.gov/pubmed/23130124
  8. Schlame M, Acehan D, Berno B, Xu Y, Valvo S, Ren M, Stokes DL, Epand RM. The physical state of lipid substrates provides transacylation specificity for tafazzin. Nat Chem Biol. 2012;8(10):862-9. PMCID: PMC3699345. http://www.ncbi.nlm.nih.gov/pubmed/22941046
  9. Topalidou I, Keller C, Kalebic N, Nguyen KC, Somhegyi H, Politi KA, Heppenstall P, Hall DH, Chalfie M. Genetically separable functions of the MEC-17 tubulin acetyltransferase affect microtubule organization. Curr Biol. 2012;22(12):1057-65. PMCID: PMC3382010. http://www.ncbi.nlm.nih.gov/pubmed/22658602
  10. Ubarretxena-Belandia I, Stokes DL. Membrane protein structure determination by electron crystallography. Curr Opin Struct Biol. 2012;22(4):520-8. PMCID: PMC3423591. http://www.ncbi.nlm.nih.gov/pubmed/22572457

2011

  1. Acehan D, Malhotra A, Xu Y, Ren M, Stokes DL, Schlame M. Cardiolipin affects the supramolecular organization of ATP synthase in mitochondria. Biophys J. 2011;100(9):2184-92. PMCID: PMC3150712. http://www.ncbi.nlm.nih.gov/pubmed/21539786
  2. Allen GS, Wu CC, Cardozo T, Stokes DL. The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking. Structure. 2011;19(9):1219-32. PMCID: PMC3168071. http://www.ncbi.nlm.nih.gov/pubmed/21820315
  3. Banerjee S, Nimigean CM. Non-vesicular transfer of membrane proteins from nanoparticles to lipid bilayers. J Gen Physiol. 2011;137(2):217-23. PMCID: PMC3032376. http://www.ncbi.nlm.nih.gov/pubmed/21282400
  4. De Carlo S, Harris JR. Negative staining and cryo-negative staining of macromolecules and viruses for TEM. Micron. 2011;42(2):117-31. PMCID: PMC2978762. http://www.ncbi.nlm.nih.gov/pubmed/20634082
  5. Durand-Heredia JM, Yu HH, De Carlo S, Lesser CF, Janakiraman A. Identification and characterization of ZapC, a stabilizer of the FtsZ ring in Escherichia coli. J Bacteriol. 2011;193(6):1405-13. PMCID: PMC3067613. http://www.ncbi.nlm.nih.gov/pubmed/21216995
  6. Leo-Macias A, Katz G, Wei H, Alimova A, Katz A, Rice WJ, Diaz-Avalos R, Hu GB, Stokes DL, Gottlieb P. Toroidal surface complexes of bacteriophage varphi12 are responsible for host-cell attachment. Virology. 2011;414(2):103-9. PMCID: PMC3095694. http://www.ncbi.nlm.nih.gov/pubmed/21489589
  7. Nans A, Einheber S, Salzer JL, Stokes DL. Electron tomography of paranodal septate-like junctions and the associated axonal and glial cytoskeletons in the central nervous system. J Neurosci Res. 2011;89(3):310-9. PMCID: PMC3128832. http://www.ncbi.nlm.nih.gov/pubmed/21259318
  8. Nans A, Mohandas N, Stokes DL. Native ultrastructure of the red cell cytoskeleton by cryo-electron tomography. Biophys J. 2011;101(10):2341-50. PMCID: PMC3218374. http://www.ncbi.nlm.nih.gov/pubmed/22098732
  9. Renzi F, Zhang X, Rice WJ, Torres-Arancivia C, Gomez-Llorente Y, Diaz R, Ahn K, Yu C, Li YM, Sisodia SS, Ubarretxena-Belandia I. Structure of gamma-secretase and its trimeric pre-activation intermediate by single-particle electron microscopy. J Biol Chem. 2011;286(24):21440-9. PMCID: PMC3122203. http://www.ncbi.nlm.nih.gov/pubmed/21454611
  10. Tian Y, Simanshu DK, Ascano M, Diaz-Avalos R, Park AY, Juranek SA, Rice WJ, Yin Q, Robinson CV, Tuschl T, Patel DJ. Multimeric assembly and biochemical characterization of the Trax-translin endonuclease complex. Nat Struct Mol Biol. 2011;18(6):658-64. PMCID: PMC3109869. http://www.ncbi.nlm.nih.gov/pubmed/21552261
  11. Wehman AM, Poggioli C, Schweinsberg P, Grant BD, Nance J. The P4-ATPase TAT-5 inhibits the budding of extracellular vesicles in C. elegans embryos. Curr Biol. 2011;21(23):1951-9. PMCID: PMC3237752. http://www.ncbi.nlm.nih.gov/pubmed/22100064

2010

  1. Diaz R, Rice WJ, Stokes DL. Fourier-Bessel reconstruction of helical assemblies. Methods Enzymol. 2010;482:131-65. PMCID: PMC3128834. http://www.ncbi.nlm.nih.gov/pubmed/20888960
  2. Filimonenko M, Isakson P, Finley KD, Anderson M, Jeong H, Melia TJ, Bartlett BJ, Myers KM, Birkeland HC, Lamark T, Krainc D, Brech A, Stenmark H, Simonsen A, Yamamoto A. The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Molecular cell. 2010;38(2):265-79. PMCID: PMC2867245. http://www.ncbi.nlm.nih.gov/pubmed/20417604
  3. Hu M, Vink M, Kim C, Derr K, Koss J, D’Amico K, Cheng A, Pulokas J, Ubarretxena-Belandia I, Stokes D. Automated electron microscopy for evaluating two-dimensional crystallization of membrane proteins. Journal of structural biology. 2010;171(1):102-10. PMCID: PMC2904827. http://www.ncbi.nlm.nih.gov/pubmed/20197095
  4. Ji H, Coleman J, Yang R, Melia TJ, Rothman JE, Tareste D. Protein determinants of SNARE-mediated lipid mixing. Biophys J. 2010;99(2):553-60. PMCID: PMC2905075. http://www.ncbi.nlm.nih.gov/pubmed/20643074
  5. Kim C, Vink M, Hu M, Love J, Stokes DL, Ubarretxena-Belandia I. An automated pipeline to screen membrane protein 2D crystallization. J Struct Funct Genomics. 2010;11(2):155-66. PMCID: PMC3128831. http://www.ncbi.nlm.nih.gov/pubmed/20349145
  6. Leal-Pinto E, Gomez-Llorente Y, Sundaram S, Tang QY, Ivanova-Nikolova T, Mahajan R, Baki L, Zhang Z, Chavez J, Ubarretxena-Belandia I, Logothetis DE. Gating of a G protein-sensitive mammalian Kir3.1 prokaryotic Kir channel chimera in planar lipid bilayers. J Biol Chem. 2010;285(51):39790-800. PMCID: PMC3000960. http://www.ncbi.nlm.nih.gov/pubmed/20937804
  7. Li G, Margueron R, Hu G, Stokes D, Wang YH, Reinberg D. Highly compacted chromatin formed in vitro reflects the dynamics of transcription activation in vivo. Molecular cell. 2010;38(1):41-53. PMCID: PMC3641559. http://www.ncbi.nlm.nih.gov/pubmed/20385088
  8. Melcher M, Muhle RA, Henrich PP, Kraemer SM, Avril M, Vigan-Womas I, Mercereau-Puijalon O, Smith JD, Fidock DA. Identification of a role for the PfEMP1 semi-conserved head structure in protein trafficking to the surface of Plasmodium falciparum infected red blood cells. Cell Microbiol. 2010;12(10):1446-62. PMCID: PMC2939972. http://www.ncbi.nlm.nih.gov/pubmed/20438573
  9. Opalka N, Brown J, Lane WJ, Twist KA, Landick R, Asturias FJ, Darst SA. Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol. 2010;8(9). PMCID: PMC2939025. http://www.ncbi.nlm.nih.gov/pubmed/20856905
  10. Owen GR, Stokes DL. Exploring the Nature of Desmosomal Cadherin Associations in 3D. Dermatol Res Pract. 2010;2010:930401. PMCID: PMC2905946. http://www.ncbi.nlm.nih.gov/pubmed/20672011
  11. Stokes DL, Rice WJ, Hu M, Kim C, Ubarretxena-Belandia I. Two-dimensional crystallization of integral membrane proteins for electron crystallography. Methods Mol Biol. 2010;654:187-205. PMCID: PMC3128833. http://www.ncbi.nlm.nih.gov/pubmed/20665267
  12. Tucker JD, Siebert CA, Escalante M, Adams PG, Olsen JD, Otto C, Stokes DL, Hunter CN. Membrane invagination in Rhodobacter sphaeroides is initiated at curved regions of the cytoplasmic membrane, then forms both budded and fully detached spherical vesicles. Mol Microbiol. 2010;76(4):833-47. http://www.ncbi.nlm.nih.gov/pubmed/20444085
  13. Ubarretxena-Belandia I, Stokes DL. Present and future of membrane protein structure determination by electron crystallography. Adv Protein Chem Struct Biol. 2010;81:33-60. PMCID: PMC3121533. http://www.ncbi.nlm.nih.gov/pubmed/21115172

2009

  1. Acehan D, Khuchua Z, Houtkooper RH, Malhotra A, Kaufman J, Vaz FM, Ren M, Rockman HA, Stokes DL, Schlame M. Distinct effects of tafazzin deletion in differentiated and undifferentiated mitochondria. Mitochondrion. 2009;9(2):86-95. PMCID: PMC2660382. http://www.ncbi.nlm.nih.gov/pubmed/19114128
  2. Haka AS, Grosheva I, Chiang E, Buxbaum AR, Baird BA, Pierini LM, Maxfield FR. Macrophages create an acidic extracellular hydrolytic compartment to digest aggregated lipoproteins. Molecular biology of the cell. 2009;20(23):4932-40. PMCID: PMC2785736. http://www.ncbi.nlm.nih.gov/pubmed/19812252
  3. Jeong H, Then F, Melia TJ, Jr., Mazzulli JR, Cui L, Savas JN, Voisine C, Paganetti P, Tanese N, Hart AC, Yamamoto A, Krainc D. Acetylation targets mutant huntingtin to autophagosomes for degradation. Cell. 2009;137(1):60-72. PMCID: PMC2940108. http://www.ncbi.nlm.nih.gov/pubmed/19345187
  4. Kampmann M, Blobel G. Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex. Nat Struct Mol Biol. 2009;16(7):782-8. PMCID: PMC2706296. http://www.ncbi.nlm.nih.gov/pubmed/19503077
  5. Mansilla-Soto J, Yoon-Robarts M, Rice WJ, Arya S, Escalante CR, Linden RM. DNA structure modulates the oligomerization properties of the AAV initiator protein Rep68. PLoS Pathog. 2009;5(7):e1000513. PMCID: PMC2702170. http://www.ncbi.nlm.nih.gov/pubmed/19593381
  6. Nagy V, Hsia KC, Debler EW, Kampmann M, Davenport AM, Blobel G, Hoelz A. Structure of a trimeric nucleoporin complex reveals alternate oligomerization states. Proceedings of the National Academy of Sciences of the United States of America. 2009;106(42):17693-8. PMCID: PMC2764879. http://www.ncbi.nlm.nih.gov/pubmed/19805193
  7. Rath U, Rogers GC, Tan D, Gomez-Ferreria MA, Buster DW, Sosa HJ, Sharp DJ. The Drosophila kinesin-13, KLP59D, impacts Pacman- and Flux-based chromosome movement. Molecular biology of the cell. 2009;20(22):4696-705. PMCID: PMC2777100. http://www.ncbi.nlm.nih.gov/pubmed/19793918
  8. Shi Y, Di Giammartino DC, Taylor D, Sarkeshik A, Rice WJ, Yates JR, 3rd, Frank J, Manley JL. Molecular architecture of the human pre-mRNA 3′ processing complex. Molecular cell. 2009;33(3):365-76. PMCID: PMC2946185. http://www.ncbi.nlm.nih.gov/pubmed/19217410
  9. Wei H, Cheng RH, Berriman J, Rice WJ, Stokes DL, Katz A, Morgan DG, Gottlieb P. Three-dimensional structure of the enveloped bacteriophage phi12: an incomplete T = 13 lattice is superposed on an enclosed T = 1 shell. PloS one. 2009;4(9):e6850. PMCID: PMC2733035. http://www.ncbi.nlm.nih.gov/pubmed/19727406

2008

  1. Acehan D, Petzold C, Gumper I, Sabatini DD, Muller EJ, Cowin P, Stokes DL. Plakoglobin is required for effective intermediate filament anchorage to desmosomes. J Invest Dermatol. 2008;128(11):2665-75. http://www.ncbi.nlm.nih.gov/pubmed/18496566
  2. Banerjee S, Huber T, Sakmar TP. Rapid incorporation of functional rhodopsin into nanoscale apolipoprotein bound bilayer (NABB) particles. J Mol Biol. 2008;377(4):1067-81. http://www.ncbi.nlm.nih.gov/pubmed/18313692
  3. Eryilmaz E, Benach J, Su M, Seetharaman J, Dutta K, Wei H, Gottlieb P, Hunt JF, Ghose R. Structure and dynamics of the P7 protein from the bacteriophage phi 12. J Mol Biol. 2008;382(2):402-22. PMCID: PMC2744460. http://www.ncbi.nlm.nih.gov/pubmed/18647606
  4. Georgescu RE, Yurieva O, Kim SS, Kuriyan J, Kong XP, O’Donnell M. Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp. Proceedings of the National Academy of Sciences of the United States of America. 2008;105(32):11116-21. PMCID: PMC2495014. http://www.ncbi.nlm.nih.gov/pubmed/18678908
  5. Hu GB, Rice WJ, Drose S, Altendorf K, Stokes DL. Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals. Journal of structural biology. 2008;161(3):411-8. PMCID: PMC2322856. http://www.ncbi.nlm.nih.gov/pubmed/17945510
  6. Hu GB, Wei H, Rice WJ, Stokes DL, Gottlieb P. Electron cryo-tomographic structure of cystovirus phi 12. Virology. 2008;372(1):1-9. PMCID: PMC2692713. http://www.ncbi.nlm.nih.gov/pubmed/18022662
  7. Milstein O, Tseng SY, Starr T, Llodra J, Nans A, Liu M, Wild MK, van der Merwe PA, Stokes DL, Reisner Y, Dustin ML. Nanoscale increases in CD2-CD48-mediated intermembrane spacing decrease adhesion and reorganize the immunological synapse. J Biol Chem. 2008;283(49):34414-22. PMCID: PMC2590684. http://www.ncbi.nlm.nih.gov/pubmed/18826951
  8. Owen GR, Acehan D, Derr KD, Rice WJ, Stokes DL. Cryoelectron tomography of isolated desmosomes. Biochem Soc Trans. 2008;36(Pt 2):173-9. http://www.ncbi.nlm.nih.gov/pubmed/18363558
  9. Tan D, Rice WJ, Sosa H. Structure of the kinesin13-microtubule ring complex. Structure. 2008;16(11):1732-9. PMCID: PMC4826039. http://www.ncbi.nlm.nih.gov/pubmed/19000825
  10. Tareste D, Shen J, Melia TJ, Rothman JE. SNAREpin/Munc18 promotes adhesion and fusion of large vesicles to giant membranes. Proceedings of the National Academy of Sciences of the United States of America. 2008;105(7):2380-5. PMCID: PMC2268145. http://www.ncbi.nlm.nih.gov/pubmed/18268324
  11. Wu CC, Rice WJ, Stokes DL. Structure of a copper pump suggests a regulatory role for its metal-binding domain. Structure. 2008;16(6):976-85. PMCID: PMC2705936. http://www.ncbi.nlm.nih.gov/pubmed/18547529

2007

  1. Acehan D, Xu Y, Stokes DL, Schlame M. Comparison of lymphoblast mitochondria from normal subjects and patients with Barth syndrome using electron microscopic tomography. Lab Invest. 2007;87(1):40-8. PMCID: PMC2215767. http://www.ncbi.nlm.nih.gov/pubmed/17043667
  2. Chuang CF, Vanhoven MK, Fetter RD, Verselis VK, Bargmann CI. An innexin-dependent cell network establishes left-right neuronal asymmetry in C. elegans. Cell. 2007;129(4):787-99. http://www.ncbi.nlm.nih.gov/pubmed/17512411
  3. Del Rio A, Dutta K, Chavez J, Ubarretxena-Belandia I, Ghose R. Solution structure and dynamics of the N-terminal cytosolic domain of rhomboid intramembrane protease from Pseudomonas aeruginosa: insights into a functional role in intramembrane proteolysis. J Mol Biol. 2007;365(1):109-22. http://www.ncbi.nlm.nih.gov/pubmed/17059825
  4. Pomfret AJ, Rice WJ, Stokes DL. Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases. Journal of structural biology. 2007;157(1):106-16. PMCID: PMC4040983. http://www.ncbi.nlm.nih.gov/pubmed/16879984
  5. Shen J, Tareste DC, Paumet F, Rothman JE, Melia TJ. Selective activation of cognate SNAREpins by Sec1/Munc18 proteins. Cell. 2007;128(1):183-95. http://www.ncbi.nlm.nih.gov/pubmed/17218264
  6. Stokes DL. Desmosomes from a structural perspective. Curr Opin Cell Biol. 2007;19(5):565-71. PMCID: PMC2211412. http://www.ncbi.nlm.nih.gov/pubmed/17945476
  7. Vanamee ES, Berriman J, Aggarwal AK. An EM view of the FokI synaptic complex by single particle analysis. J Mol Biol. 2007;370(2):207-12. PMCID: PMC2703192. http://www.ncbi.nlm.nih.gov/pubmed/17524420
  8. Vink M, Derr K, Love J, Stokes DL, Ubarretxena-Belandia I. A high-throughput strategy to screen 2D crystallization trials of membrane proteins. Journal of structural biology. 2007;160(3):295-304. PMCID: PMC2211413. http://www.ncbi.nlm.nih.gov/pubmed/17951070
  9. Yakubovskaya E, Lukin M, Chen Z, Berriman J, Wall JS, Kobayashi R, Kisker C, Bogenhagen DF. The EM structure of human DNA polymerase gamma reveals a localized contact between the catalytic and accessory subunits. EMBO J. 2007;26(19):4283-91. PMCID: PMC2230839. http://www.ncbi.nlm.nih.gov/pubmed/17762861

2006

  1. Barre P, Eliezer D. Folding of the repeat domain of tau upon binding to lipid surfaces. J Mol Biol. 2006;362(2):312-26. http://www.ncbi.nlm.nih.gov/pubmed/16908029
  2. Chen Z, Akin BL, Stokes DL, Jones LR. Cross-linking of C-terminal residues of phospholamban to the Ca2+ pump of cardiac sarcoplasmic reticulum to probe spatial and functional interactions within the transmembrane domain. J Biol Chem. 2006;281(20):14163-72. http://www.ncbi.nlm.nih.gov/pubmed/16554295
  3. Ferguson N, Becker J, Tidow H, Tremmel S, Sharpe TD, Krause G, Flinders J, Petrovich M, Berriman J, Oschkinat H, Fersht AR. General structural motifs of amyloid protofilaments. Proceedings of the National Academy of Sciences of the United States of America. 2006;103(44):16248-53. PMCID: PMC1637568. http://www.ncbi.nlm.nih.gov/pubmed/17060612
  4. Greig SL, Berriman JA, O’Brien JA, Taylor JA, Bellamy AR, Yeager MJ, Mitra AK. Structural determinants of rotavirus subgroup specificity mapped by cryo-electron microscopy. J Mol Biol. 2006;356(1):209-21. http://www.ncbi.nlm.nih.gov/pubmed/16359700
  5. Rice WJ, Kovalishin A, Stokes DL. Role of metal-binding domains of the copper pump from Archaeoglobus fulgidus. Biochem Biophys Res Commun. 2006;348(1):124-31. http://www.ncbi.nlm.nih.gov/pubmed/16876128
  6. Stokes DL, Pomfret AJ, Rice WJ, Glaves JP, Young HS. Interactions between Ca2+-ATPase and the pentameric form of phospholamban in two-dimensional co-crystals. Biophys J. 2006;90(11):4213-23. PMCID: PMC1459492. http://www.ncbi.nlm.nih.gov/pubmed/16533842

2005

  1. Alimova A, Katz A, Podder R, Minko G, Wei H, Berriman J, Alfano RR, Gottlieb P. Virus particles and receptor interaction monitored by fluorescence spectroscopy. Photochem Photobiol. 2005;81(4):879-83. http://www.ncbi.nlm.nih.gov/pubmed/15819601
  2. Eliezer D, Barre P, Kobaslija M, Chan D, Li X, Heend L. Residual structure in the repeat domain of tau: echoes of microtubule binding and paired helical filament formation. Biochemistry. 2005;44(3):1026-36. http://www.ncbi.nlm.nih.gov/pubmed/15654759
  3. Stokes DL, Delavoie F, Rice WJ, Champeil P, McIntosh DB, Lacapere JJ. Structural studies of a stabilized phosphoenzyme intermediate of Ca2+-ATPase. J Biol Chem. 2005;280(18):18063-72. http://www.ncbi.nlm.nih.gov/pubmed/15734741
  4. Wood MA, Meredith DO, Owen GR, Richards RG, Riehle MO. Utilizing atomic number contrast for FESEM imaging of colloidal nanotopography underlying biological cells. Nanotechnology. 2005;16(9):1433. http://stacks.iop.org/0957-4484/16/i=9/a=002

2003

  1. He W, Cowin P, Stokes DL. Untangling desmosomal knots with electron tomography. Science. 2003;302(5642):109-13. http://www.ncbi.nlm.nih.gov/pubmed/14526082