PUBLICATIONS 2018-04-06T15:19:52+00:00

SEMC Publications

2018

Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA.  Fidaxomicin jams M. tuberculosis RNA polymerase motions needed for initiation via RbpA contacts.  bioRxiv

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.  Mol Biol Cell. 2018 Jan 17. pii: mbc.E17-10-0596. doi: 10.1091/mbc.E17-10-0596.
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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. J Struct Biol. Feb 2 2018.  Click here to view the paper on PubMed.

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). Mol Cell Mar 28 2018. Click here to view the paper on PubMed.

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 Mar 21 2018;7.  Click here to view the paper on PubMed.

McGoldrick LL, Singh AK, Saotome K, Yelshanskaya MV, Twomey EC, Grassucci RA, Sobolevsky AI.  Opening of the human epithelial calcium channel TRPV6. Nature Jan 11 2018;553(7687):233-237. Click here to view the paper on PubMed.

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 Jan 4;13(1):e0188858. doi: 10.1371/journal.pone.0188858. eCollection 2018.
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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 CryoEM analysis. Nature. Feb 28 2018. Click here to view the paper on PubMed.

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. Proc Natl Acad Sci U S A 2018;115(7):E1419-E1428. Click here to view the paper on PubMed.

Wei H, Dandey VP, Zhang Z, Raczkowski A, Rice WJ, Carragher B, Potter CS.  Optimizing “self-wicking” nanowire grids.  Journal of Structural Biology January 2018.  DOI.

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 Mar 29 2018;7. Click here to view the paper on PubMed.

2017

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. J Struct Biol. 2017;199(3):225-236.
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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.
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Benoit MPMH, Asenjo AB, Sosa H. Cryo-EM Reveals the Structural Basis of Microtubule Depolymerization by Kinesin-13s.  bioRxiv 2017.
DOI.

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):2296-2305.
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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):3227-3236.
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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).
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Garcia-Marin V, Kelly JG, Hawken MJ.  Major Feedforward Thalamic Input Into Layer 4C of Primary Visual Cortex in Primate.  Cereb Cortex Nov 28 2017:1-16.  Click here to view the paper on PubMed.

Guo H, Bueler SA, Rubinstein JL. Atomic model for the dimeric FO region of mitochondrial ATP synthase.  Science. Oct 26 2017.
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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. Oct 5 2017;171(2):414-426 e12.
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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):8711-8719.
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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. Nov 22 2017;6.
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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):623-630.
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James ZM, Borst AJ, Haitin Y, Frenz B, DiMaio F, Zagotta WN, Veesler D.  CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel. Proc Natl Acad Sci U S A. Apr 2017;114(17):4430-4435.
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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

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):370-378.
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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):854-868.
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Noble A, 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.

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.
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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. Dec 16 2017 Dec 16. pii: S0022-2836(17)30590-9. doi: 10.1016/j.jmb.2017.11.016.
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Ren Y, Schmiege P, Blobel G.  Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1. Elife. 2017 Jan 6;6. pii: e20070. doi: 10.7554/eLife.20070.
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Scapin G, Prosise WW, Wismer MK, Strickland C.  A novel storage system for cryoEM samples. J Struct Biol. 2017 Apr 19. pii: S1047-8477(17)30058-8. doi: 10.1016/j.jsb.2017.04.005.
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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 Apr 3;27(7):968-980. doi: 10.1016/j.cub.2017.02.039. Epub 2017 Mar 16.
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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 Aug;14(8):793-796. doi: 10.1038/nmeth.4347. Epub 2017 Jul 3.  Click here to view the paper on PubMed.

Twomey EC, Yelshanskaya MV, Grassucci RA, Frank J, Sobolevsky AI.  Channel opening and gating mechanism in AMPA-subtype glutamate receptors. Nature. 2017 Sep 7;549(7670):60-65. doi: 10.1038/nature23479. Epub 2017 Jul 24.
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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. May 2017;25(3):434-445.
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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. Jan 2017;91(2).
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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. Dec 13 2017.
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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):316-324.
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2016

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.
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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.
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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.
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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):1215-1228.e25.
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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.
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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.
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Peng X, Yuan XZ, Somasundaran P, Patra P. Assessment of micro-polarity anisotrophy as a function of surfactant packing in sodium dodecyl sulphonate-hexane reverse micelles. Soft Matter. 2016;12(1):22-5.
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Razinkov I, Dandey VP, Wei H, Zhang Z, Melnekoff D, Rice WJ, Wigge C, Potter CS, Carragher B. A new method for vitrifying samples for cryoEM. J Struct Biol. 2016;195(2):190-198.
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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.
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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.
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Tan YZ, Cheng A, Potter CS, Carragher B. Automated data collection in single particle electron microscopy. Microscopy (Oxf). 2016;65(1):43-56.
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2015

(2015). Correction for Kaushal et al., Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Proc Natl Acad Sci U S A. 2015;112(20):E2736.
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Chuang JZ, Hsu YC, Sung CH. Ultrastructural visualization of trans-ciliary rhodopsin cargoes in mammalian rods. Cilia. 2015;4:4.
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Hall DH, Rice WJ. Electron Tomography Methods for C. elegans. Methods Mol Biol. 2015;1327:141-58.
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Hsu YC, Chuang JZ, Sung CH. Light regulates the ciliary protein transport and outer segment disc renewal of mammalian photoreceptors. Developmental Cell. 2015;32(6):731-742.
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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.
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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.
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Lasala R, Coudray N, Abdine A, Zhang Z, Lopez-Redondo M, Kirshenbaum R, Alexopoulos J, Zolnai A, Stokes DL, Ubarretxena-Belandia I. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Journal of structural biology. 2015;189(2):123-134.
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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):442-452.
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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. Frontiers in Physiology. 2015;6:393.
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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: the ACS journal of surfaces and colloids. 2015;31(5):1623-1631.
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2014

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 3(1):42-51.
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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 507(7490):118-123.
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Fu X, Himes BA, Ke D, Rice WJ, Ning J, Zhang P.  Controlled bacterial lysis for electron tomography of native cell membranes. Structure 22(12):1875-1882.
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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 9(2):e88288.
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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. Proc Natl Acad Sci U S A 111(20):7284-7289.
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Nguyen PA, Liou W, Hall DH, Leroux MR.  Ciliopathy proteins establish a bipartite signaling compartment in a C. elegans thermosensory neuron. J Cell Sci 127(24):5317-5330.
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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 546:33-40.
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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 24(5): 519-525.
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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 42(6):4100-4112.
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2013

Allen GS, Stokes DL, Modeling, docking, and fitting of atomic structures to 3D maps from cryo-electron microscopy. Methods Mol Biol 955:229-241.
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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 3(3):759-768.
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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. Proc Natl Acad Sci U S A 110(23): 9505-9510.
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Choi WS, Rice WJ, Stokes DL, Coller BS.  Three-dimensional reconstruction of intact human integrin alphaIIbbeta3: new implications for activation-dependent ligand binding. Blood 122(26):4165-4171.
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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. Proc Natl Acad Sci U S A 110(6):2140-2145.
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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 15(2):143-156.
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Pieper U, Schlessinger A, Kloppman 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 20(2):135-138.
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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 21(4):560-571.
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Stokes DL, Ubarretxena-Belandia I, Gonen T, Engel A.  High-throughput methods for electron crystallography. Methods Mol Biol 955:273-296.
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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 288(1): 274-284.
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2012

Cerrone M, Noorman M, Lin X, Chkourko H, Liang FX, van der Nagel R, Hund R, 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 95(4):460-468.
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Delmar M, Liang, FX, Connexin43 and the regulation of intercalated disc function. Heart Rhythm 9(5):835-838.
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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 194(12):3189-3198.
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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 196(4):419-434.
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Hom N, Mehta KR, Chou T, Foraker AB, Brodsky FM, Kireshenbaum K, Montclare JK.  Anisotropic nanocrystal arrays organized on protein lattices formed by recombinant clathrin fragments. J Mater Chem 22(44):23335-23339.
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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 7(10):e47489.
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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 1(2).
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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 8(10):862-869.
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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 22(12):1057-1065.
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Ubarretxena-Belandia I, Stokes DL (2012).  Membrane protein structure determination by electron crystallography. Curr Opin Struct Biol 22(4):520-528.
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2011

Acehan D, Malhotra A, Xu Y, Ren M, Stokes DL, Schlame M.  Cardiolipin affects the supramolecular organization of ATP synthase in mitochondria. Biophys J 100(9):2184-2192.
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Allen GS, Wu CC, Cardozo T, Stokes DL.  The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking. Structure 19(9):1219-1232.
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Banerjee S, Nimigean CM.  Non-vesicular transfer of membrane proteins from nanoparticles to lipid bilayers. J Gen Physiol 137(2):217-223.
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De Carlo S, Harris JR.  Negative staining and cryo-negative staining of macromolecules and viruses for TEM. Micron 42(2):117-131.
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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 193(6):1405-1413.
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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 414(2):103-109.
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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 89(3):310-319.
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Nans A, Mohandas N, Stokes DL.  Native ultrastructure of the red cell cytoskeleton by cryo-electron tomography. Biophys J 101(10):2341-2350.
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Renzi F, Zhang X, Rice WJ, Torres-Arancivia C, Gomez-Llorenta 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 286(24):21440-21449.
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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 18(6):658-664.
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Wehman AM, Poggioli C, Schweinsberg P, GrantBD, Nance J.  The P4-ATPase TAT-5 inhibits the budding of extracellular vesicles in C. elegans embryos. Curr Biol 21(23):1951-1959.
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2010

Diaz R, Rice WJ, Stokes DL.  Fourier-Bessel reconstruction of helical assemblies. Methods Enzymol 482: 131-165.
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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. Mol Cell 38(2): 265-279.
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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. J Struct Biol 171(1): 102-110.
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Ji H, Coleman J, Yang R, Melia TJ, Rothman JE, Tareste D.  Protein determinants of SNARE-mediated lipid mixing. Biophys J 99(2): 553-560.
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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 11(2): 155-166.
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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 285(51): 39790-39800.
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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. Mol Cell 38(1): 41-53.
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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 12(10): 1446-1462.
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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 8(9).
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Owen GR, Stokes DL.  Exploring the Nature of Desmosomal Cadherin Associations in 3D. Dermatology Research and Practice 2010.
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Stokes DL, Rice WJ, Hu M, Kim C, Ubarretxena-Belandia I.  Two-dimensional crystallization of integral membrane proteins for electron crystallography. Methods Mol Biol 654: 187-205.
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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 76(4): 833-847.
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Ubarretxena-Belandia I, Stokes DL.  Present and future of membrane protein structure determination by electron crystallography. Adv Protein Chem Struct Biol 81: 33-60.
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2009

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 9(2): 86-95.
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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. Mol Biol Cell 20(23): 4932-4940.
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Jeong H, Then F, Melia Jr. TJ, 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 137(1): 60-72.
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Kampmann M, Blobel G.  Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex. Nat Struct Mol Biol 16(7): 782-788.
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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 5(7): e1000513.
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Nagy V, Hsia KC, Debler EW, Kampmann M, Davenport AM, Blobel G, Hoelz A.  Structure of a trimeric nucleoporin complex reveals alternate oligomerization states. Proc Natl Acad Sci U S A 106(42): 17693-17698.
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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. Mol Biol Cell 20(22): 4696-4705.
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Shi Y, Di Giammartino DC, Taylor D, Sarkeshik A, Rice WJ, Yates 3rd JR, Frank J, Manley JL.  Molecular architecture of the human pre-mRNA 3′ processing complex. Mol Cell 33(3): 365-376.
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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 4(9): e6850.
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2008

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 128(11): 2665-2675.
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Banerjee S, Huber T, Sakmar TP.  Rapid incorporation of functional rhodopsin into nanoscale apolipoprotein bound bilayer (NABB) particles. J Mol Biol 377(4): 1067-1081.
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Eryilmaz E, Benach J, Su M, Seetharaman J, Dutta K, Wei H, Gottlieb P, Hunt JF, Ghose.  Structure and dynamics of the P7 protein from the bacteriophage phi 12. J Mol Biol 382(2): 402-422.
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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. Proc Natl Acad Sci U S A 105(32): 11116-11121.
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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. J Struct Biol 161(3): 411-418.
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Hu GB, Wei H, Rice WJ, Stokes DL, Gottlieb P.  Electron cryo-tomographic structure of cystovirus phi 12. Virology 372(1): 1-9.
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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 283(49): 34414-34422.
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Owen GR, Acehan D, Derr KD, Rice WJ, Stokes DL.  Cryoelectron tomography of isolated desmosomes. Biochem Soc Trans 36(Pt 2): 173-179.
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Tan D, Rice WJ, Sosa H.  Structure of the kinesin13-microtubule ring complex. Structure 16(11): 1732-1739.
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Tareste D, Shen J, Melia TJ, Rothman JE.  SNAREpin/Munc18 promotes adhesion and fusion of large vesicles to giant membranes. Proc Natl Acad Sci U S A 105(7): 2380-2385.
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Wu CC, Rice WJ, Stokes DL.  Structure of a copper pump suggests a regulatory role for its metal-binding domain. Structure 16(6): 976-985.
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2007

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 87(1): 40-48.
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Chuang CF, Vanhoven MK, Fetter RD, Verselis VK, Bargmann CI.  An innexin-dependent cell network establishes left-right neuronal asymmetry in C. elegans. Cell 129(4): 787-799.
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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. Journal of Molecular Biology 365(1): 109-122.
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Pomfret AJ, Rice WJ, Stokes DL.  Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases. J Struct Biol 157(1): 106-116.
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Shen J, Tareste DC, Paumet F, Rothman JE, Melia TJ.  Selective activation of cognate SNAREpins by Sec1/Munc18 proteins. Cell 128(1): 183-195.
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Stokes, DL.  Desmosomes from a structural perspective. Curr Opin Cell Biol 19(5): 565-571.
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Vanamee ES, Berriman J, Aggarwal AK.  An EM view of the FokI synaptic complex by single particle analysis. J Mol Biol 370(2): 207-212.
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Vink M, Derr K, Love J, Stokes DL, Ubarretxena-Belandia I.  A high-throughput strategy to screen 2D crystallization trials of membrane proteins. J Struct Biol 160(3): 295-304.
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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 26(19): 4283-4291.
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2006

Barré P, Eliezer D.  Folding of the Repeat Domain of Tau Upon Binding to Lipid Surfaces. Journal of Molecular Biology 362(2): 312-326.
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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 281(20): 14163-14172.
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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. Proc Natl Acad Sci U S A 103(44): 16248-16253.
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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 356(1): 209-221.
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Rice WJ, Kovalishin A, Stokes DL.  Role of metal-binding domains of the copper pump from Archaeoglobus fulgidus. Biochem Biophys Res Commun 348(1): 124-131.
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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 90(11): 4213-4223.
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2005

Alimova A, Katz A, Podder R, Minko G, Wei H, Berrriman J, Alfano RR, Gottlieb P.  Virus particles and receptor interaction monitored by fluorescence spectroscopy. Photochem Photobiol 81(4): 879-883.
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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 44(3): 1026-1036.
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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 280(18): 18063-18072.
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Wood MA, Meredith DO, Owen GRh, Richards RG, Riehle MO.  Utilizing atomic number contrast for FESEM imaging of colloidal nanotopography underlying biological cells. Nanotechnology 16(9): 1433.
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2003

He W, Cowin P, Stokes DL.  Untangling desmosomal knots with electron tomography. Science 302(5642): 109-113.
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