CEM Publications

Standard Institutional Abbreviations:
AECO CUNY COLU NYU NYSB

MSSM MSKC RU SUNY WADS WEIL

Authors Inst Year Title Journal Volume:Pages

He, W., Cowin, P., and Stokes, D. L. NYU
NYSB 2003 Untangling desmosomal knots with electron tomography. Science 302:109-113.

Alimova, A, Katz, A, Podder, R, Minko, G, Wei, H, Berriman, J, Alfano, R.R., Gottlieb, P. CUNY
NYSB 2005 Virus Particles and Receptor Interaction Monitored by Fluorescence Spectroscopy. Photochemistry and Photobiology 81:879-883

Stokes, D.L., F. Delavoie, W.J. Rice, P. Champeil, D.B. McIntosh, J.-J. Lacapere, NYU
NYSB 2005 Structural Studies of a Stabilized Phosphoenzyme Intermediate of Ca2+-ATPase. J. Biol. Chem. 280:18063-18072

Eliezer, D, Barré, P, Kobaslija, M, Chan, D, Li, X, Heend, L. WEIL 2005 Residual structure in the repeat domain of tau: Echoes of microtubule binding and paired helical filament formation. Biochemistry 44:1026-1036.

Del Rio, A., Dutta K., Chavez J., Ubarretxena-Belandia, I., Ghose, R., CUNY 2006 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 365: 109-122

Greig SL, Berriman JA, O'Brien JA, Taylor JA, Bellamy AR, Yeager MJ, Mitra AK. NYSB 2006 Structural determinants of rotavirus subgroup specificity mapped by cryo-electron microscopy. J Mol Biol. 356(1):209-21

Ferguson N, Becker J, Tidow H, Tremmel S, Sharpe TD, Krause G, Flinders J, Petrovich M, Berriman J, Oschkinat H, Fersht AR. NYSB 2006 General structural motifs of amyloid protofilaments. Proc Natl Acad Sci U S A. 103(44):16248-53.

Rice WJ, Kovalishin A, Stokes DL NYU
NYSB 2006 'Role of metal-binding domains of the copper pump from Archaeoglobus fulgidus.' Biochem Biophys Res Commun 348:124-131

Stokes, D.L., A.J. Pomfret, W.J. Rice, J.P. Glaves, H.S.Young. NYU
NYSB 2006 Interactions between Ca2+-ATPase and the pentameric form of phospholamban in two-dimensional co-crystals. Biophys. J. 90:4213-4223

Chen, Z., B.L. Akin , D.L. Stokes , L.R. Jones. NYU
NYSB 2006 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 281:14163-14172

Barré P, Eliezer D WEIL 2006 'Folding of the repeat domain of tau upon binding to lipid surfaces' J. Mol. Biol. 362:312-26

Wood, M.A., Meredith, D.O., Owen, G.R., Richards, R.G., Riehle, M.O. NYSB 2006 Utilizing atomic number contrast for FESEM imaging of colloidal nanotopography underlying biological cells. Nanotechnology 16:1433-1439.

Chuang CF, Vanhoven MK, Fetter RD, Verselis VK, Bargmann CI., RU 2007 An innexin-dependent cell network establishes left-right neuronal asymmetry in C. elegans. Cell. 129(4):787-99.

Yakubovskaya E, Lukin M, Chen Z, Berriman J, Wall JS, Kobayashi R, Kisker C, Bogenhagen DF. SUNY
NYSB 2007 The EM structure of human DNA polymerase gamma reveals a localized contact between the catalytic and accessory subunits. EMBO J. 26:4283-91

Vanamee ES, Berriman J, Aggarwal AK. MSSM
NYSB 2007 An EM view of the FokI synaptic complex by single particle analysis. J Mol Biol 370:207-12

Shen J, Tareste DC, Paumet F, Rothman JE, Melia TJ. COLU 2007 Selective activation of cognate SNAREpins by Sec1/Munc18 proteins. Cell 128:183-195

Vink M, Derr K, Love J, Stokes DL, Ubarretxena-Belandia I. NYSB
NYU
MSSM 2007 A high-throughput strategy to screen 2D crystallization trials of membrane proteins. J Struct Biol 160:295-304.

Stokes DL NYU
NYSB 2007 'Desmosomes from a structural perspective.' Curr Opin Cell Biol 19:565-71

Acehan D, Xu Y, Stokes DL, and Schlame, M. NYU
NYSB 2007 Comparison of lymphoblast mitochondria from normal subjects and patients with Barth syndrome using electron microscopic tomography Lab Invest. 87(1):40-48

Pomfret, A.J., W.J. Rice, D.L. Stokes, NYU
NYSB 2007 Application of the Iterative Helical Real-Space Reconstruction Method to Large Membranous Tubular Crystals of P-type ATPases. J. Struc. Biol. 57:106-116.

Tan D., Rice W.J., Sosa H. AECO
NYSB 2008 Structure of the Kinesin13 Ring Complex. Structure 16 :1732-1739

Hu GB, Wei H, Rice WJ, Stokes DL, and Gottlieb P. CUNY
NYU
NYSB 2008 Electron cryo-tomographic structure of cystovirus phi 12. Virology 372: 1-9

Eryilmaz E, Benach J, Su M, Seetharaman J, Dutta K, Wei H, Gottlieb P, Hunt JF, Ghose R. CUNY
COLU 2008 Structure and Dynamics of the P7 Protein from the Bacteriophage φ12. J Mol Biol 382 (2):402-22

Tareste D, Shen J, Melia TJ, Rothman JE. COLU
YALE 2008 SNAREpin/Munc18 promotes adhesion and fusion of large vesicles to giant membranes. Proc Natl Acad Sci U S A. 105(7):2380-5.

Milstein O., Tseng S.Y., Starr T., Llodra J., Nans A., Liu M., Wild M.K., van der Merwe P.A., Stokes D.L., Reisner Y., Dustin M.L. NYU
NYSB 2008 Nanoscale increases in CD2-CD48-mediated intermembrane spacing decrease adhesion and reorganize the immunological synapse. J Biol Chem 283(49):34414-22

Acehan D, Petzold C, Gumper I, Sabatini DD, Muller EJ, Cowin P, Stokes DL. NYU
NYSB 2008 Plakoglobin Is Required for Effective Intermediate Filament Anchorage to Desmosomes. J Invest Dermatol 128 (11):2665-75.

Wu CC, Rice WJ, Stokes DL. NYU
NYSB 2008 Structure of a copper pump suggests a regulatory role for its metal-binding domain. Structure 16:976-85.

Owen GR, Acehan D, Derr KD, Rice WJ, Stokes DL. NYSB
NYU 2008 Cryoelectron tomography of isolated desmosomes. Biochem Soc Trans 36:173-9.

Hu GB, Rice WJ, Drose S, Altendorf K, Stokes DL NYU
NYSB 2008 'Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals.' J Struct Biol 161(3):411-8

Roxana E. Georgescu, Olga Yurieva, Seung-Sup Kim, John Kuriyan, Xiang-Peng Kong, and Mike O'Donnell RU 2008 Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp. Proc Natl Acad Sci U S A. 105 (32):11116-21

Banerjee S, Huber T, and Sakmar TP. RU 2008 Rapid Incorporation of Functional Rhodopsin into Nanoscale Apolipoprotein Bound Bilayer (NABB) Particles. Journal of Molecular Biology 377:1067-1081.

Rath U, Rogers GC, Tan D, Gomez-Ferreria MA, Buster DW, Sosa HJ, Sharp DJ AECO 2009 The Drosophila kinesin-13, KLP59D, impacts Pacman- and Flux-based chromosome movement. Mol Biol Cell. 20(22):4696-705.

Wei H, Cheng RH, Berriman J, Rice WJ, Stokes DL, Katz A, Morgan DG, and Gottlieb P. CUNY
NYU
NYSB 2009 Three-dimensional structure of the enveloped bacteriophage phi12: an incomplete T = 13 lattice is superposed on an enclosed T = 1 shell. PLoS ONE 4: e6850

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. COLU
YALE 2009 Acetylation targets mutant huntingtin to autophagosomes for degradation. Cell. 137(1):60-72.

Shi Y, Di Giammartino DC, Taylor D, Sarkeshik A, Rice WJ, Yates JR, Frank J, and Manley JL. COLU
NYSB 2009 Molecular architecture of the human pre-mRNA 3' processing complex. Mol. Cell 33: 365-76.

Mansilla-Soto J, Yoon-Robarts M, Rice WJ, Arya S, Escalante CR, and Linden RM. MSSM
NYSB 2009 DNA structure modulates the oligomerization properties of the AAV initiator protein Rep68. PLoS Pathog. 5:e1000513

Acehan, D., Khuchua, Z., Houtkooper, R.H., Malhotra, A., Kaufman, J., Vaz, F.M., Ren, M., Rockman, H.A., Stokes, D.L., Schlame, M. NYU
NYSB 2009 Distinct Effects of Tafazzin Deletion in Differentiated and Undifferentiated Mitochondria. Mitochondria. 9:86-95.

Martin Kampmann and Gunter Blobel. RU 2009 Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex. Nature Structural and Molecular Biology 16(7):782-8.

Nagy V, Hsia KC, Debler EW, Kampmann M, Davenport AM, Blobel G, Hoelz A. RU 2009 Structure of a trimeric nucleoporin complex reveals alternate oligomerization states. Proc Natl Acad Sci U S A. 106(42):17693-8.

Haka A, Grosheva I, Chiang E, Buxbaum A, Baird B, Pierini L, Maxfield F. WEIL 2009 Macrophages create an acidic extracellular hydrolytic caompartment to digest aggregated lipoproteins. Mol Biol Cell 23:4932-4940

Tucker JD, Siebert CA, Escalante M, Adams PG, Olsen JD, Otto C, Stokes DL, Hunter CN. NYSB 2010 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):833-47.

Opalka N, Brown J, Lane WJ, Twist KA, Landick R, Asturias FJ, Darst SA. RU 2010 Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol. 8(9):e1000483.

Leal-Pinto E, Gómez-Llorente Y, Sundaram S, Tang QY, Ivanova-Nikolova T, Mahajan R, Baki L, Zhang Z, Chavez J, Ubarretxena-Belandia I, Logothetis DE. MSSM 2010 Gating of a G protein-sensitive mammalian Kir3.1 prokaryotic Kir channel chimera in planar lipid bilayers. J Biol Chem. 285(51):39790-800.

Melcher, M., Muhle, R., Henrich, P., Kraemer, S., Avril, M., Vigan-Womas, I., Mercereau-Puijalon, O., Fidock, D., COLU 2010 Identification of a role for the PfEMP1 semi-conserved head structure in protein trafficking to the surface of Plasmodium falciparum infected red blood cells. Cellular Microbiology 12(10):1446-1462

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. COLU
YALE 2010 The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Mol Cell. 38(2):265-79.

Ji H, Coleman J, Yang R, Melia TJ, Rothman JE, Tareste D. COLU
YALE 2010 Protein determinants of SNARE-mediated lipid mixing. Biophys J. 99(2):553-60.

Ubarretxena-Belandia I and Stokes D.L. MSSM
NYU
NYSB 2010 Present and future of membrane protein structure determination by electron crystallography Adv Protein Chem Struct Biol. 81:33-60

Stokes DL, Rice WJ, Hu M, Kim C, and Ubarretxena-Belandia I. NYSB
NYU
MSSM 2010 Two-dimensional crystallization of integral membrane proteins for electron crystallography. Methods Mol. Biol. 654: 187-205.

Owen, G.R., D.L. Stokes, NYSB
NYU 2010 Exploring the nature of desmosomal cadherin interactions in 3D. Derm. Res. Practice 2010:1-12.

Li, G, R. Margueron, G. Hu, D. Stokes, Y. Wang, D. Reinberg. NYU
NYSB 2010 Highly compacted chromatin formed in vitro reflects the dynamics of transcription activation in vivo. Mol. Cell 38:41-53.

C. Kim, M. Vink, M. Hu, D.L. Stokes, I. Ubarretxena-Belandia, NYSB
NYU
MSSM 2010 An automated pipeline to screen membrane protein 2D crystallization, J. Func. Struc. Genomics 11:155-166.

M. Hu, M. Vink, C. Kim, K. Derr, J. Koss, K. D'Amico, I. Ubarretxena-Belandia, D.L. Stokes, NYSB
NYU
MSSM 2010 Automated electron microscopy for evaluating two-dimensional crystallization of membrane proteins, J. Struct. Biol. 171:102-110.

R Diaz, WJ Rice, DL Stokes NYSB
NYU 2010 Fourier-bessel reconstruction of helical assemblies. Methods Enzymol. 2010 482:131-165

Tian Y, Simanshu DK, Ascano M, Diaz-Avalos R, Park AY, Juranek SA, Rice WJ, Yin Q, Robinson CV, Tuschl T, and Patel DJ MSKC
NYSBC 2011 Multimeric assembly and biochemical characterization of the Trax-translin endonuclease complex. Nat. Struct. Mol. Biol. 18:658-64

Leo-Macias A, Katz G, Wei H, Alimova A, Katz A, Rice W, Diaz-Avalos R, Hua G, Stokes D, Gottlieb P NYU
CUNY
NYSB 2011 Toroidal surface complexes of bacteriophage phi12 are responsible for host-cell attachment Virology 414(2):103-109

Renzi F, Zhang X, Rice WJ, Torres-Arancivia C, Gomez-Llorente Y, Diaz R, Ahn K, Li Y, Sisodia SS, Ubarretxena-Belandia I MSSM
NYSB 2011 Structure of {gamma}-secretase and its trimeric pre-activation intermediate by single-particle electron microscopy J Biol Chem 286(24):21440-9

Nans A, Einheber S, Salzer JL, Stokes DL. NYU
NYSB 2011 Electron tomography of paranodal septate-like junctions and the associated axonal and glial cytoskeletons in the central nervous system. J Neurosci Res. 89(3):310-9

Banerjee S, Nimigean CM. WEIL 2011 Non-vesicular transfer of membrane proteins from nanoparticles to lipid bilayers. J Gen Physiol. 137(2):217-23.

Allen G.S. and Stokes D.L. NYU
NYSB 2011 Modeling, Docking, Fitting of Atomic Structures to 3D Maps from Cryo-electron Microscopy Methods in Molecular Biology

-- KdDerr - 04 Jan 2011