David Stokes

Summary

Affiliation: New York University
Country: USA

Publications

  1. pmc Desmosomes from a structural perspective
    David L Stokes
    Skirball Institute and Department of Cell Biology, New York University School of Medicine, 540 First Ave, New York, NY 10016, United States
    Curr Opin Cell Biol 19:565-71. 2007
  2. pmc High-throughput methods for electron crystallography
    David L Stokes
    Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
    Methods Mol Biol 955:273-96. 2013
  3. ncbi request reprint A structural model for the catalytic cycle of Ca(2+)-ATPase
    Chen Xu
    Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, 540 First Ave, New York, NY, 10016, USA
    J Mol Biol 316:201-11. 2002
  4. ncbi request reprint Untangling desmosomal knots with electron tomography
    Wanzhong He
    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
    Science 302:109-13. 2003
  5. ncbi request reprint Structure and function of the calcium pump
    David L Stokes
    Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10012, USA
    Annu Rev Biophys Biomol Struct 32:445-68. 2003
  6. pmc Two-dimensional crystallization of integral membrane proteins for electron crystallography
    David L Stokes
    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
    Methods Mol Biol 654:187-205. 2010
  7. ncbi request reprint Role of metal-binding domains of the copper pump from Archaeoglobus fulgidus
    William J Rice
    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
    Biochem Biophys Res Commun 348:124-31. 2006
  8. pmc Interactions between Ca2+-ATPase and the pentameric form of phospholamban in two-dimensional co-crystals
    David L Stokes
    Structural Biology Program, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
    Biophys J 90:4213-23. 2006
  9. pmc Three-dimensional structure of the enveloped bacteriophage phi12: an incomplete T = 13 lattice is superposed on an enclosed T = 1 shell
    Hui Wei
    Department of Microbiology and Immunology, Sophie Davis School of Biomedical Education, The City College of New York, New York, New York, United States of America
    PLoS ONE 4:e6850. 2009
  10. pmc Structure of a copper pump suggests a regulatory role for its metal-binding domain
    Chen Chou Wu
    Skirball Institute of Biomolecular Medicine, School of Medicine, New York University, 540 First Avenue, New York, NY 10016, USA
    Structure 16:976-85. 2008

Research Grants

  1. ELECTRON MICROSCOPY OF P-TYPE ION PUMPS & PHOSPHOLAMBAN
    David Stokes; Fiscal Year: 2000
  2. Electron Microscopy of P-type Ion Pumps
    David Stokes; Fiscal Year: 2009
  3. Membrane Protein Structure by Electron Crystallography
    David Stokes; Fiscal Year: 2009
  4. Electron Microscopy of P-type Ion Pumps
    David L Stokes; Fiscal Year: 2010
  5. Electron Microscopy of P-type Ion Pumps
    David Stokes; Fiscal Year: 2009
  6. Membrane Protein Structure by Electron Crystallography
    David Stokes; Fiscal Year: 2009
  7. Electron Tomography of Adhesive Junctions
    David Stokes; Fiscal Year: 2006
  8. Electron Microscopy of P-type Ion Pumps
    David Stokes; Fiscal Year: 2005
  9. High-throughput Pipeline for Electron Crystallography
    David L Stokes; Fiscal Year: 2010

Collaborators

Detail Information

Publications23

  1. pmc Desmosomes from a structural perspective
    David L Stokes
    Skirball Institute and Department of Cell Biology, New York University School of Medicine, 540 First Ave, New York, NY 10016, United States
    Curr Opin Cell Biol 19:565-71. 2007
    ....
  2. pmc High-throughput methods for electron crystallography
    David L Stokes
    Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
    Methods Mol Biol 955:273-96. 2013
    ..In addition, the use of liquid-handling robots for making negatively stained grids and methods for automatically imaging samples in the electron microscope are described...
  3. ncbi request reprint A structural model for the catalytic cycle of Ca(2+)-ATPase
    Chen Xu
    Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, 540 First Ave, New York, NY, 10016, USA
    J Mol Biol 316:201-11. 2002
    ..If so, the reaction cycle of Ca(2+)-ATPase would have elements of a Brownian ratchet, where the chemical reactions of ATP hydrolysis are used to direct the random thermal oscillations of an innately flexible molecule...
  4. ncbi request reprint Untangling desmosomal knots with electron tomography
    Wanzhong He
    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
    Science 302:109-13. 2003
    ..This flexibility suggests a novel mechanism for generating both cis and trans interactions and for propagating these adhesive interactions along the junction...
  5. ncbi request reprint Structure and function of the calcium pump
    David L Stokes
    Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10012, USA
    Annu Rev Biophys Biomol Struct 32:445-68. 2003
    ..By comparing various structures and correlating functional data, we can now begin to associate the chemical changes constituting the reaction cycle with structural changes in these domains...
  6. pmc Two-dimensional crystallization of integral membrane proteins for electron crystallography
    David L Stokes
    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
    Methods Mol Biol 654:187-205. 2010
    ..In addition, we show examples of the different morphologies that are commonly obtained and describe basic image analysis procedures that can be used to evaluate their promise for structure determination by cryoelectron microscopy...
  7. ncbi request reprint Role of metal-binding domains of the copper pump from Archaeoglobus fulgidus
    William J Rice
    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
    Biochem Biophys Res Commun 348:124-31. 2006
    ..Alternative hypotheses are discussed by which the N-terminal MBD could influence the catalytic activity of CopA...
  8. pmc Interactions between Ca2+-ATPase and the pentameric form of phospholamban in two-dimensional co-crystals
    David L Stokes
    Structural Biology Program, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
    Biophys J 90:4213-23. 2006
    ..Furthermore, our results indicate that this pentameric form of PLB is capable of a direct interaction with Ca(2+)-ATPase...
  9. pmc Three-dimensional structure of the enveloped bacteriophage phi12: an incomplete T = 13 lattice is superposed on an enclosed T = 1 shell
    Hui Wei
    Department of Microbiology and Immunology, Sophie Davis School of Biomedical Education, The City College of New York, New York, New York, United States of America
    PLoS ONE 4:e6850. 2009
    ..The segmented dsRNA genome, the multi-layered arrangement of the capsid and the overall viral replication scheme make the Cystoviridae similar to the Reoviridae...
  10. pmc Structure of a copper pump suggests a regulatory role for its metal-binding domain
    Chen Chou Wu
    Skirball Institute of Biomolecular Medicine, School of Medicine, New York University, 540 First Avenue, New York, NY 10016, USA
    Structure 16:976-85. 2008
    ..We have built a pseudoatomic model by fitting existing crystallographic structures into the cryoelectron microscopy maps for CopA, which suggest a Cu-dependent regulatory role for the MBD...
  11. pmc Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals
    Guo Bin Hu
    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
    J Struct Biol 161:411-8. 2008
    ..These results illustrate the utility of electron tomography in structure determination of ordered assemblies, especially when disorder is severe enough to hamper conventional crystallographic analysis...
  12. ncbi request reprint Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases
    Andrew J Pomfret
    Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
    J Struct Biol 157:106-16. 2007
    ..On the other hand, IHRSR was very effective for scallop Ca(2+)-ATPase, which was too disordered to analyze by Fourier-Bessel methods...
  13. pmc Comparison of lymphoblast mitochondria from normal subjects and patients with Barth syndrome using electron microscopic tomography
    Devrim Acehan
    Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
    Lab Invest 87:40-8. 2007
    ..The data suggest that mitochondrial abnormalities of BTHS involve adhesions of inner mitochondrial membranes with subsequent collapse of the intracristae space...
  14. ncbi request reprint Structural studies of a stabilized phosphoenzyme intermediate of Ca2+-ATPase
    David L Stokes
    Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, New York, New York 10012, USA
    J Biol Chem 280:18063-72. 2005
    ..Finally, we consider the alternative possibility that phosphate transfer to fluorescein itself could explain the properties of this low fluorescence species...
  15. pmc Electron cryo-tomographic structure of cystovirus phi 12
    Guo Bin Hu
    Structural Biology Program, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
    Virology 372:1-9. 2008
    ..This second structure formed a torroidal structure termed "the donut" and appears to inhibit BHT-induced viral envelope fusion...
  16. doi request reprint Plakoglobin is required for effective intermediate filament anchorage to desmosomes
    Devrim Acehan
    Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, New York 10012, USA
    J Invest Dermatol 128:2665-75. 2008
    ....
  17. pmc Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase
    Konrad Hinsen
    Laboratoire Leon Brillouin CEA CNRS, 91191 Gif sur Yvette, France
    Biophys J 88:818-27. 2005
    ....
  18. ncbi request reprint Role of leucine 31 of phospholamban in structural and functional interactions with the Ca2+ pump of cardiac sarcoplasmic reticulum
    Zhenhui Chen
    Krannert Institute of Cardiology and the Department of Medicine, Indiana University School of Medicine, 1800 N Capitol Ave, Indianapolis, Indiana 46202, USA
    J Biol Chem 280:10530-9. 2005
    ..A model for the three-dimensional structure of the interaction site is proposed...
  19. ncbi request reprint Effect of orthophosphate, nucleotide analogues, ADP, and phosphorylation on the cytoplasmic domains of Ca(2+)-ATPase from scallop sarcoplasmic reticulum
    Chris Ryan
    Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901, USA
    J Biol Chem 279:5380-6. 2004
    ....
  20. ncbi request reprint 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
    Zhenhui Chen
    Krannert Institute of Cardiology and the Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Biol Chem 281:14163-72. 2006
    ..A model for the interaction of PLB with SERCA2a is presented, showing that Val49 fits into a constriction at the lumenal end of the M2 helix of SERCA, possibly controlling access of PLB to its binding site on SERCA...
  21. ncbi request reprint Spatial and dynamic interactions between phospholamban and the canine cardiac Ca2+ pump revealed with use of heterobifunctional cross-linking agents
    Zhenhui Chen
    Krannert Institute of Cardiology and the Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Biol Chem 278:48348-56. 2003
    ..SERCA2a are based on thapsigargin-bound SERCA, our results suggest that the nucleotide-bound, E2 conformation is substantially different and represents the key conformational state for interacting with PLB...
  22. pmc A high-throughput strategy to screen 2D crystallization trials of membrane proteins
    Martin Vink
    The New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
    J Struct Biol 160:295-304. 2007
    ....
  23. doi request reprint Cryoelectron tomography of isolated desmosomes
    Gethin Rh Owen
    New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
    Biochem Soc Trans 36:173-9. 2008
    ..Although not definitive, the resulting images provide support for the irregular groupings of cadherin molecules seen previously in mouse skin...

Research Grants22

  1. ELECTRON MICROSCOPY OF P-TYPE ION PUMPS & PHOSPHOLAMBAN
    David Stokes; Fiscal Year: 2000
    ..The family of ion pumps include those responsible for Menkes and Wilsons disease, and extrapolation of the structures will improve understanding of the molecular mechanisms for these diseases. ..
  2. Electron Microscopy of P-type Ion Pumps
    David Stokes; Fiscal Year: 2009
    ..For FxYD proteins, we will develop conditions for 2D crystallization Na/K-ATPase and phospholemman after heterologous expression and purification from yeast. ..
  3. Membrane Protein Structure by Electron Crystallography
    David Stokes; Fiscal Year: 2009
    ....
  4. Electron Microscopy of P-type Ion Pumps
    David L Stokes; Fiscal Year: 2010
    ..For FxYD proteins, we will develop conditions for 2D crystallization Na/K-ATPase and phospholemman after heterologous expression and purification from yeast. ..
  5. Electron Microscopy of P-type Ion Pumps
    David Stokes; Fiscal Year: 2009
    ..For FxYD proteins, we will develop conditions for 2D crystallization Na/K-ATPase and phospholemman after heterologous expression and purification from yeast. ..
  6. Membrane Protein Structure by Electron Crystallography
    David Stokes; Fiscal Year: 2009
    ....
  7. Electron Tomography of Adhesive Junctions
    David Stokes; Fiscal Year: 2006
    ..In our fourth aim, we will study the assembly of both adherens junctions and desmosomes in cultured keratinocytes, using calcium to initiate junction assembly between confluent cell cultures. ..
  8. Electron Microscopy of P-type Ion Pumps
    David Stokes; Fiscal Year: 2005
    ..abstract_text> ..
  9. High-throughput Pipeline for Electron Crystallography
    David L Stokes; Fiscal Year: 2010
    ..As a result, membrane proteins are implicated in many diseases. Structural information about these proteins is critical to understanding the biology behind the disease and for designing drugs to ameliorate the problems. ..