D. Stokes

发表

Outcome of the First Electron Microscopy Validation Task Force Meeting

M. Baker, W. Chiu, A. Sali, 2012, Structure.

Integrative Structure and Functional Anatomy of a Nuclear Pore Complex

David L. Stokes, Yi Shi, Steven J. Ludtke, 2018, Nature.

Structure–function mapping of a heptameric module in the nuclear pore complex

Josef D. Franke, B. Chait, A. Sali, 2012, The Journal of cell biology.

Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.

Seung Joong Kim, A. Sali, J. M. Sauder, 2013, Structure.

Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.

Seung Joong Kim, Ilan E. Chemmama, A. Sali, 2017, Structure.

Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform

Seung Joong Kim, Ilan E. Chemmama, B. Chait, 2016, Cell.

Membrane protein structure determination by electron crystallography.

D. Stokes, I. Ubarretxena-Belandia, 2012, Current opinion in structural biology.

Cardiolipin affects the supramolecular organization of ATP synthase in mitochondria.

Ashim Malhotra, David L Stokes, D. Stokes, 2011, Biophysical journal.

Deducing the symmetry of helical assemblies: Applications to membrane proteins.

N. Coudray, D. Stokes, M. Dumont, 2016, Journal of structural biology.

Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase.

Konrad Hinsen, Nathalie Reuter, Jorge Navaza, 2005, Biophysical journal.

Coordinating the impact of structural genomics on the human α-helical transmembrane proteome

Avner Schlessinger, Ursula Pieper, Wayne A Hendrickson, 2013, Nature Structural &Molecular Biology.

Native ultrastructure of the red cell cytoskeleton by cryo-electron tomography.

David L Stokes, D. Stokes, N. Mohandas, 2011, Biophysical journal.

Structural basis for potassium transport in prokaryotes by KdpFABC

D. Stokes, B. P. Pedersen, M. Schlame, 2021, Proceedings of the National Academy of Sciences.

Crystal Structure of the Potassium Importing KdpFABC Membrane Complex

D. Stokes, B. P. Pedersen, Ching-Shin Huang, 2017, Nature.

Phosphorylation and mutation of phospholamban alter physical interactions with the sarcoplasmic reticulum calcium pump.

D. Stokes, H. Young, J. Glaves, 2011, Journal of molecular biology.

Interactions between Ca2+-ATPase and the pentameric form of phospholamban in two-dimensional co-crystals.

D. Stokes, W. Rice, H. Young, 2006, Biophysical journal.

Role of Leucine 31 of Phospholamban in Structural and Functional Interactions with the Ca2+ Pump of Cardiac Sarcoplasmic Reticulum*

D. Stokes, L. Jones, Zhenhui Chen, 2005, Journal of Biological Chemistry.

Calcium transport across the sarcoplasmic reticulum: structure and function of Ca2+-ATPase and the ryanodine receptor.

T. Wagenknecht, D. Stokes, 2000, European journal of biochemistry.

Three-dimensional crystals of CaATPase from sarcoplasmic reticulum. Symmetry and molecular packing.

D. Stokes, N. Green, David L. Stokes, 1990, Biophysical journal.

Structure of the Ca2+ pump of sarcoplasmic reticulum: a view along the lipid bilayer at 9-A resolution.

H. Sasabe, D. Stokes, C. Toyoshima, 1998, Biophysical journal.

Present and future of membrane protein structure determination by electron crystallography.

David L Stokes, D. Stokes, I. Ubarretxena-Belandia, 2010, Advances in protein chemistry and structural biology.

High-throughput methods for electron crystallography.

T. Gonen, D. Stokes, I. Ubarretxena-Belandia, 2013, Methods in molecular biology.

Two-dimensional crystallization of integral membrane proteins for electron crystallography.

D. Stokes, W. Rice, I. Ubarretxena-Belandia, 2010, Methods in molecular biology.

Two-dimensional crystallization of Ca-ATPase by detergent removal.

J. Lacapère, D. Stokes, J. Rigaud, 1998, Biophysical journal.

Comparison of H+-ATPase and Ca2+-ATPase suggests that a large conformational change initiates P-type ion pump reaction cycles

Peijun Zhang, D. Stokes, W. Kühlbrandt, 1999, Current Biology.

A high-throughput strategy to screen 2D crystallization trials of membrane proteins.

David L Stokes, D. Stokes, M. Vink, 2007, Journal of structural biology.

An automated pipeline to screen membrane protein 2D crystallization

D. Stokes, M. Vink, I. Ubarretxena-Belandia, 2010, Journal of Structural and Functional Genomics.

Growth conditions control the size and order of actin bundles in vitro.

D. DeRosier, D. Stokes, David L. Stokes, 1991, Biophysical journal.

Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter

E. Tajkhorshid, R. L. Gonzalez, D. Stokes, 2022, bioRxiv.

Electron cryo-tomographic structure of cystovirus phi 12.

P. Gottlieb, D. Stokes, W. Rice, 2008, Virology.

Cyclooxygenase-2 catalysis and inhibition in lipid bilayer nanodiscs.

A. Das, D. Stokes, E. Eng, 2014, Archives of biochemistry and biophysics.

Cryoelectron tomography of isolated desmosomes.

D. Stokes, W. Rice, Devrim Acehan, 2008, Biochemical Society transactions.

Tafazzin Knockdown in Mice Leads to a Developmental Cardiomyopathy With Early Diastolic Dysfunction Preceding Myocardial Noncompaction

D. Stokes, M. Schlame, Mindong Ren, 2012, Journal of the American Heart Association.

Purified, Reconstituted Cardiac Ca2+-ATPase Is Regulated by Phospholamban but Not by Direct Phosphorylation with Ca2+/Calmodulin-dependent Protein Kinase*

D. Stokes, L. Jones, L. Reddy, 1996, The Journal of Biological Chemistry.

Role of metal-binding domains of the copper pump from Archaeoglobus fulgidus.

D. Stokes, W. Rice, A. Kovalishin, 2006, Biochemical and biophysical research communications.

Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter

E. Tajkhorshid, D. Stokes, J. Mindell, 2022, bioRxiv.

Zinc Dependent Conformational Changes in the Cation Diffusion Facilitator YiiP from S. oneidensis

A. Koide, S. Koide, D. Stokes, 2020, bioRxiv.

Functional Reconstitution of Recombinant Phospholamban with Rabbit Skeletal Ca-ATPase (*)

S. Tatulian, D. Stokes, L. Jones, 1995, The Journal of Biological Chemistry.

Phospholipase A2 activity and physical properties of lipid-bilayer substrates.

O. G. Mouritsen, D. Stokes, K. Jørgensen, 1997, Methods in enzymology.

Faculty Opinions recommendation of Global conformational rearrangements in integrin extracellular domains in outside-in and inside-out signaling.

D. Stokes, 2003 .

Comparison of lymphoblast mitochondria from normal subjects and patients with Barth syndrome using electron microscopic tomography

D. Stokes, M. Schlame, Devrim Acehan, 2007, Laboratory Investigation.

Two-Dimensional Crystallization of Membrane Proteins: Screening Strategies

Z. Zolnai, N. Coudray, D. Stokes, 2014 .

Desmosomes from a structural perspective.

D. Stokes, 2007, Current opinion in cell biology.

Plakoglobin is required for effective intermediate filament anchorage to desmosomes.

D. Stokes, C. Petzold, Devrim Acehan, 2008, The Journal of investigative dermatology.

THROMBOSIS AND HEMOSTASIS Three-dimensional reconstruction of intact human integrin a IIb b 3: new implications for activation-dependent ligand binding

D. Stokes, B. Coller, Won-Seok Choi, 2013 .

Three-dimensional crystals of Ca2+-ATPase from sarcoplasmic reticulum: merging electron diffraction tilt series and imaging the (h, k, 0) projection.

D. Stokes, H. Young, D. Shi, 1998, Journal of molecular biology.

The physical state of lipid substrates provides transacylation specificity for tafazzin.

D. Stokes, R. Epand, M. Schlame, 2012, Nature chemical biology.

Keeping calcium in its place: Ca(2+)-ATPase and phospholamban.

D. Stokes, 1997, Current opinion in structural biology.

Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy

P. Penczek, N. Coudray, D. Stokes, 2012, Proceedings of the National Academy of Sciences.

Structures and mechanism of the plant PIN-FORMED auxin transporter

D. Stokes, B. P. Pedersen, U. Hammes, 2022, Nature.

Co‐reconstitution and Co‐crystallization of Phospholamban and Ca2+‐ATPase a

D. Stokes, H. Young, L. Jones, 1998, Annals of the New York Academy of Sciences.

Two‐Dimensional Crystal Formation from Solubilized Membrane Proteins Using Bio‐Beads to Remove Detergent a

D. Stokes, G. Mosser, J. Rigaud, 1997, Annals of the New York Academy of Sciences.

Highly compacted chromatin formed in vitro reflects the dynamics of transcription activation in vivo.

D. Reinberg, R. Margueron, D. Stokes, 2010, Molecular cell.

Structures of P-type and F-type ion pumps

D. Stokes, R. Nakamoto, 1994 .

Exploring the Nature of Desmosomal Cadherin Associations in 3D

D. Stokes, G. Owen, 2010, Dermatology research and practice.

Toroidal surface complexes of bacteriophage ϕ12 are responsible for host-cell attachment.

Garrett E. Katz, Alejandra Leo-Macias, William J Rice, 2011, Virology.

Structure of the SLC4 transporter Bor1p in an inward‐facing conformation

N. Coudray, D. Stokes, A. Rohou, 2016, Protein science : a publication of the Protein Society.

Membrane invagination in Rhodobacter sphaeroides is initiated at curved regions of the cytoplasmic membrane, then forms both budded and fully detached spherical vesicles

D. Stokes, C. A. Siebert, C. Otto, 2010, Molecular microbiology.

Structure of the calcium pump from sarcoplasmic reticulum at 8-Å resolution

David L. Stokes, Koji Yonekura, Peijun Zhang, 1998, Nature.

Structureof thecalcium pump fromsarcoplasmic reticulumat 8-Å resolution

Peijun Zhang, D. Stokes, N. Green, 2022 .

Electron tomography of paranodal septate‐like junctions and the associated axonal and glial cytoskeletons in the central nervous system

D. Stokes, J. Salzer, A. Nans, 2011, Journal of neuroscience research.

Author ' s personal copy Desmosomes from a structural perspective

D. Stokes, 2007 .

Untangling Desmosomal Knots with Electron Tomography

David L Stokes, D. Stokes, P. Cowin, 2003, Science.

The ATP-binding site of Ca(2+)-ATPase revealed by electron image analysis.

H. Sasabe, D. Stokes, K. Yonekura, 1997, Biophysical journal.

Distinct effects of tafazzin deletion in differentiated and undifferentiated mitochondria.

Ashim Malhotra, David L Stokes, D. Stokes, 2009, Mitochondrion.

A structural model for the catalytic cycle of Ca(2+)-ATPase.

Chen Xu, William J Rice, David L Stokes, 2002, Journal of molecular biology.

Structure of Na+,K+-ATPase at 11-A resolution: comparison with Ca2+-ATPase in E1 and E2 states.

D. Stokes, W. Rice, D. Martin, 2001, Biophysical journal.

Three-Dimensional Structure of the Enveloped Bacteriophage Φ12: An Incomplete T = 13 Lattice Is Superposed on an Enclosed T = 1 Shell

A. Katz, P. Gottlieb, D. Stokes, 2009, PloS one.

The transmembrane domain of the p75 neurotrophin receptor stimulates phosphorylation of the TrkB tyrosine kinase receptor

D. Stokes, M. López-Redondo, M. Chao, 2017, The Journal of Biological Chemistry.

Fourier-Bessel reconstruction of helical assemblies.

William J Rice, David L Stokes, D. Stokes, 2010, Methods in enzymology.

Real-space processing of helical filaments in SPARX.

Guozhi Tao, Stefan Raunser, Pawel A Penczek, 2012, Journal of structural biology.

Image-based model of the spectrin cytoskeleton for red blood cell simulation

Thomas G. Fai, Alejandra Leo-Macias, David L. Stokes, 2017, PLoS Comput. Biol..

Polarized release of TCR-enriched microvesicles at the T cell immunological synapse

David L. Stokes, Michael L. Dustin, Eric W. Roth, 2014, Nature.

Structure of a copper pump suggests a regulatory role for its metal-binding domain.

D. Stokes, W. Rice, Chen-Chou Wu, 2008, Structure.

Purification and analysis of endogenous human RNA exosome complexes

T. Jensen, D. Stokes, M. Rout, 2016, RNA.

Nanoscale Increases in CD2-CD48-mediated Intermembrane Spacing Decrease Adhesion and Reorganize the Immunological Synapse*

Yair Reisner, Mengling Liu, David L Stokes, 2008, Journal of Biological Chemistry.

cardiovascular development Ultrasound biomicroscopy-Doppler in mouse

M. Neeman, D. Turnbull, D. Stokes, 2015 .

The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking.

D. Stokes, T. Cardozo, G. S. Allen, 2011, Structure.

Structural Studies of a Stabilized Phosphoenzyme Intermediate of Ca2+-ATPase*

D. Stokes, W. Rice, F. Delavoie, 2005, Journal of Biological Chemistry.

Locating the thapsigargin-binding site on Ca(2+)-ATPase by cryoelectron microscopy.

D. Stokes, H. Young, C. Xu, 2001, Journal of molecular biology.

Modeling a dehalogenase fold into the 8-A density map for Ca(2+)-ATPase defines a new domain structure.

D. Stokes, N. Green, 2000, Biophysical journal.

Effect of Orthophosphate, Nucleotide Analogues, ADP, and Phosphorylation on the Cytoplasmic Domains of Ca2+-ATPase from Scallop Sarcoplasmic Reticulum*

D. Stokes, P. Hardwicke, C. Ryan, 2004, Journal of Biological Chemistry.

Structure of CaATPase: electron microscopy of frozen-hydrated crystals at 6 A resolution in projection.

D. Stokes, N. Green, 1990, Journal of molecular biology.

P-type ion pumps: structure determination may soon catch up with structure predictions

D. Stokes, 1991 .

Comparison of frozen-hydrated and negatively stained crystals of Ca-ATPase suggests a shape for the intramembranous domain.

D. Stokes, N. Green, 1990, Biochemical Society transactions.

Three-dimensional reconstruction of intact human integrin αIIbβ3: new implications for activation-dependent ligand binding.

D. Stokes, W. Rice, B. Coller, 2013, Blood.

Preparation and analysis of large, flat crystals of Ca(2+)-ATPase for electron crystallography.

D. Stokes, R. C. Pace, D. Shi, 1995, Biophysical journal.

Three-dimensional cryo-electron microscopy of the calcium ion pump in the sarcoplasmic reticulum membrane

H. Sasabe, D. Stokes, C. Toyoshima, 1993, Nature.

Dendritic cell-expressed common gamma-chain recruits IL-15 for trans-presentation at the murine immunological synapse

Michael Loran Dustin, T. Springer, D. Stokes, 2018, Wellcome open research.

Dendritic cell-expressed common gamma-chain recruits IL-15 for trans-presentation at the murine immunological synapse

Michael Loran Dustin, T. Springer, D. Stokes, 2018, Wellcome open research.

Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization.

Z. Zolnai, N. Coudray, D. Stokes, 2015, Journal of structural biology.

Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals.

D. Stokes, W. Rice, K. Altendorf, 2008, Journal of structural biology.

Structure, transmembrane topology and helix packing of P‐type ion pumps

W. Taylor, D. Stokes, N. Green, 1994, FEBS Letters.

Structural basis for Potassium transport by KdpFABC

D. Stokes, B. P. Pedersen, M. Schlame, 2021, bioRxiv.

Serine phosphorylation regulates the P-type potassium pump KdpFABC

H. Erdjument-Bromage, D. Stokes, V. Dubey, 2020, bioRxiv.

The variable twist of actin and its modulation by actin-binding proteins

D. DeRosier, D. Stokes, 1987, The Journal of cell biology.

Secondary structure and orientation of phospholamban reconstituted in supported bilayers from polarized attenuated total reflection FTIR spectroscopy.

S. Tatulian, D. Stokes, L. Tamm, 1995, Biochemistry.

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*

D. Stokes, L. Jones, Zhenhui Chen, 2006, Journal of Biological Chemistry.

Locating phospholamban in co-crystals with Ca(2+)-ATPase by cryoelectron microscopy.

D. Stokes, H. Young, L. Jones, 2001, Biophysical journal.

The KdpFABC complex – K+ transport against all odds

D. Stokes, H. Apell, B. P. Pedersen, 2019, Molecular membrane biology.

Atomic force microscopy of three-dimensionl membr ' iR 6 rt eQY Ca-ATPase of sarcoplasmic reticulum A I l ; 1 8 1992 l

D. Chatenay, D. Stokes, Jean-Jacques Lacap, 2022 .

An introduction to low dose electron tomography-from specimen preparation to data collection

D. Stokes, G. Owen, 2007 .

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP

A. Koide, S. Koide, D. Stokes, 2021, The Journal of general physiology.

Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP

David L Stokes, Nicolas Coudray, N. Coudray, 2018, Proceedings of the National Academy of Sciences.

Modeling, docking, and fitting of atomic structures to 3D maps from cryo-electron microscopy.

David L Stokes, D. Stokes, G. S. Allen, 2013, Methods in molecular biology.

Actin and Flagellar Filaments: Two Helical Structures with Variable Twist

D. Stokes, E. Bullitt, S. Trachtenberg, 1986, Annals of the New York Academy of Sciences.

Structure of Na 1 , K 1-ATPase at 11-Å Resolution : Comparison with Ca 2 1-ATPase in E 1 and E 2 States

D. Stokes, W. Rice, H. Young, 2001 .

Structure and function of the calcium pump.

D. Stokes, N. Green, 2003, Annual review of biophysics and biomolecular structure.

Electron Cryo-Tomographic Structure of Cystovirus φ 12

P. Gottlieb, D. Stokes, W. Rice, 2008 .

Averaging data derived from images of helical structures with different symmetries.

D. DeRosier, D. Stokes, S. Darst, 1999, Journal of molecular biology.

How to make tubular crystals by reconstitution of detergent-solubilized Ca2(+)-ATPase.

D. Stokes, J. Rigaud, H. Young, 1997, Biophysical journal.

Energy Coupling and Stoichiometry of Zn2+/H+ Antiport by the Cation Diffusion Facilitator YiiP

Ian M. Kenney, D. Stokes, M. López-Redondo, 2023, bioRxiv.

3D Tomographic Map of Desmosome from Frozen-hydrated Skin Sections

M. Marko, D. Stokes, C. Hsieh, 2004, Microscopy and Microanalysis.

The Mechanics of Calcium Transport

D. Stokes, H. Young, 2004, The Journal of Membrane Biology.

Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases.

William J Rice, David L Stokes, D. Stokes, 2007, Journal of structural biology.

Conformation of Ca(2+)-ATPase in two crystal forms. Effects of Ca2+, thapsigargin, adenosine 5'-(beta, gamma-methylene)triphosphate), and chromium(III)-ATP on crystallization.

D. Stokes, J. Lacapere, 1994, The Journal of biological chemistry.

Automated electron microscopy for evaluating two-dimensional crystallization of membrane proteins.

Anchi Cheng, James Pulokas, Minghui Hu, 2010, Journal of structural biology.

An intracellular pathway controlled by the N-terminus of the pump subunit inhibits the bacterial KdpFABC ion pump in high K+ conditions

D. Stokes, V. Dubey, H. Khandelia, 2021, bioRxiv.

Present and future of membrane protein structure determination by electron crystallography.

D. Stokes, I. Ubarretxena-Belandia, 2010, Advances in protein chemistry and structural biology.

Lamellar stacking in three-dimensional crystals of Ca(2+)-ATPase from sarcoplasmic reticulum.

D. Stokes, C. Toyoshima, H. Ogawa, 1996, Biophysical journal.