Publications

• Coudray, N., Valvo, S., Hu, M., Lasala, R., Kim, C., Vink, M., Zhou, M., Provasi, D., Filizola, M., Tao, J., Fang, J., Penczek, P.A., Ubarretxena-Belandia, I., Stokes, D.L., 2013. Inward-Facing Conformation of the Zinc Transporter YiiP revealed by Cryo-electron Microscopy, PNAS. In press.

• Allen, G.S., Stokes, D.L. 2013. Modeling, docking and fitting of atomic structures to 3D maps from cryo-electron microscopy. Methods Mol. Biol. 955:229-241.

• Stokes, D.L., Ubarretxena-Belandia, I., Gonen, T., Engel, A. 2013. High-Throughput Methods for Electron Crystallography. Methods Mol. Biol. 955:273-296.

• Schlame, M., Acehan, A., Berno, B., Xu, Y., Valvo, S., Ren, M., Stokes, D.L., Epand, R.M. 2012. The Physical State of Lipid Substrates provides Transacylation Specificity for Tafazzin. Nat. Chem. Biol. 8:862-869. (PDF)

• Phoon, C.K.L., Acehan, D., Schlame, M., Stokes, D.L., 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: jah3-e000455. (PDF)

• Ubarretxena-Belandia, I., Stokes, D.L. 2012. Membrane protein structure determination by electron microscopy. Curr. Opin. Struct. Biol. 22:520-528. (PDF)

• 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. 2012. Structure-function mapping of a heptameric module in the nuclear pore complex. J. Cell Biol. 196:419-434. (PDF)

• Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. 2012. Outcome of the first electron microscopy validation task force meeting. Structure. 20:205-214. (PDF)

• Behrmann, E., Tao, G., Stokes, D.L., Egelman, E.H., Raunser, S., Penczek, P.A. 2012. Real-space processing of helical filaments in SPARX. J. Struct. Biol. 177:302-313. (PDF)

• Nans, A., Mohandas, N., Stokes, D.L. 2011. Native ultrastructure of the red cell cytoskeleton by cryo-electron tomography. Biophys. J. 101:2341-2350. (PDF)

• Allen, G.S. Wu, C., Cardozo, T, Stokes, D.L. 2011. The Architecture of CopA from Archeaoglobus fulgidus Studied by Cryo-Electron Microscopy and Computational Docking. Structure. 19:1219-1232. (PDF)

• Leo-Macias, A., Katz, Wei H, Alimova A, Katz A, Rice WJ, Diaz-Avalos R, Hu GB, Stokes DL, Gottlieb P., 2011. Toroidal surface complexes of bacteriophage ϕ12 are responsible for host-cell attachment. Virology. 414:103-109. (PDF)

• Glaves JP, Trieber CA, Ceholski DK, Stokes DL, Young HS. 2011. Phosphorylation and mutation of phospholamban alter physical interactions with the sarcoplasmic reticulum calcium pump. J. Mol. Biol. 405:707-723. (PDF)

• Acehan D, Malhotra A, Xu Y, Ren M, Stokes DL, Schlame M. 2011. Cardiolipin Affects the Supramolecular Organization of ATP Synthase in Mitochondria. Biophys. J. 100:2184-2192. (PDF)

• Nans A., Einheber S., Salzer J.L., Stokes D.L., 2011. Electron tomography of paranodal septate-like junctions and the associated axonal and glial cytoskeletons in the central nervous system. J. Neurosc. Res. 89:310-319. (PDF)

• Diaz, R., Rice, W.J., Stokes, D.L. 2010. Fourier-Bessel reconstruction of helical assemblies. 2010. Methods Enzmol. 482:131-165. (PDF)

• 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. PMID: 21115172. (PDF)

• 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. PMID: 20665267. (PDF)

• Owen, G.R., Stokes, D.L. 2010. Exploring the nature of desmosomal cadherin associations in 3D. Derm. Res. Practice 2010:1-12 (PDF).

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

• Tucker J.D., Siebert C.A., Escalante M., Adams P.G., Olsen J.D., Otto C., Stokes D.L., Hunter C.N. 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. 76:833-847 (PDF).

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

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

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

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

• Wei, H., Cheng R.H., Berriman, J., Rice, W.J., Stokes, D.L., Katz, A., Morgan, D. G., Gottlieb, P. 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 (PDF)

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

• Milstein O.,S.Y. Tseng, T. Starr, J. Llodra, A. Nans, M. Liu, M.K. Wild, P.A. van der Merwe, D.L. Stokes, Y. Reisner, M.L. Dustin. 2008. Nanoscale increases in CD2-CD48 mediated intermembrane spacing decrease adhesion and reorganize the immunological synapse. J. Biol. Chem. 282:34414-34422. (PDF)

• Acehan, D, C. Petzold, I. Gumper, D.D. Sabatini, E. Muller, P. Cowin and D.L. Stokes. 2008. Plakoglobin is Required for Effective Intermediate Filament Anchorage to Desmosomes. J. Invest. Derm. 128:2665-75 (PDF)

• Wu, C-C., H, Rice, W.J., Stokes, D.L. 2008. Structure of a Copper Pump Suggests a Regulatory Role for its Metal Binding Domain. Structure 16:976-985. (PDF)

• Owen, G.R, Acehan, D., Derr, K.D., Rice, W.J., Stokes, D.L. 2008. Cryoelectron Tomography of Isolated Desmosomes. Biochemical Society Transactions 36 36:173-179. (PDF)

• Hu, G. Wei, H, Rice, W.J., Stokes, D.L. Gottlieb, P. 2008. Electron Cryo-Tomographic Structure of Cystovirus phi12. Virology 372:1-9. (PDF)

• Hu, G., Rice, W.J., Droese, S., Altendorf, K., Stokes, D.L. 2008. Three-dimensional structure for KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals. J. Struct. Biol. 161;411-418. (PDF)

• Stokes, D.L. 2007. Desmosomes From A Structural Perspective. Curr. Op. Cell Biol. 19:565-571. (PDF)

• Owen, G.Rh. Stokes, D.L. 2007. An introduction to low dose electron tomography- from specimen preparation to data collection. In: Modern Research and Educational Topics in Microscopy. Méndez-Vilas, A., Diaz, J. (Eds). , Formatex Research Center, Badajoz, Spain. Vol. 2, pp. 939-950 (PDF)

• Vink, M. Derr, K., Love, J., Stokes, D.L., Ubarretxena-Belandia, I. 2007. A high-throughput strategy to screen 2D crystallization trials of membrane proteins. J. Struct. Biol. 160:295-304. (PDF)

• Acehan, D., Xu, Y., Stokes, D.L., Schlame, M., 2007. Comparison of lymphoblast mitochondria from normal subjects and patients with Barth syndrome using electron microscopic tomography. Lab. Inves. 87: 40-48. (PDF)

• Pomfret, A.J., W.J. Rice, D.L. Stokes, 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. (PDF)

• Rice, W.J., Kovalishin, A., Stokes, D.L., 2006. Role of Metal Binding Domains of the Copper Pump from Archeoglobus fulgidis. Biochem. Biophys. Res. Commun 348:124-31. (PDF)

• Chen, Z., B.L. Akin, D.L. Stokes, L.R. Jones, 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 (PDF)

• Stokes, D.L., A.J. Pomfret, W.J. Rice, J.P. Glaves, H.S. Young, 2006. Interactions Between Ca2+-ATPase and the Pentameric Form of Phospholamban in Two-Dimensional Crystals. Biophys. J. 90:4213-4223. (PDF)

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

• Chen, Z., D.L. Stokes, L.R. Jones, 2005. Role of leucine 31 of phospholamban in structural and functional interactions with the Ca2+ pump of cardiac sarcoplasmic reticulum. J. Biol. Chem. 280:10530-10539 (PDF)

• Hinsen, K., N. Reuter J. Navaza, D.L. Stokes and J.-J. Lacapere, 2005. Normal mode based fitting of atomic structure into electron density maps: application to SR Ca-ATPase. Biophys. J. 88:818-827. (PDF)

• Young, H.S., D.L. Stokes. 2004. The Mechanics of Calcium Transport. J. Membr. Biol. 198:55-63. (PDF)

• Ryan, C., D.L. Stokes, M. Chen, Z. Zhang, P.M.D. Hardwicke. 2004. Effect of orthophosphate, nucleotide analogues, ADP, and phosphorylation on the cytoplasmic domains of Ca2+-ATPase from scallop sarcoplasmic reticulum. J. Biol. Chem. 279:5380-5386. (PDF)

• Chen, Z., D.L. Stokes, W.J. Rice, L.R. Jones. 2003. Spatial and Dynamic Interactions between Phospholamban and the Canine Cardiac Ca2+ Pump Revealed with Use of Heterobifunctional Cross-Linking Agents. J. Biol. Chem. 278:48348-48356 (PDF)

• He, W., P. Cowin, D.L. Stokes. 2003. Untangling Desmosomal Knots with Electron Tomography. Science 302: 109-113 (PDF)

• Delavoie, F., D. McIntosh, F. Henao, G. Peranzi, P. Champeil, D. Stokes, J.-J. Lacapere. 2003. Projection map of covalently phosphorylated Ca-ATPase from tubular crystals. Ann. N.Y. Acad. Sci. 986:17-19 (PDF)

• Stokes, D.L., N.M. Green. 2003. Structure and function of the calcium pump. Ann. Rev. Biophys. Biomolec. Struc. 32:445-468 (PDF)

• Xu, C., W.J. Rice, W. He, D.L. Stokes. 2002. A Structural Model for the Catalytic Cycle of Ca2+-ATPase. J. Mol. Biol.   316:201-211 (PDF)

• Young, H.S., L.R. Jones, D.L. Stokes. 2001. Locating Phospholamban in Co-crystals with Ca2+-ATPase by Cryoelectron Microscopy. Biophys. J.  81:884-894. (PDF)

• Rice, W.J., H.S. Young, D.W. Martin, J.R. Sachs, D.L. Stokes. 2001. Structure of Na+,K+-ATPase at 11A Resolution: Comparison with Ca2+-ATPase in E1 and E2 States. Biophys. J. 80:2187-2197. (PDF)

• Young, H.S., C. Xu, P. Zhang, D.L Stokes. 2001. Locating the Thapsigargin Binding Site on Ca2+-ATPase by Cryoelectron Microscopy. J. Mol. Biol. 308:231-240. (PDF)

• Stokes, D.L., T. Wagenknecht  2000.  Calcium Transport across the Sarcoplasmic Reticulum: Structure and Function of Ca2+-ATPase and the Ryanodine Receptor.  Eur. J. Biochem. 267:5274-5279. (PDF)

• Stokes, D.L., N.M. Green.  2000.  Modeling a Dehalogenase Fold into the 8-Å Density Map for Ca2+-ATPase defines a new Domain Structure.  Biophys. J. 78:1765-1776. (PDF)

• Stokes, D.L., M. Auer, P. Zhang, W. Kuehlbrandt. 1999.  Comparison of H+-ATPase and Ca2+-ATPase suggests that a large conformational change initiates P-type ion pump reaction cycles.  Current Biol. 9:672-679. (PDF)

• DeRosier, D.J., D.L. Stokes, S.A. Darst.  1999.  Averaging data derived from images of helical structures with different symmetries.  J. Mol. Biol. 289:159-165. (PDF)

• Shi, D., M.R. Lewis, H.S. Young, D.L. Stokes.  1998.  Three-dimensional crystals of Ca2+-ATPase from sarcoplasmic reticulum:  Merging electron diffraction tilt series and imaging the (h,k,0) projection.  J. Mol. Biol. 284:1547-1564. (PDF)

• Zhang, P., Toyoshima, C. Yonekura, K. Green, N.M., Stokes, D.L. Stokes. 1998. Structure of the calcium pump from sarcoplasmic reticulum at 8-Å resolution. Nature 392:835-839. (PDF)

• Lacapere, J.-J., D.L. Stokes, A. Olofsson, J.-L. Rigaud.  1998.  Two-dimensional crystallization of Ca-ATPase by detergent removal.  Biophys. J. 75:1319-1329. (PDF)

• Ogawa, H., D.L. Stokes, Sasabe, H., C. Toyoshima.  1998.  Structure of the Ca2+ pump of sarcoplasmic reticulum: a view along the lipid bilayer at 9 A resolution. Biophys. J.  75:41-52. (PDF)

• Young, H.S., J.-L. Rigaud, J.-J. Lacapere, L.G. Reddy, D.L. Stokes. 1997. How to make tubular crystals by reconstitution of detergent-solubilized Ca>2+-ATPase. >Biophys. J.  72 (PDF):2545-2558.

Yonekura, K., D.L. Stokes, H. Sasabe, C. Toyoshima. 1997. The ATP-binding site of Ca2+-ATPase revealed by electron image analysis. Biophys. J. 72:997-1005. (PDF)

• Stokes, D.L. 1997. Keeping calcium in its place: Ca2+-ATPase and phospholamban. Current Opinion Struct. Biol. 7:550-556 (PDF)

• Reddy, L.G., L.R. Jones, R.C. Pace, D.L. Stokes. (1996). Purified, Reconstituted Cardiac Ca2+-ATPase is Regulated by Phospholamban but not by Direct Phosphorylation with Ca2+/Calmodulin-dependent Protein Kinase . J. Biol. Chem. 271:14964-14970. (PDF)

• Cheong, G. W., H.S. Young, H. Ogawa, C. Toyoshima, D.L. Stokes.  1996.  Lamellar stacking in three-dimensional crystals of Ca2+-ATPase from sarcoplasmic reticulum.  Biophys. J. 70:1689-1699. (PDF)

• Tatulian, S.A., L.R. Jones, L.G. Reddy, D.L. Stokes and L.K. Tamm.  1995.  Secondary structure and orientation of phospholamban reconstituted in supported bilayers from polarized attenuated total reflection FTIR spectroscopy.  Biochem.  34:4448-4456. (PDF)

• Reddy, L.G.,  L.R. Jones,  S.E. Cala,  J..J. O'Brian, S.A. Tatulian and D.L. Stokes..  1995.  Functional reconstitution of recombinant phospholamban with rabbit skeletal  Ca2+-ATPase. J. Biol. Chem. 270:9390-9397. (PDF) (PDF)

•  Shi, D., H.-H. Hsiung R.C. Pace and D. L. Stokes.  1995.  Preparation and analysis of large, flat crystals of Ca2+-ATPase for electron crystallography. Biophys. J. 68:1152-1162. (PDF)

• Stokes, D.L., W.R. Taylor, Green, N.M.  1994.  Structure, Transmembrane topology and helix packing of P-type ion pumps.  FEBS Letts346:32-38. (PDF)

• Stokes, D.L. and Nakamoto, R.K. 1994.  Structures of P- and F-type Ion Pumps.  Current Opinion in Struc. Biol. 4:197-203. (PDF)

• Stokes, D.L., Lacapere, J.-L. 1994. Conformation of Ca2+-ATPase in two crystal forms:  effects of Ca2+, thapsigargin, AMP-PCP, and Cr-ATP on crystallization. J. Biol. Chem269:11606-11613. (PDF)

• Toyoshima, C., Sasabe, H., Stokes, D.L. 1993. Three-dimensional cryo-electron microscopy of the calcium ion pump in the sarcoplasmic reticulum. Nature 362:469-471. (PDF)

• Green, N.M. and Stokes, D.L.  1992.  Structural Modelling of P-type ion pumps. Acta Physiol. Scand. 146:59-68.

• Lacapere, J.-J., Stokes, D.L., Chatenay, D. 1992. Atomic force microscopy of three-dimensional membrane protein crystals.  Biophys. J. 63:303-308. (PDF)

• Stokes, D.L. 1991.  P-type Ion Pumps: Structure determination may catch up with structure predictions. Current Opinion Struc. Biol. 1:555-561. (PDF)

• Stokes, D.L. and D.J. DeRosier. 1990. Growth Conditions Control the Size and Order of Actin Bundles In Vitro. Biophys. J. 59:456-465. (PDF)

• Stokes, D.L. and N.M. Green. 1990. The structure of CaATPase: Electron microscopy of frozen hydrated crystals at 6 A resolution in projection. J. Mol. Biol. 213:529-538.

• Stokes, D.L. and N.M. Green. 1990. Three dimensional crystals of CaATPase from sarcoplasmic reticulum: Symmetry and molecular packing. Biophys. J. 57:1-14.

• Stokes, D.L. and D.J. DeRosier. 1987. The variable twist of actin and its modulation by actin-binding proteins. J. Cell Biol. 104:1005-1017. (PDF)

• Tractenberg, S., D. Stokes, E. Bullitt and D. DeRosier. 1986. Actin and flagellar filaments: two helical structures with variable twist. Ann. N.Y. Acad. Sci. 83:88-99.

• Stokes, D.L., N.R. MacIntyre and J.A. Nadel. 1981. Nonlinear increases in diffusing capacity during exercise by seated and supine subjects. J. Appl. Physiol. 51:858-863. (PDF)