Full list of publications available from NIH NCBI:
Selected Publications
Potassium transport by KdpFABC
Sweet ME, Larsen C, Zhang X, Schlame M, Pedersen BP, Stokes DL. Structural basis for potassium transport in prokaryotes by KdpFABC. Proc Natl Acad Sci U S A. 2021 Jul 20;118(29). doi: 10.1073/pnas.2105195118.
Dubey V, Stokes DL, Pedersen BP, Khandelia H. An Intracellular Pathway Controlled by the N-terminus of the Pump Subunit Inhibits the Bacterial KdpFABC Ion Pump in High K+ Conditions. J Mol Biol. 2021 Jul 23;433(15):167008. doi: 10.1016/j.jmb.2021.167008.
Sweet ME, Zhang X, Erdjument-Bromage H, Dubey V, Khandelia H, Neubert TA, Pedersen BP, Stokes DL. Serine phosphorylation regulates the P-type potassium pump KdpFABC. Elife. 2020 Sep 21;9. doi: 10.7554/eLife.55480.
Huang CS, Pedersen BP, Stokes DL. Crystal structure of the potassium-importing KdpFABC membrane complex. Nature. 2017 Jun 29;546(7660):681-685. doi: 10.1038/nature22970.
Zn and Borate transport
Lopez-Redondo M, Fan S, Koide A, Koide S, Beckstein O, Stokes DL. Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP. J Gen Physiol. 2021 Aug 2;153(8). doi: 10.1085/jgp.202112873.
Lopez-Redondo ML, Coudray N, Zhang Z, Alexopoulos J, Stokes DL. Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP. Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):3042-3047. doi: 10.1073/pnas.1715051115.
Coudray N, L Seyler S, Lasala R, Zhang Z, Clark KM, Dumont ME, Rohou A, Beckstein O, Stokes DL. Structure of the SLC4 transporter Bor1p in an inward-facing conformation. Protein Sci. 2017 Jan;26(1):130-145. doi: 10.1002/pro.3061.
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. 2013 Feb 5;110(6):2140-5. doi: 10.1073/pnas.1215455110.
2D crystallization
Coudray N, Lasala R, Zhang Z, Clark KM, Dumont ME, Stokes DL. Deducing the symmetry of helical assemblies: Applications to membrane proteins. J Struct Biol. 2016 Aug;195(2):167-178. doi: 10.1016/j.jsb.2016.05.011.
Lasala R, Coudray N, Abdine A, Zhang Z, Lopez-Redondo M, Kirshenbaum R, Alexopoulos J, Zolnai Z, Stokes DL, Ubarretxena-Belandia I. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. J Struct Biol. 2015 Feb;189(2):123-34. doi: 10.1016/j.jsb.2014.11.008.
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. 2010 Jul;171(1):102-10. doi: 10.1016/j.jsb.2010.02.018.
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. 2007 Dec;160(3):295-304. doi: 10.1016/j.jsb.2007.09.003.
Lacapère JJ, Stokes DL, Olofsson A, Rigaud JL. Two-dimensional crystallization of Ca-ATPase by detergent removal. Biophys J. 1998 Sep;75(3):1319-29. doi: 10.1016/S0006-3495(98)74050-0.
Young HS, Rigaud JL, Lacapère JJ, Reddy LG, Stokes DL. How to make tubular crystals by reconstitution of detergent-solubilized Ca2+-ATPase. Biophys J. 1997 Jun;72(6):2545-58. doi: 10.1016/S0006-3495(97)78898-2.
Cellular tomography
Choudhuri K, Llodrá 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. 2014 Mar 6;507(7490):118-23. doi: 10.1038/nature12951.
Nans A, Mohandas N, Stokes DL. Native ultrastructure of the red cell cytoskeleton by cryo-electron tomography. Biophys J. 2011 Nov 16;101(10):2341-50. doi: 10.1016/j.bpj.2011.09.050.
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 ϕ12 are responsible for host-cell attachment. Virology. 2011 Jun 5;414(2):103-9. doi: 10.1016/j.virol.2011.03.020.
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. 2009 Apr;9(2):86-95. doi: 10.1016/j.mito.2008.12.001.
Acehan D, Petzold C, Gumper I, Sabatini DD, Müller EJ, Cowin P, Stokes DL. Plakoglobin is required for effective intermediate filament anchorage to desmosomes. J Invest Dermatol. 2008 Nov;128(11):2665-2675. doi: 10.1038/jid.2008.141.
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. 2007 Jan;87(1):40-8. doi: 10.1038/labinvest.3700480.
He W, Cowin P, Stokes DL. Untangling desmosomal knots with electron tomography. Science. 2003 Oct 3;302(5642):109-13. doi: 10.1126/science.1086957.
P-Type ATPases
Allen GS, Wu CC, Cardozo T, Stokes DL. The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking. Structure. 2011 Sep 7;19(9):1219-32. doi: 10.1016/j.str.2011.05.014.
Glaves JP, Trieber CA, Ceholski DK, Stokes DL, Young HS. Phosphorylation and mutation of phospholamban alter physical interactions with the sarcoplasmic reticulum calcium pump. J Mol Biol. 2011 Jan 21;405(3):707-23. doi: 10.1016/j.jmb.2010.11.014.
Wu CC, Rice WJ, Stokes DL. Structure of a copper pump suggests a regulatory role for its metal-binding domain. Structure. 2008 Jun;16(6):976-85. doi: 10.1016/j.str.2008.02.025.
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. 2006 Jun 1;90(11):4213-23. doi: 10.1529/biophysj.105.079640.
Stokes DL, Delavoie F, Rice WJ, Champeil P, McIntosh DB, Lacapère JJ. Structural studies of a stabilized phosphoenzyme intermediate of Ca2+-ATPase. J Biol Chem. 2005 May 6;280(18):18063-72. doi: 10.1074/jbc.M500031200.
Xu C, Rice WJ, He W, Stokes DL. A structural model for the catalytic cycle of Ca(2+)-ATPase. J Mol Biol. 2002 Feb 8;316(1):201-11. doi: 10.1006/jmbi.2001.5330.
Rice WJ, Young HS, Martin DW, Sachs JR, Stokes DL. Structure of Na+,K+-ATPase at 11-A resolution: comparison with Ca2+-ATPase in E1 and E2 states. Biophys J. 2001 May;80(5):2187-97. doi: 10.1016/S0006-3495(01)76191-7.
Stokes DL, Auer M, Zhang P, Kühlbrandt W. Comparison of H+-ATPase and Ca2+-ATPase suggests that a large conformational change initiates P-type ion pump reaction cycles. Curr Biol. 1999 Jul 1;9(13):672-9.
Shi D, Lewis MR, Young HS, Stokes DL. Three-dimensional crystals of Ca2+-ATPase from sarcoplasmic reticulum: merging electron diffraction tilt series and imaging the (h, k, 0) projection. J Mol Biol. 1998 Dec 18;284(5):1547-64. doi: 10.1006/jmbi.1998.2283.
Zhang P, Toyoshima C, Yonekura K, Green NM, Stokes DL. Structure of the calcium pump from sarcoplasmic reticulum at 8-A resolution. Nature. 1998 Apr 23;392(6678):835-9. doi: 10.1038/33959.
Toyoshima C, Sasabe H, Stokes DL. Three-dimensional cryo-electron microscopy of the calcium ion pump in the sarcoplasmic reticulum membrane. Nature. 1993 Apr 1;362(6419):467-71. doi: 10.1038/362469a0.