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A.  Methodology and technology development

Buban, J. P., Ramasse, Q. M., Gipson, B., Browning, N., Stahlberg, H. (2009). Towards high-resolution low-dose scanning transmission electron microscopy. Journal of Electron Microscopy, Submitted.

Chae, P. S.,Gotfryd, K., Pacyna, J., Miercke, L. J., Rasmussen, S. G.,Robbins, R. A., Rana, R. R, Loland, CJ, Kobilka, B, Stroud, R, Byrne, B, Gether, U, Gellman, S. H. (2010) Tandem facial amphiphiles for membrane protein stabilization. J Am Chem Soc 132, 16750-2. PMC3050673

Chapman, H. N., Fromme, P., Barty, A., White, T. A., Kirian, R. A., Aquila, A., Hunter,
M. S., Schulz, J., DePonte, D. P., Weierstall, U., Doak, R. B., Maia, F. R. N. C., Martin, A. V., Schlichting, I., Lomb, L., Coppola, N., Shoeman, R. L., Epp, S. W., Hartmann, R., Rolles, D., Rudenko, A., Foucar, L., Kimmel, N., Weidenspointner, G., Holl, P., Liang, M., Barthelmess, M., Caleman, C., Boutet, S., Bogan, M. J., Krzywinski, J., Bostedt, C., Bajt, S., Gumprecht, L., Rudek, B., Erk, B., Schmidt, C., Homke, A., Reich, C., Pietschner, D., Struder, L., Hauser, G., Gorke, H., Ullrich, J., Herrmann, S., Schaller, G., Schopper, F., Soltau, H., Kuhnel, K.-U., Messerschmidt, M., Bozek, J. D., Hau-Riege, S. P., Frank, M., Hampton, C. Y., Sierra, R. G., Starodub, D., Williams, G. J., Hajdu, J., Timneanu, N., Seibert, M. M., Andreasson, J., Rocker, A., Jonsson, O., Svenda, M., Stern, S., Nass, K., Andritschke, R., Schroter, C.-D., Krasniqi, F., Bott, M., Schmidt, K. E., Wang, X., Grotjohann, I., Holton, J. M., Barends, T. R. M., Neutze, R., Marchesini, S., Fromme, R., Schorb, S., Rupp, D., Adolph, M., Gorkhover, T., Andersson, I., Hirsemann, H., Potdevin, G., Graafsma, H., Nilsson, B. & Spence, J. C. H. (2011). Femtosecond X-ray protein nanocrystallography, Nature 470, 73-77. PMID: 21293373.

Dvir, H. Lundberg, M., Maji, S., Riek, R., Choe, S. (2009) Mistic: cellular localization, solution behavior, polymerization, and fibril formation. Protein Sci. 18, 1564-70. PMCID PMC2775223

Dvir, H., Choe, S. (2009) Bacterial expression of a eukaryotic membrane protein in fusion to various Mistic orthologs. Protein Expr Purif. PMCID: PMC2728152

Evans, J.E., Hetherington, C., Kirkland, A., Chang, L.-Y., Stahlberg, H., Browning, N. (2008). Low-dose aberration corrected cryo-electron microscopy of organic/biological specimens. Ultramicroscopy, 108(12), 1636-1644 PMID: 18703285/ PMCID: PMC2758313

Gipson, B., Zeng, X., and Stahlberg, H. (2007). 2dx_merge – Data management and merging for 2D crystal images, J. Struct. Biol., 160(3), 375-384. PMC2157552

Gipson, B., Zeng, X., Zhang, Z.Y., and Stahlberg, H. (2007) 2dx – User-friendly image processing for 2D crystals. J. Struct. Biol. 157: 64-72. PMID: 17055742

Gipson, B., Zeng, X. Stahlberg, H. (2008) Automated 3D structure reconstruction from 2D crystal data. Microscopy and Microanalysis 14(Suppl. 2), 1290-1291. PMID: 18674228

Guan, L., Smirnova, I.N., Verner, G., Nagamoni, S. and Kaback, H.R. (2006) Manipulating phospholipids for crystallization of a membrane transport protein. Proc Natl Acad Sci USA, 103, 1723-1726. PMID: 16446422/PMCID: PMC1413674

Guan, L. and Kaback, H.R. (2007) Site-directed alkylation of cysteine to test solvent accessibility. Nature Protocols, 2(8):2012-7. PMID: 17703213/ PMCID: PMC2775809

Hammon, J., Palanivelu, D.V., Chen, J., Patel, C., and Minor, D.L., Jr. (2009) A green fluorescent protein screen for identification of well-expressed membrane proteins from a cohort of extremophilic organisms. Protein Science 18 121-133. PMID: 19177357/ PMCID : PMC2708023 (Rated 'Recommended' by Faculty of 1000)

Hankamer B, Glaeser R, Stahlberg H. (2007) Electron crystallography of membrane proteins. J Struct Biol 160:263-4. PMCID: PMC2170452

Hays F, Roe-Zurz Z, Stroud R. M. (2010) Overexpression and Purification of Integral Membrane Proteins in Yeast Methods in Enzymology Chapter 29 p 697-709. PMID: 20946832.

Ho BK, Gruswitz F. (2008) (Stroud Lab) HOLLOW: generating accurate representations of channel and interior surfaces in molecular structures. BMC Struct Biol 8:49. PMID: 19014592/ PMC 2603037

Holton, J. M. (2007). XANES measurements of the rate of radiation damage to selenomethionine side chains. J. Synchrotron Radiation 14 51-72. PMID: 17211072/ PMCID: PMC2806430

Holton, J. M. (2009). A beginner's guide to radiation damage. J. Synchrotron Radiation 16: 133-142. PMID:19240325/ PMCID: PMC2651760

Holton JM and Kenneth A. Frankel. (2010) The minimum crystal size needed for a complete diffraction data set Acta Cryst.. D66, 393–408. PMID: 20382993

Howells, M. R., Beetz, T., Chapman, H. N., Chi, C., Holton, J. M., Jacobsen, C. J., Kirz, J., Lima, E., Marchesini, S., Miao, H., Sayre, D., Shapiro, D. A., Spence, J. C. H. and Starodub, D. (2008). An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy. J. Electron Spectroscopy and Related Phenomena 170: 4-12.

Kefala, G., Kwiatkowski, W. Esquivies, L., Maslennikov, I., Choe, S. (2007) Application of Mistic to improving the expression and membrane integration of histidine kinase receptors from Escherichia coli.J Struct Funct Genomics 8(4), 167-72. PMID: 17985211

Kirian RA, White TA, Holton JM, Chapman HN, Fromme P, Barty A, Lomb L, Aquila A, Maia FR, Martin AV, Fromme R, Wang X, Hunter MS, Schmidt KE, Spence JC. (2011) Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals. Acta Crystallogr A. 67(Pt 2):131-40. PMID: 21325716/PMCID: PMC3066792

Klammt C, Perrin MH, Maslennikov I, Renault L, Krupa M, Kwiatkowski W, Stahlberg H, Vale W, Choe S. (2011) Polymer-based cell-free expression of ligand-binding family B G-protein coupled receptors without detergents. Protein Sci. 20(6):1030-41. Doi: 10.1002/pro. 636. PMID: 21465615/ PMCID: PMC3104232

Lasker K, Phillips JL, Russel D, Velazquez-Muriel J, Schneidman-Duhovny D, Webb B, Schlessinger A, Sali A. (2010) Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data. Mol Cell Proteomics 9, 1689-1702. PMC2938050

Maslennikov, I., Kefala, G., Johnson, C., Riek, R., Choe, S., Kwiatkowski, W. (2007) NMR spectroscopic and analytical ultracentrifuge analysis of membrane protein detergent complexes. BMC Struct Biol. 7,74. PMID: 17988403/ PMC 2219997

Maslennikov, I., Krupa, M., Dickson, C., Esquivies, L., Blain, K., Kefala, G., Choe, S., Kwiatkowski, W. (2009). Characterization of protein detergent complexes by NMR, light scattering, and analytical ultracentrifugation. J Struct Funct Genomics 10(1), 25-35. NIHMSID: NIHMS113234.

Newby ZE, O'Connell JD 3rd, Gruswitz F, Hays FA, Harries WE, Harwood IM, Ho JD, Lee JK, Savage DF, Miercke LJ, Stroud RM. (2009). A general protocol for the crystallization of membrane proteins for X-ray structural investigation. Nat Protoc. 4(5):619-37. PMID: 19360018

Owen, R. L., Holton, J. M., Schulze-Briese, C. and Garman, E.F. (2009). Determination of X-ray flux using silicon pin diodes. J. Synchrotron Radiation 16: 143-151. PMID: 19240326/ PMCID: PMC2651761

Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. (2009) MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research 37, D347-54. PMID: 18948282/ PMC 2686492

Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A. (2011) ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 39(Database issue):D465-74. PMID: 21097780/ PMCID: PMC3013688

Savage D.F., Anderson C.L., Robles-Colmenares Y., Newby Z.E., Stroud R.M. (2007). Cell-free complements in vivo expression of the E. coli membrane proteome. Protein Sci. 16, 966-76. PMCID: PMC2206641

Schlessinger A., Geier, E.,  Fan, H., Irwin, J., Shoichet,  B., Giacomini, K., Sali, A. (2011) Structure-based Discovery of Prescription Drugs that Interact with the Norepinephrine Transporter, NET. Proc Natl Acad Sci USA 108, 15810-15815,. PMCID3179104

Spence, J. C. H., Kirian, R. A., Wang, X., Weierstall, U., Schmidt, K. E., White, T., Barty, A., Chapman, H. N., Marchesini, S. & Holton, J. (2011)."Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals", Opt. Express 19, 2866-2873. PMID: 21369108 [PubMed - in process]

Vinchurkar, M.S., Bricarello, D., Lagerstedt, J., Buban, J.P., Stahlberg, H., Voss, J.C., and Parikh, A.N. (2008). Bridging across length scales: Multiscale ordering of supported lipid bilayers via lipoprotein co-assembly and surface patterning. Journal of the American Chemical Society 130(33): 11164-11169. PMID: 18642906

Zeng, X., Gipson, B., Zheng, Z.Y., Renault, L., and Stahlberg, H. (2007). Automatic lattice determination for two-dimensional crystal images. J. Struct. Biol., 160(3), 353-361. (PMCID: PMC2265636).

Zeng, X., Stahlberg, H., Grigorieff, N.A. (2007). A maximum likelihood approach to two-dimensional crystals. J. Struct. Biol., 160(3), 362-374. (PMCID: PMC2147720).

B. Structures

Chaudhary, S., Pak, J.E., Gruswitz, F., Sharma, V., Stroud, R.M. (2012). Overexpressing Human Membrane Proteins in Stably Transfected and Clonal Human Embryonic Kidney 293S Cells. Nature Protocols 7 453-466. (PMID: 22322218)

Rosenberg, O.S., Dovey, C., Tempesta, M., Robbins, R.A., Finer-Moore, J.S., Stroud, R.M., Cox, J.S. (2011). EspR, a key regulator of Mycobacterium tuberculosis virulence, adopts a unique dimeric structure among helix-turn-helix proteins. Proc Natl Acad Sci U S A.108, 13450-5. (PMCID: PMC3158157)

Egea, P.F., Muller-Steffner, H., Kuhn, I., Cakir-Kiefer, C., Oppenheimer, N.J., Stroud, R.M., Kellenberger, E., Schuber, F. (2012). Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its michaelis complex and covalently-trapped intermediates. PLoS One 7(4):e34918. (PMCID: PMC3329556)

Metzger, L.E., Lee, J.K., Finer-Moore, J.S., Raetz, C.R., Stroud, R.M. (2012). LpxI structures reveal how a lipid A precursor is synthesized. Nat Struct Mol Biol 19: 1132-1138. (PMCID: PMC3562136)

Pedersen, B.P., Kumar, H., Waight, A.B., Risenmay, A., Roe-Zurz, Z., Chau, B., Schlessinger, A., Harries, W., Sali, A., Johri, A.K., Stroud, R.M. (2013). Crystal structure of a eukaryotic phosphate transporter. Nature. (PMID: 23542591)

Waight, A.B., Pedersen, B.P., Schlessinger, A., Bonomi, M., Chau, B.H., Roe-Zurz, Z., Risenmay, A.J., Sali, A., Stroud, R.M. (2013). Structural Basis for Alternating Access of a Eukaryotic Calcium/Proton Exchanger Nature. (in press)

Baker, K. A., Tzitzilonis, C., Kwiatkowski, W., Choe, S., and Riek, R. (2007). Conformational dynamics of the KcsA potassium channel governs gating properties. Nat. Struct. Mol. Biol 14, 1089-1095. PMID: 17922011

Chiu, P.-L., Pagel, M., Evans, J., Chou, H.-T., Zeng, X., Gipson, B., Stahlberg, H.*, Nimigean, C.* (2007) * both are corresponding authors. The structure of the prokaryotic cyclic nucleotide-modulated potassium channel MloK1 at 16Å resolution. Structure, 15(9): 1053-1064. PMCID: PMC2000844 (This article was accompanied by a "Preview") Taraska, J.W., and Zagotta, W.N. (2007). Cyclic nucleotide-regulated ion channels: Spotlight on symmetry. Structure, 15(9): 1023-1024.

De Angelis F, Lee JK, O'Connell JD, 3rd, Miercke LJ, Verschueren KH, Srinivasan V, Bauvois C, Govaerts C, Robbins RA, Ruysschaert JM, Stroud RM, Vandenbussche G.. (2010) Metal-induced conformational changes in ZneB suggest an active role of membrane fusion proteins in efflux resistance systems. Proc Natl Acad Sci USA.107, 11038-43. PMCID: PMC2890744.

Egea, P.F., and Stroud, R.M. (2010) Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes. Proc Natl Acad Sci USA 107, 17182-7. PMCID: PMC2951439.

Gruswitz F., O'Connell J., 3rd, Stroud R.M. (2007). Proc Natl Acad Sci USA 104, 42-47. Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A. PMID: 17190799/ PMCID: PMC1765473

Gruswitz F, Chaudhary S, Ho J, Schlessinger A, Bobak P, Ho C, Sali A, Westhoff C, Stroud R. (2010). Function of Human Rh based on Structure of RhCG at 2.1 Å. Proc. Natl. Acad. Sci. U. S. A. 107, 9638-9643. PMCID: PMC2906887

Guan L, Mirza O, Verner G, Iwata S, Kaback HR. (2007). Structural determination of wild-type lactose permease. Proc Natl Acad Sci USA. 104(39): 15294-8. Epub Sep 19. PMID: 17881559/ PMCID: PMC2000551

Harrington, J., Chou, H.-T., Gutsmann, T., Gelhaus, C., Stahlberg, H., Leippe, M., Armstrong, P. (2008) Membrane pore formation by pentraxin proteins from the American horshoe crab, Limulus. Biochemical J., PMID: 18370931

Ho JD, Yeh R, Sandstrom A, Chorny I, Harries WEC, Robbins RA, Miercke LJW, Stroud RM. (2009). Crystal Structure of Human Aquaporin 4 at 1.8Å and its Mechanism of Conductance. Proc Natl Acad Sci. PMID: 19383790/PMCID: PMC2678640

Kefala, G., Ahn, C., Krupa, M., Esquivies, L., Maslennikov, I., Kwiatkowski, W., Choe, S. (2010). Structures of the OmpF porin crystallized in the presence of foscholine-12. Protein Sci. 19(5), 1117-25. PMID: 2019607

Khademi S, Stroud RM. (2006). The Amt/MEPRh family: structure of AmtB and the mechanism of ammonia gas conduction. Physiology (Bethesda). 21:419-29. PMID: 17119155

Lee JK, Belogrudov GI, Stroud RM. (2008) Crystal structure of bovine mitochondrial factor B at 0.96-A resolution. Proc Natl Acad Sci USA. 105(36):13379-84. PMID: 18768789

Lee, J.K., Kozono, D., Remis, J., Kitagawa, Y., Agre, P., Stroud, R.M. (2005) Structural Basis for Conductance by the Archaeal Aquaporin AQPM at 1.68 Å. Proc. Nat Acad Sci USA 102, 18932-7. PMCID: PMC1323191

Maslennikov, I., Klammt, C., Hwang, E., Kefala, G., Okamura, M., Esquivies, L., Mörs, K., Glaubitz, C., Kwiatkowski, W., Jeon, Y.H., Choe, S. (2010) Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis. Proc Natl Acad Sci USA. 107(24):10902-7, PMCID: PMC2890740.

Menuz K., Stroud R.M., Nicoll R.A., Hays F.A. (2007). TARP auxiliary subunits switch AMPA receptor antagonists into partial agonists. Science. 318, 815-7. PMID: 17975069

Newby ZER, O'Connell III J, Robles-Colmenares Y, Khademi S, Miercke LJ, Stroud RM. (2008) Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum. Nature Structural and Molecular Biology, 15:6, 619-625. PMID: 18500352/ PMC2568999

Reyes C.L., Rutenberger E. Walter P., Stroud R.M. (2007). X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates. PLoS ONE. 11, e607. PMCID: PMC1904258

Rho, B. S., Hung, L. W., Holton, J. M., Vigil, D., Kim, S. I., Park, M. S., Terwilliger, T. C. and Pedelacq, J. D. (2006). Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis.J. Mol. Biol. 361: 850-863. PMID: 16884737

Savage DF, O'Connell JD, 3rd, Miercke LJ, Finer-Moore J, Stroud RM. (2010) Structural context shapes the aquaporin selectivity filter. Proc Natl Acad Sci USA. 107, 17164-9. PMCID: 2951435.

Shrive, A. K., Burns, I., Chou, H-T., Stahlberg, H., Armstrong, P. B., Greenhough, T. J. (2009) Crystal structures of Limulus SAP-like pentraxin reveal two molecular aggregations. J. Molec. Biol. 286, 1240-1254. PMID: 19452596

Vilar, M., Chou, H-T., Luehr, T., Maji, S.K., Riek-Loher, D., Verel, R., Manning, G., Stahlberg, H., Riek, R. (2008) The fold of α-Synuclein fibrils. PNAS, 105(25), 8637-8642 PMID: 18550842/ PMCID: PMC 2438424

Xie, W., Dickson, C., Kwiatkowski, W., Choe, S. (2010) Structure of the Cytoplasmic Segment of Histidine Kinase Receptor QseC, a Key Player in Bacterial Virulence. Protein Pept. Lett. Epub ahead of print, PMID: 20594156

C. Methodology and technology development

Classen, S., Hura, G.L., Holton, J.M., Rambo, R.P., Rodic, I., McGuire, P.J., Dyer, K., Hammel, M., Meigs, G., Frankel, K.A., Tainer, J.A. (2013). Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. Journal of Applied Crystallography 46, 1-13. (PMCID: PMC3547225)

Wittwer, M.B., Zur, A.A., Khuri, N., Kido, Y., Kosaka, A., Zhang, X., Morrissey, K.M., Sali, A., Huang, Y., Giacomini, KM. (2013). Discovery of Potent, Selective Multidrug and Toxin Extrusion Transporter 1 (MATE1, SLC47A1) Inhibitors Through Prescription Drug Profiling and Computational Modeling. J Med Chem. 56, 781-795. (PMID: 23241029/PMCID: in process)

Holton, J.M., Nielsen, C., Frankel, K.A. (2012). The point-spread function of fiber-coupled area detectors. Journal of synchrotron radiation 19, 1006-1011. (PMCID: PMC3480276)

Klammt, C., Maslennikov, I., Bayrhuber, M., Eichmann, C., Vajpai, N., Chiu, E., Blain, K., Esquivies, L., Kwon, H., Balana, B., Pieper, U., Sali, A., Slesinger, P., Kwiatkowski, W., Rick, R., Choe, S. (2012). Facile Backbone structure determination of human membrane proteins by NMR spectroscopy. Nat Methods 8, 834-839. (PMID: 22609626/PMCID TBD by Journal)

D. Other

Schlessinger, A., Wittwer, M.B., Dahlin, A., Khuri, N., Bonomi, M., Fan, H., Giacomini, K., Sali, A. (2012). High Selectivity of the γ-Aminobutyric Acid Transporter 2 (GAT-2, SLC6A13) Revealed by Structure-based Approach. J. Biol. Chem. 287, 37745-37756. (PMCID3488050)

Wu, S., Avila-Sakar, A., Kim, J., Booth, D.S., Greenberg, C.H., Rossi, A., Liao, M., Li, X., Alian, A., Griner, S.L., Juge, N., Yu, Y., Mergel, C.M., Chaparro-Riggers, J., Strop, P., Tampe, R., Edwards, R.H., Stroud, R.M., Craik, C.S., Cheng, Y. (2012) Fabs enable single particle cryoEM studies of small proteins. Structure 20: 582-92. PMCID: PMC3322386

Varrin-Doyer, M., Spencer, C.M., Schulze-Topphoff, U., Nelson, P.A., Stroud, R.M., Cree, B.A., Zamvil, S.S. (2012). Aquaporin 4-specific T cells in neuromyelitis optica exhibit a Th17 bias and recognize Clostridium ABC transporter. Ann Neurol 72: 53-64. (PMCID: PMC3405197)

Pieper, U., Schlessinger, A., Kloppmann, E., Chang, G.A., Chou, J.J., Dumont, M.E., Fox, B.G., Fromme, P., Hendrickson, W.A., Malkowski, M.G., Rees, D.C., Stokes, D.L., Stowell, M.H., Wiener, M.C., Rost, B., Stroud, R.M., Stevens, R.C., Sali, A. (2013). Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nat Struct Mol Biol 20: 135-8. (PMID: 23381628/PMCID: in process).

Petrov, E., Palanivelu, D., Nomura, T., Constantine, M., Rohde, P.R., Cox, C.D., Minor, D.L. Jr, Martinac, B. Patch-clamp characterization of the MscS-like mechanosensitive channel from Silicibacter pomeroyi. Biophysical Journal. (In Press)

Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Rout MP, Sali A. (2007) Determining the architectures of macromolecular assemblies. Nature 450: 683-94, (a). PMID: 18046405

Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Sali A, Rout MP. (2007) The molecular architecture of the nuclear pore complex. Nature 450, 695-701. PMID: 18046406

Blain KY, Kwiatkowski W, and Choe S. (2010) The functionally active Mistic-fused histidine kinase receptor, EnvZ. Biochemistry. 49, 9089-95. PMID 20849081

Chen Y., S. Zhang, M. Sorani, and K.M. Giacomini, (2007). Transport of Paraquat by Human Organic Cation Transporters and Multidrug and Toxic Compound Extrusion Family. J Pharmacol Exp Ther. 322(2):695-700. PMID:17495125

Chen Y, Teranishi K, Li S, Yee SW, Hesselson S, Stryke D, Johns SJ, Ferrin TE, Kwok P, Giacomini KM. (2009). Genetic variants in multidrug and toxic compound extrusion-1, hMATE1, alter transport function. Pharmacogenomics J. 9 (2):127-36. PMCID: PMC2949062

Chen L, Pawlikowski B, Schlessinger A, More S, Stryke D, Johns SJ, Portman M, Ferrin TE, Sali A, Giacomini K. (2010). (2010) Role of organic cation transporter 3 (SLC22A3) and Its missense variants in the pharmacologic action of metformin. Pharmacogenet Genomics 20, 687-699. PMCID: PMC2976715

Chen L, Takizawa M, Chen E, Schlessinger A, Choi JH, Segenthelar J, Sali A, Kubo M, Nakamura S, Iwamoto Y, Iwasaki N, Giacomini KM. (2010). Genetic polymorphisms in the organic cation transporter 1, ODT1, in Chinese and Japanese populations, exhibit altered function. J Pharmacol Exp Ther, 1, 42-50. PMC2957788

Chou, H.-T., Evans, J.E., and Stahlberg, H. (2006) Electron Crystallography of Membrane Proteins In: Methods in Molecular Biology: Electron Microscopy Methods and Protocols, Humana Press Totowa, New Jersey, Chapter 16, 331-343

DeVay RM, Dominguez-Ramirez L, Lackner LL, Hoppins S, Stahlberg H, Nunnari J. (2009) Coassembly of Mgm1 isoforms requires cardiolipin and mediates mitochondrial inner membrane fusion. J Cell Biol.;186(6):793-803. PMID: 19752025 [PubMed - indexed for MEDLINE]

Di Luccio, E., Petschacher, B., Voiegtli, J., Chou, H.-T., Stahlberg, H., Nidetzky, B., and Wilson, D.K. (2007) X-ray structural and kinetic studies of induced fit in xylulose kinase from E. coli. J. Mol. Biol. 365, 783-798. PMID: 17925435/ PMCID: PMC1995121

Eramian D, Eswar N, Shen M, Sali A. (2008) How well can the accuracy of comparative protein structure models be predicted? Protein Sci 17:1881-93. PMCID: PMC2578807

Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B. (2008) Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics 27;9:249. PMID: 18505562

Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. (2003) Tools for comparative protein structure modeling and analysis. Nucleic Acids Research 31, 3375-3380.

Evans, J.E., Renault, L., and Stahlberg, (2008). Structure determination using electron crystallography A review as contribution for an electronic textbook on DVD. Editors: Elena Orlova, Arie Verkleij, and Andrew Leis, 3DEM Network of Excellence (NoE)

Garcia-Celma JJ, IN Smirnova, HR Kaback, K Fendler. (2009). Electrophysiological characterization of LacY. Proc Natl Acad Sci USA. 106(18):7373-8. PMCID: PMC2671326

Garcia-Celma JJ, J, Ploch, I Smirnova, HR Kaback, K Fendler. (2010). Delineating electrogenic reactions during lactose/H+ symport. Biochemistry. 49(29):6115-21. PMCID: PMC2907097

Guan, L. and Kaback, H.R. (2005) Lessons from Lactose Permease. Annu Rev Biophys Biomol Struct. (PMID: 16343049)
Guan L, HR Kaback. (2009). Properties of a LacY efflux mutant. Biochemistry. 48(39):9250-5. PMCID: PMC2754601

Hankammer, B., Glaeser, B., Stahlberg, H. (2007). Editorial, Special issue on Electron crystallography of membrane proteins. J. Struct. Biol., 160(3): 263-264, PMCID: PMC2170452

Harrington, J., Chou, H.-T., Gutsmann, T., Gelhaus, C., Stahlberg, H., Leippe, M., Armstrong, P. (2008). Membrane pore formation by pentraxin proteins from the American horshoe crab, Limulus Biochemical J., PMID:18370931

Harrington, J.M., Chou, H.-T., Gutsmann, T., Gelhaus, C., Stahlberg, H., Leippe, M., Armstrong, (2009) Membrane activity of C-reactive protein. P.B. FEBS Letters. PMID: 19230837

Hays FA, Roe-Zurz Z, Li M, Kelly L, Gruswitz F, Sali A, Stroud RM. (2009). Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination. Journal of Structural and Functional Genomics 10, 9-16. PMID: 19031011/ NIHMSID 136939

Jiang X, Nie Y, Kaback HR. (2011) Site-directed alkylation studies with LacY provide evidence for the alternating access model of transport. Biochemistry 50(10):1634-40. PMID: 21254783/ PMCID: PMC3057939

Kaback HR, Smirnova I, Kasho V, Nie Y, Zhou Y. (2011) The alternating access transport mechanism in LacY. J Membr Biol. 239(1-2):85-93. PMID: 21161516/ PMCID: PMC3030946

Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz D, Giacomini KM, Stroud RM, Sali A. (2009) A survey of integral alpha-helical membrane proteins. J Struct Funct Genomics 10, 269-280. PMC2780624

Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. (2010). Functional Hot Spots in Human ABC Transporter Nucleotide Binding Domains. Protein Sci, 19, 2110-2121, 2010. PMC3005782.

Kelly L., Karchin R., Sali A. (2007) Protein interactions and disease phenotypes in the ABC transporter superfamily. Pacific Symposium on Biocomputing. (PMID 17990484).

Khademi S, Stroud RM. (2006). The Amt/MEPRh family: structure of AmtB and the mechanism of ammonia gas conduction. Physiology (Bethesda). 21:419-29. (PMID: 17119155)

Kroetz D. L., Ahituv N., Burchard E. G., Guo S., Sali A., and Giacomini K M.( 2009) The Pharmacogenomics Center of the University of California, San Francisco: At the interface of genomics, biological mechanism and drug therapy. Pharmacogenomics, 10, 1569-1576. PMC2923222.

Lee JK, Stroud RM. (2010) Unlocking the eukaryotic membrane protein structural proteome. Curr Opin Struct Biol 20, 464-70. PMID: 20739007 [PMCID – in process].

Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD 3rd, Miercke LJ, Giacomini KM, Sali A, Stroud RM. (2009) Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. Journal of Molecular Biology 385, 820-30. PMC2659619

Liu Z, MG Madej, HR Kaback. (2010). Helix dynamics in LacY: helices II and IV. J Mol Biol. 396(3):617-26.

Majumdar DS, Smirnovaa I, Kasho V, Nir E, Kong X, Weiss S, Kaback HR. (2007). Single-molecule FRET reveals sugar-induced conformational dynamics in LacY. Proc Natl Acd Sci USA. 104(31): 12640-5. Epub May 14. PMID: 17502603.

Minematsu T, Giacomini KM. (2011) Interactions of tyrosine kinase inhibitors with organic cation transporters and multidrug and toxic compound extrusion proteins. Mol Cancer Ther 10(3):531-9. PMID: 21252289/PMCID: PMC3063525.

Mirza, O., Guan, L., Verner, G., Iwata, S. and Kaback, H.R. (2006) Structural evidence for induced fit and a mechanism for sugar/H (+) symport in LacY. Embo J. 25, 1177-83. PMID: 16525509; PMC1422171

Nie Y, Ermolova N, Kaback HR. (2007). Site-directed alkylation of Lac Y: effect of the proton electrochemical gradient. J Mol Biol. 374(2): 356-64. Sep 11. (PMID: 17920075).

Nie, Y., F.E. Sabetfard, and H.R. Kaback. (2008). The Cys154-->Gly mutation in LacY causes constitutive opening of the hydrophilic periplasmic pathway. J Mol Biol, 379: 695-703. PMID: 18485365 NIHMSID: 141221

Nie Y, HR Kaback. (2010). Sugar binding induces the same global conformational change in purified LacY as in the native bacterial membrane. Proc Natl Acad Sci USA. 107(21):9903-8.

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Nie, Y., Y. Zhou, and H.R. Kaback. (2009). Clogging the periplasmic pathway in LacY. Biochemistry 48(4): 738-43. PMID: 19128028, PMC2654236

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Renault, L., and Stahlberg, H. (2007). Book review: Three-dimensional transmission electron microscopy of Macromolecular Assemblies (by J. Frank). Scanning 29(1), 37.

Roosild TP, Vega M, Castronovo S, Choe S. (2006) Characterization of the family of MISTIC homologues. BMC Struct Biol. 6,10. PMCID: PMC1471793

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Sali A, Lima CD, Kostic M. (2007) Editorial: Structural genomics. Structure 15, 1341.

Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A. (2010) Comparison of Human Solute Carriers. Protein Sci. 19, 412-428. PMC2866268

Shaya, D., Kreir, M., Robbins, R., Wong, S., Hammon, J., Brüggemann, A., and Minor, D.L., Jr., (2011) Voltage-gated sodium channel (NaV) protein dissection creates a set of functional 'pore-only' proteins Proc Natl Acad Sci USA 108 12313-12318 PMID: 21746903: PMCID: PMC3145705

Smirnova I, Kasho V, Choe JY, Altenbach C, Hubbell WL, Kaback HR. (2007). Sugar binding induces and outward facing conformation of LacY. Proc Natl Acad Sci USA. 104(42): 16504-9. PMID: 17925435

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Smirnova I, V Kasho, J Sugihara, HR Kaback. (2009). Probing of the rates of alternating access in LacY with Trp fluorescence. Proc Natl Acad Sci USA. 106(51):21561-6. PMCID: PMC2799877

Smirnova I, V Kasho, J Sugihara, JY Choe, HR Kaback. (2009). Residues in the H+ translocation site define the pKa for sugar binding to LacY. Biochemistry. 48(37):8852-60. PMCID: PMC2769999

Stahlberg, H., and Walz, T. (2008). Molecular electron microscopy – State of the art and future directions. ACS Chem. Biol., 3(5), 268-281 PMCID: PMC2660199

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Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, Harries W. 2007 Annual Progress Report Synopsis of the Center for Structures of Membrane Proteins. Journal of Structural and Functional Genomics 10, 193-208, 2009. PMID: 19148774/ PMC2705707

Tao, L., Mogilner, A., Civelokoglu-Scholey, G., Wollman, R., Evans, J.E., Stahlberg, H., and Scholey, J.M. (2006). The homotetrameric kinesin-5, KLP61F, forms crossbridges between microtubules and antagonizes Ncd in motility assays. Current Biology 16, 2293-2302. PMID: 17141610

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Zhou Y, Guan L, Freites JA, and Kaback HR. (2008). Opening and closing of the periplasmic gate in lactose permease. Proc Natl Acad Sci USA. 105(10): 3774-8. Epub Mar 4. PMID: 18319336/ PMCID: PMC2268789

Zhou Y, Y Nie, HR Kaback. (2009). Residues gating the periplasmic pathway of LacY. J Mol Biol. 394(2):219-25. PMCID: PMC2784193

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