Publications

260.

260. NMR characterization of HtpG, the E. coli Hsp90, using sparse labeling with 13C-methyl alanine. Pederson K, Chalmers GR, Gao Q, Elnatan D, Ramelot TA, Ma LC, Montelione GT, Kennedy MA, Agard DA, Prestegard JH. J Biomol NMR. 2017 Jul;68(3):225-236. doi: 10.1007/s10858-017-0123-8. Epub 2017 Jun 26. PMID: 28653216(html)

259. "Design of Allosteric Stimulators of the Hsp90 ATPase as New Anticancer Leads," D'Annessa I, Sattin S, Tao J, Pennati M, Sànchez-Martìn C, Moroni E, Rasola A, Zaffaroni N, Agard DA, Bernardi A, Colombo G. Chemistry. 2017 Apr 19;23(22):5188-5192. doi: 10.1002/chem.201700169. Epub 2017 Mar 22. PMID: 28207175  (html)

258. "Internal Structure and Preferential Protein Binding of Colloidal Aggregates," Duan D, Torosyan H, Elnatan D, McLaughlin CK, Logie J, Shoichet MS, Agard DA, Shoichet BK. ACS Chem Biol. 2017 Jan 20;12(1):282-290. doi: 10.1021/acschembio.6b00791. Epub 2016 Dec 16. PMID: 27983786 (html)

257. "Assembly of a nucleus-like structure during viral replication in bacteria," Chaikeeratisak V, Nguyen K, Khanna K, Brilot AF, Erb ML, Coker JK, Vavilina A, Newton GL, Buschauer R, Pogliano K, Villa E, Agard DA, Pogliano J. Science. 2017 Jan 13;355(6321):194-197. doi: 10.1126/science.aal2130. PMID: 28082593 (html)

256. "Higher-order oligomerization of Spc110p drives γ-tubulin ring complex assembly," Lyon AS, Morin G, Moritz M, Yabut KC, Vojnar T, Zelter A, Muller E, Davis TN, Agard DA. Mol Biol Cell. 2016 Jul 15;27(14):2245-58. doi: 10.1091/mbc.E16-02-0072. Epub 2016 May 25. PMID: 27226487

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255. "Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase," Verba KA, Wang RY, Arakawa A, Liu Y, Shirouzu M, Yokoyama S, Agard DA. Science. 2016 Jun 24;352(6293):1542-7. doi: 10.1126/science.aaf5023. PMID: 27339980

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254. "The Seckel syndrome and centrosomal protein Ninein localizes asymmetrically to stem cell centrosomes but is not required for normal development, behavior, or DNA damage response in Drosophila," Zheng Y, Mennella V, Marks S, Wildonger J, Elnagdi E, Agard D, Megraw TL. Mol Biol Cell. 2016 Jun 1;27(11):1740-52. doi: 10.1091/mbc.E15-09-0655. Epub 2016 Apr 6. PMID: 27053665

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253."Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure," Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. J Struct Biol. 2016 Jun;194(3):303-10. doi: 10.1016/j.jsb.2016.03.006. Epub 2016 Mar 8. PMID: 26968363

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252. "Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands," Vettoretti G, Moroni E, Sattin S, Tao J, Agard DA, Bernardi A, Colombo G. Sci Rep. 2016 Apr 1;6:23830. doi: 10.1038/srep23830. PMID: 27032695 

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251. "Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference," Pimentel-Elardo SM, Sørensen D, Ho L, Ziko M, Bueler SA, Lu S, Tao J, Moser A, Lee R, Agard D, Fairn G, Rubinstein JL, Shoichet BK, Nodwell JR.ACS Chem Biol. 2015 Nov 20;10(11):2616-23. doi: 10.1021/acschembio.5b00612. Epub 2015 Sep 18.PMID: 26352211 (html)

250. "Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage," Li X, Zheng S, Agard DA, Cheng Y. J Struct Biol. 2015 Nov;192(2):174-8. doi: 10.1016/j.jsb.2015.09.003. Epub 2015 Sep 11. PMID: 26370395 (html)

249. "Evaluation of super-resolution performance of the K2 electron-counting camera using 2D crystals of aquaporin-0. Chiu PL, Li X, Li Z, Beckett B, Brilot AF, Grigorieff N, Agard DA, Cheng Y, Walz T. J Struct Biol. 2015 Nov;192(2):163-73. doi: 10.1016/j.jsb.2015.08.015. Epub 2015 Aug 28. PMID: 26318383 (html)

248. "Extensions to the MRC format header for electron cryo-microscopy and tomography," MRC2014 Cheng A, Henderson R, Mastronarde D, Ludtke SJ, Schoenmakers RH, Short J, Marabini R, Dallakyan S, Agard D, Winn M. J Struct Biol. 2015 Nov;192(2):146-50. doi: 10.1016/j.jsb.2015.04.002. Epub 2015 Apr 13. PMID: 25882513 (html)

247. "Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands," Sattin S, Tao J, Vettoretti G, Moroni E, Pennati M, Lopergolo A, Morelli L, Bugatti A, Zuehlke A, Moses M, Prince T, Kijima T, Beebe K, Rusnati M, Neckers L, Zaffaroni N, Agard DA, Bernardi A, Colombo G. Chemistry. 2015 Sep 21;21(39):13598-608. doi: 10.1002/chem.201502211. Epub 2015 Aug 18. PMID: 26286886  (html, )

246. "Synthesis of Functionalized 2-(4-Hydroxyphenyl)-3-methylbenzofuran Allosteric Modulators of Hsp90 Activity," Sattin, Sara; Panza, Matteo; Vasile, Francesca; Berni, Francesca; Goti, Giulio; Tao, Jiahui; Moroni, Elisabetta; Agard, David; Colombo, Giorgio; Bernardi, Anna, European Journal of Organic Chemistry (2016) 20, 3349-64.(html, pdf)

245. "Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hps90 traps and stabilizes an unfolded kinase," Verba, Kliment A.; Wang, Ray Yu-Ruei; Arakawa, Akihiko; Liu, Yanxin; Shirouzu, Mikako; Yokoyama, Shigeyuki; Agard, David A., Science. (2016) 352(6293), 1542-7.(html, pdf)

244. "Higher-order oligomerization of Spc110p drives gamma-tubulin ring complex assembly," Lyon Andrew S; Moritz Michelle; Agard David A; Morin Genevieve; Yabut King Clyde B; Vojnar Tamira; Zelter Alex; Muller Eric; Davis Trisha N, M Biol Cell. (2016) 27:14, 2245-58.(html, pdf)

243. "Interaction of CK1δ with γTuSCensures proper microtubule assembly and spindle positioning," Peng, Y., M. Moritz, X. Han, T.H. Giddings, A. Lyon, J. Kollman, M. Winey, J. Yates III, D.A. Agard, D.G. Drubin, G. Barnes, Mol. Biol. Cell. (2015) 26:2505-2518.html, pdf

242. "Asynchronous data acquisitionand on-the-fly analysis of dose fractionated cryoEM images by UCSFImage," Li Xueming; Zheng Shawn; Agard David A; Cheng Yifan, Journal of Structural Biology. (2015).(html, pdf)

241. "Evaluation of super-resolution performance of the K2 electron-counting camera using 2D crystals of aquaporin-0," Chiu, Po-Lin; Li, Xueming; Li, Zongli; Beckett, Brian; Brilot, Axel F.; Grigorieff, Nikolaus; Agard, David A.; Cheng, Yifan; Walz, Thomas, Journal of Structural Biology (2015). (html, pdf)

240. "Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands," Sattin, Sara; Tao, Jiahui; Vettoretti, Gerolamo; Moroni, Elisabetta; Pennati, Marzia; Lopergolo, Alessia; Morelli, Laura; Bugatti, Antonella; Zuehlke, Abbey; Moses, Mike; Prince, Thomas; Kijima, Toshiki; Beebe, Kristin; Rusnati, Marco; Neckers, Len; Zaffaroni, Nadia; Agard, David A.; Bernardi, Anna; Colombo, Giorgio, Chemistry - A European Journal, 21(39), 13598-13608. (html, pdf)

239. "The Cancer Cell Map Initiative: Defining the Hallmark Networks of Cancer," Krogan, Nevan J; Lippman, Scott; Agard, David A.; Ashworth, Alan; Ideker, Trey, Molecular Cell (2015), 58(4), 690-8. (html, pdf)

238. "Hsp70 Forms Antiparallel Dimers Stabilized by Post-translational Modifications to Position Clients for Transfer to Hsp90," Morgner, Nina; Schmidt, Carla; Beilsten-Edmands, Victoria; Ebong, Ima-obong; Patel, Nisha A.; Clerico, Eugenia M; Kirschke, Elaine; Daturpalli, Soumya; Jackson, Sophie E; Agard, David; Robinson, Carol V., Cell Reports (2015), 11(5), 759-69. (html, pdf)

237. "Ring closure activates yeast g-TuRC for species-specific microtubule nucleation," Justin M Kollman, Charles H Greenberg, Sam Li, Michelle Moritz, Alex Zelter, Kimberly K Fong, Jose-Jesus Fernandez, Andrej Sali, John Kilmartin, Trisha N Davis & David A Agard, Nature Structural & Molecular Biology (2015), 22(2), 132-7. (html, pdf)

236. "A bacteriophage tubulin harnesses dynamic instability to center DNA in infected cells," Erb Marcella L; Coker Joanna K C; Chaikeeratisak Vorrapon; Nonejuie Poochit; Pogliano Joe; Kraemer James A; Agard David A, eLife (2014), 3. (html, pdf)

235. "Glucocorticoid Receptor Function Regulated by Coordinated Action of the Hsp90 and Hsp70 Chaperone Cycles," Kirschke, Elaine; Goswami, Devrishi; Southworth, Daniel; Griffin, Patrick R.; Agard, David A., Cell (2014), 157(7), 1685-97. (html, pdf).

234. "Microarray-based screening of heat shock protein inhibitors," Emilia Schax, Johanna-Gabriela Walter, Helene Märzhäuser, Frank Stahl, Thomas Scheper, David A. Agard, Simone Eichner, Andreas Kirschning, Carsten Zeilinger, Journal of Biotechnology, (2014), 180, 1-9. (html, pdf)

233. "Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone," Street Timothy O; Zeng Xiaohui; Chu Feixia; Pellarin Riccardo; Bonomi Massimiliano; Sali Andrej; Kelly Mark J S; Agard David A, Journal of Molecular Biology (2014), 426(12), 2393-2404. (html, pdf).

232. "Sparse labeling of proteins: Structural characterization from long range constraints," Prestegard James H; Agard David A; Lavery Laura A; Moremen Kelley W; Morris Laura C; Pederson Kari, Journal of Magnetic Resonance (2014), 241, 32-40. (html, pdf)

231. "The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery," Lili X. Peng, Monica T. Hsu, Massimiliano Bonomi, David A. Agard, Matthew P. Jacobson, PLoS (2014), e1003464/1-e1003464/13, 13 pp (html, pdf)

230. "The Structure and Assembly Mechanism of a Novel Three-Stranded Tubulin Filament that Centers Phage DNA," Elena A. Zehr, James A. Kraemer, Marcella L. Erb, Joanna K.C. Coker, Elizabeth A. Montabana, Joe Pogliano, David A. Agard, Structure (2014), 22(4), 539-548. (html, pdf)

229. "Bacterial tubulin TubZ- Bt transitions between a two- stranded intermediate and a four- stranded filament upon GTP hydrolysis," Montabana, Elizabeth A.; Agard, David A., Proceedings of the National Academy of Sciences of the United States of America (2014), 111(9), 3407-3412. (html, pdf)

228. "Structural Asymmetry in the Closed State of Mitochondrial Hsp90 (TRAP1) Supports a Two-Step ATP Hydrolysis Mechanism," Laura A. Lavery, James R. Partridge, Theresa A. Ramelot, Daniel Elnatan, Michael A. Kennedy, David A. Agard, Molecular Cell, Volume 53, Issue 2, 23 January 2014, Pages 330-343 (html, pdf)

227. "Cell-cycle regulation of formin-mediated actin cable assembly," Miao Y, Wong CC, Mennella V, Michelot A, Agard DA, Holt LJ, Yates JR 3rd, Drubin DG., Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):E4446-55 (html, pdf)

226. "Amorphous no more: subdiffraction view of the pericentriolar material architecture," Vito Mennella, David A. Agard, Bo Huang, Laurence Pelletier, Trends in Cell Biology, 2013. (html, pdf)

225. "High-resolution restoration of 3D structrues from widefield images wiht extreme low signal-to-noise ratio," Muthuvel Arigovindan, Jennifer C. Fung, Daniel Elnatan, Vito Mennella, Yee-Hung Mark Chan, Michael Pollard, Eric Branlund, John W. Sedat, and David A. Agard, Proc Nat Assoc Sci., 2013, Oct 22, 110(43), 17344-9. (pdf, html)

224. "Influence of electron dose rate on electron counting images recorded with the K2 camera," Li X, Zheng SQ, Egami K, Agard DA, Cheng Y., J Struct Biol. 2013 Aug 20 (html, pdf)

223. "Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM," Li, Xueming; Mooney, Paul; Zheng, Shawn; Booth, Christopher R.; Braunfeld, Michael B.; Gubbens, Sander; Agard, David A.; Cheng, Yifan, Nature Methods (2013), 10(6), 584-590. (html, pdf)

222. "The bacterial actin MamK: in vitro assembly behavior and filament architecture," Ozyamak E, Kollman J, Agard DA, Komeili A., J Biol Chem. 2013, 288(6), 4265-77. (pdf)

221. "Uncovering a region of heat shock protein 90 important for client binding in E. coli and chaperone function in yeast." Genest O, Reidy M, Street TO, Hoskins JR, Camberg JL, Agard DA, Masison DC, Wickner S., Mol Cell. 2013, 49(3), 464-73. (pdf)

220. "Fast multicolor 3D imaging using aberration-corrected multifocus microscopy," Sara Abrahamsson, Jiji Chen, Bassam Hajj, Sjoerd Stallinga, Alexander Y Katsov, Jan Wisniewski, Gaku Mizuguchi, Pierre Soule, Florian Mueller, Claire Dugast Darzacq, Xavier Darzacq, Carl Wu , Cornelia I Bargmann , David A Agard , Maxime Dahan, & Mats G L Gustafsson, Nature Methods, 2013, 10(1), 60-3 (pdf)

219. "Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization," Mennella V, Keszthelyi B, McDonald KL, Chhun B, Kan F, Rogers GC, Huang B and Agard DA, Nature Cell Biology, 2012, 14, 1159-68. (html, pdf).

218. "The bacterial actin MamK: in vitro assembly behavior and filament architecture," Ertan Ozyamak, Justin Kollman, David A. Agard, and Arash Komeili, J. Biological Chem., Nov 2012. (html, pdf).

217. "A Method for Integrative Structure Determination of Protein-Protein Complexes," Schneidman-Duhovny Dina; Rossi Andrea; Avila-Sakar Agustin; Kim Seung Joong; Velazquez-Muriel Javier; Strop Pavel; Liang Hong; Krukenberg Kristin A; Liao Maofu; Kim Ho Min; Sobhanifar Solmaz; Dötsch Volker; Rajpal Arvind; Pons Jaume; Agard David A; Cheng Yifan; and Sali Andrej, Bioinformatics (Oxford, England) (2012) (html, pdf).

216. "A phage tubulin assembles dynamic filaments by a novel mechanism to center viral DNA within the host cell," J. Kraemer, M.L. Erb, C.A. Waddling, E.A. Montabana, E.A. Zehr, H. Wang, K. Nguyen, D.S.L. Pham, D. Agard, and J. Pogliano, Cell, 2012, 149(7), 1488-99 (html, pdf).

215. "The conserved arginine 380 of Hsp90 is not a catalytic residue, but stabilizes the closed conformation required for ATP hydrolysis." Cunningham CN, Southworth DR, Krukenberg KA, Agard DA. Protein Sci. 2012 May 31. (html, pdf)

214. "Functional modulation of a protein folding landscape via side-chain distortion." Kelch BA, Salimi NL, Agard DA. Proc Natl Acad Sci U S A. (2012), 109(24), 9414-9.(pdf)

213. "Effect of depth dependent spherical aberrations in 3D structured illumination microscopy." Arigovindan M, Sedat JW, Agard DA. Opt Express. (2012), 20(6), 6527-41. (pdf)

212. Interferometer-based structured-illumination microscopy utilizing complementary phase relationship through constructive and destructive image detection by two cameras, Shao L; Winoto L; Agard D A; Gustafsson M G L; Sedat J W, Journal of microscopy (2012), 246(3), 229-36.

211. "Three-dimensional structure of basal body triplet revealed by electron cryo-tomography." Li S, Fernandez JJ, Marshall WF, Agard DA. EMBO J. (2011), 31(3), 552-62. (pdf)

210. "Cross-Monomer Substrate Contacts Reposition the Hsp90 N-Terminal Domain and Prime the Chaperone Activity." Street TO, Lavery LA, Verba KA, Lee CT, Mayer MP, Agard DA. J Mol Biol. (2012), 415(1), 3-15. (pdf)

209. "A small molecule that preferentially binds the closed conformation of Hsp90," Alexander LD, Partridge JR, Agard DA, McAlpine SR. Bioorg Med Chem Lett. (2011), 21(23), 7068-71. (pdf)

208. "A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction," Zheng, Shawn Q.; Branlund, Eric; Kesthelyi, Bettina; Braunfeld, Michael B.; Cheng, Yifan; Sedat, John W.; Agard, David A., Ultramicroscopy (2011), 111(8), 1137-1143. (pdf)

207. "Architecture and assembly of a divergent member of the ParM family of bacterial actin-like proteins," Rivera, Christopher R.; Kollman, Justin M.; Polka, Jessica K.; Agard, David A.; Mullins, R. Dyche, Journal of Biological Chemistry (2011), 286(16), 14282-14290. (pdf)

206. "Client-Loading Conformation of the Hsp90 Molecular Chaperone Revealed in the Cryo-EM Structure of the Human Hsp90:Hop Complex," Southworth, Daniel R.; Agard, David A., Molecular Cell (2011), 42(6), 771-781. (pdf)

205. "Conformational dynamics of the molecular chaperone Hsp90," Krukenberg, Kristin A.; Street, Timothy O.; Lavery, Laura A.; Agard, David A., Quarterly Reviews of Biophysics (2011), 44(2), 229-255. (html, pdf)

204. "Crystal structure of g-tubulin complex protein GCP4 provides insight into microtubule nucleation," Guillet, Valerie; Knibiehler, Martine; Gregory-Pauron, Lynn; Remy, Marie-Helene; Chemin, Cecile; Raynaud-Messina, Brigitte; Bon, Cecile; Kollman, Justin M.; Agard, David A.; Merdes, Andreas; et al, Nature Structural & Molecular Biology (2011), 18(8), 915-919. (pdf)

203. "Microtubule nucleation by g-tubulin complexes," Kollman, Justin M.; Merdes, Andreas; Mourey, Lionel; Agard, David A., Nature Reviews Molecular Cell Biology (2011), 12(11), 709-721. (html, pdf)

202. "Sas-4 provides a scaffold for cytoplasmic complexes and tethers them in a centrosome," Gopalakrishnan Jayachandran; Mennella Vito; Blachon Stephanie; Zhai Bo; Smith Andrew H; Megraw Timothy L; Nicastro Daniela; Gygi Steven P; Agard David A; Avidor-Reiss Tomer, Nature communications (2011), 2, 359. (html)

201. "Substrate Binding Drives Large-Scale Conformational Changes in the Hsp90 Molecular Chaperone," Street, Timothy O.; Lavery, Laura A.; Agard, David A., Molecular Cell (2011), 42(1), 96-105. (pdf)

200. Zheng, Shawn Q.; Sedat, J. W.; Agard, D. A.. "Automated data collection for electron microscopic tomography." Methods in Enzymology (2010), 481(Cryo-EM, Part A), 283-315. (pdf)

199. Ho, Bosco K.; Agard, David A. "An improved strategy for generating forces in Steered Molecular Dynamics: the mechanical unfolding of titin, e2lip3 and ubiquitin." PLoS One (2010), 5(9), No pp. given. (pdf)

198. Matsuda, Atsushi; Shao, Lin; Boulanger, Jerome; Kervrann, Charles; Carlton, Peter M.; Kner, Peter; Agard, David; Sedat, John W. "Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP- histones." PLoS One (2010), 5(9), No pp. given. (pdf)

197. Carlton PM, Boulanger J, Kervrann C, Sibarita JB, Salamero J, Gordon-Messer S, Bressan D, Haber JE, Haase S, Shao L, Winoto L, Matsuda A, Kner P, Uzawa S, Gustafsson M, Kam Z, Agard DA, Sedat JW., "Inaugural Article: From the Cover: Fast live simultaneous multiwavelength four-dimensional optical microscopy," Proc Natl Acad Sci U S A. (2010), 107(37), 16016-22. (html, pdf, commentary)

196. Kollman JM, Polka JK, Zelter A, Davis TN, Agard DA, "Microtubule nucleating gamma-TuSC assembles structures with 13-fold microtubule-like symmetry," Nature (2010), (html, pdf)

195. Xu, W., Xu, F., Jones, M., Keszthelyi, B., Sedat, J.W., Agard, D.A., Mueller, K, "High-performance iterative electron tomography reconstruction with long-object compensation using graphics processing units (GPUs),"  J. Structural Biology (2010), 171(2), 142-153 (html, pdf)

194. Kner, P; Winoto, L; Agard, DA.; Sedat, JW.; Conchello, J-A; Cogswell, CJ.; Wilson, T; Brown, TG., "Closed loop adaptive optics for microscopy without a wavefront sensor," Proceedings of SPIE (2010), 7570, 757006-757006-9. (pdf)

193. Arigovindan M, Shaevitz J, McGowan J, Sedat JW, Agard DA., "A Parallel Product-Convolution approach for representing the depth varying Point Spread Functions in 3D widefield microscopy based on principal component analysis," Opt Express., 2010 Mar 29, 18(7), 6461-76. (pdf)

192. Kner P, Sedat JW, Agard DA, Kam Z., "High-resolution wide-field microscopy with adaptive optics for spherical aberration correction and motionless focusing," J Microsc., 2010, 237(2), 136-47. (html, pdf)

191. Salimi NL, Ho B, and Agard DA, "Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable a-Lytic Protease," PLoS Computational Biology, 2010, 6(2), e1000689 (pdf)

190. Gopalakrishnan J, Guichard P, Smith AH, Schwarz H, Agard DA, Marco S, and Avidor-Reiss, T, "Self-Assembling SAS-6 Multimer is a Core Centriole Building Block," J Biol Chem., 2010, 285(12), 8759-70. (html, pdf)

189. Vasko RC, Rodriguez RA, Cunningham CN, Ardi VC, Agard DA, and McAlpine, SR, "Mechanistic Studies of Sansalvamide A-Amide: An Allosteric Modulator of Hsp90," ACS Med. Chem. Lett, 2010, 1(1), 4-8. (html, pdf)

188. Ho BK, Agard DA, "Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility," Protein Sci. 2010 Jan 5. (html, pdf)

187. Street TO, Krukenberg KA, Rosgen J, Bolen DW, Agard DA, "Osmolyte-induced conformational changes in the Hsp90 molecular chaperone, " Protein Sci.2010, 19, 57-65. (html, pdf)

186. Xu F, Xu W, Jones M, Keszthelyi B, Sedat J, Agard D, Mueller K, "On the efficiency of iterative ordered subset reconstruction algorithms for acceleration on GPUs," Comp Met Prog Biomed, 2009. (html, pdf)

185. Choy RM, Kollman JM, Zelter A, Davis TN, Agard DA, "Localization and orientation of the gamma-Tubulin Small Complex components using protein tags as labels for single particle EM," J Struct Biol. 2009 Dec, 168(3):571-4. (html, pdf)

184. Polka JK, Kollman JM, Agard DA, Mullins RD, "The Structure and Assembly Dynamics of Plasmid Actin AlfA Imply a Novel Mechanism of DNA Segregation," J Bacteriol. 2009 Oct, 191(20), 6219-30. (html, pdf)

183. Krukenberg KA, Böttcher UM, Southworth DR, Agard DA, "Grp94, the endoplasmic reticulum Hsp90, has a similar solution conformation to cytosolic Hsp90 in the absence of nucleotide," Protein Sci. 2009 Jun 24, 18(9), 1815-27. (html, pdf)

182. Zheng SQ, Matsuda A, Braunfeld MB, Sedat JW, Agard DA, "Dual-axis target mapping and automated sequential acquisition of dual-axis EM tomographic data," J Struct Biol. 2009 Nov, 168(2), 323-31. (html, pdf)

181. Krukenberg KA, Southworth DR, Street TO, Agard DA, "pH-Dependent Conformational Changes in Bacterial Hsp90 Reveal a Grp94-Like Conformation at pH 6 That Is Highly Active in Suppression of Citrate Synthase Aggregation," J Mol Biol. (2009) Jul 10; 390(2): pp 278-91. (html, pdf)

180. Suloway C, Shi J, Cheng A, Pulokas J, Carragher B, Potter CS, Zheng SQ, Agard DA, Jensen GJ, "Fully automated, sequential tilt-series acquisition with Leginon," J Struct Biol. (2009) Jul, 167(1): pp11-18. (html, pdf)

179. Ho BK, Agard DA., "Probing the flexibility of large conformational changes in protein structures through local perturbations," PLoS Comput Biol. (2009) Apr, 5(4):e1000343. (html, pdf)

178. Southworth DR, Agard DA, "Species-dependent ensembles of conserved conformational states define the Hsp90 chaperone ATPase cycle," Mol Cell. (2008) Dec 5, 32(5):631-40 (html, pdf)

177. Ho BK and Agard DA, "Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms," BMC Structural Biology (2008), 8:41 (html, pdf)

176. Förster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, Sali A., "Integration of Small-Angle X-Ray Scattering Data into Structural Modeling of Proteins and Their Assemblies." J Mol Biol. (2008), 382(4), 1089-106 (html, pdf)

175. Shao L, Isaac B, Uzawa S, Agard DA, Sedat JW, Gustafsson MG., "I5S: wide-field light microscopy with 100-nm-scale resolution in three dimensions," Biophys J. (2008), 94(12), 4971-83 (html, pdf)

174. Gustafsson MG, Shao L, Carlton PM, Wang CJ, Golubovskaya IN, Cande WZ, Agard DA, Sedat JW., "Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination," Biophys J. (2008), 94(12), 4957-70. (html, pdf)

173. Schermelleh L, Carlton PM, Haase S, Shao L, Winoto L, Kner P, Burke B, Cardoso MC, Agard DA, Gustafsson MG, Leonhardt H, Sedat JW., "Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy." Science (2008), 320(5881), 1332-6. (html, pdf)

172. Nölting B, Agard DA., "How general is the nucleation-condensation mechanism?" Proteins. (2008) 73(3), 754-64. (html, pdf)

171. Cunningham CN, Krukenberg KA, Agard DA., " Intra- and inter-monomer interactions are required to synergistically facilitate ATP hydrolysis in Hsp90.", J Biol Chem. (2008) 283(30), 21170-8. (html, pdf, supplemental data)

170. Krukenberg KA, Förster F, Rice LM, Sali A, Agard DA., "Multiple Conformations of E. coli Hsp90 in Solution: Insights into the Conformational Dynamics of Hsp90." Structure. (2008), 16(5), 755-65. (pdf, supplemental data)

169. Trammell MA, Mahoney NM, Agard DA, Vale RD., "Mob4 plays a role in spindle focusing in Drosophila S2 cells." J Cell Sci. (2008), 121(8), 1284-92. (pdf)

168. Rice, Luke M., Montabana, Elizabeth A., Agard, David A., "The lattice as allosteric effector: structural studies of ab- and g-tubulin clarify the role of GTP in microtubule assembly." Proceedings of the National Academy of Sciences of the United States of America (2008), 105(14), 5378-5383. (pdf)

167. Kollman JM, Zelter A, Muller EG, Fox B, Rice LM, Davis TN, Agard DA., "The Structure of the g-Tubulin Small Complex: Implications of Its Architecture and Flexibility for Microtubule Nucleation", Mol Biol Cell. 2008, 19(1), 207-15 (pdf)

166. B.A. Kelch and D.A. Agard, "Mesophile versus Thermophile: Insights Into the Structural Mechanisms of Kinetic Stability," J. Mol. Biol., 2007, 370(4), 784-95. (pdf).

165. E.F. Hom, F. Marchis, T.K. Lee, S. Haase, D.A. Agard, and J.W. Sedat, "AIDA: an adaptive image deconvolution algorithm with application to multi-frame and three-dimensional data," J Opt Soc Am A Opt Image Sci Vis. 2007, 24(6), 1580-600. (pdf).

164. Brian A. Kelch, Kyle P. Eagen, F. Pinar Erciyas, Elisabeth L. Humphris, Adam R. Thomason, Shinji Mitsuiki and David A. Agard, "Structural and Mechanistic Exploration of Acid Resistance: Kinetic Stability Facilitates Evolution of Extremophilic Behavior," Journal of Molecular Biology, (2007), 368(3), 870-883. (pdf).

163. Peter König, Michael B. Braunfeld, John W. Sedat and David A. Agard, "The three-dimensional structure of in vitro reconstituted Xenopus laevis chromosomes by EM tomography, " Chromosoma 2007, 116(4), 349-372. (pdf).

162. Zheng SQ, Kollman JM, Braunfeld MB, Sedat JW, Agard DA, "Automated acquisition of electron microscopic random conical tilt sets," J Struct Biol. 2007, 157(1), 148-55. (html or pdf).

161. Shiau AK, Harris SF, Southworth DR, Agard DA, "Structural Analysis of E. coli hsp90 Reveals Dramatic Nucleotide-Dependent Conformational Rearrangements," Cell. 2006, 127(2), 329-340. (html or pdf).

160. Wei B, Lam PG, Braunfeld MB, Agard DA, Genzer J, Spontak RJ., "Tunable instability mechanisms of polymer thin films by molecular self-assembly," Langmuir. 2006, 22(21), 8642-5 (html or pdf).

159. Yonekura K, Braunfeld MB, Maki-Yonekura S, and Agard DA"Electron energy filtering significantly improves amplitude contrast of frozen-hydrated protein at 300kV," J Struct Biol. 2006, 156(3), 524-536. (html or pdf).

158. Zheng SQ, Keszthelyi B, Branlund E, Lyle JM, Braunfeld MB, Sedat JW, and Agard DA,"UCSF tomography: An integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction," J Struct Biol. 2006 157(1), 138-147. (html or pdf).

157. Fuhrmann, C.N., Daugherty, M.D., and Agard, D.A., "Subangstrom Crystallography Reveals that Short Ionic Hydrogen Bonds, and Not a His-Asp Low-Barrier Hydrogen Bond, Stabilize the Transition State in Serine Protease Catalysis," JACS, 2006, 128(28), 9086-102. (pdf).

156. Truhlar, S.M.E. and Agard, D.A., "The Folding Landscape of an α-Lytic Protease Variant Reveals the Role of a Conserved Beta-Hairpin in the Development of Kinetic Stability." Proteins: Structure, Function, and Bioinformatics (2005), 61, 105-114. (pdf).

155. W. C. Moss, S. Haase, J. M. Lyle, D. A. Agard & J. W. Sedat, "A novel 3D wavelet-based filter for visualizing features in noisy biological data," J. Microscopy, (2005), 219, 43-49. (pdf).

154. Ota N, Agard DA. "Intramolecular Signaling Pathways Revealed by Modeling Anisotropic Thermal Diffusion." J Mol Biol. 2005 Jul 7; (html or pdf).

153. Aldaz H, Rice LM, Stearns T, Agard DA. "Insights into microtubule nucleation from the crystal structure of human gamma-tubulin." Nature. 2005 May 26;435(7041):523-7. (html or pdf).

152. Koenig P, Braunfeld M, Agard DA., "Use of surface affinity enrichment and cryo-embedding to prepare in vitro reconstituted mitotic chromosomes for EM tomography." Ultramicroscopy. 2005 Jul;103(4):261-74. (html or pdf).

151. Jaswal SS, Truhlar SM, Dill KA, Agard DA., "Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases." J Mol Biol. 2005 Mar 25;347(2):355-66. (html or pdf).

150. Satoru Uzawa, Fei Li, Ye Jin, Kent L. McDonald, Michael B. Braunfeld , David A. Agard , and W. Zacheus Cande, "Spindle Pole Body Duplication in Fission Yeast Occurs at the G1/S Boundary but Maturation Is Blocked until Exit from S by an Event Downstream of Cdc10⁺." Mol. Biol. Cell, 2004, 15(12), 5219-5230. (html or pdf).

149. Alastair A. MacDowell, Rich S. Celestre, Malcolm Howells, Wayne McKinney, James Krupnick, Daniella Cambie, Edward E. Domning, Robert M. Duarte, Nicholas Kelez, David W. Plate, Carl W. Cork, Thomas N. Earnest, Jeffery Dickert, George Meigs, Corie Ralston, James M. Holton, Tom Alber, James M. Berger, David A. Agard and Howard A. Padmore, "Suite of three protein crystallography beamlines with single superconducting bend magnet as the source." J. Synch. Rad., 2004, 11, 447-455. (pdf).

148. Hanser BM, Gustafsson MG, Agard DA, Sedat JW, "Phase-retrieved pupil functions in wide-field fluorescence microscopy." J Microsc. 2004 Oct;216(Pt 1):32-48 (html or pdf).

147. Seth F. Harris, Andrew K. Shiau and David A. Agard, "The Crystal Structure of the Carboxy-Terminal Dimerization Domain of htpG, the Escherichia coli Hsp90, Reveals a Potential Substrate Binding Site," Structure, (2004) 12(6):1087-1097 (pdf).

146. Zheng, Q.S., Braunfeld, M.B., Sedat, J.W, and Agard, DA. "An improved strategy for automated electron microscopic tomography," J. Struct. Biol., (2004) 147(2):91-101 (html or pdf).

145. Fuhrmann, C.N., Kelch, B.A., Ota, N., Agard, D.A. "The 0.83Å resolution crystal structure of α-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain," J. Mol Biol. (2004);338(5):999-1013. (html or pdf).

144. Stephanie M.E. Truhlar, Erin L. Cunningham and David A. Agard. The folding landscape of Streptomyces griseus protease B reveals the energetic costs and benefits associated with evolving kinetic stability. Protein Science (2004), 13:381-390 (pdf).

143. Erin L. Cunningham and David A. Agard. Disabling the folding catalyst is the last critical step in α-lytic protease folding. Protein Science (2004), 13:325-331(pdf).

142. Kuntz Irwin D; Agard David A Assessment of the role of computations in structural biology. Advances in protein chemistry (2003), 66 1-25.

141. Wilder, Elizabeth A.; Braunfeld, Michael B.; Jinnai, Hiroshi; Hall, Carol K.; Agard, David A.; Spontak, Richard J. Nano-fibrillar networks in poly(ethyl methacrylate) and its silica nanocomposites. Journal of Physical Chemistry B (2003), 107(42), 11633-11642.(pdf).

140. Erin L. Cunningham and David A. Agard. Interdependent Folding of the N- and C-Terminal Domains Defines the Cooperative Folding of α-Lytic Protease. Biochemistry; 2003, 42, 13212-13219 (html and pdf).

139. Hanser BM, Gustafsson MG, Agard DA, Sedat JW. (2003). Phase retrieval for high-numerical-aperture optical systems. Opt Lett. 2003 May 15;28(10):801-3 (pdf).

138. Jinnai, H., Nishikawa, Y., Ito, M., Agard, D.A., Smith, S.D., and Spontak, R.J. (2002). Topological Similarity of Sponge-like Bicontinuous Morphologies Differing in Length Scale. Advanced Materials, 14(22), 1615-18 (pdf).

137. Chih-Ying Chen, Michael L. Reese, Peter K. Hwang, Nobuyuki Ota, David Agard, and Frances M. Brodsky (2002). Clathrin light and heavy chain interface: α-helix binding superhelix loops via critical tryptophans, The EMBO Journal, 21(22), 6072-6082 (html, pdf).

136. Rice, L. and Agard, D. (2002). Centriole duplication: centrin in on answers? Curr Biol 2002 Sep 17;12(18), R618-9. (pdf).

135. Cunningham, E., Mau, T., Truhlar, S.M.E., Agard, D.A. (2002). The Pro Region N-Terminal Domain Provides Specific Interactions Required for Catalysis of α-Lytic Protease Folding. Biochemistry 41(28), 8860-7, (html or pdf).

134. Wille, H., Michelitsch, M.M., Guenebaut, V., Supattapone, S., Serban, A., Cohen, F.E., Agard, D.A., Prusiner, S.B. (2002). Structural Studies of the Scrapie Prion Protein by Electron Crystallography. Proc. Natl. Acad. Sci 99: 3563-3568 (html or pdf).

133. Shiau, A.K., Barstad, D., Radek, J.T., Meyers, M.J., Katzenellenbogen, B.S., Katzenellenbogen, J.A., Agard, D.A., and Greene, G.L. (2002). Structural Characterization of a Subtype-Selective Ligand Reveals a Novel Mode of Estrogen Receptor Antagonism. Nature Structural Biology 9(5), 359-64 (html or pdf).

132. Jaswal, Sheila S.; Sohl, Julie L. Davis, Jonathan H.; Agard, David A. "Energetic landscape of α-lytic protease optimzes longevity through kinetic stability." Nature 415 (2002) 343-6 (pdf).

131. Tonelli, Marco; Peters, Reuben J.; James, Thomas L.; Agard, David A. "The solution structure of the viral binding domain of Tva, the cellular receptor for subgroup A avian leukosis and sarcoma virus." FEBS Letters 509 (2001) 161-168 (html or pdf).

130. Ota, Nobuyuki and Agard, David A., Binding Mode Prediction for a Flexible Ligand in a Flexible Pocket using Multi-Conformation Simulated Annealing Pseudo Crystallographic Refinement, J. Mol. Biol. (2001), 314(3), 607-17 (pdf or html).

129. Murphy, S.M, Preble, A.M., Patel, U.K., O'Connell, K.L., Dias, D.P., Moritz, M., Agard, D.A., Stults, J.T., and Stearns, T., GCP5 and GCP6: Two New Members of the Human gamma -Tubulin Complex, Mol. Biol. Cell (2001)12 3340-3352, (html or pdf).

128. Ota, N., Agard, D.A. (2001) Enzyme specificity under dynamic control II: Principal component analysis of α-lytic protease using global and local solvent boundary conditions. Protein Sci. 2001 Jul;10(7):1403-14 (pdf).

127. Marshall, W.F., Marko, J.F., Agard, D.A., Sedat, J.W. (2001) Chromosome elasticity and mitotic polar ejection force measured in living Drosophila embryos by four-dimensional microscopy-based motion analysis. Curr Biol. 2001 Apr 17;11(8):569-78 (html or pdf).

126. Moritz, M., Agard, D.A. (2001) -Tubulin complexes and microtubule nucleation. Curr Opin Struct Biol. 11(2):174-81 (pdf or html).

125. Kam Z., Hanser, B., Gustafsson, M.G., Agard, D.A., Sedat, J.W. (2001) Computational adaptive optics for live three-dimensional biological imaging. Proc Natl Acad Sci U S A. 98(7):3790-5 (pdf).

124. Kushner, Peter J.; Agard, David; Feng, Wei-Jun; Lopez, Gabriela; Schiau, Andrew; Uht, Rosalie; Webb, Paul; Greene, Geoffrey. Oestrogen receptor function at classical and alternative response elements. Novartis Foundation Symposium (2000), 230(Neuronal and Cognitive Effects of Oestrogens), 20-32. (pdf).

123. Kushner, P.J., Agard D.A., Greene G.L., Scanlan T.S., Shiau, A.K., Uht R.M., Webb P. (2000) Estrogen receptor pathways to AP-1. J Steroid Biochem Mol Biol. 74(5):311-7 (pdf).

122. Moritz, M., Braunfeld, M.B., Guenebaut, V., Heuser, J., Agard, D.A. (2000) Structure of the gamma-tubulin ring complex: a template for microtubule nucleation. Nat Cell Biol. 2(6):365-70 (pdf).

121. Derman, A.I., Agard, D.A. (2000) Two energetically disparate folding pathways of α-lytic protease share a single transition state. Nat Struct Biol. 7(5):394-7 (pdf).

120. Bass, H.W., Riera-Lizarazu, O., Ananiev, E.V., Bordoli, S.J., Rines, H.W., Phillips, R.L., Sedat, J.W., Agard, D.A., Cande, W.Z. (2000) Evidence for the coincident initiation of homolog pairing and synapsis during the telomere-clustering (bouquet) stage of meiotic prophase. J Cell Sci. 113(6):1033-42 (pdf).

119. Jinnai H, Nishikawa Y, Spontak R.J., Smith S.D., Agard D.A., Hashimoto T. Direct measurement of interfacial curvature distributions in a bicontinuous block copolymer morphology. Phys Rev Lett. 2000 Jan 17;84(3):518-21 (pdf).

118. Cunningham, E.L., Jaswal, S.S., Sohl J.L., Agard D.A. (1999) Kinetic stability as a mechanism for protease longevity. Proc Natl Acad Sci U S A. 96(20):11008-14 (pdf).

117. Gustafsson, M.G., Agard, D.A., Sedat, J.W. (1999) I5M: 3D widefield light microscopy with better than 100 nm axial resolution. J Microsc. 195 ( Pt 1):10-6 (pdf).

116. Miller, D.W. and Agard, D.A. (1999). Enzyme Specificity Under Dynamic Control: A Normal Mode Analysis of α-Lytic Protease. Journal of Molecular Biology 286(1); 267-78 (pdf).

115. Anderson, D.E., Peters, R.J., Wilk, B., Agard, D.A. (1999). α-lytic protease precursor: characterization of a structured folding intermediate. Biochemistry 38(15); 4728-35 (pdf).

114. Moritz, M., Braunfeld, M.B., Alberts, B.M., Agard, D.A. (1998) Reconstitution of centrosome microtubule nucleation in Drosophila. Methods Cell Biol. (1998) 67:141-8. (pdf).

113. Shiau, A., Barstad,D., Loria,P.M., Cheng,L., Kushner,P.J., Agard,D.A., and Greene, G.L. (1998) The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by taxoxifen. Cell 95(7):927-37 (pdf).

112. Sauter, N.K., Mau, T., Rader, S.D., and Agard, D.A. (1998). Molecular architecture of a folding catalyst:α-lytic protease complexed with its pro region. Nature Structural Biology 5: 945-950 (pdf).

111. Sohl, J.L., Jaswal, S.S., and Agard, D.A. (1998). Unfolded conformations are more stable than the native state of α-lytic protease. Nature 395: 817-819 (pdf).

110. Peters, R.J., Shiau, A.K., Sohl, J.L., Anderson, D.E., Tang, G., Silen, J.L., Agard, D.A. (1998). Pro region C-terminus: protease active site interactions are critical in catalyzing the folding of α-lytic protease. Biochemistry. 37:12058-12067 (pdf).

109. Fung, J.C., Marshall, W.F., Dernburg, A., Agard, D.A., Sedat, J.W. (1998). Homologous Chromosome Pairing in Drosophila Melanogaster Proceeds through Multiple Independent Initiations. J. Cell Biol. 141:5-20 (pdf).

108. Davis, J.H. and Agard, D.A. (1998). Relationship between enzyme specificity and the backbone dynamics of free and inhibited α-lytic protease. Biochemistry. 37:7696-7707 (pdf).

107. Han K F; Sedat J W; Agard D A Practical image restoration of thick biological specimens using multiple focus levels in transmission electron microscopy. Journal of Structural Biology (1997), 120(3), 237-44. (pdf).

106. Davis, Jonathan H.; Agard, David A.; Handel, Tracy M.; Basus, Vladimir J. Alterations in chemical shifts and exchange broadening upon peptide boronic acid inhibitor binding to α-lytic protease. Journal of Biomolecular NMR (1997), 10(1), 21-27. (pdf).

105. Herrnandez, L.D., Delos, S.E., Peters, R. R., Agard, D.A., Bates, P., Young, J.A.T., and White, J.M. (1997). Activation of a retroviral membrane fusion protein: receptor-induced liposome binding. J. Cell Biol. 139: 1455-1464 (pdf).

104. Marshall, W.F., Straight, A., Marko, J.F., Swedlow, J.R., Dernburg, A.F., Murray, A.W., Belmont, A.S., Agard, D.A., and Sedat, J.W. (1997). Interphase chromosomes undergoes large-scale diffusional motion in living cells. Current Biology. 7:930-939. (pdf).

103. Laurer, J.H., Fung, J.C., Sedat, J.W., Smith, S.D., Agard, D.A., Samseth, Mortensen, K., and Spontak, R.J. (1997). From micelles to randomly connected, bilayered membranes in dilute block copolymer beads. Langmuir 13: 2177-2180 (pdf).

102. Bass, H.W., Marshall, W.F., Sedat, J.W., Agard, D.A., and Cande, W.Z. (1997). Telomeres cluster de novo before the initiation of synapsis; a 3-dimensional spatial analysis of telomere positions before and during meiotic prophase. J. Cell. Biol. 137: 5-18 (pdf).

101. Rader, S.D. and Agard, D.A. (1997). Conformational substrates in enzyme mechanism: the 120K structure of α-lytic protease at 1.5 Å resolution. Protein Science 6: 1375-1386. (pdf).

100. Laurer, J.H., Hajduk, D.A., Fung, F.C., Sedat, J.W., Smith, S.D., Gruner, S.M., Agard, D.A., and Spontak, R.J. (1997). Microstructural Analysis of a Cubic Bicontinuous Morphology in a Neat SIS Triblock Copolymer. Macromols. 30: 3938-3941 (pdf).

99. Sohl, J.L.α-lytic protease by pro region c-terminal steric occlusion of the active site. Biochemistry 36(13): 3894-3902 (pdf).

98. Fung, J.C., Kane, L., Smith, S.D., Sedat, J.W., Agard, D.A., and Spontak, R.J. (1997). Phase behavior of complex diblock copolymer blends: a transmission electron microscopy study. Materials Science Forum 239-241: 170-184. (pdf).

97. Kam, Z., Margolis, H.J., Agard, D.A., and Sedat, J.W. (1996). Three-dimensional microscopy in thick biological samples: a fresh approach for adjusting focus and correcting spherical aberration. Bioimaging 5: 40-49. (pdf).

96. Gustafsson, Mats G. L.; Sedat, John W.; Agard, David A.. Method and apparatus for three-dimensional microscopy with enhanced depthresolution. PCT Int. Appl. (1996), No pp. given.

95. Boggs, Amy Fujishige; Agard, David A.. Bacterial extracellular secretion: transport of α-lytic protease across the outer membrane of Escherichia coli. Membrane Protein Transport (1996), 3 165-179. (pdf).

94. Spontak, R.J., Fung, J.C., Braunfeld, M.B., Sedat, J.W., Agard, D.A., Ashraf, A., and Smith, S.D. (1996). Architecture-induced phase immiscibility in a diblock/multiblock copolymer blend. Macromolecules 29(8): 2850-2856 (pdf).

93. Spontak, R.J., Fung, J.C., Braunfeld, M.B., Sedat, J.W., Agard, D.A., Kane, L., Smith, S.D., Satkowski, M.M., Ashraf, A., Hajduk, D.A., and Gruner, S.M. (1996). Phase behavior of ordered diblock copolymer blends: effects of compositional heterogeneity. Macromols. 29 (13): 4494-4507 (pdf).

92. Marshall, W.F., Dernburg, A.F., Harmon, B., Agard, D.A., and Sedat, J.W. (1996). Specific interactions of chromatin with the nuclear envelope: Positional determination within the nucleus in D. melanogaster. Mol. Biol. Cell 7: 825-842. (pdf).

91. Dernburg, A.F., Broman, K.W., Fung, J.C., Marshall, W.F., Philips, J., Agard, D.A., and Sedat, J.W. (1996). Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85: 745-759 (pdf).

90. Han, K.F., Gubbens, A.J., Sedat, J.W., and Agard, D.A. (1996). Optimal strategies for imaging thick biological specimens: exit wavefront reconstruction and energy-filtered imaging. J. Microscopy 183 (2): 124-132.(pdf).

89. Paddy, M.R., Saumweber, H., Agard, D.A., and Sedat, J.W. (1996). Time-resolved, in vivo studies of mitotic spindle formation and nuclear lamina breakdown in Drosophila early embryos. J. Cell Science 109: 591-607 (pdf).

88. Fung, J.C., De Ruijter, W.J., Chen, H., Abbey, C.K., Sedat, J.W., and Agard, D.A. (1996). Toward fully automated high-resolution electron tomography. J. Struct. Biol. 116(1): 181-9 (pdf).

87. Chen, H., Hughes, D.D., Chan, T.-A., Sedat, J.W. and Agard, D.A. (1996). IVE (image visualization environment): a software platform for all three-dimensional microscopy applications. J. Struct. Biol. 116: 56-60 (pdf).

86. Scalettar, B.A., Swedlow, J.R., Sedat, J.W., and Agard, D.A. (1996). Dispersion, aberration and deconvolution in multi-wavelength fluorescence images. J. Microscopy 182 (1): 55-60.(pdf).

85. Moritz, M., Braunfeld, M.B., Sedat, J.W., Alberts, B., and Agard, D.A. (1995). Microtubule nucleation by gamma-tubulin-containing rings in the centrosome. Nature 378: 638-640. (pdf).

84. Mace, J.E. and Agard, D.A. (1995). Kinetic and structural characterization of mutations of glycine 216 in α-lytic protease: a new target for engineering substrate specificity. J. Mol. Biol. 254: 720-736.(pdf).

83. Urata, Y., Parmelee, S.J., Agard, D.A., and Sedat, J.W. (1995). A three-dimensional structural dissection of Drosophila polytene chromosomes. J. Cell. Biol. 131: 279-295. (pdf).

82. Moritz, M., Braunfeld, M.B., Fung, J.C., Sedat, J.W., Alberts, B.M., and Agard, D.A. (1995). Three-dimensional structural characterization of centrosomes from early Drosophila embryos. J. Cell Biol. 130: 1149-1159. (pdf).

81. Mace, J.E., Wilk, B.J., and Agard, D.A. (1995). Functional linkage between the active site of α-lytic protease and distant regions of structure: scanning alanine mutagenesis of a surface loop affects activity and substrate specificity. J. Mol. Biol. 251: 116-134.(pdf).

80. Zingler, K., Belanger, C., Peters, R., Agard, D.A., and Young, J.A.T. (1995). Identification and characterization of the viral interaction determinant of the subgroup A avian leukosis virus receptor. J. Virology 69 (7): 4261-6 (pdf).

79. Marshall, W.F., Agard, D.A., and Sedat, J.W. (1995). Quantitative analysis of chromosome motion in Drosophila melanogaster. proc. SPIE 2412: 33042.

78. Gustafsson, M.G.L., Agard, D.A., and Sedat, J.W. (1995). Seven-fold improvement of axial resolution in 3-D widefield microscopy using two objective lenses. proc. SPIE 2412: 145-156.

77. Han, K.F., Sedat, J.W., and Agard, D.A. (1995). Mechanism of image formation for thick biological specimens: exit wavefront reconstruction and electron energy-loss spectroscopic imaging. J. Microscopy 178 (2): 107-119. (pdf).

76. Han, K. F.; Sedat, J. W.; Agard, D. A.. Image restoration for thick biological specimens using a through focus series as applied to electron tomography. Electron Microscopy 1994, Proceedings of the International Congress on Electron Microscopy, 13th, Paris, July 17-22, 1994 (1994), 1 503-504.

75. Baker, D. and Agard, D.A. (1994). Influenza hemagglutinin: kinetic control of protein function. Structure 2: 907-910 (html).

74. Dong, L-M., Wilson, C., Wardell, M.R., Simmons, T., Mahley, R.W., Weisgraber, K.H., and Agard, D.A. (1994). Human Apolipoprotein E. The role of arginine-61 in mediating the lipoprotein preferences of the E3 and E4 isoforms. Journal of Biological Chemistry 269: 22358-22365 (pdf).

73. Wilson, C., Mau, T.E., Weisgraber, K.H., Wardell, M.R., Mahley, R.W., and Agard, D.A. (1994). Salt bridge relay triggers defective LDL receptor binding by a mutant apolipoprotein. Structure 2(8): 713-718 (html).

72. Baker, D. and Agard, D.A. (1994). Kinetics versus thermodynamics in protein folding. Biochem. 33: 7505-7509.(pdf).

71. Horowitz, R.A., Agard, D.A., Sedat, J.W., and Woodcock, C.L. (1994). The three-dimensional architecture of chromatin in situ: electron tomography of reveals fibers composed of a continuously zig-zag nucleosomal ribbon. J. Cell Biol. 125: 1-10. (pdf).

70. Braunfeld, M.B., Koster, A.J., Sedat, J.W., and Agard, D.A. (1994). Cryo automated electron tomography: towards high resolution reconstructions of plastic embedded structures. J. Microscopy 174: 75-84. (pdf).

69. Dawe, R.K., Sedat, J.W., Agard, D.A., and Cande, W.Z. (1994). Meiotic chromosome pairing in maize is associated with a novel chromatin organization. Cell 76: 901-912. (pdf).

68. Hiraoka, Yasushi; Dernburg, Abby F.; Parmelee, Susan J.; Rykowski, Mary C.; Agard, David A.; Sedat, John W. The onset of homologous chromosome pairing during Drosophila melanogaster embryogenesis. Journal of Cell Biology (1993), 120(3), 591-600.(pdf).

67. Wardell, Mark R.; Wilson, Charles; Agard, David A.; Mahley, Robert W.; Weisgraber, Karl H. Crystal structures of the common apolipoprotein E variants: insights into functional mechanisms. NATO ASI Series, Series H: Cell Biology (1993), 73(Human Apolipoprotein Mutants III), 81-96.

66. Baker, D., Shiau, A.K., and Agard, D.A. (1993). The role of pro regions in protein folding. The role of pro regions in protein folding. Curr. Opinion Cell Biol. 5: 966-970. (pdf).

65. Swedlow, J.R., Agard, D.A., and Sedat, J.W. (1993). Chromosome structure inside the nucleus. Curr. Opinion Cell Biol. 5: 412-416. (pdf).

64. Agard, D. A. (1993). To fold or not to fold... Science, 260:1903-1904. (pdf).

63. Kam, Z, Jones, M.O., Chen, H., Agard, D.A., and Sedat, J.W. (1993). Design and construction of an optimal illumination system for quantitative wide-field multi-dimensional microscopy. J. Bioimaging 1: 71-81. (pdf).

62. Bystroff, C., Baker, D., Fletterick, R.J., and Agard, D.A. (1993). PRISM: Application to the solution of two protein structures. Acta Crystallographica, D49: 440-448. (pdf).

61. Baker, D., Bystroff, C., Fletterick, R.J., and Agard, D.A. (1993). PRISM: Topologically constrained phase refinement for macromolecular crystallography. Acta Crystallographica, D49: 429-439. (pdf).

60. Koster, A.J., Braunfeld, M.B., Fung, J.C., Abbey, C.K., Han, K.F., Liu, W., Chen, H., Sedat, J.W., and Agard, D.A. (1993). Towards automatic three-dimensional imaging of large biological structures using intermediate voltage electron microscopy. EMSA Bulletin 23: 176-188. (pdf).

59. Swedlow, J.R., Sedat, J.W., and Agard, D.A. (1993). Multiple chromosomal populations of topoisomerase II detected in vivo by time-lapse, three-dimensional wide field microscopy. Cell 73: 97-108. (pdf).

58. Wilson, C., Gregoret, L.M., and Agard, D.A. (1993). Modelling side chain conformation for homologous proteins using an energy based rotamer search. J. Mol. Biol. 229: 996-1006.(pdf).

57. Baker, D., Krukowski, A.E., and Agard, D.A. (1993). Uniqueness and the ab initio phase problem in macromolecular crystallography. Acta Crystallographica. D49: 186-192. (pdf).

56. Wilson, C. and Agard, D.A. (1993). PRISM: Automated crystallographic phase refinement by iterative skeletonization. Acta Crystallographica A49: 97-104. (pdf).

55. Koster, A.J., Braunfeld, M.B., Sedat, J.W., and Agard, D.A. (1992). Automated TEM control for electron tomography. Electron Microscopy 1: 119-123. (pdf).

54. Chen, H., Clyborne, W., Sedat, J.W., and Agard, D. A. (1992). PRISM: An integrated system for display and analysis of three-dimensional microscope images. SPIE Biomedical Image Processing and Three-Dimensional Microscopy 1660: 784-790. (pdf).

52. Koster, A.J., Chen, H., Sedat, J.W., and Agard, D.A. (1992). Automated microscopy for electron tomography. Ultramicroscopy 46: 207-227. (pdf).

51. Fujishige, A., Smith, K., Silen, J.L., and Agard, D.A. (1992). Correct folding of α-lytic protease is required for its extracellular secretion from E. coli. J.C.B. 118:33-42. (pdf).

50. Baker, D., Sohl, J.L., and Agard, D.A. (1992). A protein-folding reaction under kinetic control. Nature 356: 263-265. (pdf).

49. Paddy, M.R., Agard, D.A., and Sedat, J.W. (1992). An extended view of nuclear lamin structure, function and dynamics. Sems. in Cell Biol. 3: 255-266.

48. Baker, D., Silen, J.L., and Agard, D.A. (1992). Protease pro region required for folding is a potent inhibitor of the mature enzyme. Proteins 12: 339-344.

47. Holmes, T.J., Liu, Y-H., Khosla, D., and Agard, D.A. (1991). Increased depth-of-field and stereo pairs of fluorescence micrographs via inverse filtering and maximum likelihood estimation. J. Microscopy 164 (3): 217-237. (pdf).

46. Kam Z; Minden J S; Agard D A; Sedat J W; Leptin M Drosophila gastrulation: analysis of cell shape changes in living embryos by three-dimensional fluorescence microscopy. Development (Cambridge, England) (1991), 112(2), 365-70.

45. Bone R; Sampson N S; Bartlett P A; Agard D A, Crystal structures of α-lytic protease complexes with irreversibly bound phosphonate esters. Biochemistry (1991), 30(8), 2263-72.(pdf).

44. Bone, R., Fujishige, A., Kettner, C.A., and Agard, D.A. (1991). Structural basis for broad specificity in α-lytic protease mutants. Biochem. 30: 10388-10398.(pdf).

43. Wilson, C., Mace, J.E., and Agard, D.A. (1991). A computational method for the design of enzymes with altered substrate specificity. J. Mol. Biol. 220: 495-506. (pdf).

42. Wilson, C. and Agard, D.A. (1991). Engineering substrate specificity. Curr. Opinions Cell Biol. 1: 617-623. (pdf).

41. Caldwell, J.W., Agard, D.A., and Kollman, P.A. (1991). Free energy calculations on binding and catalysis by α-lytic protease: the role of substrate size in the P1 pocket. Proteins 10: 140-148.

40. Bone, R. and Agard, D.A. (1991). Mutational remodeling enzyme specificity. Methods Enzymol. 202: 643-672. (pdf).

39. Wilson, C., Wardell, M.R., Weisgraber, K.H., Mahley, R.W., and Agard, D.A. (1991). Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E. Science 252: 1817-1822.

38. Kam, Z., Minden, J.S., Agard, D.A., Sedat, J.W., and Leptin, M. (1991). Drosophila gastrulation: analysis of cell shape changes in living embryos by three-dimensional fluorescence microscopy. Development 112: 365-370. (pdf).

37. Paddy, M.R., Belmont, A.S., Saumweber, H., Agard, D.A., and Sedat, J.W. (1990). Interphase nuclear envelope lamins form a discontinuous network that interacts with only a fraction of the chromatin in the nuclear periphery. Cell 62: 89-106 (pdf).

36. Minden, Jonathan; Kam, Zvi; Agard, David; Sedat, John; Alberts, Bruce. Embryonic lineage analysis using three-dimensional, time lapse in vivo fluorescent microscopy. Proceedings of SPIE-The International Society for Optical Engineering (1990), 1205(Bioimaging Two-Dimens. Spectrosc.), 29-42. (pdf).

35. Hiraoka, Y., Agard, D.A., and Sedat, J.W. (1990). Temporal and spatial coordination of chromosome movement, spindle formation and nuclear envelope breakdown during prometaphase in Drosophila melanogaster embryos. J. Cell Biol., 111: 2815-2828. (pdf).

34. Hiraoka, Y., Rykowski, M.C., Lefstin, J.A., Agard, D.A., and Sedat, J.W. (1990). Three-dimensional organization of chromosomes studied by in situ hybridization and optical sectioning microscopy. SPIE Bioimaging & Two-dimens. Spectroscopy 1205: 11-19. (pdf).

33. Hiraoka, Y., Sedat, J.W., and Agard, D.A. (1990). Determination of the three-dimensional imaging properties of an optical microscope system: partial confocal behavior in epi-fluorescence microscopy. Biophys. J., 57: 325-333.

32. Chen, H., Sedat, J.W., and Agard, D.A. (1989). Software and hardware for 3-D gray-level image analysis and quantization. SPIE New Methods in Microscopy and Low Light Imaging 1161: 31-41. (pdf).

31. Agard, D.A., Hiraoka, Y., and Sedat, J.W. (1989). Three-dimensional microscopy: image processing for high-resolution subcellular imaging. SPIE New Methods in Microscopy and Low Light Imaging 1161: 24-30. (pdf).

30. Hiraoka, Y., Minden, J.S., Agard, D.A., and Sedat, J.W. (1989). Focal points for chromosome condensation and decondensation on the nuclear envelope revealed by three-dimensional in vivo microscopy. Nature 342: 392-296. (pdf).

29. Silen, J.L. and Agard, D.A. (1989). The α-lytic protease pro region does not require a physical linkage to activate the protease domain in vivo. Nature 341: 462-464. (pdf).

28. Minden, J.S., Agard, D.A., Sedat, J.W., and Alberts, M.B. (1989). Direct cell lineage in Drosophila melanogaster by time-lapse, three-dimensional optical microscopy of living embryos. J. Cell Biol. 109: 505-516.

27. Bone, R., Frank, D., Kettner, C., and Agard, D.A. (1989). Structural analysis of specificity: α-lytic protease complexes with analogs of reaction intermediates. Biochem. 28: 7600-7609 (pdf).

26. Bone, R., Silen, J.L., and Agard, D.A. (1989). Structural plasticity broadens the specificity of an engineered protease. Nature 339: 191-195.(pdf).

25. Silen, J.L., Frank, D., Fujishige, A., Bone, R., and Agard, D.A. (1989). Analysis of prepro α-lytic protease expression in E. coli reveals that the pro region is required for activity. J. Bact. 171: 1320-1325.(pdf).

24. Shaw, P.J., Agard, D.A., Hiraoka, Y., and Sedat, J.W. (1989). Tilted view reconstruction in optical microscopy. Three-dimensional reconstruction of Drosophila melanogaster embryo nuclei. Biophys. J. 55: 101-110. (pdf).

23. Belmont, A., Braunfeld, M.B., Sedat, J.W., and Agard, D.A. (1989). Large-scale chromatin structural domains within mitotic and interphase chromosomes in vivo and in vitro. Chromosoma, 98:129-143. (pdf).

22. Rykowksi, M.C., Parmalee, S.J., Agard, D.A., and Sedat, J.W. (1988). Precise determination of the molecular limits of a polytene chromosome band: regulatory sequences for the Notch gene are in the interband. Cell 54: 461-472.(pdf).

21. Aggerbeck, L.P., Wetterau, J.R., Weisgraber, K.H., Mahley, R.W., and Agard, D.A. (1988). Crystallization and preliminary x-ray diffraction studies on the amino-terminal (receptor binding) domain of human apolipoprotein E3 from serum very low density lipoproteins. J. Mol. Biol. 202: 279-181.(pdf).

20. Agard, D.A., Hiraoka, Y., Shaw, P., and Sedat, J.W. (1988). Three-dimensional light microscopy of diploid Drosophila chromosomes. Cell Motility & Cytoskeleton 10: 18-27.(pdf).

19. Silen, J.L., McGrath, C.N., Smith, K.R., and Agard, D.A. (1988). Molecular analysis of the gene encoding α-lytic protease: evidence for a preproenzyme. Gene 69: 237-244. (pdf).

18. Kettner, C.A., Bone, R., Agard, D.A., and Bachovchin, W.W. (1988). Kinetic properties of the binding of α-lytic protease to peptide boronic acids. Biochem. 27: 7682-7688.(pdf).

17. Spontak, R.J., Williams, M.C., and Agard, D.A. (1988). Three-dimensional study of cylindrical morphology in an styrene-butadiene-styrene block copolymer. Polymer 29: 387-395.(pdf).

16. Spontak, R.J., Williams, M.C., and Agard, D.A. (1988). The interphase composition profile in SB/SBS block copolymers, measured with electron microscopy, and microstructural implications. Macromols. 21(5): 1377-1387.(pdf).

15. Bone, R., Shenvi, A.R., Kettner, C.A., and Agard, D.A. (1987). Serine protease mechanism: the structure of an inhibitory complex of α-lytic protease and a tightly bound peptide boronic acid. Biochem. 26: 7609-7614.(pdf).

14. Hiraoka, Y., Sedat, J.W., and Agard, D.A. (1987). The use of a charge-coupled device for quantitative optical microscopy of biological structures. Science 238: 36-41.(pdf).

13. Belmont, A., Sedat, J.W., and Agard, D.A. (1987). A 3-D approach to mitotic chromosome structure: evidence for a hierarchical organization. J. Cell Biol. 105: 77-92 (pdf).

12. Gruenbaum, Y., Hochstrasser, M., Mathog, D., Saumweber, H., Agard, D.A., and Sedat, J.W. (1984). Spatial organisation of the drosophila nucleus: a three-dimensional cytogenetic study. J. Cell Science Suppl. 1: 223-234. (pdf).

11. Thomas, G.J., Jr. and Agard, D.A.. (1984). Quantitative analysis of nucleic acids, proteins and viruses by raman band deconvolution. Biophys. J., 46: 763-768.(pdf).

10. Agard, D.A. (1983). A least-squares method for determining structure factor in three-dimensional tilted-view reconstruction. J. Mol. Biol. 167: 849-852. (pdf).

9. Agard, D.A. and Sedat, J.W. (1983). Three-dimensional architecture of a polytene nucleus. Nature 302: 676-681.(pdf).

8. Agard, D.A. and Stroud, R.M. (1982). Linking regions between helices in bacteriorhodopsin revealed. Biophys. J. 37: 589-602.(pdf).

7. Agard, D.A. and Stroud, R.M. (1982). α-bungarotoxin structure revealed by a rapid method or averaging electron density of non-crystallographically, translationally-related molecules. Acta Cryst. A38: 186-194.(pdf).

6. Steinberg, R.A. and Agard, D.A. (1981). Turnover of regulatory subunit of cyclic AMP-dependent protein kinase in S49 mouse lymphoma cells: regulation by catalytic subunit and analogs of cyclic AMP. J.B.C. 256: 10731-10734.(pdf).

5. Steinberg, R.A. and Agard, D.A. (1981). Studies on the phosphorylation and synthesis of Type I regulatory subunit of cyclic AMP-dependent protein kinase in intact S49 mouse lymphoma cells. J.B.C. 256: 11356-11364.(pdf).

4. Agard, D.A., Steinberg, R.A., and Stroud, R.M. (1980). Quantitative analysis of electrophoretograms: a mathematical approach to super-resolution. Analyt. Biochem. 111: 257-268. (pdf).

3. Agard, D.A. and Sedat, J.W. (1980). Progress in the three-dimensional analysis of biological specimens utilizing image processing techniques. J. SPIE 264: 110-117.

2. Stroud, R.M. and Agard, D.A. (1979). Structure determination of asymmetric membrane profiles using an iterative fourier method. Biophys. J. 25(3): 495-512. (pdf).

1. Ross, M.J., Klymkowsky, M.W., Agard, D.A., and Stroud, R.M. (1977). Structural studies of a membrane-bound acetylcholine receptor from Torpedo californica. J. Mol. Biol. 116: 635-659. (pdf).