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Dave Agard, PhD

Title(s)Professor, Biochemistry and Biophysics
SchoolSchool of Medicine
Phone415-476-2521
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    Other Positions
    Title(s)Howard Hughes Investigator, Biochemistry and Biophysics


    Collapse Biography 
    Collapse Education and Training
    University of California, San FranciscoPostdoctoral StudiesGraduate Division - Biochemistry

    Collapse Research 
    Collapse Research Activities and Funding
    Structure & Mechanism: microtubule nucleation, centrosomes, phage cytoskeleton
    NIH R35GM118099Jun 1, 2016 - May 31, 2021
    Role: Principal Investigator
    The Yeast Centrosome - Structure Assembly & Function
    NIH P01GM105537Sep 1, 2014 - Aug 31, 2019
    Role: Co-Investigator
    Characterization of a bacteriophage tubulin involved in viral replication
    NIH/NIGMS R01GM104556Aug 1, 2013 - Apr 30, 2017
    Role: Principal Investigator
    Structural Basis of Protein Homeostasis
    NIH/NIGMS U01GM098254Sep 30, 2012 - Jul 31, 2015
    Role: Principal Investigator
    National Resource for Automated Molecular Microscopy
    NIH P41RR017573Sep 30, 2002 - Jul 31, 2012
    Role: Co-Investigator
    STRUCTURE AND DYNAMICS OF NUCLEAR RECEPTORS
    NIH/NIDDK P01DK058390Aug 15, 2000 - Jul 31, 2006
    Role: Co-Investigator
    FASEB CONFERENCE: PROTEIN FOLDING AND ASSEMBLY IN CELLS
    NIH R13GM061717Jul 1, 2000 - Jun 30, 2001
    Role: Principal Investigator
    GATAN IMAGING ENERGY FILTER WITH CCD CAMERA FOR IVEM
    NIH S10RR013926Feb 1, 2000 - Jan 31, 2001
    Role: Principal Investigator
    Comprehensive Biology: Exploiting the Yeast Genome
    NIH P41RR011823Sep 30, 1996 - Jun 30, 2016
    Role: Co-Investigator
    BioCAT - Biophysics Collaborative Access Team
    NIH P41RR008630Sep 30, 1995 - Mar 31, 2012
    Role: Co-Investigator
    Molecular Biophysics Training Grant
    NIH/NIGMS T32GM008284Sep 30, 1988 - Jun 30, 2023
    Role: Principal Investigator
    National Biomedical NMR Resource at Madison
    NIH P41RR002301Jul 1, 1985 - Feb 28, 2015
    Role: Co-Investigator
    Macromolecular Diffraction Resource: MacCHESS
    NIH P41RR001646Sep 1, 1983 - Jun 30, 2013
    Role: Co-Investigator
    Centrosome structure and mechanism of MT nucleation by gamma-tubulin complexes
    NIH R01GM031627Mar 1, 1983 - Dec 31, 2016
    Role: Principal Investigator
    Bio-Organic Biomedical Mass Spectrometry Resource
    NIH P41RR001614Mar 1, 1982 - May 31, 2015
    Role: Co-Investigator
    A Synchroton Radiation Structural Biology Resource
    NIH P41RR001209Mar 1, 1980 - Feb 28, 2015
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Global Health

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Fernandez JJ, Li S, Agard DA. Consideration of sample motion in cryo-tomography based on alignment residual interpolation. J Struct Biol. 2019 Jan 25. PMID: 30690142.
      View in: PubMed
    2. Freilich R, Betegon M, Tse E, Mok SA, Julien O, Agard DA, Southworth DR, Takeuchi K, Gestwicki JE. Competing protein-protein interactions regulate binding of Hsp27 to its client protein tau. Nat Commun. 2018 Nov 01; 9(1):4563. PMID: 30385828.
      View in: PubMed
    3. Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell. 2018 Jul 26; 174(3):505-520. PMID: 30053424.
      View in: PubMed
    4. Palovcak E, Wang F, Zheng SQ, Yu Z, Li S, Betegon M, Bulkley D, Agard DA, Cheng Y. A simple and robust procedure for preparing graphene-oxide cryo-EM grids. J Struct Biol. 2018 Oct; 204(1):80-84. PMID: 30017701.
      View in: PubMed
    5. Elnatan D, Agard DA. Calcium binding to a remote site can replace magnesium as cofactor for mitochondrial Hsp90 (TRAP1) ATPase activity. J Biol Chem. 2018 Aug 31; 293(35):13717-13724. PMID: 29991590.
      View in: PubMed
    6. Fernandez JJ, Li S, Bharat TAM, Agard DA. Cryo-tomography tilt-series alignment with consideration of the beam-induced sample motion. J Struct Biol. 2018 Jun; 202(3):200-209. PMID: 29410148.
      View in: PubMed
    7. Moroni E, Agard DA, Colombo G. The Structural Asymmetry of Mitochondrial Hsp90 (Trap1) Determines Fine Tuning of Functional Dynamics. J Chem Theory Comput. 2018 Feb 13; 14(2):1033-1044. PMID: 29320629.
      View in: PubMed
    8. Citron YR, Fagerstrom CJ, Keszthelyi B, Huang B, Rusan NM, Kelly MJS, Agard DA. The centrosomin CM2 domain is a multi-functional binding domain with distinct cell cycle roles. PLoS One. 2018; 13(1):e0190530. PMID: 29315319.
      View in: PubMed
    9. Verba KA, Agard DA. Protein Expression and Purification of the Hsp90-Cdc37-Cdk4 Kinase Complex from Saccharomyces cerevisiae. Bio Protoc. 2017 Oct 05; 7(19). PMID: 29104897.
      View in: PubMed
    10. Verba KA, Agard DA. How Hsp90 and Cdc37 Lubricate Kinase Molecular Switches. Trends Biochem Sci. 2017 10; 42(10):799-811. PMID: 28784328.
      View in: PubMed
    11. Elnatan D, Betegon M, Liu Y, Ramelot T, Kennedy MA, Agard DA. Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1. Elife. 2017 07 25; 6. PMID: 28742020.
      View in: PubMed
    12. Pederson K, Chalmers GR, Gao Q, Elnatan D, Ramelot TA, Ma LC, Montelione GT, Kennedy MA, Agard DA, Prestegard JH. NMR characterization of HtpG, the E. coli Hsp90, using sparse labeling with 13C-methyl alanine. J Biomol NMR. 2017 Jul; 68(3):225-236. PMID: 28653216.
      View in: PubMed
    13. Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. Liquid droplet formation by HP1a suggests a role for phase separation in heterochromatin. Nature. 2017 07 13; 547(7662):236-240. PMID: 28636604.
      View in: PubMed
    14. D'Annessa I, Sattin S, Tao J, Pennati M, Sànchez-Martìn C, Moroni E, Rasola A, Zaffaroni N, Agard DA, Bernardi A, Colombo G. Design of Allosteric Stimulators of the Hsp90 ATPase as New Anticancer Leads. Chemistry. 2017 Apr 19; 23(22):5188-5192. PMID: 28207175.
      View in: PubMed
    15. Zheng SQ, Palovcak E, Armache JP, Verba KA, Cheng Y, Agard DA. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods. 2017 Apr; 14(4):331-332. PMID: 28250466.
      View in: PubMed
    16. 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. Assembly of a nucleus-like structure during viral replication in bacteria. Science. 2017 01 13; 355(6321):194-197. PMID: 28082593.
      View in: PubMed
    17. Duan D, Torosyan H, Elnatan D, McLaughlin CK, Logie J, Shoichet MS, Agard DA, Shoichet BK. Internal Structure and Preferential Protein Binding of Colloidal Aggregates. ACS Chem Biol. 2017 01 20; 12(1):282-290. PMID: 27983786.
      View in: PubMed
    18. Verba KA, Wang RY, Arakawa A, Liu Y, Shirouzu M, Yokoyama S, Agard DA. Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase. Science. 2016 Jun 24; 352(6293):1542-7. PMID: 27339980.
      View in: PubMed
    19. Lyon AS, Morin G, Moritz M, Yabut KC, Vojnar T, Zelter A, Muller E, Davis TN, Agard DA. Higher-order oligomerization of Spc110p drives ?-tubulin ring complex assembly. Mol Biol Cell. 2016 07 15; 27(14):2245-58. PMID: 27226487; PMCID: PMC4945142 [Available on 09/30/16].
    20. Thabouillot O, Perrier P, Roche NC, Agard D, Barbier O, Martin G, Viant E, Leclere JB. A Fortunate Story of an Unusual AK-47 Bullet Trajectory: Always Keep a Smartphone in Your Pocket. Prehosp Disaster Med. 2016 Jun; 31(3):343-5. PMID: 27086713.
      View in: PubMed
    21. Zheng Y, Mennella V, Marks S, Wildonger J, Elnagdi E, Agard D, Megraw TL. 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. Mol Biol Cell. 2016 06 01; 27(11):1740-52. PMID: 27053665; PMCID: PMC4884065.
    22. Vettoretti G, Moroni E, Sattin S, Tao J, Agard DA, Bernardi A, Colombo G. Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands. Sci Rep. 2016 Apr 01; 6:23830. PMID: 27032695; PMCID: PMC4817115.
    23. Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. Structure of ?-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. J Struct Biol. 2016 06; 194(3):303-10. PMID: 26968363.
      View in: PubMed
    24. 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. Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference. ACS Chem Biol. 2015 Nov 20; 10(11):2616-23. PMID: 26352211; PMCID: PMC4658348 [Available on 11/20/16].
    25. Li X, Zheng S, Agard DA, Cheng Y. Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage. J Struct Biol. 2015 Nov; 192(2):174-8. PMID: 26370395; PMCID: PMC4633327 [Available on 11/01/16].
    26. Chiu PL, Li X, Li Z, Beckett B, Brilot AF, Grigorieff N, Agard DA, Cheng Y, Walz T. Evaluation of super-resolution performance of the K2 electron-counting camera using 2D crystals of aquaporin-0. J Struct Biol. 2015 Nov; 192(2):163-73. PMID: 26318383; PMCID: PMC4633381 [Available on 11/01/16].
    27. 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. Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands. Chemistry. 2015 Sep 21; 21(39):13598-608. PMID: 26286886.
      View in: PubMed
    28. Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. The cancer cell map initiative: defining the hallmark networks of cancer. Mol Cell. 2015 May 21; 58(4):690-8. PMID: 26000852.
      View in: PubMed
    29. Peng Y, Moritz M, Han X, Giddings TH, Lyon A, Kollman J, Winey M, Yates J, Agard DA, Drubin DG, Barnes G. Interaction of CK1d with ?TuSC ensures proper microtubule assembly and spindle positioning. Mol Biol Cell. 2015 Jul 01; 26(13):2505-18. PMID: 25971801; PMCID: PMC4571304.
    30. Morgner N, Schmidt C, Beilsten-Edmands V, Ebong IO, Patel NA, Clerico EM, Kirschke E, Daturpalli S, Jackson SE, Agard D, Robinson CV. Hsp70 forms antiparallel dimers stabilized by post-translational modifications to position clients for transfer to Hsp90. Cell Rep. 2015 May 05; 11(5):759-69. PMID: 25921532; PMCID: PMC4431665.
    31. Cheng A, Henderson R, Mastronarde D, Ludtke SJ, Schoenmakers RH, Short J, Marabini R, Dallakyan S, Agard D, Winn M. MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography. J Struct Biol. 2015 Nov; 192(2):146-50. PMID: 25882513; PMCID: PMC4642651.
    32. Kollman JM, Greenberg CH, Li S, Moritz M, Zelter A, Fong KK, Fernandez JJ, Sali A, Kilmartin J, Davis TN, Agard DA. Ring closure activates yeast ?TuRC for species-specific microtubule nucleation. Nat Struct Mol Biol. 2015 Feb; 22(2):132-7. PMID: 25599398; PMCID: PMC4318760.
    33. Partridge JR, Lavery LA, Elnatan D, Naber N, Cooke R, Agard DA. A novel N-terminal extension in mitochondrial TRAP1 serves as a thermal regulator of chaperone activity. Elife. 2014 Dec 22; 3. PMID: 25531069; PMCID: PMC4381864.
    34. Erb ML, Kraemer JA, Coker JK, Chaikeeratisak V, Nonejuie P, Agard DA, Pogliano J. A bacteriophage tubulin harnesses dynamic instability to center DNA in infected cells. Elife. 2014 Nov 27; 3. PMID: 25429514; PMCID: PMC4244570.
    35. Kirschke E, Goswami D, Southworth D, Griffin PR, Agard DA. Glucocorticoid receptor function regulated by coordinated action of the Hsp90 and Hsp70 chaperone cycles. Cell. 2014 Jun 19; 157(7):1685-97. PMID: 24949977; PMCID: PMC4087167.
    36. Street TO, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly MJ, Chu F, Agard DA. Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone. J Mol Biol. 2014 Jun 12; 426(12):2393-404. PMID: 24726919.
      View in: PubMed
    37. Prestegard JH, Agard DA, Moremen KW, Lavery LA, Morris LC, Pederson K. Sparse labeling of proteins: structural characterization from long range constraints. J Magn Reson. 2014 Apr; 241:32-40. PMID: 24656078.
      View in: PubMed
    38. Schax E, Walter JG, Märzhäuser H, Stahl F, Scheper T, Agard DA, Eichner S, Kirschning A, Zeilinger C. Microarray-based screening of heat shock protein inhibitors. J Biotechnol. 2014 Jun 20; 180:1-9. PMID: 24667540.
      View in: PubMed
    39. Zehr EA, Kraemer JA, Erb ML, Coker JK, Montabana EA, Pogliano J, Agard DA. The structure and assembly mechanism of a novel three-stranded tubulin filament that centers phage DNA. Structure. 2014 Apr 08; 22(4):539-48. PMID: 24631461; PMCID: PMC3999902.
    40. Montabana EA, Agard DA. Bacterial tubulin TubZ-Bt transitions between a two-stranded intermediate and a four-stranded filament upon GTP hydrolysis. Proc Natl Acad Sci U S A. 2014 Mar 04; 111(9):3407-12. PMID: 24550513; PMCID: PMC3948286.
    41. Peng LX, Hsu MT, Bonomi M, Agard DA, Jacobson MP. The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery. PLoS Comput Biol. 2014 Feb; 10(2):e1003464. PMID: 24516374; PMCID: PMC3916224.
    42. Lavery LA, Partridge JR, Ramelot TA, Elnatan D, Kennedy MA, Agard DA. Structural asymmetry in the closed state of mitochondrial Hsp90 (TRAP1) supports a two-step ATP hydrolysis mechanism. Mol Cell. 2014 Jan 23; 53(2):330-43. PMID: 24462206.
      View in: PubMed
    43. Mennella V, Agard DA, Huang B, Pelletier L. Amorphous no more: subdiffraction view of the pericentriolar material architecture. Trends Cell Biol. 2014 Mar; 24(3):188-97. PMID: 24268653; PMCID: PMC3991556.
    44. Gordon DA, Smith ME, Wratschko M, Agard D, Holden L, Wilcox S, Lazorchak JM. A new approach for the laboratory culture of the fathead minnow, Pimephales promelas. Environ Toxicol Chem. 2014 Jan; 33(1):126-33. PMID: 24115165.
      View in: PubMed
    45. Miao Y, Wong CC, Mennella V, Michelot A, Agard DA, Holt LJ, Yates JR, Drubin DG. Cell-cycle regulation of formin-mediated actin cable assembly. Proc Natl Acad Sci U S A. 2013 Nov 19; 110(47):E4446-55. PMID: 24133141.
      View in: PubMed
    46. Arigovindan M, Fung JC, Elnatan D, Mennella V, Chan YH, Pollard M, Branlund E, Sedat JW, Agard DA. High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio. Proc Natl Acad Sci U S A. 2013 Oct 22; 110(43):17344-9. PMID: 24106307; PMCID: PMC3808589.
    47. Li X, Zheng SQ, Egami K, Agard DA, Cheng Y. Influence of electron dose rate on electron counting images recorded with the K2 camera. J Struct Biol. 2013 Nov; 184(2):251-60. PMID: 23968652; PMCID: PMC3854003.
    48. Li X, Mooney P, Zheng S, Booth CR, Braunfeld MB, Gubbens S, Agard DA, Cheng Y. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods. 2013 Jun; 10(6):584-90. PMID: 23644547; PMCID: PMC3684049.
    49. Genest O, Reidy M, Street TO, Hoskins JR, Camberg JL, Agard DA, Masison DC, Wickner S. Uncovering a region of heat shock protein 90 important for client binding in E. coli and chaperone function in yeast. Mol Cell. 2013 Feb 07; 49(3):464-73. PMID: 23260660.
      View in: PubMed
    50. Abrahamsson S, Chen J, Hajj B, Stallinga S, Katsov AY, Wisniewski J, Mizuguchi G, Soule P, Mueller F, Dugast Darzacq C, Darzacq X, Wu C, Bargmann CI, Agard DA, Dahan M, Gustafsson MG. Fast multicolor 3D imaging using aberration-corrected multifocus microscopy. Nat Methods. 2013 Jan; 10(1):60-3. PMID: 23223154; PMCID: PMC4161287.
    51. Ozyamak E, Kollman J, Agard DA, Komeili A. The bacterial actin MamK: in vitro assembly behavior and filament architecture. J Biol Chem. 2013 Feb 08; 288(6):4265-77. PMID: 23204522; PMCID: PMC3567678.
    52. Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A. A method for integrative structure determination of protein-protein complexes. Bioinformatics. 2012 Dec 15; 28(24):3282-9. PMID: 23093611; PMCID: PMC3519461.
    53. Mennella V, Keszthelyi B, McDonald KL, Chhun B, Kan F, Rogers GC, Huang B, Agard DA. Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization. Nat Cell Biol. 2012 Nov; 14(11):1159-68. PMID: 23086239; PMCID: PMC3767400.
    54. Cunningham CN, Southworth DR, Krukenberg KA, Agard DA. The conserved arginine 380 of Hsp90 is not a catalytic residue, but stabilizes the closed conformation required for ATP hydrolysis. Protein Sci. 2012 Aug; 21(8):1162-71. PMID: 22653663; PMCID: PMC3537237.
    55. Kraemer JA, Erb ML, Waddling CA, Montabana EA, Zehr EA, Wang H, Nguyen K, Pham DS, Agard DA, Pogliano J. A phage tubulin assembles dynamic filaments by an atypical mechanism to center viral DNA within the host cell. Cell. 2012 Jun 22; 149(7):1488-99. PMID: 22726436.
      View in: PubMed
    56. Kelch BA, Salimi NL, Agard DA. Functional modulation of a protein folding landscape via side-chain distortion. Proc Natl Acad Sci U S A. 2012 Jun 12; 109(24):9414-9. PMID: 22635267.
      View in: PubMed
    57. Shao L, Winoto L, Agard DA, Gustafsson MG, Sedat JW. Interferometer-based structured-illumination microscopy utilizing complementary phase relationship through constructive and destructive image detection by two cameras. J Microsc. 2012 Jun; 246(3):229-36. PMID: 22472010; PMCID: PMC3447539.
    58. Arigovindan M, Sedat JW, Agard DA. Effect of depth dependent spherical aberrations in 3D structured illumination microscopy. Opt Express. 2012 Mar 12; 20(6):6527-41. PMID: 22418536.
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    59. Li S, Fernandez JJ, Marshall WF, Agard DA. Three-dimensional structure of basal body triplet revealed by electron cryo-tomography. EMBO J. 2012 Feb 01; 31(3):552-62. PMID: 22157822; PMCID: PMC3273388.
    60. Street TO, Lavery LA, Verba KA, Lee CT, Mayer MP, Agard DA. Cross-monomer substrate contacts reposition the Hsp90 N-terminal domain and prime the chaperone activity. J Mol Biol. 2012 Jan 06; 415(1):3-15. PMID: 22063096.
      View in: PubMed
    61. Kollman JM, Merdes A, Mourey L, Agard DA. Microtubule nucleation by ?-tubulin complexes. Nat Rev Mol Cell Biol. 2011 Oct 12; 12(11):709-21. PMID: 21993292.
      View in: PubMed
    62. Alexander LD, Partridge JR, Agard DA, McAlpine SR. A small molecule that preferentially binds the closed conformation of Hsp90. Bioorg Med Chem Lett. 2011 Dec 01; 21(23):7068-71. PMID: 22014826.
      View in: PubMed
    63. Guillet V, Knibiehler M, Gregory-Pauron L, Remy MH, Chemin C, Raynaud-Messina B, Bon C, Kollman JM, Agard DA, Merdes A, Mourey L. Crystal structure of ?-tubulin complex protein GCP4 provides insight into microtubule nucleation. Nat Struct Mol Biol. 2011 Jul 03; 18(8):915-9. PMID: 21725292; PMCID: PMC3703858.
    64. Southworth DR, Agard DA. Client-loading conformation of the Hsp90 molecular chaperone revealed in the cryo-EM structure of the human Hsp90:Hop complex. Mol Cell. 2011 Jun 24; 42(6):771-81. PMID: 21700222; PMCID: PMC3144320.
    65. Gopalakrishnan J, Mennella V, Blachon S, Zhai B, Smith AH, Megraw TL, Nicastro D, Gygi SP, Agard DA, Avidor-Reiss T. Sas-4 provides a scaffold for cytoplasmic complexes and tethers them in a centrosome. Nat Commun. 2011 Jun 21; 2:359. PMID: 21694707; PMCID: PMC3677532.
    66. Street TO, Lavery LA, Agard DA. Substrate binding drives large-scale conformational changes in the Hsp90 molecular chaperone. Mol Cell. 2011 Apr 08; 42(1):96-105. PMID: 21474071.
      View in: PubMed
    67. Zheng SQ, Branlund E, Kesthelyi B, Braunfeld MB, Cheng Y, Sedat JW, Agard DA. A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction. Ultramicroscopy. 2011 Jul; 111(8):1137-43. PMID: 21741915; PMCID: PMC3190582.
    68. Krukenberg KA, Street TO, Lavery LA, Agard DA. Conformational dynamics of the molecular chaperone Hsp90. Q Rev Biophys. 2011 May; 44(2):229-55. PMID: 21414251.
      View in: PubMed
    69. Rivera CR, Kollman JM, Polka JK, Agard DA, Mullins RD. Architecture and assembly of a divergent member of the ParM family of bacterial actin-like proteins. J Biol Chem. 2011 Apr 22; 286(16):14282-90. PMID: 21339292.
      View in: PubMed
    70. Ho BK, Agard DA. An improved strategy for generating forces in steered molecular dynamics: the mechanical unfolding of titin, e2lip3 and ubiquitin. PLoS One. 2010 Sep 29; 5(9). PMID: 20927369; PMCID: PMC2947501.
    71. Matsuda A, Shao L, Boulanger J, Kervrann C, Carlton PM, Kner P, Agard D, Sedat JW. Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP- histones. PLoS One. 2010 Sep 15; 5(9):e12768. PMID: 20856676; PMCID: PMC2939896.
    72. 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. Fast live simultaneous multiwavelength four-dimensional optical microscopy. Proc Natl Acad Sci U S A. 2010 Sep 14; 107(37):16016-22. PMID: 20705899; PMCID: PMC2941331.
    73. Kollman JM, Polka JK, Zelter A, Davis TN, Agard DA. Microtubule nucleating gamma-TuSC assembles structures with 13-fold microtubule-like symmetry. Nature. 2010 Aug 12; 466(7308):879-82. PMID: 20631709; PMCID: PMC2921000.
    74. Xu W, Xu F, Jones M, Keszthelyi B, Sedat J, Agard D, Mueller K. High-performance iterative electron tomography reconstruction with long-object compensation using graphics processing units (GPUs). J Struct Biol. 2010 Aug; 171(2):142-53. PMID: 20371381; PMCID: PMC2885506.
    75. 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. PMID: 20389670.
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    76. Ho BK, Agard DA. Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility. Protein Sci. 2010 Mar; 19(3):398-411. PMID: 20052683; PMCID: PMC2866267.
    77. Salimi NL, Ho B, Agard DA. Unfolding simulations reveal the mechanism of extreme unfolding cooperativity in the kinetically stable alpha-lytic protease. PLoS Comput Biol. 2010 Feb 26; 6(2):e1000689. PMID: 20195497; PMCID: PMC2829044.
    78. Kner P, Winoto L, Agard DA, Sedat JW. Closed loop adaptive optics for microscopy without a wavefront sensor. Proc SPIE Int Soc Opt Eng. 2010 Feb 24; 7570. PMID: 24392198.
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    79. 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 Feb; 237(2):136-47. PMID: 20096044; PMCID: PMC2897157.
    80. Gopalakrishnan J, Guichard P, Smith AH, Schwarz H, Agard DA, Marco S, Avidor-Reiss T. Self-assembling SAS-6 multimer is a core centriole building block. J Biol Chem. 2010 Mar 19; 285(12):8759-70. PMID: 20083610; PMCID: PMC2838298.
    81. Street TO, Krukenberg KA, Rosgen J, Bolen DW, Agard DA. Osmolyte-induced conformational changes in the Hsp90 molecular chaperone. Protein Sci. 2010 Jan; 19(1):57-65. PMID: 19890989; PMCID: PMC2817839.
    82. Zheng SQ, Sedat JW, Agard DA. Automated data collection for electron microscopic tomography. Methods Enzymol. 2010; 481:283-315. PMID: 20887862.
      View in: PubMed
    83. Vasko RC, Rodriguez RA, Cunningham CN, Ardi VC, Agard DA, McAlpine SR. Mechanistic studies of Sansalvamide A-amide: an allosteric modulator of Hsp90. ACS Med Chem Lett. 2010 Jan 01; 1(1):4-8. PMID: 20730035.
      View in: PubMed
    84. 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. Comput Methods Programs Biomed. 2010 Jun; 98(3):261-70. PMID: 19850372; PMCID: PMC2871068.
    85. 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 Sep; 18(9):1815-27. PMID: 19554567; PMCID: PMC2777357.
    86. 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. PMID: 19723581.
      View in: PubMed
    87. 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. PMID: 19666709; PMCID: PMC2753045.
    88. 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. PMID: 19545637; PMCID: PMC2776717.
    89. 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):278-91. PMID: 19427321; PMCID: PMC2735500.
    90. 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):11-8. PMID: 19361558; PMCID: PMC2724967.
    91. 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. PMID: 19343225; PMCID: PMC2660149.
    92. Southworth DR, Agard DA. Species-dependent ensembles of conserved conformational states define the Hsp90 chaperone ATPase cycle. Mol Cell. 2008 Dec 05; 32(5):631-40. PMID: 19061638; PMCID: PMC2633443.
    93. Nölting B, Agard DA. How general is the nucleation-condensation mechanism? Proteins. 2008 Nov 15; 73(3):754-64. PMID: 18498109; PMCID: PMC2776727.
    94. Ho BK, Agard DA. Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms. BMC Struct Biol. 2008 Oct 07; 8:41. PMID: 18840291; PMCID: PMC2569941.
    95. 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 Oct 17; 382(4):1089-106. PMID: 18694757; PMCID: PMC2745287.
    96. 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 Jun 06; 320(5881):1332-6. PMID: 18535242; PMCID: PMC2916659.
    97. Cunningham CN, Krukenberg KA, Agard DA. Intra- and intermonomer interactions are required to synergistically facilitate ATP hydrolysis in Hsp90. J Biol Chem. 2008 Jul 25; 283(30):21170-8. PMID: 18492664; PMCID: PMC2475720.
    98. 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 May; 16(5):755-65. PMID: 18462680; PMCID: PMC2600884.
    99. Trammell MA, Mahoney NM, Agard DA, Vale RD. Mob4 plays a role in spindle focusing in Drosophila S2 cells. J Cell Sci. 2008 Apr 15; 121(Pt 8):1284-92. PMID: 18388316; PMCID: PMC2851640.
    100. Rice LM, Montabana EA, Agard DA. The lattice as allosteric effector: structural studies of alphabeta- and gamma-tubulin clarify the role of GTP in microtubule assembly. Proc Natl Acad Sci U S A. 2008 Apr 08; 105(14):5378-83. PMID: 18388201.
      View in: PubMed
    101. 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 Jun; 94(12):4957-70. PMID: 18326650; PMCID: PMC2397368.
    102. 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 Jun; 94(12):4971-83. PMID: 18326649; PMCID: PMC2397336.
    103. Kollman JM, Zelter A, Muller EG, Fox B, Rice LM, Davis TN, Agard DA. The structure of the gamma-tubulin small complex: implications of its architecture and flexibility for microtubule nucleation. Mol Biol Cell. 2008 Jan; 19(1):207-15. PMID: 17978090.
      View in: PubMed
    104. Hom EF, Marchis F, Lee TK, Haase S, Agard DA, Sedat JW. 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 Jun; 24(6):1580-600. PMID: 17491626; PMCID: PMC3166524.
    105. Kelch BA, Agard DA. Mesophile versus thermophile: insights into the structural mechanisms of kinetic stability. J Mol Biol. 2007 Jul 20; 370(4):784-95. PMID: 17543987.
      View in: PubMed
    106. Kam Z, Kner P, Agard D, Sedat JW. Modelling the application of adaptive optics to wide-field microscope live imaging. J Microsc. 2007 Apr; 226(Pt 1):33-42. PMID: 17381707.
      View in: PubMed
    107. König P, Braunfeld MB, Sedat JW, Agard DA. The three-dimensional structure of in vitro reconstituted Xenopus laevis chromosomes by EM tomography. Chromosoma. 2007 Aug; 116(4):349-72. PMID: 17333236.
      View in: PubMed
    108. Kelch BA, Eagen KP, Erciyas FP, Humphris EL, Thomason AR, Mitsuiki S, Agard DA. Structural and mechanistic exploration of acid resistance: kinetic stability facilitates evolution of extremophilic behavior. J Mol Biol. 2007 May 04; 368(3):870-83. PMID: 17382344.
      View in: PubMed
    109. Zheng SQ, Kollman JM, Braunfeld MB, Sedat JW, Agard DA. Automated acquisition of electron microscopic random conical tilt sets. J Struct Biol. 2007 Jan; 157(1):148-55. PMID: 17169745; PMCID: PMC2556511.
    110. Shiau AK, Harris SF, Southworth DR, Agard DA. Structural Analysis of E. coli hsp90 reveals dramatic nucleotide-dependent conformational rearrangements. Cell. 2006 Oct 20; 127(2):329-40. PMID: 17055434.
      View in: PubMed
    111. 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 Oct 10; 22(21):8642-5. PMID: 17014099.
      View in: PubMed
    112. Yonekura K, Braunfeld MB, Maki-Yonekura S, Agard DA. Electron energy filtering significantly improves amplitude contrast of frozen-hydrated protein at 300kV. J Struct Biol. 2006 Dec; 156(3):524-36. PMID: 16987672.
      View in: PubMed
    113. Fuhrmann CN, Daugherty MD, Agard DA. 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. J Am Chem Soc. 2006 Jul 19; 128(28):9086-102. PMID: 16834383.
      View in: PubMed
    114. Zheng SQ, Keszthelyi B, Branlund E, Lyle JM, Braunfeld MB, Sedat JW, Agard DA. UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction. J Struct Biol. 2007 Jan; 157(1):138-47. PMID: 16904341.
      View in: PubMed
    115. Truhlar SM, Agard DA. The folding landscape of an alpha-lytic protease variant reveals the role of a conserved beta-hairpin in the development of kinetic stability. Proteins. 2005 Oct 01; 61(1):105-14. PMID: 16044461.
      View in: PubMed
    116. Ota N, Agard DA. Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J Mol Biol. 2005 Aug 12; 351(2):345-54. PMID: 16005893.
      View in: PubMed
    117. Moss WC, Haase S, Lyle JM, Agard DA, Sedat JW. A novel 3D wavelet-based filter for visualizing features in noisy biological data. J Microsc. 2005 Aug; 219(Pt 2):43-9. PMID: 16159339.
      View in: PubMed
    118. 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. PMID: 15917813.
      View in: PubMed
    119. 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. PMID: 15740746.
      View in: PubMed
    120. König 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. PMID: 15885431.
      View in: PubMed
    121. MacDowell AA, Celestre RS, Howells M, McKinney W, Krupnick J, Cambie D, Domning EE, Duarte RM, Kelez N, Plate DW, Cork CW, Earnest TN, Dickert J, Meigs G, Ralston C, Holton JM, Alber T, Berger JM, Agard DA, Padmore HA. Suite of three protein crystallography beamlines with single superconducting bend magnet as the source. J Synchrotron Radiat. 2004 Nov 01; 11(Pt 6):447-55. PMID: 15496731.
      View in: PubMed
    122. 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. PMID: 15369481.
      View in: PubMed
    123. Uzawa S, Li F, Jin Y, McDonald KL, Braunfeld MB, Agard DA, Cande WZ. 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 Dec; 15(12):5219-30. PMID: 15385623.
      View in: PubMed
    124. Zheng QS, Braunfeld MB, Sedat JW, Agard DA. An improved strategy for automated electron microscopic tomography. J Struct Biol. 2004 Aug; 147(2):91-101. PMID: 15193638.
      View in: PubMed
    125. Harris SF, Shiau AK, Agard DA. The crystal structure of the carboxy-terminal dimerization domain of htpG, the Escherichia coli Hsp90, reveals a potential substrate binding site. Structure. 2004 Jun; 12(6):1087-97. PMID: 15274928.
      View in: PubMed
    126. Fuhrmann CN, Kelch BA, Ota N, Agard DA. The 0.83 A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain. J Mol Biol. 2004 May 14; 338(5):999-1013. PMID: 15111063.
      View in: PubMed
    127. Cunningham EL, Agard DA. Disabling the folding catalyst is the last critical step in alpha-lytic protease folding. Protein Sci. 2004 Feb; 13(2):325-31. PMID: 14739318; PMCID: PMC2286698.
    128. Truhlar SM, Cunningham EL, Agard DA. The folding landscape of Streptomyces griseus protease B reveals the energetic costs and benefits associated with evolving kinetic stability. Protein Sci. 2004 Feb; 13(2):381-90. PMID: 14718653; PMCID: PMC2286692.
    129. Cunningham EL, Agard DA. Interdependent folding of the N- and C-terminal domains defines the cooperative folding of alpha-lytic protease. Biochemistry. 2003 Nov 18; 42(45):13212-9. PMID: 14609332.
      View in: PubMed
    130. Hanser BM, Gustafsson MG, Agard DA, Sedat JW. Phase retrieval for high-numerical-aperture optical systems. Opt Lett. 2003 May 15; 28(10):801-3. PMID: 12779151.
      View in: PubMed
    131. Kuntz ID, Agard DA. Assessment of the role of computations in structural biology. Adv Protein Chem. 2003; 66:1-25. PMID: 14631815.
      View in: PubMed
    132. Chen CY, Reese ML, Hwang PK, Ota N, Agard D, Brodsky FM. Clathrin light and heavy chain interface: alpha-helix binding superhelix loops via critical tryptophans. EMBO J. 2002 Nov 15; 21(22):6072-82. PMID: 12426379.
      View in: PubMed
    133. Rice LM, Agard DA. Centriole duplication: centrin in on answers? Curr Biol. 2002 Sep 17; 12(18):R618-9. PMID: 12372266.
      View in: PubMed
    134. Cunningham EL, Mau T, Truhlar SM, Agard DA. The pro region N-terminal domain provides specific interactions required for catalysis of alpha-lytic protease folding. Biochemistry. 2002 Jul 16; 41(28):8860-7. PMID: 12102628.
      View in: PubMed
    135. Shiau AK, Barstad D, Radek JT, Meyers MJ, Nettles KW, Katzenellenbogen BS, Katzenellenbogen JA, Agard DA, Greene GL. Structural characterization of a subtype-selective ligand reveals a novel mode of estrogen receptor antagonism. Nat Struct Biol. 2002 May; 9(5):359-64. PMID: 11953755.
      View in: PubMed
    136. Wille H, Michelitsch MD, Guenebaut V, Supattapone S, Serban A, Cohen FE, Agard DA, Prusiner SB. Structural studies of the scrapie prion protein by electron crystallography. Proc Natl Acad Sci U S A. 2002 Mar 19; 99(6):3563-8. PMID: 11891310; PMCID: PMC122563.
    137. Jaswal SS, Sohl JL, Davis JH, Agard DA. Energetic landscape of alpha-lytic protease optimizes longevity through kinetic stability. Nature. 2002 Jan 17; 415(6869):343-6. PMID: 11797014.
      View in: PubMed
    138. Tonelli M, Peters RJ, James TL, Agard DA. The solution structure of the viral binding domain of Tva, the cellular receptor for subgroup A avian leukosis and sarcoma virus. FEBS Lett. 2001 Dec 07; 509(2):161-8. PMID: 11768384.
      View in: PubMed
    139. Ota N, Agard DA. Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement. J Mol Biol. 2001 Nov 30; 314(3):607-17. PMID: 11846570.
      View in: PubMed
    140. Murphy SM, Preble AM, Patel UK, O'Connell KL, Dias DP, Moritz M, Agard D, Stults JT, Stearns T. GCP5 and GCP6: two new members of the human gamma-tubulin complex. Mol Biol Cell. 2001 Nov; 12(11):3340-52. PMID: 11694571.
      View in: PubMed
    141. Ota N, Agard DA. Enzyme specificity under dynamic control II: Principal component analysis of alpha-lytic protease using global and local solvent boundary conditions. Protein Sci. 2001 Jul; 10(7):1403-14. PMID: 11420442.
      View in: PubMed
    142. Marshall WF, Marko JF, Agard DA, Sedat JW. 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. PMID: 11369201.
      View in: PubMed
    143. Moritz M, Agard DA. Gamma-tubulin complexes and microtubule nucleation. Curr Opin Struct Biol. 2001 Apr; 11(2):174-81. PMID: 11297925.
      View in: PubMed
    144. Kam Z, Hanser B, Gustafsson MG, Agard DA, Sedat JW. Computational adaptive optics for live three-dimensional biological imaging. Proc Natl Acad Sci U S A. 2001 Mar 27; 98(7):3790-5. PMID: 11274396; PMCID: PMC31131.
    145. Moritz M, Braunfeld MB, Alberts BM, Agard DA. Reconstitution of centrosome microtubule nucleation in Drosophila. Methods Cell Biol. 2001; 67:141-8. PMID: 11550465.
      View in: PubMed
    146. Kushner PJ, Agard DA, Greene GL, Scanlan TS, Shiau AK, Uht RM, Webb P. Estrogen receptor pathways to AP-1. J Steroid Biochem Mol Biol. 2000 Nov 30; 74(5):311-7. PMID: 11162939.
      View in: PubMed
    147. Moritz M, Braunfeld MB, Guénebaut V, Heuser J, Agard DA. Structure of the gamma-tubulin ring complex: a template for microtubule nucleation. Nat Cell Biol. 2000 Jun; 2(6):365-70. PMID: 10854328.
      View in: PubMed
    148. Derman AI, Agard DA. Two energetically disparate folding pathways of alpha-lytic protease share a single transition state. Nat Struct Biol. 2000 May; 7(5):394-7. PMID: 10802737.
      View in: PubMed
    149. Bass HW, Riera-Lizarazu O, Ananiev EV, Bordoli SJ, Rines HW, Phillips RL, Sedat JW, Agard DA, Cande WZ. Evidence for the coincident initiation of homolog pairing and synapsis during the telomere-clustering (bouquet) stage of meiotic prophase. J Cell Sci. 2000 Mar; 113 ( Pt 6):1033-42. PMID: 10683151.
      View in: PubMed
    150. Jinnai H, Nishikawa Y, Spontak RJ, Smith SD, Agard DA, Hashimoto T. Direct measurement of interfacial curvature distributions in a bicontinuous block copolymer morphology. Phys Rev Lett. 2000 Jan 17; 84(3):518-21. PMID: 11015953.
      View in: PubMed
    151. Kushner PJ, Agard D, Feng WJ, Lopez G, Schiau A, Uht R, Webb P, Greene G. Oestrogen receptor function at classical and alternative response elements. Novartis Found Symp. 2000; 230:20-6; discussion 27-40. PMID: 10965500.
      View in: PubMed
    152. Cunningham EL, Jaswal SS, Sohl JL, Agard DA. Kinetic stability as a mechanism for protease longevity. Proc Natl Acad Sci U S A. 1999 Sep 28; 96(20):11008-14. PMID: 10500115; PMCID: PMC34233.
    153. Gustafsson MG, Agard DA, Sedat JW. I5M: 3D widefield light microscopy with better than 100 nm axial resolution. J Microsc. 1999 Jul; 195(Pt 1):10-6. PMID: 10444297.
      View in: PubMed
    154. Anderson DE, Peters RJ, Wilk B, Agard DA. alpha-lytic protease precursor: characterization of a structured folding intermediate. Biochemistry. 1999 Apr 13; 38(15):4728-35. PMID: 10200160.
      View in: PubMed
    155. Miller DW, Agard DA. Enzyme specificity under dynamic control: a normal mode analysis of alpha-lytic protease. J Mol Biol. 1999 Feb 12; 286(1):267-78. PMID: 9931265.
      View in: PubMed
    156. Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA, Greene GL. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell. 1998 Dec 23; 95(7):927-37. PMID: 9875847.
      View in: PubMed
    157. Sauter NK, Mau T, Rader SD, Agard DA. Structure of alpha-lytic protease complexed with its pro region. Nat Struct Biol. 1998 Nov; 5(11):945-50. PMID: 9808037.
      View in: PubMed
    158. Sohl JL, Jaswal SS, Agard DA. Unfolded conformations of alpha-lytic protease are more stable than its native state. Nature. 1998 Oct 22; 395(6704):817-9. PMID: 9796818.
      View in: PubMed
    159. Peters RJ, Shiau AK, Sohl JL, Anderson DE, Tang G, Silen JL, Agard DA. Pro region C-terminus:protease active site interactions are critical in catalyzing the folding of alpha-lytic protease. Biochemistry. 1998 Sep 01; 37(35):12058-67. PMID: 9724517.
      View in: PubMed
    160. Davis JH, Agard DA. Relationship between enzyme specificity and the backbone dynamics of free and inhibited alpha-lytic protease. Biochemistry. 1998 May 26; 37(21):7696-707. PMID: 9601029.
      View in: PubMed
    161. Fung JC, Marshall WF, Dernburg A, Agard DA, Sedat JW. Homologous chromosome pairing in Drosophila melanogaster proceeds through multiple independent initiations. J Cell Biol. 1998 Apr 06; 141(1):5-20. PMID: 9531544; PMCID: PMC2132734.
    162. Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A, Belmont A, Murray AW, Agard DA, Sedat JW. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol. 1997 Dec 01; 7(12):930-9. PMID: 9382846.
      View in: PubMed
    163. Han KF, Sedat JW, Agard DA. Practical image restoration of thick biological specimens using multiple focus levels in transmission electron microscopy. J Struct Biol. 1997 Dec; 120(3):237-44. PMID: 9441929.
      View in: PubMed
    164. Davis JH, Agard DA, Handel TM, Basus VJ. Alterations in chemical shifts and exchange broadening upon peptide boronic acid inhibitor binding to alpha-lytic protease. J Biomol NMR. 1997 Jul; 10(1):21-7. PMID: 9335113.
      View in: PubMed
    165. Rader SD, Agard DA. Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution. Protein Sci. 1997 Jul; 6(7):1375-86. PMID: 9232638; PMCID: PMC2143753.
    166. Bass HW, Marshall WF, Sedat JW, Agard DA, Cande WZ. Telomeres cluster de novo before the initiation of synapsis: a three-dimensional spatial analysis of telomere positions before and during meiotic prophase. J Cell Biol. 1997 Apr 07; 137(1):5-18. PMID: 9105032; PMCID: PMC2139864.
    167. Sohl JL, Shiau AK, Rader SD, Wilk BJ, Agard DA. Inhibition of alpha-lytic protease by pro region C-terminal steric occlusion of the active site. Biochemistry. 1997 Apr 01; 36(13):3894-902. PMID: 9092819.
      View in: PubMed
    168. Han KF, Gubbens AJ, Sedat JW, Agard DA. Optimal strategies for imaging thick biological specimens: exit wavefront reconstruction and energy-filtered imaging. J Microsc. 1996 Aug; 183(Pt 2):124-32. PMID: 8805824.
      View in: PubMed
    169. Dernburg AF, Broman KW, Fung JC, Marshall WF, Philips J, Agard DA, Sedat JW. Perturbation of nuclear architecture by long-distance chromosome interactions. Cell. 1996 May 31; 85(5):745-59. PMID: 8646782.
      View in: PubMed
    170. Marshall WF, Dernburg AF, Harmon B, Agard DA, Sedat JW. Specific interactions of chromatin with the nuclear envelope: positional determination within the nucleus in Drosophila melanogaster. Mol Biol Cell. 1996 May; 7(5):825-42. PMID: 8744953; PMCID: PMC275932.
    171. Scalettar BA, Swedlow JR, Sedat JW, Agard DA. Dispersion, aberration and deconvolution in multi-wavelength fluorescence images. J Microsc. 1996 Apr; 182(Pt 1):50-60. PMID: 8632447.
      View in: PubMed
    172. Paddy MR, Saumweber H, Agard DA, Sedat JW. Time-resolved, in vivo studies of mitotic spindle formation and nuclear lamina breakdown in Drosophila early embryos. J Cell Sci. 1996 Mar; 109 ( Pt 3):591-607. PMID: 8907705.
      View in: PubMed
    173. Chen H, Hughes DD, Chan TA, Sedat JW, Agard DA. IVE (Image Visualization Environment): a software platform for all three-dimensional microscopy applications. J Struct Biol. 1996 Jan-Feb; 116(1):56-60. PMID: 8742723.
      View in: PubMed
    174. Fung JC, Liu W, de Ruijter WJ, Chen H, Abbey CK, Sedat JW, Agard DA. Toward fully automated high-resolution electron tomography. J Struct Biol. 1996 Jan-Feb; 116(1):181-9. PMID: 8742742.
      View in: PubMed
    175. Mace JE, Agard DA. Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity. J Mol Biol. 1995 Dec 08; 254(4):720-36. PMID: 7500345.
      View in: PubMed
    176. Moritz M, Braunfeld MB, Sedat JW, Alberts B, Agard DA. Microtubule nucleation by gamma-tubulin-containing rings in the centrosome. Nature. 1995 Dec 07; 378(6557):638-40. PMID: 8524401.
      View in: PubMed
    177. Urata Y, Parmelee SJ, Agard DA, Sedat JW. A three-dimensional structural dissection of Drosophila polytene chromosomes. J Cell Biol. 1995 Oct; 131(2):279-95. PMID: 7593159; PMCID: PMC2199990.
    178. Moritz M, Braunfeld MB, Fung JC, Sedat JW, Alberts BM, Agard DA. Three-dimensional structural characterization of centrosomes from early Drosophila embryos. J Cell Biol. 1995 Sep; 130(5):1149-59. PMID: 7657699; PMCID: PMC2120545.
    179. Mace JE, Wilk BJ, Agard DA. Functional linkage between the active site of alpha-lytic protease and distant regions of structure: scanning alanine mutagenesis of a surface loop affects activity and substrate specificity. J Mol Biol. 1995 Aug 04; 251(1):116-34. PMID: 7643381.
      View in: PubMed
    180. Han KF, Sedat JW, Agard DA. Mechanism of image formation for thick biological specimens: exit wavefront reconstruction and electron energy-loss spectroscopic imaging. J Microsc. 1995 May; 178(Pt 2):107-19. PMID: 7783184.
      View in: PubMed
    181. Baker D, Agard DA. Influenza hemagglutinin: kinetic control of protein function. Structure. 1994 Oct 15; 2(10):907-10. PMID: 7866741.
      View in: PubMed
    182. Dong LM, Wilson C, Wardell MR, Simmons T, Mahley RW, Weisgraber KH, Agard DA. Human apolipoprotein E. Role of arginine 61 in mediating the lipoprotein preferences of the E3 and E4 isoforms. J Biol Chem. 1994 Sep 02; 269(35):22358-65. PMID: 8071364.
      View in: PubMed
    183. Wilson C, Mau T, Weisgraber KH, Wardell MR, Mahley RW, Agard DA. Salt bridge relay triggers defective LDL receptor binding by a mutant apolipoprotein. Structure. 1994 Aug 15; 2(8):713-8. PMID: 7994571.
      View in: PubMed
    184. Baker D, Agard DA. Kinetics versus thermodynamics in protein folding. Biochemistry. 1994 Jun 21; 33(24):7505-9. PMID: 8011615.
      View in: PubMed
    185. Braunfeld MB, Koster AJ, Sedat JW, Agard DA. Cryo automated electron tomography: towards high-resolution reconstructions of plastic-embedded structures. J Microsc. 1994 May; 174(Pt 2):75-84. PMID: 8051698.
      View in: PubMed
    186. Horowitz RA, Agard DA, Sedat JW, Woodcock CL. The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon. J Cell Biol. 1994 Apr; 125(1):1-10. PMID: 8138564; PMCID: PMC2120010.
    187. Dawe RK, Sedat JW, Agard DA, Cande WZ. Meiotic chromosome pairing in maize is associated with a novel chromatin organization. Cell. 1994 Mar 11; 76(5):901-12. PMID: 8124724.
      View in: PubMed
    188. Baker D, Shiau AK, Agard DA. The role of pro regions in protein folding. Curr Opin Cell Biol. 1993 Dec; 5(6):966-70. PMID: 8129949.
      View in: PubMed
    189. Bystroff C, Baker D, Fletterick RJ, Agard DA. PRISM: application to the solution of two protein structures. Acta Crystallogr D Biol Crystallogr. 1993 Sep 01; 49(Pt 5):440-8. PMID: 15299503.
      View in: PubMed
    190. Baker D, Bystroff C, Fletterick RJ, Agard DA. PRISM: topologically constrained phased refinement for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 1993 Sep 01; 49(Pt 5):429-39. PMID: 15299502.
      View in: PubMed
    191. Agard DA. To fold or not to fold.... Science. 1993 Jun 25; 260(5116):1903-4. PMID: 8100365.
      View in: PubMed
    192. Swedlow JR, Agard DA, Sedat JW. Chromosome structure inside the nucleus. Curr Opin Cell Biol. 1993 Jun; 5(3):412-6. PMID: 8352957.
      View in: PubMed
    193. Swedlow JR, Sedat JW, Agard DA. Multiple chromosomal populations of topoisomerase II detected in vivo by time-lapse, three-dimensional wide-field microscopy. Cell. 1993 Apr 09; 73(1):97-108. PMID: 8384932.
      View in: PubMed
    194. Wilson C, Gregoret LM, Agard DA. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J Mol Biol. 1993 Feb 20; 229(4):996-1006. PMID: 8445659.
      View in: PubMed
    195. Hiraoka Y, Dernburg AF, Parmelee SJ, Rykowski MC, Agard DA, Sedat JW. The onset of homologous chromosome pairing during Drosophila melanogaster embryogenesis. J Cell Biol. 1993 Feb; 120(3):591-600. PMID: 8425892; PMCID: PMC2119536.
    196. Baker D, Krukowski AE, Agard DA. Uniqueness and the ab initio phase problem in macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 1993 Jan 01; 49(Pt 1):186-92. PMID: 15299560.
      View in: PubMed
    197. Koster AJ, Chen H, Sedat JW, Agard DA. Automated microscopy for electron tomography. Ultramicroscopy. 1992 Oct; 46(1-4):207-27. PMID: 1481272.
      View in: PubMed
    198. Paddy MR, Agard DA, Sedat JW. An extended view of nuclear lamin structure, function, and dynamics. Semin Cell Biol. 1992 Aug; 3(4):255-66. PMID: 1421171.
      View in: PubMed
    199. Fujishige A, Smith KR, Silen JL, Agard DA. Correct folding of alpha-lytic protease is required for its extracellular secretion from Escherichia coli. J Cell Biol. 1992 Jul; 118(1):33-42. PMID: 1618906; PMCID: PMC2289522.
    200. Baker D, Silen JL, Agard DA. Protease pro region required for folding is a potent inhibitor of the mature enzyme. Proteins. 1992 Apr; 12(4):339-44. PMID: 1579568.
      View in: PubMed
    201. Baker D, Sohl JL, Agard DA. A protein-folding reaction under kinetic control. Nature. 1992 Mar 19; 356(6366):263-5. PMID: 1552947.
      View in: PubMed
    202. Bone R, Fujishige A, Kettner CA, Agard DA. Structural basis for broad specificity in alpha-lytic protease mutants. Biochemistry. 1991 Oct 29; 30(43):10388-98. PMID: 1931963.
      View in: PubMed
    203. Wilson C, Mace JE, Agard DA. Computational method for the design of enzymes with altered substrate specificity. J Mol Biol. 1991 Jul 20; 220(2):495-506. PMID: 1856870.
      View in: PubMed
    204. Wilson C, Wardell MR, Weisgraber KH, Mahley RW, Agard DA. Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E. Science. 1991 Jun 28; 252(5014):1817-22. PMID: 2063194.
      View in: PubMed
    205. Kam Z, Minden JS, Agard DA, Sedat JW, Leptin M. Drosophila gastrulation: analysis of cell shape changes in living embryos by three-dimensional fluorescence microscopy. Development. 1991 Jun; 112(2):365-70. PMID: 1794308.
      View in: PubMed
    206. Hiraoka Y, Swedlow JR, Paddy MR, Agard DA, Sedat JW. Three-dimensional multiple-wavelength fluorescence microscopy for the structural analysis of biological phenomena. Semin Cell Biol. 1991 Jun; 2(3):153-65. PMID: 1720334.
      View in: PubMed
    207. Bone R, Sampson NS, Bartlett PA, Agard DA. Crystal structures of alpha-lytic protease complexes with irreversibly bound phosphonate esters. Biochemistry. 1991 Feb 26; 30(8):2263-72. PMID: 1998685.
      View in: PubMed
    208. Caldwell JW, Agard DA, Kollman PA. Free energy calculations on binding and catalysis by alpha-lytic protease: the role of substrate size in the P1 pocket. Proteins. 1991; 10(2):140-8. PMID: 1896427.
      View in: PubMed
    209. Hiraoka Y, Agard DA, Sedat JW. Temporal and spatial coordination of chromosome movement, spindle formation, and nuclear envelope breakdown during prometaphase in Drosophila melanogaster embryos. J Cell Biol. 1990 Dec; 111(6 Pt 2):2815-28. PMID: 2125300; PMCID: PMC2116368.
    210. Paddy MR, Belmont AS, Saumweber H, Agard DA, Sedat JW. Interphase nuclear envelope lamins form a discontinuous network that interacts with only a fraction of the chromatin in the nuclear periphery. Cell. 1990 Jul 13; 62(1):89-106. PMID: 2194675.
      View in: PubMed
    211. Hiraoka Y, Sedat JW, Agard DA. Determination of three-dimensional imaging properties of a light microscope system. Partial confocal behavior in epifluorescence microscopy. Biophys J. 1990 Feb; 57(2):325-33. PMID: 2317554; PMCID: PMC1280673.
    212. Hiraoka Y, Minden JS, Swedlow JR, Sedat JW, Agard DA. Focal points for chromosome condensation and decondensation revealed by three-dimensional in vivo time-lapse microscopy. Nature. 1989 Nov 16; 342(6247):293-6. PMID: 2509947.
      View in: PubMed
    213. Silen JL, Agard DA. The alpha-lytic protease pro-region does not require a physical linkage to activate the protease domain in vivo. Nature. 1989 Oct 05; 341(6241):462-4. PMID: 2507926.
      View in: PubMed
    214. Bone R, Frank D, Kettner CA, Agard DA. Structural analysis of specificity: alpha-lytic protease complexes with analogues of reaction intermediates. Biochemistry. 1989 Sep 19; 28(19):7600-9. PMID: 2611204.
      View in: PubMed
    215. Belmont AS, Braunfeld MB, Sedat JW, Agard DA. Large-scale chromatin structural domains within mitotic and interphase chromosomes in vivo and in vitro. Chromosoma. 1989 Aug; 98(2):129-43. PMID: 2476279.
      View in: PubMed
    216. Minden JS, Agard DA, Sedat JW, Alberts BM. Direct cell lineage analysis in Drosophila melanogaster by time-lapse, three-dimensional optical microscopy of living embryos. J Cell Biol. 1989 Aug; 109(2):505-16. PMID: 2503522; PMCID: PMC2115721.
    217. Bone R, Silen JL, Agard DA. Structural plasticity broadens the specificity of an engineered protease. Nature. 1989 May 18; 339(6221):191-5. PMID: 2716847.
      View in: PubMed
    218. Silen JL, Frank D, Fujishige A, Bone R, Agard DA. Analysis of prepro-alpha-lytic protease expression in Escherichia coli reveals that the pro region is required for activity. J Bacteriol. 1989 Mar; 171(3):1320-5. PMID: 2646278; PMCID: PMC209748.
    219. Agard DA, Hiraoka Y, Shaw P, Sedat JW. Fluorescence microscopy in three dimensions. Methods Cell Biol. 1989; 30:353-77. PMID: 2494418.
      View in: PubMed
    220. Shaw PJ, Agard DA, Hiraoka Y, Sedat JW. Tilted view reconstruction in optical microscopy. Three-dimensional reconstruction of Drosophila melanogaster embryo nuclei. Biophys J. 1989 Jan; 55(1):101-10. PMID: 2495031; PMCID: PMC1330446.
    221. Aikens RS, Agard DA, Sedat JW. Solid-state imagers for microscopy. Methods Cell Biol. 1989; 29:291-313. PMID: 2643764.
      View in: PubMed
    222. Kettner CA, Bone R, Agard DA, Bachovchin WW. Kinetic properties of the binding of alpha-lytic protease to peptide boronic acids. Biochemistry. 1988 Oct 04; 27(20):7682-8. PMID: 3207699.
      View in: PubMed
    223. Silen JL, McGrath CN, Smith KR, Agard DA. Molecular analysis of the gene encoding alpha-lytic protease: evidence for a preproenzyme. Gene. 1988 Sep 30; 69(2):237-44. PMID: 3234766.
      View in: PubMed
    224. Rykowski MC, Parmelee SJ, Agard DA, Sedat JW. Precise determination of the molecular limits of a polytene chromosome band: regulatory sequences for the Notch gene are in the interband. Cell. 1988 Aug 12; 54(4):461-72. PMID: 3135939.
      View in: PubMed
    225. Aggerbeck LP, Wetterau JR, Weisgraber KH, Mahley RW, Agard DA. 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. 1988 Jul 05; 202(1):179-81. PMID: 3172212.
      View in: PubMed
    226. Agard DA, Hiraoka Y, Sedat JW. Three-dimensional light microscopy of diploid Drosophila chromosomes. Cell Motil Cytoskeleton. 1988; 10(1-2):18-27. PMID: 3141069.
      View in: PubMed
    227. Bone R, Shenvi AB, Kettner CA, Agard DA. Serine protease mechanism: structure of an inhibitory complex of alpha-lytic protease and a tightly bound peptide boronic acid. Biochemistry. 1987 Dec 01; 26(24):7609-14. PMID: 3122831.
      View in: PubMed
    228. Hiraoka Y, Sedat JW, Agard DA. The use of a charge-coupled device for quantitative optical microscopy of biological structures. Science. 1987 Oct 02; 238(4823):36-41. PMID: 3116667.
      View in: PubMed
    229. Belmont AS, Sedat JW, Agard DA. A three-dimensional approach to mitotic chromosome structure: evidence for a complex hierarchical organization. J Cell Biol. 1987 Jul; 105(1):77-92. PMID: 3112167; PMCID: PMC2114920.
    230. Thomas GJ, Agard DA. Quantitative analysis of nucleic acids, proteins, and viruses by Raman band deconvolution. Biophys J. 1984 Dec; 46(6):763-8. PMID: 6083811; PMCID: PMC1435106.
    231. Gruenbaum Y, Hochstrasser M, Mathog D, Saumweber H, Agard DA, Sedat JW. Spatial organization of the Drosophila nucleus: a three-dimensional cytogenetic study. J Cell Sci Suppl. 1984; 1:223-34. PMID: 6442295.
      View in: PubMed
    232. Agard DA, Sedat JW. Three-dimensional architecture of a polytene nucleus. Nature. 1983 Apr 21; 302(5910):676-81. PMID: 6403872.
      View in: PubMed