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Stewart, Phoebe L., Ph.D.
Position:
Associate Professor of Molecular Physiology & Biophysics
Department:
Molecular Physiology & Biophysics
Lab Url:
N/A
Phone Number:
615-322-7908
Email Address:
phoebe.stewart@vanderbilt.edu
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| Office
Address |
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Mailing
Address |
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710 Light Hall
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710 Light Hall 0615
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| Research
Keywords |
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Cryo-Electron Microscopy,Cryo-EM,Protein Structure,Structural Biology,Virus |
| Research
Specialty |
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Structure of macromolecular assemblies by cryo-electron microscopy and three-dimensional image processing |
| Research
Description |
Cryo-electron microscopy (cryo-EM) combined with computer image reconstruction is a powerful way to visualize the structure of large macromolecular assemblies. The technique involves freezing a droplet of sample in a cryogen, which preserves the sample in an amorphous ice layer on an EM sample grid. The grid is kept frozen (at liquid nitrogen or helium temperatures) while it is imaged in an electron microscope and digital images are collected. Image analysis software is then used to synthesize images of thousands of particles into a detailed three-dimensional structure. Atomic resolution structures of component molecules or domains can often be mapped into the cryo-EM density. This approach has been successfully applied to icosahedral viruses as well as symmetric and asymmetric protein assemblies (>200 kDa). Recent advances in liquid helium cryo-microscopy, automation of data acquisition, and image processing on multi-processor computers, offer the potential of reaching near atomic resolution (3-5 Angstroms) by cryo-EM methods.
Ongoing and new projects include:
1. Adenovirus, adenovirus-receptor and antibody complexes, engineered adenovirus vectors
2. The DNA-dependent protein kinase, DNA-PK, an enzyme involved in DNA double-strand break repair and immunoglobulin gene rearrangement
3. The vault particle, a ubiquitous cytoplasmic RNA-protein complex implicated in cancer cell multi-drug resistance
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Kendall, A, McDonald, M, Bian, W, Bowles, T, Baumgarten, SC, Shi, J, Stewart, PL, Bullitt, E, Gore, D, Irving, TC, Havens, WM, Ghabrial, SA, Wall, JS, Stubbs, G. Structure of Flexible Filamentous Plant Viruses. J Virol, , , 2008 Pattanayek, R, Williams, DR, Pattanayek, S, Mori, T, Johnson, CH, Stewart, PL, Egli, M. Structural model of the circadian clock KaiB-KaiC complex and mechanism for modulation of KaiC phosphorylation. EMBO J, 27(12), 1767-78, 2008 Shi, J, Williams, DR, Stewart, PL. A Script-Assisted Microscopy (SAM) package to improve data acquisition rates on FEI Tecnai electron microscopes equipped with Gatan CCD cameras. J Struct Biol, , , 2008 Williams, DR, Lee, KJ, Shi, J, Chen, DJ, Stewart, PL. Cryo-EM structure of the DNA-dependent protein kinase catalytic subunit at subnanometer resolution reveals alpha helices and insight into DNA binding. Structure, 16(3), 468-77, 2008 Mori, T, Williams, DR, Byrne, MO, Qin, X, Egli, M, Mchaourab, HS, Stewart, PL, Johnson, CH. Elucidating the ticking of an in vitro circadian clockwork. PLoS Biol, 5(4), e93, 2007 Stewart, PL, Nemerow, GR. Cell integrins: commonly used receptors for diverse viral pathogens. Trends Microbiol, 15(11), 500-7, 2007 Mathis JM, Stewart PL, Zhu ZB, Curiel DT. The Biology Behind: Advanced Generation Adenoviral Virotherapy Agents Embody Enhanced Potency Based Upon CAR-Independent Tropism. Clinical Cancer Research, 12, 2651-2656, 2006 Pattanayek, R, Williams, DR, Pattanayek, S, Xu, Y, Mori, T, Johnson, CH, Stewart, PL, Egli, M. Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian clock using hybrid structural methods. EMBO J, 25(9), 2017-28, 2006 Saban, SD, Silvestry, M, Nemerow, GR, Stewart, PL. Visualization of alpha-helices in a 6-angstrom resolution cryoelectron microscopy structure of adenovirus allows refinement of capsid protein assignments. J Virol, 80(24), 12049-59, 2006 Shi, J, Koteiche, HA, McHaourab, HS, Stewart, PL. Cryoelectron microscopy and EPR analysis of engineered symmetric and polydisperse Hsp16.5 assemblies reveals determinants of polydispersity and substrate binding. J Biol Chem, 281(52), 40420-8, 2006 Kickhoefer VA, Garcia Y, Mikyas Y, Johansson E, Zhou JC, Raval-Fernandes S, Minoofar P, Zink JI, Dunn B, Stewart PL, Rome LH. Engineering of Vault Nanocapsules with Enzymatic and Fluorescent Properties. PNAS, 102, 4348-4352, 2005 Koteiche, HA, Chiu, S, Majdoch, RL, Stewart, PL, Mchaourab, HS. Atomic models by cryo-EM and site-directed spin labeling: application to the N-terminal region of Hsp16.5. Structure, 13(8), 1165-71, 2005 Saban, SD, Nepomuceno, RR, Gritton, LD, Nemerow, GR, Stewart, PL. CryoEM structure at 9A resolution of an adenovirus vector targeted to hematopoietic cells. J Mol Biol, 349(3), 526-37, 2005 Stewart, PL, Makabi, M, Lang, J, Dickey-Sims, C, Robertson, AJ, Coffman, JA, Suprenant, KA. Sea urchin vault structure, composition, and differential localization during
development. BMC Dev Biol, 5(1), 3, 2005 Mikyas Y, Makabi M, Raval-Fernandes S, Harrington L, Kickhoefer VA, Rome LH, Stewart, PL. Cryoelectron microscopy imaging of recombinant and tissue derived vaults: localization
of the MVP N termini and VPARP. J Mol Biol, 344(1), 91-105, 2004 Varghese R, Mikyas Y, Stewart PL, Ralston R. Postentry neutralization of adenovirus type 5 by an antihexon antibody. J Virol, 78(22), 12320-32, 2004 Stewart PL, Dermody TS, Nemerow GR. Structural basis of nonenveloped virus cell entry. Adv Protein Chem, 64, 455-91, 2003 Wu E, Pache L, Von Seggern DJ, Mullen T-M, Mikyas Y, Stewart PL, Nemerow GR. Flexibility of the adenovirus fiber is required for efficient receptor interaction. J Virol, 77, 7225-35, 2003 Chiu, C Y, Wu, E, Brown, S L, Von Seggern, D J, Nemerow, G R, Stewart, P L. Structural analysis of a fiber-pseudotyped adenovirus with ocular tropism suggests
differential modes of cell receptor interactions. J Virol, 75(11), 5375-80, 2001 Kickhoefer, V A, Liu, Y, Kong, L B, Snow, B E, Stewart, P L, Harrington, L, Rome, L H. The Telomerase/vault-associated protein TEP1 is required for vault RNA stability
and its association with the vault particle. J Cell Biol, 152(1), 157-64, 2001 Miyoshi, E K, Stewart, P L, Kincade, P W, Lee, M B, Thompson, A A, Wall, R. Aberrant expression and localization of the cytoskeleton-binding pp52 (LSP1)
protein in hairy cell leukemia. Leuk Res, 25(1), 57-67, 2001 Montesano-Roditis, L, Glitz, D G, Traut, R R, Stewart, P L. Cryo-electron microscopic localization of protein L7/L12 within the Escherichia
coli 70 S ribosome by difference mapping and Nanogold labeling. J Biol Chem, 276(17), 14117-23, 2001 Nemerow, G R, Stewart, P L. Antibody neutralization epitopes and integrin binding sites on nonenveloped viruses. Virology, 288, 189-91, 2001 Haley, D A, Bova, M P, Huang, Q L, Mchaourab, H S, Stewart, P L. Small heat-shock protein structures reveal a continuum from symmetric to variable
assemblies. J Mol Biol, 298(2), 261-72, 2000 Kong, L B, Siva, A C, Kickhoefer, V A, Rome, L H, Stewart, P L. RNA location and modeling of a WD40 repeat domain within the vault. RNA, 6(6), 890-900, 2000 Stewart, P L, Cary, R B, Peterson, S R, Chiu, C Y. Digitally collected cryo-electron micrographs for single particle reconstruction. Microsc Res Tech, 49(3), 224-32, 2000 Bova, M P, Yaron, O, Huang, Q, Ding, L, Haley, D A, Stewart, P L, Horwitz, J. Mutation R120G in alphaB-crystallin, which is linked to a desmin-related myopathy,
results in an irregular structure and defective chaperone-like function. Proc Natl Acad Sci U S A, 96(11), 6137-42, 1999 Chiu, C Y, Mathias, P, Nemerow, G R, Stewart, P L. Structure of adenovirus complexed with its internalization receptor, alphavbeta5
integrin. J Virol, 73(8), 6759-68, 1999 Haley, D A, Horwitz, J, Stewart, P L. Image restrained modeling of alphaB-crystallin. Exp Eye Res, 68(1), 133-6, 1999 Horwitz, J, Bova, M P, Ding, L L, Haley, D A, Stewart, P L. Lens alpha-crystallin: function and structure. Eye, 13 ( Pt 3b), 403-8, 1999 Kong, L B, Siva, A C, Rome, L H, Stewart, P L. Structure of the vault, a ubiquitous celular component. Structure Fold Des, 7(4), 371-9, 1999 Nemerow, G R, Stewart, P L. Role of alpha(v) integrins in adenovirus cell entry and gene delivery. Microbiol Mol Biol Rev, 63(3), 725-34, 1999 Pace, K E, Lee, C, Stewart, P L, Baum, L G. Restricted receptor segregation into membrane microdomains occurs on human
T cells during apoptosis induced by galectin-1. J Immunol, 163(7), 3801-11, 1999 Stewart, P L, Chiu, C Y, Haley, D A, Kong, L B, Schlessman, J L. Review: resolution issues in single-particle reconstruction. J Struct Biol, 128(1), 58-64, 1999 Von Seggern, D J, Chiu, C Y, Fleck, S K, Stewart, P L, Nemerow, G R. A helper-independent adenovirus vector with E1, E3, and fiber deleted: structure
and infectivity of fiberless particles. J Virol, 73(2), 1601-8, 1999 Chiu, C Y, Cary, R B, Chen, D J, Peterson, S R, Stewart, P L. Cryo-EM imaging of the catalytic subunit of the DNA-dependent protein kinase. J Mol Biol, 284(4), 1075-81, 1998 Haley, D A, Horwitz, J, Stewart, P L. The small heat-shock protein, alphaB-crystallin, has a variable quaternary
structure. J Mol Biol, 277(1), 27-35, 1998 Keith, D E, Anton, B, Murray, S R, Zaki, P A, Chu, P C, Lissin, D V, Monteillet-Agius, G, Stewart, P L, Evans, C J, von Zastrow, M. mu-Opioid receptor internalization: opiate drugs have differential effects
on a conserved endocytic mechanism in vitro and in the mammalian brain. Mol Pharmacol, 53(3), 377-84, 1998 Kong, L B, An, D, Ackerson, B, Canon, J, Rey, O, Chen, I S, Krogstad, P, Stewart, P L. Cryoelectron microscopic examination of human immunodeficiency virus type 1
virions with mutations in the cyclophilin A binding loop. J Virol, 72(5), 4403-7, 1998 Shah, A K, Stewart, P L. QVIEW: software for rapid selection of particles from digital electron micrographs. J Struct Biol, 123(1), 17-21, 1998 Prigozy, T I, Sieling, P A, Clemens, D, Stewart, P L, Behar, S M, Porcelli, S A, Brenner, M B, Modlin, R L, Kronenberg, M. The mannose receptor delivers lipoglycan antigens to endosomes for presentation
to T cells by CD1b molecules. Immunity, 6(2), 187-97, 1997 Stewart, P L, Chiu, C Y, Huang, S, Muir, T, Zhao, Y, Chait, B, Mathias, P, Nemerow, G R. Cryo-EM visualization of an exposed RGD epitope on adenovirus that escapes
antibody neutralization. EMBO J, 16(6), 1189-98, 1997 Stewart, P L, Nemerow, G R. Recent structural solutions for antibody neutralization of viruses. Trends Microbiol, 5(6), 229-33, 1997 Stewart, P L, Burnett, R M. Adenovirus structure by X-ray crystallography and electron microscopy. Curr Top Microbiol Immunol, 199 ( Pt 1), 25-38, 1995 Stewart, P L. Integrating cryo-electron microscopy into drug-design strategies. Trends Biotechnol, 12(11), 429-31, 1994 Stewart, P L, Fuller, S D, Burnett, R M. Difference imaging of adenovirus: bridging the resolution gap between X-ray
crystallography and electron microscopy. EMBO J, 12(7), 2589-99, 1993 Stewart, P L, Ghosh, S, Bamford, D H, Burnett, R M. Crystallization of the major coat protein of PRD1, a bacteriophage with an
internal membrane. J Mol Biol, 230(1), 349-52, 1993 Stewart, P L, Burnett, R M, Cyrklaff, M, Fuller, S D. Image reconstruction reveals the complex molecular organization of adenovirus. Cell, 67(1), 145-54, 1991 Opella, S J, Stewart, P L. Solid-state nuclear magnetic resonance structural studies of proteins. Methods Enzymol, 176, 242-75, 1989 Opella, S J, Stewart, P L, Valentine, K G. Protein structure by solid-state NMR spectroscopy. Q Rev Biophys, 19(1-2), 7-49, 1987 |
| Postdoctoral
Position Available |
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| Postdoctoral
Position Details |
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N/A |
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