Past Journal Clubs
02/25/00 Three-dimensional Structure of Bovine NADH:Ubiquinone Oxidoreductase
(Complex I) at 22A in Ice (1998) Grigorieff. JMB, 277, 1033-1046.
[Carolyn]
David's presentation on
indexing helical diffraction patterns
04/06/01 Single particle reconstruction of RNA PolII
[John Craighead]
03/10/00 Structure of a-latrotoxin oligomers reveals that divalent cation-
dependent tetramers form membrane pores (2000) Orlova et al. Nat. Struct. Biol.,
7, 48-53.
[Anchi]
03/24/00 Clathrin coats at 21A resolution: a cellular assembly desgined to
recycle multiple membrane receptors (1998) Smith et al. EMBO J., 17, 4943-4953.
Functional Organization of Clathrin in Coats: Combining Electron Cryomicroscopy
and X-ray Crystallography (1999) Musacchio et al. Molecular Cell, 3, 761-770.
[Jawdat]
04/07/00 Scaling Structure Factor Amplitudes in Electron Cryomicropscopy Using
X-ray Solution Scattering (1999) Schmid et al. J. Struct. Biol., 128, 51-57.
[Mark D.]
05/05/00 Three-dimensional structure of poliovirus receptor bound to poliovirus
(2000) Belnap et al. Proc. Natl. Acad. Sci. 97, 73-78. Interaction of the
poliovirus receptor with poliovirus (2000) He et al. Proc. Natl. Acad. Sci. 97,
79-84.
[Kelly]
06/02/00 Electron-crystallographic Refinement of the Structure of
Bacteriorhodopsin (1996) Grigorieff et al. JMB 259, 393-421.
[Gary]
06/16/00 Crystal structure of the calcium pump of sarcoplasmic reticulum
at 2.6A resolution (2000) Toyoshima et al. Nature 405, 647-655.
[Alok]
07/14/00 Three-Dimensional Structure of the Human TFIID-IIA Complex (1999)
Andel et al. Science 286, 2153-2156.
[Isabelle]
08/11/00 Assembly and Analysis of Conical Models for the HIV-1 Core (1999)
Ganser et al. Science 283, 80-83.
[Barbie Ganser]
08/25/00 Mapping and fuzzy classification of macromolecular images using
self-organising neural networks (2000) Pascual et al. Ultramicroscopy 84, 85-99.
[Jose-Maria Carazo]
09/08/00 Three conformations of an Archael Chaperonin, TF55 from Sulfolobus
shibatae (2000) Schoehn et al. JMB 296, 813-819
[Josh]
09/22/00 Three-dimensional Structure of Ryanodine Receptor Isoform Three
in Two Conformational States as Visualized by Cryo-electron Microscopy (2000)
Sharma et al. JBC 275, 9485-9491.
[Daniel]
10/20/00 Group II chaperonin in an open conformation examined by electron
tomography (1998) Nitsch et al. Nat. Struct. Biol. 5, 855-857.
[Brian]
11/03/00 Scientific Writing : My Approach and Irreverent Opinions
[Mark Y.]
11/17/00 (1968) DeRosier & Klug Nature, 217, 130-.
[Carolyn]
12/15/00 Eukaryotic chaperonin CCT stabilizes actin and tubulin folding
intermediates in open quasi-native conformations (2000) Llorca et al. EMBO J.,
22, 5971-5979.
[Pablo]
01/21/01 Structure of Membran-bound Annexin A5 Trimers: A Hybrid Cryo-EM-
X-ray Crystallography Study (2000) Oling et al. JMB 304, 561-573.
[Anchi]
01/26/01 Small Heat-Shock Protein Structures Reveal a Continuum from Symmetric
to Variable Assemblies (2000) Haley et al. JMB 298, 261-272.
[Isabelle]
02/23/01 Leginon: An Automated System for Acquisition of Images from Vitreous
Ice Specimens (2000) Caragher et al. JSB 132, 33-45.
[Abel]
03/09/01 Computer Image Processing of Electron Micrographs of Biological
Structures with Helical Symmetry (1988) Stewart. J. Electron Microscopy
Technique 9, 325-358.
[David DeRosier]
05/04/01 Using EM reconstructions of viruses to phase Xray data
[Vijay Reddy]
05/18/01 Fitting methods I
[Willy Wriggers]
06/01/01 Fitting methods II
[Niels Volkmann]
06/15/01 Nature 386:88-91; Nature 386:91-94; Molecular Cell 3:771-780
[Kelly]
07/16/01 Jean Lepault, Isabelle Petitpas, Inge Erk, Jorge Navaza, Dominique
Bigot, Michel Dona, Patrice Vachette, Jean Cohen, and Felix A. Rey
Structural polymorphism of the major capsid protein of rotavirus
EMBO J. 2001 20: 1498-1507.
[Jawdat]
07/30/01
'Perspectives of Molecular and Cellular Electron Tomography'
AJ Koster, R Grimm, D Typke, R Hegerl, A Stoschek, J Walz, W Baumeister
(1997) Journal of Structural Biology 120: 276-308.
'3D reconstruction with CTF correction from energy-filtered CryoEM
micrographs: procedure and application to the 70S E.coli ribosome'
J Zhu, PA Penczek, R Schroder, J Frank (1997) Journal of Structural
Biology 118: 197-219.
'Zero-loss energy filtering as improved imaging mode in cryoEM of
frozen-hydrated specimens'
RR Schroder, W Hofmann and JF Menetret (1990) Journal of Structural
Biology 105: 28-34.
[Mark D.]
08/13/01
1.
Hesse J, Hebert H, Koeck PJ. Related Articles
Evaluation of scanners and CCD cameras for high-resolution TEM of protein
crystals and single particles.
Microsc Res Tech. 2000 May 1;49(3):292-300.
2.
Zuo JM. Related Articles
Electron detection characteristics of a slow-scan CCD camera, imaging plates
and film, and electron image restoration.
Microsc Res Tech. 2000 May 1;49(3):245-68.
3.
Stewart PL, Cary RB, Peterson SR, Chiu CY. Related Articles
Digitally collected cryo-electron micrographs for single particle
reconstruction.
Microsc Res Tech. 2000 May 1;49(3):224-32.
Article, in PDF format, please copy it from
4.
Brink J, Wei Tam M. Related Articles
Processing of electron diffraction patterns acquired on a slow-scan CCD
camera.
J Struct Biol. 1996 Jan-Feb;116(1):144-9.
[Gary]
09/10/01
1.
The structure of pariacoto virus reveals a dodecahedral cage of duplex
RNA.
Tang L, Johnson KN, Ball LA, Lin T, Yeager M, Johnson JE.
Nat Struct Biol. 2001 Jan;8(1):77-83.
2.
Enhanced genome annotation using structural profiles in the program
3D-PSSM.
Kelley LA, MacCallum RM, Sternberg MJ.
J Mol Biol. 2000 Jun 2;299(2):499-520.
[Liang]
10/08/01
Automated Identification of Filaments in Cryo-electron Microscopy Images.
Zhu et al.
J. Struct. Biol., 2002. In press.
[Yuanxin]
10/22/01
Single-Particle Approaches in the Analysis of Small 2D Crystals of the
Mitochondrial Channel VDAC.
Verschoor et al.,
J. Struct. Biol. 2001. 133, 254-265.
[Anchi]
11/19/01
Cryoelectron-Microscopy Image Reconstruction of Symmetry
Mismatches in Bacteriophage 029.
Morais et al.
J. Struct. Biol. 2001. 135, 38-46 (2001)
[Carolyn]
12/03/01
A robust algorithm for the reconstruction of helical filaments using
single-particle methods.
Egelman
Ultramicroscopy, 2000, 85, 225-234
[Mark D.]
12/17/01
1. Identification of spherical virus particles in digitized images of
entire electron micrographs.
Boier Martin IM, Marinescu DC, Lynch RE, Baker TS.
J Struct Biol 1997 Nov;120(2):146-57
2. Local average intensity-based method for identifying spherical
particles in electron micrographs.
Kivioja T, Ravantti J, Verkhovsky A, Ukkonen E, Bamford D.
J Struct Biol 2000 Aug;131(2):126-34
[Brian]
02/11/02
Correspondence analysis of sinogram lines. Sinogram trajectories in factor
space replace raw images in the orientation of projections of
macromolecular assemblies.
Bellon PR, Cantele F, and Lanzavecchia S. (2001)
Ultramicroscopy 87. 187-97.
[Josh]
02/25/02
"Fast Rotational Matching"
"The Fast Rotation Function", in "The Molecular Replacement Method",
RA Crowther, edited by M.G.Rossmann (Gordon and Breach, 1972).
[Julio]
03/11/02
Ruben Abagyan
Flexible docking and molecular modelling
03/25/02
Escherichia coli 70S ribosome at 15A resolution by cryo-electron
microscopy: localalization of fMET-tRNA and fitting of L1 protein
Malhotra et al, 1998. JMB 280, 103-116.
[Carolyn]
04/08/02
Cryo-negative staining
Adrian M, Dubochet J, Fuller SD, Harris JR.
Micron 1998 Apr-Jun;29(2-3):145-60
[Gary]
05/20/02
Estimation of variance distribution in three-dimensional
reconstruction. II. Applications
Weiping Liu, Nicolas Boisset, and Joachim Frank (1995)
J. Opt. Soc. Am. A /Vol.12, 2628-2635
[Anchi]
06/03/02
Acehan D., Jiang X., Morgan D.G., Heuser J., Wang X., Akey C.;
Three-Dimensional Structure of the Apoptosome: Implications for
Assembly, Procaspase-9 Binding, and Activation;
Molecular Cell 2002 9: 423-432
[Jawdat]
06/17/02
"Perforated support films with pre-defined hole size, shape and
arrangement"
E. Ermantraut, K. Wohlfart, and W. Tichelaar
Ultramicroscopy 74:75-81 (1998)
[Kelly]
07/29/02
Electron tomography of single ice-embedded Macromolecules:
Three-dimensional alignement and classification. Walz et al., 1997.
Journal of structural biology 120, 387-395.
[Isabelle]
08/12/02
New Insights into the Spring-Loaded Conformational Change of Influenza
Virus Hemagglutinin
by Jennifer A. Gruenke, R. Todd Armstrong, William W. Newcomb, Jay C.
Brown, and Judith M. White
Journal of Virology, May 2002, p. 4456-4466, Vol. 76, No. 9
[Ben]
09/09/02
William V. Nicholson and Robert M. Glaeser (2001) Review: automatic
particle detection in electron microscopy. Journal of Structure Biology
133, 90-101.
[Yuanxin]
10/07/02
"Hepatitis C Virus IRES RNA-Induced Changes in the Conformation of the 40S
Ribosomal Subunit" Christian M. T. Spahn, Jeffrey S. Kieft, Robert A.
Grassucci, Pawel A. Penczek, Kaihong Zhou, Jennifer A. Doudna, and Joachim
Frank Science 291: 1959 (2001)
[John]
10/21/02
The Structure of the Archeabacterial Flagellar Filament of the
Extreme Halophile Halobacterium salinarum R1M1 and its Relation to
Eubacterial Flagellar Filaments and Type IV Pili. S. Cohen-Krausz
and S. Trachtenberg, JMB 2002, 321, pp. 383-395.
[Lisa]
11/04/02
Resch et al. "Visualization of the actin cytoskeleton by
cryo-electron microscopy" J Cell Science 115: 1877-1882.
[Kim]
11/18/02
Flicker, P.F., Robinson, J.P., DasGupta, B.R. (1999) Is Formation of
Visible Channels in a Phospholipid Bilayer by Botulinum Neurotoxin
Type B Sensitive to its Disulfide?, J. Struct. Biol. 128, 297-304.
[Chris A.]
12/02/02
Efficiency of 2D alignment methods
Laurent Joyeux, Pawel A. Penczek
Ultramicroscopy 92 (2002) 33-46.
[Yao]
01/13/03
URMILA B. S. RAWAT, ANDREY V. ZAVIALOV, JAYATI SENGUPTA, MIKEL
VALLE, ROBERT A. GRASSUCCI, JAMIE LINDE, BENTE VESTERGAARD, MNS
EHRENBERG & JOACHIM FRANK
Nature 421, 87 - 90 (2003)
A cryo-electron microscopic study of ribosome-bound
termination factor RF2
[Anchi]
01/27/03
Tutorial on Odd-Axis Electron Holography
Michael Lehman and Hannes Lichte
Microscopy and Microannalysis, 8(2002) 447-466
Two related papers will be used during the talk. There are
--- The potential and limitations of neutrons, electrons and X-rays for atomic
resolution microscopy of unstained biological molecules.
Richard Henderson
Quarterly Reviews of Biophysics, 28, 2(1995) 171-193
--- Electron holographic observation for biological specimens: electron
holography of bio-specimens
K. Aoyama and Q. Ru
J. Microscopy, 182(1996) 177-185
[Gary]
02/24/03
GroEL JMB paper:
Steven J. Ludtke, Joanita Jakana, Jiu-Li Song, David T. Chuang, and Wah Chiu
"A 11.5 A Single Particle Reconstruction of GroEL Using EMAN"
JMB, 2001, vol. 315, p.253-262
[Francisco G.]
03/10/03
Interaction of the Vibrio cholerae cytolysin (VCC) with cholesterol, some
cholesterol esters, and cholesterol derivatives: a TEM study
Journal of Structural Biology vol 139:2, 122-135(Oct 2002)
[Thanh]
03/24/03
Rice, et.al., Structure of Na, K-ATPase at 11A Resolution: Comparison with
Ca-ATPase in E1, E2 States. Biophysics Journal. May 2001. pp 2187-2197.
Volume 80, No. 5.
[Andrew]
04/07/03
Cryo-negative staining reduces electron-beam sensitivity of
vitrified biological particles" S. De Carlo et. al. Journal of
Structural Biology Vol 138, Issue 3, June 2002, pages 216-226.
[Joel]
04/28/03
Methods for reconstructing density maps of "single" particles from
cryoelectron micrographs to subnanometer resolution.
Conway JF, Steven AC.
J Struct Biol 1999 Dec 1;128(1):106-18
[Brian]
06/02/03
An automatic particle pickup method using a neural network applicable to
low-contrast electron micrographs
(Ogura and Sato, Journal of Structural Biology 136, 227-238 (2001))
[Marco]
06/16/03
Burgess et al. "Dynein structure and power stroke". Nature 421, 715-718
(2003).
[Carolyn]
07/14/03
Molecular Architecture of the Multiprotein Splicing Factor SF3b
Monika M. Golas, Bjoern Sander, Cindy L. Will, Reinhard Lührmann, and
Holger Stark
Science 2003 May 9; 300: 980-984.
[Barbie]
08/25/03
"Myosin VI is an actin-based motor that moves backwards"
Nature 401, 505 - 508 (1999)
"The core of the motor domain determines the direction of myosin movement"
Nature 412, 831 - 834 (2001).
[Josh]
09/08/03
"Fourier Amplitude Decay of Electron Cryomicroscopic Images
of Single Particles and Effects on Structure Determination"
Ali Saad, Steven J. Ludtke, Joanita Jakana, Frazer J. Rixon, Hiro Tsuruta, and
Wah Chiu
Journal of Structural Biology 133, 32^Ö42 (2001)
[Gary]
09/22/03
Science. 2002 Nov 8;298(5596):1209-13.
Macromolecular architecture in eukaryotic cells visualized by
cryoelectron tomography.
Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W
[Isabelle]
10/06/03
"A method for estimating the CTF in electron microscopy based on ARMA
models and parameter adjustment"
Ultramicroscopy 96:17-35
[Kelly]
10/20/03
"Practical aspects of overexpressing bacterial secondary
membrane transporters for structural studies"
Biochimica et Biophysica Acta (2003) vol. 1610, p. 23-36
[Mark D.]
11/03/03
1) Zhao FQ, Craig R. "Capturing time-resolved changes in molecular structure by negative staining." J Struct Biol. 2003 Jan;141(1):43-52.
2) Zhao FQ, Craig R. "Ca2+ causes release of myosin heads from the thick
filament surface on the milliseconds time scale" J Mol Biol. 2003 Mar
14;327(1):145-58.
[Andrei]
12/15/03
1) Watson, J.D., and Crick, F.H.C. "A Structure for Deoxyribose Nucleic Acid" Nature (1953) 171, 737-738.
2) Franklin, R.E., and Gosing R.G. "Molecular configuration of Sodium Thymonucleate" (1953) 171, 740-741.
[Anchi]
01/13/04
Cameron, G.J., Wess,T.J., Bonser,R.H.C. Young's modulus varies with differential orientation of keratin in feathers J. Struct.
Biol. (2003) 143, 118-123.
[Francisco G.]
01/26/04
Huang, Z., Baldwin, P.R., Mullapudi, S., Penczek, P.A. Automated determination of parameters describing power spectra of
micrograph images in electron microscopy J. Struct. Biol. (2003) 144, 79-94.
[Yuanxin]
02/23/04
Heymann, J.A.W., Hirai,T., Shi, D., Subramaniam, S. Projection structure of
the bacterial oxalate transporter OxlT at 3.4 A resolution. J Struct. Biol.
(2003) 144, 320-326.
[Andrew Ward]
03/22/04
Lee, S., Sowa, M.E., Watanabe, Y.-H., Sigler, P.B., Chiu, W. Yoshida, M.,
Tsai, F.T.F. The structure of ClpB: A molecular chaperone that rescues proteins
from an aggregated state. Cell (2003) 115, 229-240.
[Scott Stagg]
04/05/04
Sweitzer, S.M., and Hinshaw, J.E. Dynamin undergoes a GTP-dependent
conformational change causing vesiculation. Cell (1998) 93, 1021-29.
Zhang, P., and Hinshaw, J.E. Three dimensional reconstruction of dynamin in the
constricted state. Nature Cell Biology (2001) 3, 922-26.
[Josh Chappie]
04/19/04
White, H.E., Saibil, H.R., Ignatiou, A., Orlova, E.V. Recognition and separation of single particles with size variation by
statistical analysis of their images. J Mol Biol (2004) 336, 453-60.
[Joel Quispe]
05/04/04
Hewat and Blaas Cyroelectron microscopy analysis of the structural changes
associated with human rhinovirus type 14 uncoating. J Virology (2004) 78,
2935-42
[Kelly Dryden]
06/07/04
Mark Yeager, M.D.-Special presentation on Scientific Writing. You may access the pdf
of this presentation by clicking on this link: scientific writing
presentation.pdf
07/12/04
1) Halic M, Becker T, Pool MR, Spahn CM, Grassucci RA, Frank J, Beckmann R.
Structure of the signal recognition particle interacting with the elongation-arrested ribosome.
Nature. 2004 Feb 26;427(6977):808-14.
2) Gilbert RJ, Fucini P, Connell S, Fuller SD, Nierhaus KH, Robinson CV, Dobson CM, Stuart DI.
Three-dimensional structures of translating ribosomes by Cryo-EM.
Mol Cell. 2004 Apr 9;14(1):57-66.
[Barbie Gansen]
07/26/04
1) Qingxiong Zheng, Michael B. Braunfeld, John W. Sedat, and David A. Agard.
An improved strategy for automated electron microscopic tomography.
2) http://www.bio.umass.edu/microscopy/tecnai/
[Anchi Cheng]
08/09/04
C. O. S. Sorzano, S. Joni, C. El-Bez, J. M. Carazo, S. De Carlo, P. Thévenaz, and M. Unser.
A multiresolution approach to orientation assignment in 3D electron microscopy of single particles.
[Andrei Efimov]
09/27/04
Zheng Liu, et al.
Location of Divergent Region 2 on the Three-dimensional Structure of Cardiac Muscle Ryanodine Receptor/Calcium Release Channel
[Francisco Guerra]
10/11/04
Ricardo A. Bernal and Daniela Stock
Three-Dimensional Structure of the Intact Thermus thermophilus H+-ATPase/Synthase by Electron Microscopy
[Scott Stagg]
11/08/04
C.O.S. Sorzano, L.G. de la Fraga, R. Clackdoyle, J.M. Carazo
Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy
[Francisco Guerra]
11/22/04
Fotin A, Cheng Y, Sliz P, Grigorieff N, Harrison SC, Kirchhausen T, Walz T.
Molecular model for a complete clathrin lattice from electron cryomicroscopy.
[Josh Chappie]
1/24/05
[Anchi Cheng]
3/21/05
Cyrklaff, M., Carrascosa, J.L., et. al.
Cryo-electron Tomography of Vaccinia Virus
[Craig ]