Transcript Atomic models of complexes - Cryo

Data Mining
Text mining, e.g.:
• Structures at specific resolution
• Structures by negative staining
• Structures by vitrification
Mining structural data, e.g.:
• Segmentation
• 3D shape recognition
• Secondary structure recognition
• Fold modules recognition
Goals
• Atomic scale model of a cell
• Atomic models of interacting complexes
• Conformational dynamics
Difficulties
• Range of size
• Range of resolution
• Range of complexity
Towards the atomic model of a cell
Wolfgang Baumeister
Segmentation
Actin
mesh &
aldolase
Niels
Volkmann
Volkmann, 2002, JSB 138:123
Atomic models of complexes
15 Å
10 Å
Helixhunter
Situs
5Å
b sheets
Helix orientation
Wah Chiu
If no structure available:
SCOP: 1.65 released December 2003.
CATH: 2.5.1: Released January 2004
Atomic models of complexes
10 Å
structure
of HBV
Fitting
of FAB
Alasdair Steven
Helix orientation: the fold
The directionality of the helices
was determined by collecting the
best-ftting orientations resulting
from a search through the 3D
experimental map for a large
number of a-helical fragments.
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3D cryo EM
4.5 Å resolution
Mitsuoka et al. J. Struct. Biol. (1999)
De Groot et al., J. Mol. Biol (2000)
How to describe protein motion without
sequence and atomic coordinates
The 3D continuous object is decomposed into a set of Voronoi
cells that approximate its shape and density distribution. The
anisotropic elastic network theory allows the thermal fluctuations
to be predicted.
Ming et al. PNAS (2002) 99: 8620-25
Tama et al. J. Mol. Biol. (2002) 321: 297–305
Scheuring et al. E. Biophys J, 2001