PMID- 22291925
OWN - NLM
STAT- MEDLINE
DCOM- 20120604
LR  - 20211021
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 7
IP  - 1
DP  - 2012
TI  - IPET and FETR: experimental approach for studying molecular structure dynamics by 
      cryo-electron tomography of a single-molecule structure.
PG  - e30249
LID - 10.1371/journal.pone.0030249 [doi]
LID - e30249
AB  - The dynamic personalities and structural heterogeneity of proteins are essential for 
      proper functioning. Structural determination of dynamic/heterogeneous proteins is 
      limited by conventional approaches of X-ray and electron microscopy (EM) of 
      single-particle reconstruction that require an average from thousands to millions 
      different molecules. Cryo-electron tomography (cryoET) is an approach to determine 
      three-dimensional (3D) reconstruction of a single and unique biological object such 
      as bacteria and cells, by imaging the object from a series of tilting angles. 
      However, cconventional reconstruction methods use large-size whole-micrographs that 
      are limited by reconstruction resolution (lower than 20 Å), especially for small and 
      low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse 
      effects from image distortion and the measuring tilt-errors (including tilt-axis and 
      tilt-angle errors) both play a major role in limiting the reconstruction resolution. 
      Therefore, we developed a "focused electron tomography reconstruction" (FETR) 
      algorithm to improve the resolution by decreasing the reconstructing image size so 
      that it contains only a single-instance protein. FETR can tolerate certain levels of 
      image-distortion and measuring tilt-errors, and can also precisely determine the 
      translational parameters via an iterative refinement process that contains a series 
      of automatically generated dynamic filters and masks. To describe this method, a set 
      of simulated cryoET images was employed; to validate this approach, the real 
      experimental images from negative-staining and cryoET were used. Since this approach 
      can obtain the structure of a single-instance molecule/particle, we named it 
      individual-particle electron tomography (IPET) as a new robust strategy/approach 
      that does not require a pre-given initial model, class averaging of multiple 
      molecules or an extended ordered lattice, but can tolerate small tilt-errors for 
      high-resolution single "snapshot" molecule structure determination. Thus, FETR/IPET 
      provides a completely new opportunity for a single-molecule structure determination, 
      and could be used to study the dynamic character and equilibrium fluctuation of 
      macromolecules.
FAU - Zhang, Lei
AU  - Zhang L
AD  - Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, 
      United States of America.
FAU - Ren, Gang
AU  - Ren G
LA  - eng
GR  - R01 GM104427/GM/NIGMS NIH HHS/United States
GR  - R01 HL115153/HL/NHLBI NIH HHS/United States
PT  - Evaluation Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PT  - Validation Study
DEP - 20120124
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Macromolecular Substances)
SB  - IM
MH  - Algorithms
MH  - Computer Simulation
MH  - Cryoelectron Microscopy/*methods
MH  - Crystallography, X-Ray
MH  - Electron Microscope Tomography/*methods
MH  - Image Processing, Computer-Assisted/*methods
MH  - Imaging, Three-Dimensional/methods
MH  - Macromolecular Substances/analysis/chemistry
MH  - Models, Molecular
MH  - *Molecular Dynamics Simulation
MH  - *Molecular Structure
MH  - Protein Structure, Quaternary
MH  - Protein Structure, Secondary
PMC - PMC3265479
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2012/02/01 06:00
MHDA- 2012/06/05 06:00
CRDT- 2012/02/01 06:00
PHST- 2011/07/06 00:00 [received]
PHST- 2011/12/14 00:00 [accepted]
PHST- 2012/02/01 06:00 [entrez]
PHST- 2012/02/01 06:00 [pubmed]
PHST- 2012/06/05 06:00 [medline]
AID - PONE-D-11-12734 [pii]
AID - 10.1371/journal.pone.0030249 [doi]
PST - ppublish
SO  - PLoS One. 2012;7(1):e30249. doi: 10.1371/journal.pone.0030249. Epub 2012 Jan 24.