@article {2110, title = {Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules.}, journal = {J Struct Biol}, volume = {166}, year = {2009}, month = {05/2009}, pages = {126-32}, abstract = {

Attempts to develop efficient classification approaches to the problem of heterogeneity in single-particle reconstruction of macromolecules require phantom data with realistic noise models. We have estimated the signal-to-noise ratios and spectral signal-to-noise ratios for three steps in the electron microscopic image formation from data obtained experimentally. An important result is that structural noise, i.e., the irreproducible component of the object prior to image formation, is substantial, and of the same order of magnitude as the reproducible signal. Based on this result, the noise modeling for testing new classification techniques can be improved.

}, keywords = {Cryoelectron Microscopy, Image Processing, Computer-Assisted}, issn = {1095-8657}, doi = {10.1016/j.jsb.2009.02.012}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19269332}, author = {Baxter, Bill and Grassucci, Robert A and Gao, Haixiao and Frank, Joachim} } @article {2111, title = {Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.}, journal = {Proc Natl Acad Sci U S A}, volume = {106}, year = {2009}, month = {01/2009}, pages = {1063-8}, abstract = {

In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism.

}, keywords = {Cryoelectron Microscopy, Enzyme Activation, Escherichia coli, Escherichia coli Proteins, Guanosine Triphosphate, Histidine, Hydrolysis, Hydrophobic and Hydrophilic Interactions, Models, Molecular, Peptide Elongation Factor Tu, Protein Structure, Secondary, Ribosomal Proteins, Ribosomes, RNA, Transfer, Signal Transduction}, issn = {1091-6490}, doi = {10.1073/pnas.0811370106}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19122150}, author = {Villa, Elizabeth and Sengupta, Jayati and Trabuco, Leonardo G and LeBarron, Jamie and Baxter, Bill and Shaikh, Tanvir R and Grassucci, Robert A and Nissen, Poul and Ehrenberg, M{\r a}ns and Schulten, Klaus and Frank, Joachim} } @article {2114, title = {Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.}, journal = {J Struct Biol}, volume = {164}, year = {2008}, month = {10/2008}, pages = {24-32}, abstract = {

A number of image processing parameters in the 3D reconstruction of a ribosome complex from a cryo-EM data set were varied to test their effects on the final resolution. The parameters examined were pixel size, window size, and mode of Fourier amplitude enhancement at high spatial frequencies. In addition, the strategy of switching from large to small pixel size during angular refinement was explored. The relationship between resolution (in Fourier space) and the number of particles was observed to follow a lin-log dependence, a relationship that appears to hold for other data, as well. By optimizing the above parameters, and using a lin-log extrapolation to the full data set in the estimation of resolution from half-sets, we obtained a 3D map from 131,599 ribosome particles at 6.7A resolution (FSC=0.5).

}, keywords = {Cryoelectron Microscopy, Escherichia coli, Image Enhancement, Image Processing, Computer-Assisted, Ribosomes}, issn = {1095-8657}, doi = {10.1016/j.jsb.2008.05.007}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18606549}, author = {LeBarron, Jamie and Grassucci, Robert A and Shaikh, Tanvir R and Baxter, Bill and Sengupta, Jayati and Frank, Joachim} } @article {2115, title = {Particle picking by segmentation: a comparative study with SPIDER-based manual particle picking.}, journal = {J Struct Biol}, volume = {152}, year = {2005}, month = {12/2005}, pages = {211-20}, abstract = {

Boxing hundreds of thousands of particles in low-dose electron micrographs is one of the major bottle-necks in advancing toward achieving atomic resolution reconstructions of biological macromolecules. We have shown that a combination of pre-processing operations and segmentation can be used as an effective, automatic tool for identifying and boxing single-particle images. This paper provides a brief description of how this method has been applied to a large data set of micrographs of ice-embedded ribosomes, including a comparative analysis of the efficiency of the method. Some results on processing micrographs of tripeptidyl peptidase II particles are also shown. In both cases, we have achieved our goal of selecting at least 80\% of the particles that an expert would select with less than 10\% false positives.

}, keywords = {Algorithms, Aminopeptidases, Cryoelectron Microscopy, Dipeptidyl-Peptidases and Tripeptidyl-Peptidases, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Internet, Particle Size, Ribosomes, Serine Endopeptidases, Software, Software Validation}, issn = {1047-8477}, doi = {10.1016/j.jsb.2005.09.007}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16330229}, author = {Adiga, Umesh and Baxter, Bill and Hall, Richard J and Rockel, Beate and Rath, Bimal K and Frank, Joachim and Glaeser, Robert M} }