01443nas a2200205 4500008004100000022001400041245010400055210006900159260001200228300001100240490000800251520078400259653002801043653004001071100001701111700002501128700001701153700001901170856004801189 2009 eng d a1095-865700aDetermination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules.0 aDetermination of signaltonoise ratios and spectral SNRs in cryoE c05/2009 a126-320 v1663 a
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.
10aCryoelectron Microscopy10aImage Processing, Computer-Assisted1 aBaxter, Bill1 aGrassucci, Robert, A1 aGao, Haixiao1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/1926933202370nas a2200445 4500008004100000022001400041245009000055210006900145260001200214300001100226490000800237520103400245653002801279653002201307653002101329653003001350653002701380653001401407653001501421653004501436653002201481653003301503653003301536653002301569653001401592653001801606653002401624100002101648700002101669700002501690700002001715700001701735700002201752700002501774700001701799700002101816700002001837700001901857856004801876 2009 eng d a1091-649000aRibosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.0 aRibosomeinduced changes in elongation factor Tu conformation con c01/2009 a1063-80 v1063 aIn 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.
10aCryoelectron Microscopy10aEnzyme Activation10aEscherichia coli10aEscherichia coli Proteins10aGuanosine Triphosphate10aHistidine10aHydrolysis10aHydrophobic and Hydrophilic Interactions10aModels, Molecular10aPeptide Elongation Factor Tu10aProtein Structure, Secondary10aRibosomal Proteins10aRibosomes10aRNA, Transfer10aSignal Transduction1 aVilla, Elizabeth1 aSengupta, Jayati1 aTrabuco, Leonardo, G1 aLeBarron, Jamie1 aBaxter, Bill1 aShaikh, Tanvir, R1 aGrassucci, Robert, A1 aNissen, Poul1 aEhrenberg, Måns1 aSchulten, Klaus1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/1912215001752nas a2200265 4500008004100000022001400041245010100055210006900156260001200225300001000237490000800247520093400255653002801189653002101217653002201238653004001260653001401300100002001314700002501334700002201359700001701381700002101398700001901419856004801438 2008 eng d a1095-865700aExploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.0 aExploration of parameters in cryoEM leading to an improved densi c10/2008 a24-320 v1643 aA 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).
10aCryoelectron Microscopy10aEscherichia coli10aImage Enhancement10aImage Processing, Computer-Assisted10aRibosomes1 aLeBarron, Jamie1 aGrassucci, Robert, A1 aShaikh, Tanvir, R1 aBaxter, Bill1 aSengupta, Jayati1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/18606549