02370nas 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 a

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.

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/1912215001670nas a2200289 4500008004100000022001400041245011900055210006900174260001200243300001200255490000600267520076600273653004001039653002501079653002201104653002401126653001301150653002801163100002201191700001701213700001701230700002701247700002101274700001801295700001901313856004801332 2008 eng d a1750-279900aSPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.0 aSPIDER image processing for singleparticle reconstruction of bio c10/2008 a1941-740 v33 a

This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Computation here is performed using the image-processing software SPIDER and can be managed using a graphical user interface, termed the SPIDER Reconstruction Engine. Two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines. Once an existing model is available, reference-based alignment can be used, a procedure that can be iterated. Also described is supervised classification, a method to look for homogeneous subsets when multiple known conformations of the molecule may coexist.

10aImage Processing, Computer-Assisted10aMicroscopy, Electron10aModels, Molecular10aMolecular Structure10aSoftware10aUser-Computer Interface1 aShaikh, Tanvir, R1 aGao, Haixiao1 aBaxter, Bill1 aAsturias, Francisco, J1 aBoisset, Nicolas1 aLeith, ArDean1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/19180078