Molecular Machines

The use of EM and image analysis techniques, particularly the single particle methodology, has opened the door to the structural characterization of large protein complexes in the megadalton range. This review covers the basic principles of single particle EM and recent examples of its application

[1]  Andreas Engel,et al.  Structural determinants of water permeation through aquaporin-1 , 2000, Nature.

[2]  Wei-Hau Chang,et al.  Electron Crystal Structure of the Transcription Factor and DNA Repair Complex, Core TFIIH , 2000, Cell.

[3]  D. Moras,et al.  Molecular Structure of Human TFIIH , 2000, Cell.

[4]  Joachim Frank,et al.  A ratchet-like inter-subunit reorganization of the ribosome during translocation , 2000, Nature.

[5]  W. Baumeister,et al.  The Regulatory Complex of Drosophila melanogaster 26s Proteasomes , 2000, The Journal of cell biology.

[6]  J M Carazo,et al.  Mapping and fuzzy classification of macromolecular images using self-organizing neural networks. , 2000, Ultramicroscopy.

[7]  G. Harauz,et al.  Angular reconstitution of the Staphylothermus marinus phosphoenolpyruvate synthase , 2000, Microscopy research and technique.

[8]  S. Harrison,et al.  Structure of the reovirus core at 3.6 Å resolution , 2000, Nature.

[9]  L. Amos,et al.  Focusing-in on microtubules. , 2000, Current opinion in structural biology.

[10]  H. Saibil,et al.  Molecular chaperones: containers and surfaces for folding, stabilising or unfolding proteins. , 2000, Current opinion in structural biology.

[11]  J. Frank,et al.  Solution Structure of the E. coli 70S Ribosome at 11.5 Å Resolution , 2000, Cell.

[12]  B. Böttcher,et al.  Direct visualisation of conformational changes in EF(0)F(1) by electron microscopy. , 2000, Journal of molecular biology.

[13]  M. Heel,et al.  Large-Scale Movement of Elongation Factor G and Extensive Conformational Change of the Ribosome during Translocation , 2000, Cell.

[14]  Masahide Kikkawa,et al.  15 Å Resolution Model of the Monomeric Kinesin Motor, KIF1A , 2000, Cell.

[15]  R. Tjian,et al.  Three-dimensional structure of the human TFIID-IIA-IIB complex. , 1999, Science.

[16]  M. Brand,et al.  Three-dimensional structures of the TAFII-containing complexes TFIID and TFTC. , 1999, Science.

[17]  Julie Grantham,et al.  Eukaryotic type II chaperonin CCT interacts with actin through specific subunits , 1999, Nature.

[18]  J. Frank,et al.  Animation of the dynamical events of the elongation cycle based on cryoelectron microscopy of functional complexes of the ribosome. , 1999, Journal of structural biology.

[19]  Lanzavecchia,et al.  Fast and accurate three-dimensional reconstruction from projections with random orientations via radon transforms , 1999, Journal of structural biology.

[20]  R. Glaeser.  Review: electron crystallography: present excitement, a nod to the past, anticipating the future. , 1999, Journal of structural biology.

[21]  W Chiu,et al.  EMAN: semiautomated software for high-resolution single-particle reconstructions. , 1999, Journal of structural biology.

[22]  M G Rossmann,et al.  X-ray crystallographic structure of the Norwalk virus capsid. , 1999, Science.

[23]  M. Heel,et al.  Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallograhy. , 1999, Structure.

[24]  C. Yip,et al.  Quaternary structure of the insulin-insulin receptor complex. , 1999, Science.

[25]  Michael Radermacher,et al.  3D reconstruction of the ATP-bound form of CCT reveals the asymmetric folding conformation of a type II chaperonin , 1999, Nature Structural Biology.

[26]  J Pulokas,et al.  Leginon: a system for fully automated acquisition of 1000 electron micrographs a day. , 1999, Ultramicroscopy.

[27]  S. Harrison,et al.  Functional organization of clathrin in coats: combining electron cryomicroscopy and X-ray crystallography. , 1999, Molecular cell.

[28]  Helen R. Saibil,et al.  GroEL-GroES Cycling ATP and Nonnative Polypeptide Direct Alternation of Folding-Active Rings , 1999, Cell.

[29]  N. Volkmann,et al.  Quantitative fitting of atomic models into observed densities derived by electron microscopy. , 1999, Journal of structural biology.

[30]  J. Mccammon,et al.  Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. , 1999, Journal of structural biology.

[31]  N Grigorieff,et al.  Clathrin coats at 21 Å resolution: a cellular assembly designed to recycle multiple membrane receptors , 1998, The EMBO journal.

[32]  Niels Volkmann,et al.  A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units , 1998, Nature Structural Biology.

[33]  J Frank,et al.  Escherichia coli 70 S ribosome at 15 A resolution by cryo-electron microscopy: localization of fMet-tRNAfMet and fitting of L1 protein. , 1998, Journal of molecular biology.

[34]  Joachim Frank,et al.  A 9 Å Resolution X-Ray Crystallographic Map of the Large Ribosomal Subunit , 1998, Cell.

[35]  J Frank,et al.  Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[36]  N Grigorieff,et al.  Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice. , 1998, Journal of molecular biology.

[37]  A. McGough.  F-actin-binding proteins. , 1998, Current opinion in structural biology.

[38]  K. Leonard,et al.  Consistent structure between bacterial and mitochondrial NADH:ubiquinone oxidoreductase (complex I). , 1998, Journal of molecular biology.

[39]  B. Alberts.  The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists , 1998, Cell.

[40]  W. Chiu,et al.  Determination of the gelsolin binding site on F-actin: implications for severing and capping. , 1998, Biophysical journal.

[41]  C. Akey,et al.  Active nuclear pore complexes in Chironomus: visualization of transporter configurations related to mRNP export. , 1998, Journal of cell science.

[42]  Kenneth H. Downing,et al.  Structure of the αβ tubulin dimer by electron crystallography , 1998, Nature.

[43]  F. Sigworth.  A maximum-likelihood approach to single-particle image refinement. , 1998, Journal of structural biology.

[44]  W. Baumeister,et al.  26S proteasome structure revealed by three-dimensional electron microscopy. , 1998, Journal of structural biology.

[45]  C. Akey,et al.  Three-dimensional architecture of the isolated yeast nuclear pore complex: functional and evolutionary implications. , 1998, Molecular cell.

[46]  J Frank,et al.  Alignment of conduits for the nascent polypeptide chain in the ribosome-Sec61 complex. , 1997, Science.

[47]  D. DeRosier,et al.  Evidence for a Conformational Change in Actin Induced by Fimbrin (N375) Binding , 1997, The Journal of cell biology.

[48]  W. Lehman,et al.  3-D image reconstruction of reconstituted smooth muscle thin filaments containing calponin: visualization of interactions between F-actin and calponin. , 1997, Journal of molecular biology.

[49]  R. Brimacombe,et al.  Visualization of elongation factor Tu on the Escherichia coli ribosome , 1997, Nature.

[50]  Akinori Kidera,et al.  Surface of bacteriorhodopsin revealed by high-resolution electron crystallography , 1997, Nature.

[51]  Wah Chiu,et al.  Cofilin Changes the Twist of F-Actin: Implications for Actin Filament Dynamics and Cellular Function , 1997, The Journal of cell biology.

[52]  M. Goldberg,et al.  Three-dimensional visualization of the route of protein import: the role of nuclear pore complex substructures. , 1997, Experimental cell research.

[53]  P. Wingfield,et al.  Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy , 1997, Nature.

[54]  B. Böttcher,et al.  Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy , 1997, Nature.

[55]  R. Vincentelli,et al.  Three-dimensional structure of NADH-dehydrogenase from Neurospora crassa by electron microscopy and conical tilt reconstruction. , 1997, Journal of molecular biology.

[56]  J. Frank,et al.  Direct Visualization of A-, P-, and E-Site Transfer RNAs in the Escherichia coli Ribosome , 1996, Science.

[57]  W. Chiu,et al.  A 7-A projection map of frozen, hydrated acrosomal bundle from Limulus sperm. , 1995, Journal of structural biology.

[58]  M van Heel,et al.  The 70S Escherichia coli ribosome at 23 A resolution: fitting the ribosomal RNA. , 1995, Structure.

[59]  R. Henderson.  The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules , 1995, Quarterly Reviews of Biophysics.

[60]  C. Akey.  Structural plasticity of the nuclear pore complex. , 1995, Journal of molecular biology.

[61]  Neil A. Ranson,et al.  Location of a folding protein and shape changes in GroEL–GroES complexes imaged by cryo-electron microscopy , 1994, Nature.

[62]  Yoshinori Fujiyoshi,et al.  Atomic Model of Plant Light‐Harvesting Complex by Electron Crystallography. , 1994 .

[63]  D. DeRosier,et al.  Determination of the alpha-actinin-binding site on actin filaments by cryoelectron microscopy and image analysis , 1994, The Journal of cell biology.

[64]  R A Milligan,et al.  Structure of the actin-myosin complex and its implications for muscle contraction. , 1993, Science.

[65]  M. Chmeissani.  Determination of Alpha , 1991 .

[66]  R. Henderson,et al.  Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. , 1990, Journal of molecular biology.

[67]  J. Frank,et al.  A new non-crystallographic image-processing technique reveals the architecture of ribosomes. , 1988, Trends in biochemical sciences.

[68]  Andreas Engel,et al.  Structural determinants of water permeation through aquaporin-1 , 2000, Nature.

[69]  Wei-Hau Chang,et al.  Electron Crystal Structure of the Transcription Factor and DNA Repair Complex, Core TFIIH , 2000, Cell.

[70]  Joachim Frank,et al.  A ratchet-like inter-subunit reorganization of the ribosome during translocation , 2000, Nature.

[71]  W. Baumeister,et al.  The Regulatory Complex of Drosophila melanogaster 26s Proteasomes , 2000, The Journal of cell biology.

[72]  J M Carazo,et al.  Mapping and fuzzy classification of macromolecular images using self-organizing neural networks. , 2000, Ultramicroscopy.

[73]  G. Harauz,et al.  Angular reconstitution of the Staphylothermus marinus phosphoenolpyruvate synthase , 2000, Microscopy research and technique.

[74]  S. Harrison,et al.  Structure of the reovirus core at 3.6 Å resolution , 2000, Nature.

[75]  L. Amos,et al.  Focusing-in on microtubules. , 2000, Current opinion in structural biology.

[76]  H. Saibil,et al.  Molecular chaperones: containers and surfaces for folding, stabilising or unfolding proteins. , 2000, Current opinion in structural biology.

[77]  B. Böttcher,et al.  Direct visualisation of conformational changes in EF(0)F(1) by electron microscopy. , 2000, Journal of molecular biology.

[78]  M. Heel,et al.  Large-Scale Movement of Elongation Factor G and Extensive Conformational Change of the Ribosome during Translocation , 2000, Cell.

[79]  Masahide Kikkawa,et al.  15 Å Resolution Model of the Monomeric Kinesin Motor, KIF1A , 2000, Cell.

[80]  R. Tjian,et al.  Three-dimensional structure of the human TFIID-IIA-IIB complex. , 1999, Science.

[81]  M. Brand,et al.  Three-dimensional structures of the TAFII-containing complexes TFIID and TFTC. , 1999, Science.

[82]  Julie Grantham,et al.  Eukaryotic type II chaperonin CCT interacts with actin through specific subunits , 1999, Nature.

[83]  J. Frank,et al.  Animation of the dynamical events of the elongation cycle based on cryoelectron microscopy of functional complexes of the ribosome. , 1999, Journal of structural biology.

[84]  Lanzavecchia,et al.  Fast and accurate three-dimensional reconstruction from projections with random orientations via radon transforms , 1999, Journal of structural biology.

[85]  R. Glaeser.  Review: electron crystallography: present excitement, a nod to the past, anticipating the future. , 1999, Journal of structural biology.

[86]  W Chiu,et al.  EMAN: semiautomated software for high-resolution single-particle reconstructions. , 1999, Journal of structural biology.

[87]  M G Rossmann,et al.  X-ray crystallographic structure of the Norwalk virus capsid. , 1999, Science.

[88]  M. Heel,et al.  Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallograhy. , 1999, Structure.

[89]  C. Yip,et al.  Quaternary structure of the insulin-insulin receptor complex. , 1999, Science.

[90]  Michael Radermacher,et al.  3D reconstruction of the ATP-bound form of CCT reveals the asymmetric folding conformation of a type II chaperonin , 1999, Nature Structural Biology.

[91]  J Pulokas,et al.  Leginon: a system for fully automated acquisition of 1000 electron micrographs a day. , 1999, Ultramicroscopy.

[92]  S. Harrison,et al.  Functional organization of clathrin in coats: combining electron cryomicroscopy and X-ray crystallography. , 1999, Molecular cell.

[93]  Helen R. Saibil,et al.  GroEL-GroES Cycling ATP and Nonnative Polypeptide Direct Alternation of Folding-Active Rings , 1999, Cell.

[94]  N. Volkmann,et al.  Quantitative fitting of atomic models into observed densities derived by electron microscopy. , 1999, Journal of structural biology.

[95]  J. Mccammon,et al.  Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. , 1999, Journal of structural biology.

[96]  Niels Volkmann,et al.  A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units , 1998, Nature Structural Biology.

[97]  N Grigorieff,et al.  Clathrin coats at 21 Å resolution: a cellular assembly designed to recycle multiple membrane receptors , 1998, The EMBO journal.

[98]  J Frank,et al.  Escherichia coli 70 S ribosome at 15 A resolution by cryo-electron microscopy: localization of fMet-tRNAfMet and fitting of L1 protein. , 1998, Journal of molecular biology.

[99]  J Frank,et al.  Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[100]  N Grigorieff,et al.  Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice. , 1998, Journal of molecular biology.

[101]  A. McGough.  F-actin-binding proteins. , 1998, Current opinion in structural biology.

[102]  K. Leonard,et al.  Consistent structure between bacterial and mitochondrial NADH:ubiquinone oxidoreductase (complex I). , 1998, Journal of molecular biology.

[103]  B. Alberts.  The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists , 1998, Cell.

[104]  W. Chiu,et al.  Determination of the gelsolin binding site on F-actin: implications for severing and capping. , 1998, Biophysical journal.

[105]  C. Akey,et al.  Active nuclear pore complexes in Chironomus: visualization of transporter configurations related to mRNP export. , 1998, Journal of cell science.

[106]  Kenneth H. Downing,et al.  Structure of the αβ tubulin dimer by electron crystallography , 1998, Nature.

[107]  F. Sigworth.  A maximum-likelihood approach to single-particle image refinement. , 1998, Journal of structural biology.

[108]  W. Baumeister,et al.  26S proteasome structure revealed by three-dimensional electron microscopy. , 1998, Journal of structural biology.

[109]  C. Akey,et al.  Three-dimensional architecture of the isolated yeast nuclear pore complex: functional and evolutionary implications. , 1998, Molecular cell.

[110]  J Frank,et al.  Alignment of conduits for the nascent polypeptide chain in the ribosome-Sec61 complex. , 1997, Science.

[111]  D. DeRosier,et al.  Evidence for a Conformational Change in Actin Induced by Fimbrin (N375) Binding , 1997, The Journal of cell biology.

[112]  W. Lehman,et al.  3-D image reconstruction of reconstituted smooth muscle thin filaments containing calponin: visualization of interactions between F-actin and calponin. , 1997, Journal of molecular biology.

[113]  R. Brimacombe,et al.  Visualization of elongation factor Tu on the Escherichia coli ribosome , 1997, Nature.

[114]  Akinori Kidera,et al.  Surface of bacteriorhodopsin revealed by high-resolution electron crystallography , 1997, Nature.

[115]  Wah Chiu,et al.  Cofilin Changes the Twist of F-Actin: Implications for Actin Filament Dynamics and Cellular Function , 1997, The Journal of cell biology.

[116]  M. Goldberg,et al.  Three-dimensional visualization of the route of protein import: the role of nuclear pore complex substructures. , 1997, Experimental cell research.

[117]  P. Wingfield,et al.  Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy , 1997, Nature.

[118]  B. Böttcher,et al.  Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy , 1997, Nature.

[119]  R. Vincentelli,et al.  Three-dimensional structure of NADH-dehydrogenase from Neurospora crassa by electron microscopy and conical tilt reconstruction. , 1997, Journal of molecular biology.

[120]  J. Frank,et al.  Direct Visualization of A-, P-, and E-Site Transfer RNAs in the Escherichia coli Ribosome , 1996, Science.

[121]  W. Chiu,et al.  A 7-A projection map of frozen, hydrated acrosomal bundle from Limulus sperm. , 1995, Journal of structural biology.

[122]  M van Heel,et al.  The 70S Escherichia coli ribosome at 23 A resolution: fitting the ribosomal RNA. , 1995, Structure.

[123]  R. Henderson.  The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules , 1995, Quarterly Reviews of Biophysics.

[124]  C. Akey.  Structural plasticity of the nuclear pore complex. , 1995, Journal of molecular biology.

[125]  Neil A. Ranson,et al.  Location of a folding protein and shape changes in GroEL–GroES complexes imaged by cryo-electron microscopy , 1994, Nature.

[126]  Yoshinori Fujiyoshi,et al.  Atomic Model of Plant Light‐Harvesting Complex by Electron Crystallography. , 1994 .

[127]  R A Milligan,et al.  Structure of the actin-myosin complex and its implications for muscle contraction. , 1993, Science.

[128]  R. Henderson,et al.  Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. , 1990, Journal of molecular biology.

[129]  J. Frank,et al.  A new non-crystallographic image-processing technique reveals the architecture of ribosomes. , 1988, Trends in biochemical sciences.