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Volumn 36, Issue , 2007, Pages 43-62

Visualizing flexibility at molecular resolution: Analysis of heterogeneity in single-particle electron microscopy reconstructions

Author keywords

3D variance; Conformational flexibility; Cryo EM; Macromolecular assemblies; Maximum likelihood

Indexed keywords

CAMERA; CONFORMATION; CONFORMATIONAL TRANSITION; CRYOELECTRON MICROSCOPY; DIGITAL IMAGING; IMAGE ANALYSIS; IMAGE DISPLAY; IMAGE PROCESSING; IMAGE QUALITY; IMAGE RECONSTRUCTION; IMAGING SYSTEM; MACROMOLECULE; MAXIMUM LIKELIHOOD METHOD; MOLECULAR IMAGING; MULTIVARIATE ANALYSIS; PRIORITY JOURNAL; REVIEW; SINGLE PARTICLE ELECTRON MICROSCOPY; VARIANCE;

EID: 34347236451     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.36.040306.132742     Document Type: Review
Times cited : (69)

References (49)
  • 3
    • 0032982866 scopus 로고    scopus 로고
    • EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome
    • Agrawal RK, Heagle AB, Penczek P, Grassucci RA, Frank J. 1999. EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. Nat. Struct. Biol. 6:643-47
    • (1999) Nat. Struct. Biol , vol.6 , pp. 643-647
    • Agrawal, R.K.1    Heagle, A.B.2    Penczek, P.3    Grassucci, R.A.4    Frank, J.5
  • 4
    • 4544268556 scopus 로고    scopus 로고
    • Performance evaluation of a transmission scintillator-based lens-coupled 4K CCD camera for use in low-dose electron cryo-microscopy
    • Bailey B, Agard DA, Sedat JW, Barfels M, Chao H, Mooney PE. 2004. Performance evaluation of a transmission scintillator-based lens-coupled 4K CCD camera for use in low-dose electron cryo-microscopy. Microsc. Microanal. 10:1204-5
    • (2004) Microsc. Microanal , vol.10 , pp. 1204-1205
    • Bailey, B.1    Agard, D.A.2    Sedat, J.W.3    Barfels, M.4    Chao, H.5    Mooney, P.E.6
  • 5
    • 1842409555 scopus 로고    scopus 로고
    • Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy
    • Bottcher B, Wynne SA, Crowther RA. 1997. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature 386:26-27
    • (1997) Nature , vol.386 , pp. 26-27
    • Bottcher, B.1    Wynne, S.A.2    Crowther, R.A.3
  • 6
    • 1242351230 scopus 로고    scopus 로고
    • Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis
    • Brink J, Ludtke SJ, Kong Y, Wakil SJ, Ma J, Chiu W. 2004. Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis. Structure 12:185-91
    • (2004) Structure , vol.12 , pp. 185-191
    • Brink, J.1    Ludtke, S.J.2    Kong, Y.3    Wakil, S.J.4    Ma, J.5    Chiu, W.6
  • 8
    • 0032599786 scopus 로고    scopus 로고
    • Performance of a 2k CCD camera designed for electron crystallography at 400 kV
    • Downing KH, Hendrickson FM. 1999. Performance of a 2k CCD camera designed for electron crystallography at 400 kV. Ultramicroscopy 75:215-33
    • (1999) Ultramicroscopy , vol.75 , pp. 215-233
    • Downing, K.H.1    Hendrickson, F.M.2
  • 9
    • 33845305513 scopus 로고    scopus 로고
    • The iterative helical real space reconstruction method: Surmounting the problems posed by real polymers
    • Egelman EH. 2007. The iterative helical real space reconstruction method: surmounting the problems posed by real polymers. J. Struct. Biol. 157:83-94
    • (2007) J. Struct. Biol , vol.157 , pp. 83-94
    • Egelman, E.H.1
  • 10
    • 0036089703 scopus 로고    scopus 로고
    • Single-particle imaging of macromolecules by cryo-electron microscopy
    • Frank J. 2002. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31:303-19
    • (2002) Annu. Rev. Biophys. Biomol. Struct , vol.31 , pp. 303-319
    • Frank, J.1
  • 12
    • 0034691576 scopus 로고    scopus 로고
    • A ratchet-like intersubunit reorganization of the ribosome during translocation
    • Frank J, Agrawal RK. 2000. A ratchet-like intersubunit reorganization of the ribosome during translocation. Nature 406:318-22
    • (2000) Nature , vol.406 , pp. 318-322
    • Frank, J.1    Agrawal, R.K.2
  • 13
    • 4344605740 scopus 로고    scopus 로고
    • Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset
    • Gao H, Valle M, Ehrenberg M, Frank J. 2004. Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset. J. Struct. Biol. 147:283-90
    • (2004) J. Struct. Biol , vol.147 , pp. 283-290
    • Gao, H.1    Valle, M.2    Ehrenberg, M.3    Frank, J.4
  • 14
    • 0038670209 scopus 로고    scopus 로고
    • Molecular architecture of the multiprotein splicing factor SF3b
    • Golas MM, Sander B, Will CL, Luhrmann R, Stark H. 2003. Molecular architecture of the multiprotein splicing factor SF3b. Science 300:980-84
    • (2003) Science , vol.300 , pp. 980-984
    • Golas, M.M.1    Sander, B.2    Will, C.L.3    Luhrmann, R.4    Stark, H.5
  • 15
    • 33644838451 scopus 로고    scopus 로고
    • Cryo-electron microscopy studies of human TFIID: Conformational breathing in the integration of gene regulatory cues
    • Grob P, Cruse MJ, Inouye C, Peris M, Penczek PA, et al. 2006. Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues. Structure 14:511-20
    • (2006) Structure , vol.14 , pp. 511-520
    • Grob, P.1    Cruse, M.J.2    Inouye, C.3    Peris, M.4    Penczek, P.A.5
  • 17
    • 0037406441 scopus 로고    scopus 로고
    • Dynamics of herpes simplex virus capsid maturation visualized by time-lapse cryoelectron microscopy
    • Heymann JB, Cheng N, Newcomb WW, Trus BL, Brown JC, Steven AC. 2003. Dynamics of herpes simplex virus capsid maturation visualized by time-lapse cryoelectron microscopy. Nat. Struct. Biol. 10:334-41
    • (2003) Nat. Struct. Biol , vol.10 , pp. 334-341
    • Heymann, J.B.1    Cheng, N.2    Newcomb, W.W.3    Trus, B.L.4    Brown, J.C.5    Steven, A.C.6
  • 18
    • 18844378344 scopus 로고    scopus 로고
    • Electron tomography reveals diverse conformations of integrin alphaIIbbeta3 in the active state
    • Iwasaki K, Mitsuoka K, Fujiyoshi Y, Fujisawa Y, Kikuchi M, et al. 2005. Electron tomography reveals diverse conformations of integrin alphaIIbbeta3 in the active state. J. Struct. Biol. 150:259-67
    • (2005) J. Struct. Biol , vol.150 , pp. 259-267
    • Iwasaki, K.1    Mitsuoka, K.2    Fujiyoshi, Y.3    Fujisawa, Y.4    Kikuchi, M.5
  • 20
    • 0034695668 scopus 로고    scopus 로고
    • Maturation dynamics of a viral capsid: Visualization of transitional intermediate states
    • Lata R, Conway JF, Cheng N, Duda RL, Hendrix RW, et al. 2000. Maturation dynamics of a viral capsid: visualization of transitional intermediate states. Cell 100:253-63
    • (2000) Cell , vol.100 , pp. 253-263
    • Lata, R.1    Conway, J.F.2    Cheng, N.3    Duda, R.L.4    Hendrix, R.W.5
  • 21
    • 15444370401 scopus 로고    scopus 로고
    • Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope
    • Lei J, Frank J. 2005. Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope. J. Struct. Biol. 150:69-80
    • (2005) J. Struct. Biol , vol.150 , pp. 69-80
    • Lei, J.1    Frank, J.2
  • 22
    • 32544460568 scopus 로고    scopus 로고
    • The orthogonal tilt reconstruction method: An approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles
    • Leschziner AE, Nogales E. 2006. The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles. J. Struct. Biol. 153:284-99
    • (2006) J. Struct. Biol , vol.153 , pp. 284-299
    • Leschziner, A.E.1    Nogales, E.2
  • 23
    • 33748286733 scopus 로고    scopus 로고
    • Electron tomography of swollen rigor fibers of insect flight muscle reveals a short and variably angled s2 domain
    • Liu J, Wu S, Reedy MC, Winkler H, Lucaveche C, et al. 2006. Electron tomography of swollen rigor fibers of insect flight muscle reveals a short and variably angled s2 domain. J. Mol. Biol. 362:844-60
    • (2006) J. Mol. Biol , vol.362 , pp. 844-860
    • Liu, J.1    Wu, S.2    Reedy, M.C.3    Winkler, H.4    Lucaveche, C.5
  • 24
    • 0032479177 scopus 로고    scopus 로고
    • Escherichia coli 70S ribosome at 15 Å resolution by cryo-electron microscopy: Localization of fMet-tRNAfMet and fitting of L1 protein
    • Malhotra A, Penczek P, Agrawal RK, Gabashvili IS, Grassucci RA, et al. 1998. Escherichia coli 70S ribosome at 15 Å resolution by cryo-electron microscopy: localization of fMet-tRNAfMet and fitting of L1 protein. J. Mol. Biol. 280:103-16
    • (1998) J. Mol. Biol , vol.280 , pp. 103-116
    • Malhotra, A.1    Penczek, P.2    Agrawal, R.K.3    Gabashvili, I.S.4    Grassucci, R.A.5
  • 25
    • 2342662152 scopus 로고    scopus 로고
    • Negative staining and image classification: Powerful tools in modern electron microscopy
    • Ohi M, Li Y, Cheng Y, Walz T. 2004. Negative staining and image classification: powerful tools in modern electron microscopy. Biol. Proc. Online 6:23-34
    • (2004) Biol. Proc. Online , vol.6 , pp. 23-34
    • Ohi, M.1    Li, Y.2    Cheng, Y.3    Walz, T.4
  • 26
    • 0031583477 scopus 로고    scopus 로고
    • Structure of keyhole limpet hemocyanin type 1 (KLH1) at 15 Å resolution by electron cryomicroscopy and angular reconstitution
    • Orlova EV, Dube P, Harris JR, Beckman E, Zemlin F, et al. 1997. Structure of keyhole limpet hemocyanin type 1 (KLH1) at 15 Å resolution by electron cryomicroscopy and angular reconstitution. J. Mol. Biol. 271:417-37
    • (1997) J. Mol. Biol , vol.271 , pp. 417-437
    • Orlova, E.V.1    Dube, P.2    Harris, J.R.3    Beckman, E.4    Zemlin, F.5
  • 27
    • 33646042904 scopus 로고    scopus 로고
    • A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation
    • Penczek PA, Frank J, Spahn CM. 2006. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol. 154:184-94
    • (2006) J. Struct. Biol , vol.154 , pp. 184-194
    • Penczek, P.A.1    Frank, J.2    Spahn, C.M.3
  • 28
    • 0028393194 scopus 로고
    • The ribosome at improved resolution: New techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles
    • Penczek PA, Grassucci RA, Frank J. 1994. The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy 53:251-70
    • (1994) Ultramicroscopy , vol.53 , pp. 251-270
    • Penczek, P.A.1    Grassucci, R.A.2    Frank, J.3
  • 29
    • 33644847296 scopus 로고    scopus 로고
    • Estimation of variance in single-particle reconstruction using the bootstrap technique
    • Penczek PA, Yang C, Frank J, Spahn CM. 2006. Estimation of variance in single-particle reconstruction using the bootstrap technique. J. Struct. Biol. 154:168-83
    • (2006) J. Struct. Biol , vol.154 , pp. 168-183
    • Penczek, P.A.1    Yang, C.2    Frank, J.3    Spahn, C.M.4
  • 30
    • 0001339881 scopus 로고
    • Three-dimensional reconstruction of single particles from random and nonrandom tilt series
    • Radermacher M. 1988. Three-dimensional reconstruction of single particles from random and nonrandom tilt series. J. Electron Microsc. Tech. 9:359-94
    • (1988) J. Electron Microsc. Tech , vol.9 , pp. 359-394
    • Radermacher, M.1
  • 31
    • 0035782681 scopus 로고    scopus 로고
    • The structure of the V(1)-ATPase determined by three-dimensional electron microscopy of single particles
    • Radermacher M, Ruiz T, Wieczorek H, Gruber G. 2001. The structure of the V(1)-ATPase determined by three-dimensional electron microscopy of single particles. J. Struct. Biol. 135:26-37
    • (2001) J. Struct. Biol , vol.135 , pp. 26-37
    • Radermacher, M.1    Ruiz, T.2    Wieczorek, H.3    Gruber, G.4
  • 32
    • 84985231782 scopus 로고
    • Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli
    • Radermacher M, Wagenknecht T, Verschoor A, Frank J. 1987. Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 146(Pt. 2):113-36
    • (1987) J. Microsc , vol.146 , Issue.PART. 2 , pp. 113-136
    • Radermacher, M.1    Wagenknecht, T.2    Verschoor, A.3    Frank, J.4
  • 33
    • 0142042865 scopus 로고    scopus 로고
    • Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy
    • Rosenthal PB, Henderson R. 2003. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333:721-45
    • (2003) J. Mol. Biol , vol.333 , pp. 721-745
    • Rosenthal, P.B.1    Henderson, R.2
  • 34
    • 0041334007 scopus 로고    scopus 로고
    • The 10.8 Å structure of Saccharomyces cerevisiae phosphofructokinase determined by cryoelectron microscopy: Localization of the putative fructose 6-phosphate binding sites
    • Ruiz T, Mechin I, Bar J, Rypniewski W, Kopperschlager G, Radermacher M. 2003. The 10.8 Å structure of Saccharomyces cerevisiae phosphofructokinase determined by cryoelectron microscopy: localization of the putative fructose 6-phosphate binding sites. J. Struct. Biol. 143:124-34
    • (2003) J. Struct. Biol , vol.143 , pp. 124-134
    • Ruiz, T.1    Mechin, I.2    Bar, J.3    Rypniewski, W.4    Kopperschlager, G.5    Radermacher, M.6
  • 35
    • 0033617129 scopus 로고    scopus 로고
    • GroEL-GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings
    • Rye HS, Roseman AM, Chen S, Furtak K, Fenton WA, et al. 1999. GroEL-GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings. Cell 97:325-38
    • (1999) Cell , vol.97 , pp. 325-338
    • Rye, H.S.1    Roseman, A.M.2    Chen, S.3    Furtak, K.4    Fenton, W.A.5
  • 36
    • 20544469627 scopus 로고    scopus 로고
    • Advantages of CCD detectors for de novo three-dimensional structure determination in single-particle electron microscopy
    • Sander B, Golas MM, Stark H. 2005. Advantages of CCD detectors for de novo three-dimensional structure determination in single-particle electron microscopy. J. Struct. Biol. 151:92-105
    • (2005) J. Struct. Biol , vol.151 , pp. 92-105
    • Sander, B.1    Golas, M.M.2    Stark, H.3
  • 37
    • 33845939047 scopus 로고    scopus 로고
    • Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization
    • Scheres SH, Gao H, Valle M, Herman GT, Eggermont PPB, et al. 2007. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat. Methods 4:27
    • (2007) Nat. Methods , vol.4 , pp. 27
    • Scheres, S.H.1    Gao, H.2    Valle, M.3    Herman, G.T.4    Eggermont, P.P.B.5
  • 38
    • 16244396466 scopus 로고    scopus 로고
    • Maximum-likelihood multi-reference refinement for electron microscopy images
    • Scheres SH, Valle M, Nunez R, Sorzano CO, Marabini R, et al. 2005. Maximum-likelihood multi-reference refinement for electron microscopy images. J. Mol. Biol. 348:139-49
    • (2005) J. Mol. Biol , vol.348 , pp. 139-149
    • Scheres, S.H.1    Valle, M.2    Nunez, R.3    Sorzano, C.O.4    Marabini, R.5
  • 39
    • 0031704540 scopus 로고    scopus 로고
    • A maximum-likelihood approach to single-particle image refinement
    • Sigworth FJ. 1998. A maximum-likelihood approach to single-particle image refinement. J. Struct. Biol. 122:328-39
    • (1998) J. Struct. Biol , vol.122 , pp. 328-339
    • Sigworth, F.J.1
  • 40
    • 28544439977 scopus 로고    scopus 로고
    • Structural roles for human translation factor eIF3 in initiation of protein synthesis
    • Siridechadilok B, Fraser CS, Hall RJ, Doudna JA, Nogales E. 2005. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 310:1513-15
    • (2005) Science , vol.310 , pp. 1513-1515
    • Siridechadilok, B.1    Fraser, C.S.2    Hall, R.J.3    Doudna, J.A.4    Nogales, E.5
  • 41
    • 33748775731 scopus 로고    scopus 로고
    • Automated cryoEM data acquisition and analysis of 284742 particles of GroEL
    • Stagg SM, Lander GC, Pulokas J, Fellmann D, Cheng A, et al. 2006. Automated cryoEM data acquisition and analysis of 284742 particles of GroEL. J. Struct. Biol. 155:470-81
    • (2006) J. Struct. Biol , vol.155 , pp. 470-481
    • Stagg, S.M.1    Lander, G.C.2    Pulokas, J.3    Fellmann, D.4    Cheng, A.5
  • 43
    • 33745024278 scopus 로고    scopus 로고
    • Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
    • Tama F, Brooks CL. 2006. Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu. Rev. Biophys. Biomol. Struct. 35:115-33
    • (2006) Annu. Rev. Biophys. Biomol. Struct , vol.35 , pp. 115-133
    • Tama, F.1    Brooks, C.L.2
  • 44
    • 0017140343 scopus 로고
    • Electron microscopy of frozen hydrated biological specimens
    • Taylor KA, Glaeser RM. 1976. Electron microscopy of frozen hydrated biological specimens. J. Ultrastruct. Res. 55:448-56
    • (1976) J. Ultrastruct. Res , vol.55 , pp. 448-456
    • Taylor, K.A.1    Glaeser, R.M.2
  • 45
    • 0023102907 scopus 로고
    • Angular reconstitution: A posteriori assignment of projection directions for 3D reconstruction
    • Van Heel M. 1987. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy 21:111-23
    • (1987) Ultramicroscopy , vol.21 , pp. 111-123
    • Van Heel, M.1
  • 46
    • 0031423486 scopus 로고    scopus 로고
    • Electron tomography of single ice-embedded macromolecules: Three-dimensional alignment and classification
    • Walz J, Typke D, Nitsch M, Koster AJ, Hegerl R, Baumeister W. 1997. Electron tomography of single ice-embedded macromolecules: three-dimensional alignment and classification. J. Struct. Biol. 120:387-95
    • (1997) J. Struct. Biol , vol.120 , pp. 387-395
    • Walz, J.1    Typke, D.2    Nitsch, M.3    Koster, A.J.4    Hegerl, R.5    Baumeister, W.6
  • 47
    • 0742272143 scopus 로고    scopus 로고
    • Recognition and separation of single particles with size variation by statistical analysis of their images
    • White HE, Saibil HR, Ignatiou A, Orlova EV. 2004. Recognition and separation of single particles with size variation by statistical analysis of their images. J. Mol. Biol. 336:453-60
    • (2004) J. Mol. Biol , vol.336 , pp. 453-460
    • White, H.E.1    Saibil, H.R.2    Ignatiou, A.3    Orlova, E.V.4
  • 48
    • 0035783259 scopus 로고    scopus 로고
    • Automated data collection with a Tecnai 12 electron microscope: Applications for molecular imaging by cryomicroscopy
    • Zhang P, Beatty A, Milne JL, Subramaniam S. 2001. Automated data collection with a Tecnai 12 electron microscope: applications for molecular imaging by cryomicroscopy. J. Struct. Biol. 135:251-61
    • (2001) J. Struct. Biol , vol.135 , pp. 251-261
    • Zhang, P.1    Beatty, A.2    Milne, J.L.3    Subramaniam, S.4
  • 49
    • 0035877764 scopus 로고    scopus 로고
    • Direct evidence for the size and conformational variability of the pyruvate dehydrogenase complex revealed by three-dimensional electron microscopy. The "breathing" core and its functional relationship to protein dynamics
    • Zhou ZH, Liao W, Cheng RH, Lawson JE, McCarthy DB, et al. 2001. Direct evidence for the size and conformational variability of the pyruvate dehydrogenase complex revealed by three-dimensional electron microscopy. The "breathing" core and its functional relationship to protein dynamics. J. Biol. Chem. 276:21704-13
    • (2001) J. Biol. Chem , vol.276 , pp. 21704-21713
    • Zhou, Z.H.1    Liao, W.2    Cheng, R.H.3    Lawson, J.E.4    McCarthy, D.B.5


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