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Volumn 166, Issue 1, 2009, Pages 67-78

A method for the alignment of heterogeneous macromolecules from electron microscopy

Author keywords

2D alignment; EM reconstruction; Heterogeneous data; Particle alignment

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA;

EID: 60649101018     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2008.12.008     Document Type: Article
Times cited : (47)

References (45)
  • 1
    • 0027730441 scopus 로고
    • Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate
    • Beese L.S., Friedman J.M., and Steitz T.A. Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate. Biochemistry 32 (1993) 14095-14101
    • (1993) Biochemistry , vol.32 , pp. 14095-14101
    • Beese, L.S.1    Friedman, J.M.2    Steitz, T.A.3
  • 2
    • 84975624414 scopus 로고
    • Classification of image data in conjugate representation spaces
    • Borland L., and van Heel M. Classification of image data in conjugate representation spaces. J. Opt. Soc. Am. A7 (1990) 601
    • (1990) J. Opt. Soc. Am. , vol.A7 , pp. 601
    • Borland, L.1    van Heel, M.2
  • 3
    • 1242351230 scopus 로고    scopus 로고
    • Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis
    • Brink J., Ludtke S.J., Kong Y., Wakil S.J., Ma J., and Chiu W. Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis. Structure (Camb) 12 (2004) 185-191
    • (2004) Structure (Camb) , 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
  • 4
    • 4344620779 scopus 로고    scopus 로고
    • Use of negative stain and single-particle image processing to explore dynamic properties of flexible macromolecules
    • Burgess S.A., Walker M.L., Thirumurugan K., Trinick J., and Knight P.J. Use of negative stain and single-particle image processing to explore dynamic properties of flexible macromolecules. J. Struct. Biol. 147 (2004) 247-258
    • (2004) J. Struct. Biol. , vol.147 , pp. 247-258
    • Burgess, S.A.1    Walker, M.L.2    Thirumurugan, K.3    Trinick, J.4    Knight, P.J.5
  • 5
    • 41649087227 scopus 로고    scopus 로고
    • Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections
    • Elad N., Clare D.K., Saibil H.R., and Orlova E.V. Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections. J. Struct. Biol. 162 (2008) 108-120
    • (2008) J. Struct. Biol. , vol.162 , pp. 108-120
    • Elad, N.1    Clare, D.K.2    Saibil, H.R.3    Orlova, E.V.4
  • 6
    • 19844377583 scopus 로고    scopus 로고
    • The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy
    • Falke S., Tama F., Brooks III C.L., Gogol E.P., and Fisher M.T. The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. J. Mol. Biol. 348 (2005) 219-230
    • (2005) J. Mol. Biol. , vol.348 , pp. 219-230
    • Falke, S.1    Tama, F.2    Brooks III, C.L.3    Gogol, E.P.4    Fisher, M.T.5
  • 8
    • 0036089703 scopus 로고    scopus 로고
    • Single-particle imaging of macromolecules by cryo-electron microscopy
    • Frank J. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31 (2002) 303-319
    • (2002) Annu. Rev. Biophys. Biomol. Struct. , vol.31 , pp. 303-319
    • Frank, J.1
  • 9
    • 0036089703 scopus 로고    scopus 로고
    • Single-particle imaging of macromolecules by cryo-electron microscopy
    • Frank J. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31 (2002) 303-319
    • (2002) Annu. Rev. Biophys. Biomol. Struct. , vol.31 , pp. 303-319
    • Frank, J.1
  • 10
    • 0346495979 scopus 로고    scopus 로고
    • Toward an understanding of the structural basis of translation
    • Frank J. Toward an understanding of the structural basis of translation. Genome Biol. 4 (2003) 237
    • (2003) Genome Biol. , vol.4 , pp. 237
    • Frank, J.1
  • 11
    • 33845340157 scopus 로고    scopus 로고
    • Unsupervised classification of single particles by cluster tracking in multi-dimensional space
    • Fu J., Gao H., and Frank J. Unsupervised classification of single particles by cluster tracking in multi-dimensional space. J. Struct. Biol. 157 (2007) 226-239
    • (2007) J. Struct. Biol. , vol.157 , pp. 226-239
    • Fu, J.1    Gao, H.2    Frank, J.3
  • 13
    • 15244359121 scopus 로고    scopus 로고
    • Major conformational change in the complex SF3b upon integration into the spliceosomal U11/U12 di-snRNP as revealed by electron cryomicroscopy
    • Golas M.M., Sander B., Will C.L., Luhrmann R., and Stark H. Major conformational change in the complex SF3b upon integration into the spliceosomal U11/U12 di-snRNP as revealed by electron cryomicroscopy. Mol. Cell 17 (2005) 869-883
    • (2005) Mol. Cell , vol.17 , pp. 869-883
    • Golas, M.M.1    Sander, B.2    Will, C.L.3    Luhrmann, R.4    Stark, H.5
  • 14
    • 0033777020 scopus 로고    scopus 로고
    • Resolution measurement in structures derived from single particles
    • Grigorieff N. Resolution measurement in structures derived from single particles. Acta Crystallogr. D 56 (2000) 1270-1277
    • (2000) Acta Crystallogr. D , vol.56 , pp. 1270-1277
    • Grigorieff, N.1
  • 15
    • 34548359171 scopus 로고    scopus 로고
    • Cross-correlation of common lines: a novel approach for single-particle reconstruction of a structure containing a flexible domain
    • Hall R.J., Siridechadilok B., and Nogales E. Cross-correlation of common lines: a novel approach for single-particle reconstruction of a structure containing a flexible domain. J. Struct. Biol. 159 (2007) 474-482
    • (2007) J. Struct. Biol. , vol.159 , pp. 474-482
    • Hall, R.J.1    Siridechadilok, B.2    Nogales, E.3
  • 16
    • 0000313739 scopus 로고
    • Exact filters for general geometry 3-dimensional reconstruction
    • Harauz G., and van Heel M. Exact filters for general geometry 3-dimensional reconstruction. Optik 73 (1986) 146-156
    • (1986) Optik , vol.73 , pp. 146-156
    • Harauz, G.1    van Heel, M.2
  • 17
    • 0036289516 scopus 로고    scopus 로고
    • Efficiency of 2D alignment methods
    • Joyeux L., and Penczek P.A. Efficiency of 2D alignment methods. Ultramicroscopy 92 (2002) 33-46
    • (2002) Ultramicroscopy , vol.92 , pp. 33-46
    • Joyeux, L.1    Penczek, P.A.2
  • 18
    • 34347236451 scopus 로고    scopus 로고
    • Visualizing flexibility at molecular resoluiton: Analysis of heterogeneity in single-paticle electron microscopy reconstructions
    • in press
    • Leschziner, A., Nogales, E., in press. Visualizing flexibility at molecular resoluiton: analysis of heterogeneity in single-paticle electron microscopy reconstructions. Ann. Rev. Biophys. Biomol. Struct.
    • Ann. Rev. Biophys. Biomol. Struct
    • Leschziner, A.1    Nogales, E.2
  • 23
    • 0000167776 scopus 로고    scopus 로고
    • Appendix: measures of resolution using Fourier shell correlation
    • Penczek P. Appendix: measures of resolution using Fourier shell correlation. J. Mol. Biol. 280 (1998) 115-116
    • (1998) J. Mol. Biol. , vol.280 , pp. 115-116
    • Penczek, P.1
  • 24
    • 0028393194 scopus 로고
    • The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles
    • Penczek P.A., Grassucci R.A., and Frank J. The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy 53 (1994) 251-270
    • (1994) Ultramicroscopy , vol.53 , pp. 251-270
    • Penczek, P.A.1    Grassucci, R.A.2    Frank, J.3
  • 25
    • 0030198739 scopus 로고    scopus 로고
    • A common-lines based method for determining orientations for N > 3 particle projections simultaneously
    • Penczek P.A., Zhu J., and Frank J. A common-lines based method for determining orientations for N > 3 particle projections simultaneously. Ultramicroscopy 63 (1996) 205-218
    • (1996) Ultramicroscopy , vol.63 , pp. 205-218
    • Penczek, P.A.1    Zhu, J.2    Frank, J.3
  • 26
    • 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 P.A., Frank J., and Spahn C.M. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol. 154 (2006) 184-194
    • (2006) J. Struct. Biol. , vol.154 , pp. 184-194
    • Penczek, P.A.1    Frank, J.2    Spahn, C.M.3
  • 27
    • 33644847296 scopus 로고    scopus 로고
    • Estimation of variance in single-particle reconstruction using the bootstrap technique
    • Penczek P.A., Yang C., Frank J., and Spahn C.M. Estimation of variance in single-particle reconstruction using the bootstrap technique. J. Struct. Biol. 154 (2006) 168-183
    • (2006) J. Struct. Biol. , vol.154 , pp. 168-183
    • Penczek, P.A.1    Yang, C.2    Frank, J.3    Spahn, C.M.4
  • 29
    • 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., and Frank J. Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 146 (1987) 113-136
    • (1987) J. Microsc. , vol.146 , pp. 113-136
    • Radermacher, M.1    Wagenknecht, T.2    Verschoor, A.3    Frank, J.4
  • 30
    • 0035783162 scopus 로고    scopus 로고
    • Structures of unliganded and ATP-bound states of the Escherichia coli chaperonin GroEL by cryoelectron microscopy
    • Roseman A.M., Ranson N.A., Gowen B., Fuller S.D., and Saibil H.R. Structures of unliganded and ATP-bound states of the Escherichia coli chaperonin GroEL by cryoelectron microscopy. J. Struct. Biol. 135 (2001) 115-125
    • (2001) J. Struct. Biol. , vol.135 , pp. 115-125
    • Roseman, A.M.1    Ranson, N.A.2    Gowen, B.3    Fuller, S.D.4    Saibil, H.R.5
  • 31
    • 0035715944 scopus 로고    scopus 로고
    • Allostery and protein substrate conformational change during GroEL/GroES-mediated protein folding
    • Saibil H.R., Horwich A.L., and Fenton W.A. Allostery and protein substrate conformational change during GroEL/GroES-mediated protein folding. Adv. Protein Chem. 59 (2001) 45-72
    • (2001) Adv. Protein Chem. , vol.59 , pp. 45-72
    • Saibil, H.R.1    Horwich, A.L.2    Fenton, W.A.3
  • 33
    • 28544439977 scopus 로고    scopus 로고
    • Structural roles for human translation factor eIF3 in initiation of protein synthesis
    • Siridechadilok B., Fraser C.S., Hall R.J., Doudna J.A., and Nogales E. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 310 (2005) 1513-1515
    • (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
  • 34
    • 0032489021 scopus 로고    scopus 로고
    • Mechanical devices of the spliceosome: motors, clocks, springs, and things
    • Staley J.P., and Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92 (1998) 315-326
    • (1998) Cell , vol.92 , pp. 315-326
    • Staley, J.P.1    Guthrie, C.2
  • 35
    • 0023523524 scopus 로고
    • Object recognition and localization via pose clustering
    • Stockman G. Object recognition and localization via pose clustering. Comput. Vis. Graph. Image Process. 40 (1987) 361-387
    • (1987) Comput. Vis. Graph. Image Process. , vol.40 , pp. 361-387
    • Stockman, G.1
  • 39
    • 0023102907 scopus 로고
    • Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction
    • van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy 21 (1987) 111-123
    • (1987) Ultramicroscopy , vol.21 , pp. 111-123
    • van Heel, M.1
  • 43
    • 0742272143 scopus 로고    scopus 로고
    • Recognition and separation of single particles with size variation by statistical analysis of their images
    • White H.E., Saibil H.R., Ignatiou A., and Orlova E.V. Recognition and separation of single particles with size variation by statistical analysis of their images. J. Mol. Biol. 336 (2004) 453-460
    • (2004) J. Mol. Biol. , vol.336 , pp. 453-460
    • White, H.E.1    Saibil, H.R.2    Ignatiou, A.3    Orlova, E.V.4
  • 45
    • 0036173417 scopus 로고    scopus 로고
    • Influence of implementation parameters on registration of MR and SPECT brain images by maximization of mutual information
    • Zhu Y.-M., and Cochoff S.M. Influence of implementation parameters on registration of MR and SPECT brain images by maximization of mutual information. J. Nucl. Med. 43 (2002) 160-166
    • (2002) J. Nucl. Med. , vol.43 , pp. 160-166
    • Zhu, Y.-M.1    Cochoff, S.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.